Diff of the two buildlogs:

--
--- b1/build.log	2025-01-23 06:36:24.251930394 +0000
+++ b2/build.log	2025-01-23 08:57:47.710923572 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Tue Feb 24 22:45:23 -12 2026
-I: pbuilder-time-stamp: 1772016323
+I: Current time: Thu Jan 23 20:36:28 +14 2025
+I: pbuilder-time-stamp: 1737614188
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -37,52 +37,84 @@
 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/640563/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/770555/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos1-amd64.
+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 23 06:36 /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/770555/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/770555/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='amd64'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
-  DISTRIBUTION='trixie'
-  HOME='/root'
-  HOST_ARCH='amd64'
+  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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.2.37(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=amd64
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
+  DIRSTACK=()
+  DISTRIBUTION=trixie
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='0a309341bd7140e095b5d03f4dd432cd'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  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='640563'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=139ee6ae855344739602e41fddc7efa1
+  LANG=C
+  LANGUAGE=et_EE:et
+  LC_ALL=C
+  MACHTYPE=x86_64-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=770555
   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.fXt1A25E/pbuilderrc_1u3p --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.fXt1A25E/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-5.dsc'
-  SUDO_GID='111'
-  SUDO_UID='106'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://213.165.73.152:3128'
+  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.fXt1A25E/pbuilderrc_ZfxK --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.fXt1A25E/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-5.dsc'
+  SUDO_GID=110
+  SUDO_UID=105
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://46.16.76.132:3128
 I: uname -a
-  Linux ionos15-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/640563/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/770555/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -614,7 +646,7 @@
 Get: 434 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB]
 Get: 435 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB]
 Get: 436 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.7 [108 kB]
-Fetched 346 MB in 8s (41.0 MB/s)
+Fetched 346 MB in 15s (22.9 MB/s)
 Preconfiguring packages ...
 Selecting previously unselected package libapparmor1:amd64.
 (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 ... 19856 files and directories currently installed.)
@@ -2044,8 +2076,8 @@
 Setting up tzdata (2024b-6) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Wed Feb 25 10:46:33 UTC 2026.
-Universal Time is now:  Wed Feb 25 10:46:33 UTC 2026.
+Local time is now:      Thu Jan 23 06:38:36 UTC 2025.
+Universal Time is now:  Thu Jan 23 06:38:36 UTC 2025.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up libxcb-present0:amd64 (1.17.0-2+b1) ...
@@ -2612,7 +2644,11 @@
 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/770555/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/770555/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
@@ -2626,7 +2662,7 @@
 	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 '>'
@@ -3448,15 +3484,15 @@
 [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] ^
@@ -5386,26 +5422,26 @@
 [INFO] ------------------------------------------------------------------------
 [INFO] Reactor Summary for biojava 6.1.0:
 [INFO] 
-[INFO] biojava ............................................ SUCCESS [ 37.801 s]
-[INFO] biojava-core ....................................... SUCCESS [  8.637 s]
-[INFO] biojava-forester ................................... SUCCESS [  8.552 s]
-[INFO] biojava-alignment .................................. SUCCESS [  2.982 s]
-[INFO] biojava-structure .................................. SUCCESS [  9.603 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [  1.512 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [  4.653 s]
-[INFO] biojava-genome ..................................... SUCCESS [  2.680 s]
-[INFO] biojava-modfinder .................................. SUCCESS [  2.098 s]
-[INFO] biojava-ws ......................................... SUCCESS [  1.824 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [  1.606 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [  2.358 s]
-[INFO] biojava-survival ................................... SUCCESS [  2.487 s]
-[INFO] biojava-ontology ................................... SUCCESS [  2.105 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [  1.182 s]
+[INFO] biojava ............................................ SUCCESS [ 42.216 s]
+[INFO] biojava-core ....................................... SUCCESS [ 17.597 s]
+[INFO] biojava-forester ................................... SUCCESS [ 18.948 s]
+[INFO] biojava-alignment .................................. SUCCESS [  6.874 s]
+[INFO] biojava-structure .................................. SUCCESS [ 22.054 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [  3.520 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [ 23.855 s]
+[INFO] biojava-genome ..................................... SUCCESS [ 21.074 s]
+[INFO] biojava-modfinder .................................. SUCCESS [ 17.720 s]
+[INFO] biojava-ws ......................................... SUCCESS [ 15.231 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [  5.036 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [ 11.178 s]
+[INFO] biojava-survival ................................... SUCCESS [ 11.970 s]
+[INFO] biojava-ontology ................................... SUCCESS [  4.972 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [  2.553 s]
 [INFO] ------------------------------------------------------------------------
 [INFO] BUILD SUCCESS
 [INFO] ------------------------------------------------------------------------
-[INFO] Total time:  01:30 min
-[INFO] Finished at: 2026-02-24T22:48:57-12:00
+[INFO] Total time:  03:46 min
+[INFO] Finished at: 2025-01-23T20:43:45+14:00
 [INFO] ------------------------------------------------------------------------
 make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
    dh_auto_test
@@ -5469,295 +5505,295 @@
 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.util.StringManipulationHelperTest
+[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: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.317 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
-[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
-[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
-[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest
+getAlignment
+hashCode
+equals
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.search.io.HspTest
+[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
-[INFO] Running org.biojava.nbio.core.util.XMLHelperTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.224 s - in org.biojava.nbio.core.search.io.SearchIOTest
+[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.
