Diff of the two buildlogs:

--
--- b1/build.log	2024-12-09 16:26:56.532656919 +0000
+++ b2/build.log	2024-12-09 18:36:45.288128695 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Mon Dec  9 02:05:24 -12 2024
-I: pbuilder-time-stamp: 1733753124
+I: Current time: Mon Jan 12 12:49:58 +14 2026
+I: pbuilder-time-stamp: 1768171798
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -41,54 +41,86 @@
 dpkg-source: info: applying remove_tests_needing_junitx.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/55354/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/61093/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos16-i386.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Jan 11 22:50 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/61093/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/61093/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='i386'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
-  DISTRIBUTION='trixie'
-  HOME='/root'
-  HOST_ARCH='i386'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
+  BASH_VERSION='5.2.32(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=i386
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 '
+  DIRSTACK=()
+  DISTRIBUTION=trixie
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=i686
+  HOST_ARCH=i386
   IFS=' 	
   '
-  INVOCATION_ID='69bd4d8100e74530acceb49ddd804a10'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
-  LD_PRELOAD='libeatmydata.so'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='55354'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=2e815d7d26cf46e29764187c8dae71a3
+  LANG=C
+  LANGUAGE=de_CH:de
+  LC_ALL=C
+  LD_LIBRARY_PATH=/usr/lib/libeatmydata
+  LD_PRELOAD=libeatmydata.so
+  MACHTYPE=i686-pc-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=61093
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.1RPBW0ww/pbuilderrc_ovPv --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1RPBW0ww/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-5.dsc'
-  SUDO_GID='112'
-  SUDO_UID='107'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://46.16.76.132:3128'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.1RPBW0ww/pbuilderrc_vjsz --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1RPBW0ww/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-5.dsc'
+  SUDO_GID=112
+  SUDO_UID=107
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://213.165.73.152:3128
 I: uname -a
-  Linux ionos12-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/55354/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/61093/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -610,7 +642,7 @@
 Get: 424 http://deb.debian.org/debian trixie/main i386 maven-repo-helper all 1.11 [142 kB]
 Get: 425 http://deb.debian.org/debian trixie/main i386 unzip i386 6.0-28 [166 kB]
 Get: 426 http://deb.debian.org/debian trixie/main i386 maven-debian-helper all 2.6.5 [108 kB]
-Fetched 354 MB in 12s (30.6 MB/s)
+Fetched 354 MB in 5s (70.9 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package libapparmor1:i386.
 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19954 files and directories currently installed.)
@@ -2010,8 +2042,8 @@
 Setting up tzdata (2024b-4) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Mon Dec  9 14:08:56 UTC 2024.
-Universal Time is now:  Mon Dec  9 14:08:56 UTC 2024.
+Local time is now:      Sun Jan 11 22:50:48 UTC 2026.
+Universal Time is now:  Sun Jan 11 22:50:48 UTC 2026.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up libxcb-present0:i386 (1.17.0-2+b1) ...
@@ -2561,7 +2593,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../biojava6-live_6.1.0+dfsg-5_source.changes
+I: user script /srv/workspace/pbuilder/61093/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/61093/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../biojava6-live_6.1.0+dfsg-5_source.changes
 dpkg-buildpackage: info: source package biojava6-live
 dpkg-buildpackage: info: source version 6.1.0+dfsg-5
 dpkg-buildpackage: info: source distribution unstable
@@ -2575,7 +2611,7 @@
 	bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done"
 	mh_unpatchpoms -plibbiojava6-java
    jh_clean
-Duplicate specification "u=s" for option "u"
+Duplicate specification "unlink|u" for option "u"
    debian/rules override_dh_clean
 make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
 dpkg: warning: --compare-versions used with obsolete relation operator '>'
@@ -3077,11 +3113,11 @@
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/MainPanelApplets.java:[34,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:[19,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/tools/Blast.java:[36,19] javax.swing.JApplet in javax.swing has been deprecated and marked for removal
+[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/io/parsers/phyloxml/XmlElement.java:[130,19] Boolean(java.lang.String) in java.lang.Boolean has been deprecated and marked for removal
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[69,28] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[75,22] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[76,34] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/phylogeny/data/DomainArchitecture.java:[77,40] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
-[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/io/parsers/phyloxml/XmlElement.java:[130,19] Boolean(java.lang.String) in java.lang.Boolean has been deprecated and marked for removal
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/util/BasicDescriptiveStatistics.java:[57,20] Double(double) in java.lang.Double has been deprecated and marked for removal
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java:[106,31] Double(java.lang.String) in java.lang.Double has been deprecated and marked for removal
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/ControlPanel.java:[494,34] Integer(int) in java.lang.Integer has been deprecated and marked for removal
@@ -3256,8 +3292,8 @@
 [WARNING] source value 8 is obsolete and will be removed in a future release
 [WARNING] target value 8 is obsolete and will be removed in a future release
 [WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
-[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java: Some input files use or override a deprecated API.
-[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java: Recompile with -Xlint:deprecation for details.
+[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java: Some input files use or override a deprecated API.
+[INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java: Recompile with -Xlint:deprecation for details.
 [INFO] 
 [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-alignment ---
 [INFO] Tests are skipped.
@@ -3397,15 +3433,15 @@
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
 [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
 [WARNING] ^
+[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
+[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
+[WARNING] ^
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
 [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
 [WARNING] ^
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: reference not found: Profile
 [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
 [WARNING] ^
-[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: reference not found: Profile
-[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
-[WARNING] ^
 [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: reference not found: Profile
 [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
 [WARNING] ^
@@ -5335,26 +5371,26 @@
 [INFO] ------------------------------------------------------------------------
 [INFO] Reactor Summary for biojava 6.1.0:
 [INFO] 
-[INFO] biojava ............................................ SUCCESS [ 45.138 s]
-[INFO] biojava-core ....................................... SUCCESS [ 25.940 s]
-[INFO] biojava-forester ................................... SUCCESS [ 28.333 s]
-[INFO] biojava-alignment .................................. SUCCESS [  6.954 s]
-[INFO] biojava-structure .................................. SUCCESS [ 24.989 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [  3.216 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [ 11.353 s]
-[INFO] biojava-genome ..................................... SUCCESS [  7.551 s]
-[INFO] biojava-modfinder .................................. SUCCESS [  5.138 s]
-[INFO] biojava-ws ......................................... SUCCESS [  4.830 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [  3.796 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [  4.964 s]
-[INFO] biojava-survival ................................... SUCCESS [  5.583 s]
-[INFO] biojava-ontology ................................... SUCCESS [  4.275 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [  2.202 s]
+[INFO] biojava ............................................ SUCCESS [ 50.920 s]
+[INFO] biojava-core ....................................... SUCCESS [01:29 min]
+[INFO] biojava-forester ................................... SUCCESS [01:18 min]
+[INFO] biojava-alignment .................................. SUCCESS [ 26.749 s]
+[INFO] biojava-structure .................................. SUCCESS [01:34 min]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 10.367 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [ 26.028 s]
+[INFO] biojava-genome ..................................... SUCCESS [ 13.790 s]
+[INFO] biojava-modfinder .................................. SUCCESS [ 10.033 s]
+[INFO] biojava-ws ......................................... SUCCESS [  6.904 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [  5.720 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [  8.202 s]
+[INFO] biojava-survival ................................... SUCCESS [  9.426 s]
+[INFO] biojava-ontology ................................... SUCCESS [  8.302 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [  4.788 s]
 [INFO] ------------------------------------------------------------------------
 [INFO] BUILD SUCCESS
 [INFO] ------------------------------------------------------------------------
-[INFO] Total time:  03:05 min
-[INFO] Finished at: 2024-12-09T02:12:50-12:00
+[INFO] Total time:  07:37 min
+[INFO] Finished at: 2026-01-12T13:01:53+14:00
 [INFO] ------------------------------------------------------------------------
 make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
    dh_auto_test
@@ -5418,295 +5454,295 @@
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest
+[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
-[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.361 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.73 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.529 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
-[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.294 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.TranslationTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.671 s - in org.biojava.nbio.core.sequence.TranslationTest
-[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.nbio.core.sequence.SequenceViewTest
-[INFO] Running org.biojava.nbio.core.sequence.StrandTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.core.sequence.StrandTest
-[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
+[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.178 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
+[INFO] Running org.biojava.nbio.core.sequence.DNATest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.nbio.core.sequence.EditSequenceTest
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 s - in org.biojava.nbio.core.sequence.DNATest
+[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.095 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.sequence.location.LocationTest
-[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.012 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.285 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
-[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.core.sequence.SequenceViewTest
+[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.25 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
-[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
+[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.188 s - in org.biojava.nbio.core.sequence.RNASequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.DNATest
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.081 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.TranslationTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.157 s - in org.biojava.nbio.core.sequence.DNATest
-[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.347 s - in org.biojava.nbio.core.sequence.TranslationTest
+[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals
+[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
+[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
-[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.nbio.core.sequence.location.LocationTest
+[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.163 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
+[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.231 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
-[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
+[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest
+[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.156 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.202 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
+[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