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.422 s - in org.biojava.nbio.core.util.XMLHelperTest
-[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
+getFileExtensions
+setFile
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.646 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
+[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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.util.TestUncompressInputStream
-[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>
-
+setFile
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.031 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
+[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: 0.147 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
-[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest
+[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.178 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.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.064 s - in org.biojava.nbio.core.util.SoftHashMapTest
-[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
+[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.056 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
+[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.555 s - in org.biojava.nbio.core.util.FlatFileCacheTest
-[INFO] Running org.biojava.nbio.core.util.EqualsTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.13 s - in org.biojava.nbio.core.util.EqualsTest
-[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.25 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
+[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.
-[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.543 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
-[INFO] Running org.biojava.nbio.core.util.HashcoderTest
-[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.core.util.HashcoderTest
-[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
+[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.
-[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.445 s - in org.biojava.nbio.core.util.SequenceToolsTest
-[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.255 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
+[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.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.174 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.StrandTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.nbio.core.sequence.StrandTest
-[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.335 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[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.
-[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.261 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
-[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[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.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
+[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.446 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.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.555 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
+[INFO] Running org.biojava.nbio.core.util.EqualsTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.core.util.EqualsTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
-[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.065 s - in org.biojava.nbio.core.util.SoftHashMapTest
+[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: 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.SequenceViewTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.288 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: 0.142 s - in org.biojava.nbio.core.util.HashcoderTest
+[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.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.SequenceViewTest
-[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.289 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
-[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.3 s - in org.biojava.nbio.core.util.XMLHelperTest
+[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
+[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.nbio.core.util.TestUncompressInputStream
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest
+[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.495 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
+[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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
-[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.311 s - in org.biojava.nbio.core.util.FlatFileCacheTest
+[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.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.743 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 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.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
+[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
+[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.244 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[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: 0.121 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 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] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.919 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
+[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.
-[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.187 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
+[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] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
-[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
-[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
+[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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.core.sequence.RNASequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.613 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.EditSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.232 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
+[INFO] Running org.biojava.nbio.core.sequence.StrandTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 s - in org.biojava.nbio.core.sequence.StrandTest
+[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: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
+[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.656 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
+[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.
-[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.373 s - in org.biojava.nbio.core.sequence.RNASequenceTest
+[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 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: 0.005 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.TranslationTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[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: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.269 s - in org.biojava.nbio.core.sequence.TranslationTest
-[INFO] Running org.biojava.nbio.core.sequence.DNATest
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.525 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
+[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: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.core.sequence.DNATest
-[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.232 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
-[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in 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: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.147 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 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: 0.035 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
+[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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.638 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.552 s - in org.biojava.nbio.core.sequence.DNATest
+[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.
-[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.064 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.036 s - in 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.
-[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.082 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
+[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.248 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: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
-[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.684 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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.nbio.core.fasta.TestFASTAReader
-[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
+[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.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.035 s - in org.biojava.nbio.core.search.io.SearchIOTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-createObjects
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.nbio.core.sequence.SequenceViewTest
+[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.