-[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.316 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.471 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
-[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
+[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.245 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
+[INFO] Running org.biojava.nbio.core.sequence.StrandTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.core.sequence.StrandTest
+[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
-[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.core.sequence.EditSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.184 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-getFileExtensions
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.185 s - in org.biojava.nbio.core.sequence.RNASequenceTest
+[INFO] Running org.biojava.nbio.core.util.HashcoderTest
+[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.224 s - in org.biojava.nbio.core.util.HashcoderTest
+[INFO] Running org.biojava.nbio.core.util.EqualsTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.core.util.EqualsTest
+[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-setFile
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.047 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-createObjects
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 s - in org.biojava.nbio.core.util.FlatFileCacheTest
+[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-getFileExtensions
-setFile
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.068 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.412 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
+[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.104 s - in org.biojava.nbio.core.search.io.SearchIOTest
-[INFO] Running org.biojava.nbio.core.search.io.HspTest
+[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.267 s - in org.biojava.nbio.core.util.SequenceToolsTest
+[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest
+<to>
+  <a>22</a>
+  <b>43.22</b>
+  <text>some text</text>
+  <dt tz="UTC">2021-08-15</dt>
+</to>
+
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-getAlignment
-hashCode
-equals
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 s - in org.biojava.nbio.core.search.io.HspTest
-[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
+[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.163 s - in org.biojava.nbio.core.fasta.TestFASTAReader
-[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.056 s - in org.biojava.nbio.core.util.SoftHashMapTest
+[INFO] Running org.biojava.nbio.core.util.XMLHelperTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.032 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.606 s - in org.biojava.nbio.core.util.XMLHelperTest
+[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.638 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
+[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.757 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
+[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
+[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
+[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.456 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
+[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.61 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.nbio.core.util.TestUncompressInputStream
+[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.239 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.core.fasta.TestFASTAReader
+[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.327 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
+[INFO] Running org.biojava.nbio.core.search.io.HspTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.268 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
-[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
+getAlignment
+hashCode
+equals
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.nbio.core.search.io.HspTest
+[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
+getFileExtensions
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 3.348 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
-[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest
+setFile
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.02 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
+[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
+createObjects
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.636 s - in org.biojava.nbio.core.util.SequenceToolsTest
-[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
-[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.093 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
-[INFO] Running org.biojava.nbio.core.util.EqualsTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.569 s - in org.biojava.nbio.core.util.EqualsTest
-[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
+getFileExtensions
+setFile
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.958 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
+[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.core.util.TestUncompressInputStream
-[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.042 s - in org.biojava.nbio.core.search.io.SearchIOTest
+[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.24 s - in org.biojava.nbio.core.util.SoftHashMapTest
-[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest
+[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
-[INFO] Running org.biojava.nbio.core.util.HashcoderTest
-[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.665 s - in org.biojava.nbio.core.util.HashcoderTest
-[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.559 s - in org.biojava.nbio.core.util.FlatFileCacheTest
-[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.185 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.628 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
-[INFO] Running org.biojava.nbio.core.util.XMLHelperTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.277 s - in org.biojava.nbio.core.util.XMLHelperTest
-[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest
-<to>
-  <a>22</a>
-  <b>43.22</b>
-  <text>some text</text>
-  <dt tz="UTC">2021-08-15</dt>
-</to>
-
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
-[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet
+[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.072 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
+[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.633 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
+[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.041 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -5759,86 +5795,86 @@
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.387 s - in org.biojava.nbio.phylo.TestForesterWrapper
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.phylo.TestForesterWrapper
 [INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
-[INFO] Running org.biojava.nbio.alignment.GuideTreeTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
+[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.48 s - in org.biojava.nbio.alignment.GuideTreeTest
-[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.462 s - in org.biojava.nbio.alignment.TestDNAAlignment
-[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
+[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
+[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.328 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
-[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.28 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
-[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.271 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
+[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.472 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
-[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
-[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.105 s - in org.biojava.nbio.alignment.SmithWatermanTest
 [INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.318 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
-[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
+[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.498 s - in org.biojava.nbio.alignment.LocalAlignmentTest
-[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.993 s - in org.biojava.nbio.alignment.TestDNAAlignment
+[INFO] Running org.biojava.nbio.alignment.GuideTreeTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.904 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
-[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.alignment.GuideTreeTest
+[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.876 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
-[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.394 s - in org.biojava.nbio.alignment.SmithWatermanTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.129 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
 [INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.623 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
-[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
+[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.651 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
-[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.487 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
-[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.alignment.LocalAlignmentTest
+[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.525 s - in org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -5870,353 +5906,353 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
-SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-SLF4J: Defaulting to no-operation (NOP) logger implementation
-SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.447 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
-[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.029 s - in org.biojava.nbio.structure.TestDNAAlignment
-[INFO] Running org.biojava.nbio.structure.HetatomImplTest
+[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
+[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
+[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
+[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestTitleParsing
+[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
+[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 s - in org.biojava.nbio.structure.HetatomImplTest
-[INFO] Running org.biojava.nbio.structure.TestNucleotides
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.037 s - in org.biojava.nbio.structure.TestNucleotides
-[INFO] Running org.biojava.nbio.structure.SiteTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
+[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
+[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
+[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
+[INFO] Running org.biojava.nbio.structure.io.TestShortLines
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.19 s - in org.biojava.nbio.structure.SiteTest
-[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.033 s - in org.biojava.nbio.structure.TestExperimentalTechniques
-[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.028 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[INFO] Running org.biojava.nbio.structure.TestCalc
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.359 s - in org.biojava.nbio.structure.io.TestShortLines
+[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestHardBioUnits
+[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 s - in org.biojava.nbio.structure.TestCalc
-[INFO] Running org.biojava.nbio.structure.TestBond
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.028 s - in org.biojava.nbio.structure.TestBond
-[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.151 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.415 s - in org.biojava.nbio.structure.ResidueRangeTest
-[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.047 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
-[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.066 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.232 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest
-[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.885 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.169 s - in org.biojava.nbio.structure.align.client.TestStructureName
-[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
+Using PDB_DIR=/tmp as temporary file directory
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.36 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.166 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.173 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.032 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.04 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.026 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.377 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
-[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest
+[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.079 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
-[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
-[INFO] Running org.biojava.nbio.structure.TestAltLocs
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.864 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
+[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 4.288 s - in org.biojava.nbio.structure.TestAltLocs
-[INFO] Running org.biojava.nbio.structure.Test4hhb
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.io.TestDBRefParsing
+[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestSiftsParsing
+[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.956 s - in org.biojava.nbio.structure.Test4hhb
-[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.067 s - in org.biojava.nbio.structure.contact.TestContactCalc
-[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.877 s - in org.biojava.nbio.structure.io.TestHeaderOnly
+[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-Interface <A, B>
-<CA R 0 3.0 3.0 3.0, CA R 0 7.0 3.0 3.0> - 4.0
-Interface <A, C>
-<CA R 0 3.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
-Interface <B, C>
-<CA R 0 7.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.237 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
-[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.nbio.structure.ResidueNumberTest
-[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.473 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
+[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.592 s - in org.biojava.nbio.structure.TestStructureSerialization
-[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.032 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.022 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