-getFileExtensions
-setFile
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.559 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-getFileExtensions
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.365 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
+[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.
-setFile
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.017 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-[INFO] Running org.biojava.nbio.core.search.io.HspTest
+[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.556 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
+[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.
-getAlignment
-hashCode
-equals
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.search.io.HspTest
-[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.biojava.nbio.core.sequence.EditSequenceTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -5806,90 +5842,90 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.alignment.GuideTreeTest
+[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper
 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: 0.111 s - in org.biojava.nbio.alignment.GuideTreeTest
-[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.355 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: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
-[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.252 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.
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.11 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
-[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.412 s - in org.biojava.nbio.alignment.io.TestStockholmParser
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.nbio.alignment.io.TestStockholmParser
-[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.623 s - in org.biojava.nbio.alignment.LocalAlignmentTest
+[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: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
-[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.484 s - in org.biojava.nbio.alignment.TestDNAAlignment
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
-[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.432 s - in org.biojava.nbio.alignment.SmithWatermanTest
+[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.319 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
+[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
 [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: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 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: 0.054 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
-[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.24 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
+[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: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 s - in org.biojava.nbio.alignment.SmithWatermanTest
-[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.203 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
+[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
-[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.592 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[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.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.187 s - in org.biojava.nbio.alignment.TestDNAAlignment
-[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.LocalAlignmentTest
-[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
-[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.233 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
+[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: 0.181 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
-[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.5 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
-[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.752 s - in org.biojava.nbio.alignment.GuideTreeTest
+[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.phylo.TestForesterWrapper
-[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.432 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.744 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -5925,349 +5961,349 @@
 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: 0.037 s - in org.biojava.nbio.structure.TestVeryLongFileName
-[INFO] Running org.biojava.nbio.structure.TestCloning
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestCloning
-[INFO] Running org.biojava.nbio.structure.TestStructureImpl
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 s - in org.biojava.nbio.structure.TestVeryLongFileName
+[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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.structure.TestStructureImpl
-[INFO] Running org.biojava.nbio.structure.TestAltLocs
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 4.959 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
+[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.
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.336 s - in org.biojava.nbio.structure.TestAltLocs
-[INFO] Running org.biojava.nbio.structure.HetatomImplTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.488 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
+[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.structure.HetatomImplTest
-[INFO] Running org.biojava.nbio.structure.TestAtomCache
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.407 s - in org.biojava.nbio.structure.io.TestShortLines
+[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: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.358 s - in org.biojava.nbio.structure.TestAtomCache
-[INFO] Running org.biojava.nbio.structure.TestAtomIterator
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 s - in org.biojava.nbio.structure.TestAtomIterator
-[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
-[INFO] Running org.biojava.nbio.structure.ElementTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ElementTest
-[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.898 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 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: 0.018 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.527 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[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.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
-[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
+Using PDB_DIR=/tmp as temporary file directory
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.49 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
+[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
+[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[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.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.121 s - in org.biojava.nbio.structure.TestURLIdentifier
-[INFO] Running org.biojava.nbio.structure.ChemCompTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.nbio.structure.io.TestDBRefParsing
+[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.047 s - in org.biojava.nbio.structure.io.TestTitleParsing
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[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.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.547 s - in org.biojava.nbio.structure.ChemCompTest
-[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.591 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: 0.012 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
+[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: 1.387 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.01 s - in org.biojava.nbio.structure.TestStructureSerialization
+[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.1 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
 [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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
-[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
-[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[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] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 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: 0.006 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
-[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.06 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
+[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.TestHardBioUnits
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.TestHardBioUnits
+[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.
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.718 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
-[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 4.968 s - in org.biojava.nbio.structure.io.TestHeaderOnly
+[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.TestMMcifOrganismParsing
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
+[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.TestURLBasedFileParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
+[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.234 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
-[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 s - in org.biojava.nbio.structure.io.TestTitleParsing
-[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestHardBioUnits
-[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 7.539 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[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.
-[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.425 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.099 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.032 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.076 s - in org.biojava.nbio.structure.TestDNAAlignment
+[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.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.74 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 2.903 s - in org.biojava.nbio.structure.ChemCompTest
+[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.