 [INFO] Running org.biojava.nbio.structure.TestStructureImpl
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.408 s - in org.biojava.nbio.structure.TestStructureImpl
-[INFO] Running org.biojava.nbio.structure.TestCloning
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.045 s - in org.biojava.nbio.structure.TestCloning
-[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.043 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.structure.TestStructureImpl
 [INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.056 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
 [INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
-[INFO] Running org.biojava.nbio.structure.TestKeywords
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
+[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.328 s - in org.biojava.nbio.structure.TestKeywords
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.028 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.239 s - in org.biojava.nbio.structure.TestStructureSerialization
+[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.032 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
-[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.089 s - in org.biojava.nbio.structure.TestURLIdentifier
+[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
-[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.025 s - in org.biojava.nbio.structure.AtomPositionMapTest
-[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.096 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.033 s - in org.biojava.nbio.structure.asa.TestAsaCalc
+[INFO] Running org.biojava.nbio.structure.Test2JA5
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.Test2JA5
+[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.structure.ResidueNumberTest
+[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestStructureCrossReferences
+[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[INFO] Running org.biojava.nbio.structure.Test4hhb
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.167 s - in org.biojava.nbio.structure.asa.TestAsaCalc
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.024 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.944 s - in org.biojava.nbio.structure.Test4hhb
+[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.44 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
-[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.228 s - in org.biojava.nbio.structure.SourceCompoundTest
+[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestDNAAlignment
+[INFO] Running org.biojava.nbio.structure.HetatomImplTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 23.59 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
-[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.structure.HetatomImplTest
+[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
+[INFO] Running org.biojava.nbio.structure.TestCloning
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestCloning
 [INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.044 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
 [INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.244 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
-[INFO] Running org.biojava.nbio.structure.Test2JA5
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.008 s - in org.biojava.nbio.structure.Test2JA5
-[INFO] Running org.biojava.nbio.structure.ElementTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.structure.ElementTest
-[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.438 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
+[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.363 s - in org.biojava.nbio.structure.PdbFileFormat30Test
-[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 2.963 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
+[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestParsingCalcium
+[INFO] Running org.biojava.nbio.structure.TestPdbId
+[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100]
+[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
+[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.structure.TestPdbId
+[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.324 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
-[INFO] Running org.biojava.nbio.structure.TestAtomIterator
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.014 s - in org.biojava.nbio.structure.TestAtomIterator
-[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.271 s - in org.biojava.nbio.structure.TestURLIdentifier
-[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.021 s - in org.biojava.nbio.structure.TestParsingCalcium
-[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
+[INFO] Running org.biojava.nbio.structure.TestKeywords
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 16.128 s - in org.biojava.nbio.structure.SourceCompoundTest
-[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.998 s - in org.biojava.nbio.structure.TestKeywords
+[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.54 s - in org.biojava.nbio.structure.TestEntityHeuristics
-[INFO] Running org.biojava.nbio.structure.ChemCompTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.428 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
+[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 2.362 s - in org.biojava.nbio.structure.ChemCompTest
-[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.112 s - in org.biojava.nbio.structure.TestStructureCrossReferences
-[INFO] Running org.biojava.nbio.structure.TestChargeAdder
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.048 s - in org.biojava.nbio.structure.TestChargeAdder
-[INFO] Running org.biojava.nbio.structure.TestAtomCache
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.054 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest
+[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
+[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 3.928 s - in org.biojava.nbio.structure.TestAtomCache
-[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.49 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
-[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.195 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
-[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.074 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
+[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.167 s - in org.biojava.nbio.structure.TestVeryLongFileName
-[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.TestHardBioUnits
-[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.031 s - in org.biojava.nbio.structure.io.TestSiftsParsing
-[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
+[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.069 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
+[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 4.982 s - in org.biojava.nbio.structure.io.TestHeaderOnly
-[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.03 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.024 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
-[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.061 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
-[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.107 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
-[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.031 s - in org.biojava.nbio.structure.align.client.TestStructureName
+[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
+[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.026 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
-[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.245 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
-[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.036 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
-[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.989 s - in org.biojava.nbio.structure.PdbFileFormat30Test
+[INFO] Running org.biojava.nbio.structure.TestBond
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestBond
+[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 8.06 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
-[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.183 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
+[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 3.037 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
-[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestTitleParsing
-[INFO] Running org.biojava.nbio.structure.io.TestShortLines
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.029 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
+[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.013 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[INFO] Running org.biojava.nbio.structure.TestCalc
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.427 s - in org.biojava.nbio.structure.io.TestShortLines
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.02 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.103 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.nbio.structure.TestCalc
+[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.007 s - in org.biojava.nbio.structure.AtomPositionMapTest
+[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 15.76 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.032 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.059 s - in org.biojava.nbio.structure.ResidueRangeTest
+[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestExperimentalTechniques
+[INFO] Running org.biojava.nbio.structure.ElementTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.nbio.structure.ElementTest
+[INFO] Running org.biojava.nbio.structure.TestAtomIterator
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestAtomIterator
+[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
+[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.215 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.122 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
+[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.346 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
-[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.68 s - in org.biojava.nbio.structure.TestEntityHeuristics
+[INFO] Running org.biojava.nbio.structure.TestAtomCache
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.387 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
-[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
-[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.402 s - in org.biojava.nbio.structure.TestAtomCache
+[INFO] Running org.biojava.nbio.structure.TestAltLocs
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.415 s - in org.biojava.nbio.structure.io.TestDBRefParsing
-[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.391 s - in org.biojava.nbio.structure.TestAltLocs
+[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
+[INFO] Running org.biojava.nbio.structure.TestChargeAdder
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestChargeAdder
+[INFO] Running org.biojava.nbio.structure.TestNucleotides
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestNucleotides
+[INFO] Running org.biojava.nbio.structure.SiteTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.775 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.structure.SiteTest
+[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-Using PDB_DIR=/tmp as temporary file directory
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.564 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.243 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
+[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 11.143 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.024 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.032 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.TestVeryLongFileName
+[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.632 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+Interface <A, B>
+<CA R 0 3.0 3.0 3.0, CA R 0 7.0 3.0 3.0> - 4.0
+Interface <A, C>
+<CA R 0 3.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
+Interface <B, C>
+<CA R 0 7.0 3.0 3.0, CA R 0 5.0 8.0 4.0> - 5.477225575051661
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
+[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.007 s - in org.biojava.nbio.structure.contact.TestContactCalc
+[INFO] Running org.biojava.nbio.structure.ChemCompTest
+SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
+SLF4J: Defaulting to no-operation (NOP) logger implementation
+SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.265 s - in org.biojava.nbio.structure.ChemCompTest
 [INFO] Running org.biojava.nbio.structure.PDBStatusTest
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.027 s - in org.biojava.nbio.structure.PDBStatusTest
-[INFO] Running org.biojava.nbio.structure.TestPdbId
-[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100]
-[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
-[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.435 s - in org.biojava.nbio.structure.TestPdbId
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.PDBStatusTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6265,21 +6301,21 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.733 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
+[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.structure.gui.RenderStyleTest
+[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.nbio.structure.gui.StructureViewerTest
 [INFO] Running org.biojava.nbio.structure.gui.TestAtomInfo
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.833 s - in org.biojava.nbio.structure.gui.TestAtomInfo
-[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.544 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.structure.gui.TestAtomInfo
 [INFO] Running org.biojava.nbio.structure.gui.ViewerTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.287 s - in org.biojava.nbio.structure.gui.ViewerTest
-[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.252 s - in org.biojava.nbio.structure.gui.RenderStyleTest
-[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 s - in org.biojava.nbio.structure.gui.StructureViewerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.structure.gui.ViewerTest
+[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
+[INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6308,51 +6344,51 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.genome.io.fastq.FastqTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.138 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.787 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
-[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.101 s - in org.biojava.nbio.genome.TestGenomeMapping
-[INFO] Running org.biojava.nbio.genome.FeatureListTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.931 s - in org.biojava.nbio.genome.FeatureListTest
+[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.102 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
 [INFO] Running org.biojava.nbio.genome.TestChromosomeMappingTools
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.395 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
-[INFO] Running org.biojava.nbio.genome.TestIssue355
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 s - in org.biojava.nbio.genome.TestIssue355
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
 [INFO] Running org.biojava.nbio.genome.TestLocation
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 s - in org.biojava.nbio.genome.TestLocation
-[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
-[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.164 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.24 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
-[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.169 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 s - in org.biojava.nbio.genome.io.fastq.FastqTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.817 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.285 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.genome.TestLocation
+[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.737 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
-[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.733 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.532 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.609 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
+[INFO] Running org.biojava.nbio.genome.FeatureListTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.genome.FeatureListTest
+[INFO] Running org.biojava.nbio.genome.TestIssue355
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.genome.TestIssue355
+[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.049 s - in org.biojava.nbio.genome.TestGenomeMapping
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6381,20 +6417,20 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.55 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
 [INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 3.551 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.247 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
+[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.053 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
 [INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.471 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.215 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
 [INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.115 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.049 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6424,7 +6460,7 @@
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
 [INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.1 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.051 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6453,13 +6489,13 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.141 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
 [INFO] Running org.biojava.nbio.ronn.JronnTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.613 s - in org.biojava.nbio.ronn.JronnTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.214 s - in org.biojava.nbio.ronn.JronnTest
+[INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.052 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6488,31 +6524,43 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest
+[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.458 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
+[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.822 s - in org.biojava.nbio.aaproperties.xml.ElementTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
+[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.403 s - in org.biojava.nbio.aaproperties.xml.ElementTest
+[INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.913 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
-[INFO] Running org.biojava.nbio.aaproperties.CookBookTest
+[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.486 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
+[INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.643 s - in org.biojava.nbio.aaproperties.CookBookTest
+SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
+SAOV_0114,53660.5723,41370.0,41370.0,4.986
+SAOV_0094,45884.0164,57760.0,57760.0,8.5193
+SAA6008_00126,95002.026,55240.0,55740.0,5.7263
+SequenceName,A,N,MolecularWeight
+SAOV_0114,0.101,0.0525,53660.5723
+SAOV_0094,0.0537,0.0767,45884.0164
+SAA6008_00126,0.0955,0.0414,95002.026
+SequenceName,A,N,MolecularWeight
+SAOV_0114,0.101,0.0525,53660.5723
+SAOV_0094,0.0537,0.0767,45884.0164
+SAA6008_00126,0.0955,0.0414,95002.026
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.433 s - in org.biojava.nbio.aaproperties.CommandPromptTest
 [INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
@@ -6523,29 +6571,17 @@
 NP_000257                133 aa            linear   PRI 27-MAR-2008,0.0451,0.0075,15043.5262
 SequenceName,A,N,MolecularWeight
 NP_000257                133 aa            linear   PRI 27-MAR-2008,0.0451,0.0075,15043.5262
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.717 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
-[INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.409 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
+[INFO] Running org.biojava.nbio.aaproperties.CookBookTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.887 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
-[INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.356 s - in org.biojava.nbio.aaproperties.CookBookTest
+[INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
-SAOV_0114,53660.5723,41370.0,41370.0,4.986
-SAOV_0094,45884.0164,57760.0,57760.0,8.5193
-SAA6008_00126,95002.026,55240.0,55740.0,5.7263
-SequenceName,A,N,MolecularWeight
-SAOV_0114,0.101,0.0525,53660.5723
-SAOV_0094,0.0537,0.0767,45884.0164
-SAA6008_00126,0.0955,0.0414,95002.026
-SequenceName,A,N,MolecularWeight
-SAOV_0114,0.101,0.0525,53660.5723
-SAOV_0094,0.0537,0.0767,45884.0164
-SAA6008_00126,0.0955,0.0414,95002.026
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.773 s - in org.biojava.nbio.aaproperties.CommandPromptTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6594,21 +6630,21 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.ontology.TestParseOBO
+[INFO] Running org.biojava.nbio.ontology.TestParseSBO
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.235 s - in org.biojava.nbio.ontology.TestParseOBO
-[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 s - in org.biojava.nbio.ontology.TestParseSBO
+[INFO] Running org.biojava.nbio.ontology.TestParseOBO
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.472 s - in org.biojava.nbio.ontology.TestOboFileParsing
-[INFO] Running org.biojava.nbio.ontology.TestParseSBO
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.ontology.TestParseOBO
+[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
 SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.26 s - in org.biojava.nbio.ontology.TestParseSBO
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.nbio.ontology.TestOboFileParsing
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6637,26 +6673,26 @@
 [INFO] ------------------------------------------------------------------------
 [INFO] Reactor Summary for biojava 6.1.0:
 [INFO] 
-[INFO] biojava ............................................ SUCCESS [  0.004 s]
-[INFO] biojava-core ....................................... SUCCESS [32:27 min]
-[INFO] biojava-forester ................................... SUCCESS [ 11.044 s]
-[INFO] biojava-alignment .................................. SUCCESS [09:51 min]
-[INFO] biojava-structure .................................. SUCCESS [  01:00 h]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 19.763 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [03:53 min]
-[INFO] biojava-genome ..................................... SUCCESS [10:39 min]
-[INFO] biojava-modfinder .................................. SUCCESS [02:33 min]
-[INFO] biojava-ws ......................................... SUCCESS [ 31.388 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [01:17 min]
-[INFO] biojava-aa-prop .................................... SUCCESS [04:11 min]
-[INFO] biojava-survival ................................... SUCCESS [  0.096 s]
-[INFO] biojava-ontology ................................... SUCCESS [01:33 min]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.381 s]
+[INFO] biojava ............................................ SUCCESS [  0.002 s]
+[INFO] biojava-core ....................................... SUCCESS [30:37 min]
+[INFO] biojava-forester ................................... SUCCESS [  0.278 s]
+[INFO] biojava-alignment .................................. SUCCESS [09:13 min]
+[INFO] biojava-structure .................................. SUCCESS [50:48 min]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.153 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [03:03 min]
+[INFO] biojava-genome ..................................... SUCCESS [09:11 min]
+[INFO] biojava-modfinder .................................. SUCCESS [02:02 min]
+[INFO] biojava-ws ......................................... SUCCESS [ 30.664 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [01:10 min]
+[INFO] biojava-aa-prop .................................... SUCCESS [04:07 min]
+[INFO] biojava-survival ................................... SUCCESS [  0.026 s]
+[INFO] biojava-ontology ................................... SUCCESS [01:32 min]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.055 s]
 [INFO] ------------------------------------------------------------------------
 [INFO] BUILD SUCCESS
 [INFO] ------------------------------------------------------------------------
-[INFO] Total time:  02:08 h
-[INFO] Finished at: 2024-12-09T04:20:54-12:00
+[INFO] Total time:  01:52 h
+[INFO] Finished at: 2026-01-12T14:54:14+14:00
 [INFO] ------------------------------------------------------------------------
    create-stamp debian/debhelper-build-stamp
    dh_prep
@@ -6888,26 +6924,26 @@
 [INFO] ------------------------------------------------------------------------
 [INFO] Reactor Summary for biojava 6.1.0:
 [INFO] 
-[INFO] biojava ............................................ SUCCESS [  0.644 s]
-[INFO] biojava-core ....................................... SUCCESS [  0.082 s]
-[INFO] biojava-forester ................................... SUCCESS [  0.077 s]
-[INFO] biojava-alignment .................................. SUCCESS [  0.049 s]
-[INFO] biojava-structure .................................. SUCCESS [  0.057 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.041 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [  0.048 s]
-[INFO] biojava-genome ..................................... SUCCESS [  0.045 s]
-[INFO] biojava-modfinder .................................. SUCCESS [  0.043 s]
-[INFO] biojava-ws ......................................... SUCCESS [  0.043 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [  0.045 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [  0.042 s]
-[INFO] biojava-survival ................................... SUCCESS [  0.043 s]
-[INFO] biojava-ontology ................................... SUCCESS [  0.050 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.045 s]
+[INFO] biojava ............................................ SUCCESS [  0.346 s]
+[INFO] biojava-core ....................................... SUCCESS [  0.046 s]
+[INFO] biojava-forester ................................... SUCCESS [  0.043 s]
+[INFO] biojava-alignment .................................. SUCCESS [  0.026 s]
+[INFO] biojava-structure .................................. SUCCESS [  0.032 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.023 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [  0.028 s]
+[INFO] biojava-genome ..................................... SUCCESS [  0.025 s]
+[INFO] biojava-modfinder .................................. SUCCESS [  0.024 s]
+[INFO] biojava-ws ......................................... SUCCESS [  0.024 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [  0.025 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [  0.024 s]
+[INFO] biojava-survival ................................... SUCCESS [  0.023 s]
+[INFO] biojava-ontology ................................... SUCCESS [  0.029 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.031 s]
 [INFO] ------------------------------------------------------------------------
 [INFO] BUILD SUCCESS
 [INFO] ------------------------------------------------------------------------
-[INFO] Total time:  1.721 s
-[INFO] Finished at: 2024-12-09T04:20:59-12:00
+[INFO] Total time:  0.962 s
+[INFO] Finished at: 2026-01-12T14:54:17+14:00
 [INFO] ------------------------------------------------------------------------
 	mh_resolve_dependencies --non-interactive --offline --build -plibbiojava6-java --javadoc --base-directory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg --non-explore
 Analysing pom.xml...
@@ -7128,15 +7164,15 @@
    jh_installlibs
    jh_classpath
 Duplicate specification "version|V" for option "V"
+Duplicate specification "version|V" for option "V"
+Duplicate specification "V:s" for option "V"
 Duplicate specification "V:s" for option "V"
 Duplicate specification "V:s" for option "V"
 Duplicate specification "version|V" for option "V"
 Duplicate specification "version|V" for option "V"
-Duplicate specification "version|V" for option "V"
-Duplicate specification "version|V" for option "V"
-Duplicate specification "version|V" for option "V"
-Duplicate specification "version|V" for option "V"
-Duplicate specification "version|V" for option "V"
+Duplicate specification "V:s" for option "V"
+Duplicate specification "V:s" for option "V"
+Duplicate specification "V:s" for option "V"
 Duplicate specification "V:s" for option "V"
 Duplicate specification "version|V" for option "V"
    jh_manifest
@@ -7164,12 +7200,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/61093/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/61093/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/55354 and its subdirectories
-I: Current time: Mon Dec  9 04:26:55 -12 2024
-I: pbuilder-time-stamp: 1733761615
+I: removing directory /srv/workspace/pbuilder/61093 and its subdirectories
+I: Current time: Mon Jan 12 14:59:43 +14 2026
+I: pbuilder-time-stamp: 1768179583