-Using PDB_DIR=/tmp as temporary file directory
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.305 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
-[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.TestParseMmcifHeader
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.292 s - in org.biojava.nbio.structure.TestURLIdentifier
+[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.031 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.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.748 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
-[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.327 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
+[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.192 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
+[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.099 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
+[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.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.structure.io.TestDBRefParsing
-[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestSiftsParsing
-[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.TestWriteLargeCoordinatePDB
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
-[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
-[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.035 s - in org.biojava.nbio.structure.PdbFileFormat30Test
+[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.045 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
+[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.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.11 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.612 s - in org.biojava.nbio.structure.TestStructureSerialization
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[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.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 4.292 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
-[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.TestMmtfStructureWriter
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 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: 0.048 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.08 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
+[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.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.851 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
-[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.TestMmtfUtils
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[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.
-[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.069 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[INFO] Running org.biojava.nbio.structure.io.TestShortLines
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.52 s - in org.biojava.nbio.structure.TestKeywords
+[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: 0.265 s - in org.biojava.nbio.structure.io.TestShortLines
-[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 1.668 s - in org.biojava.nbio.structure.TestAltLocs
+[INFO] Running org.biojava.nbio.structure.TestBond
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.044 s - in org.biojava.nbio.structure.TestBond
+[INFO] Running org.biojava.nbio.structure.TestAtomIterator
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.023 s - in org.biojava.nbio.structure.TestAtomIterator
+[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.032 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[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: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.832 s - in org.biojava.nbio.structure.io.TestHeaderOnly
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.096 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
 [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.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.926 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
-[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.021 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.415 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
+[INFO] Running org.biojava.nbio.structure.TestChargeAdder
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.012 s - in org.biojava.nbio.structure.TestChargeAdder
+[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.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.027 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
-[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 s - in org.biojava.nbio.structure.SiteTest
+[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.055 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[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: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.031 s - in org.biojava.nbio.structure.asa.TestAsaCalc
-[INFO] Running org.biojava.nbio.structure.TestNucleotides
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestNucleotides
-[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestExperimentalTechniques
-[INFO] Running org.biojava.nbio.structure.TestChargeAdder
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.TestChargeAdder
-[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.005 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: 0.006 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
-[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.847 s - in org.biojava.nbio.structure.TestEntityHeuristics
+[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: 0.404 s - in org.biojava.nbio.structure.TestPdbId
+[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.
-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: 0.066 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
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 2.272 s - in org.biojava.nbio.structure.TestAtomCache
+[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.056 s - in org.biojava.nbio.structure.TestParsingCalcium
+[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.028 s - in org.biojava.nbio.structure.AtomPositionMapTest
 [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: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.25 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: 0.005 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.017 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
+[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: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.074 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.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.
-[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.047 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
+[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.284 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
 [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.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
 [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.006 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.044 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
 [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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.68 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
 [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[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
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.035 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
 [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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
-[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.align.client.TestStructureName
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.488 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
+[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.029 s - in org.biojava.nbio.structure.TestStructureCrossReferences
+[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.093 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[INFO] Running org.biojava.nbio.structure.Test2JA5
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.092 s - in org.biojava.nbio.structure.Test2JA5
+[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.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.027 s - in org.biojava.nbio.structure.align.client.TestStructureName
-[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
-[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.272 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
+[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: 1.012 s - in org.biojava.nbio.structure.PdbFileFormat30Test
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.022 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 27.851 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: 0.052 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.017 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
+[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.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.368 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
-[INFO] Running org.biojava.nbio.structure.SiteTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 5.818 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
+[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.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.structure.SiteTest
-[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.432 s - in org.biojava.nbio.structure.ResidueRangeTest
+[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.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.162 s - in org.biojava.nbio.structure.SourceCompoundTest
-[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: 0.297 s - in org.biojava.nbio.structure.TestPdbId
-[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.288 s - in org.biojava.nbio.structure.Test4hhb
+[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: 8.955 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: 0.023 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
-[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.031 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
-[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.68 s - in org.biojava.nbio.structure.HetatomImplTest
+[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.nbio.structure.ResidueNumberTest
+[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: 2.998 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.097 s - in org.biojava.nbio.structure.asa.TestAsaCalc
 [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: 4.423 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
-[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: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.349 s - in org.biojava.nbio.structure.TestCalc
-[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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.915 s - in org.biojava.nbio.structure.Test4hhb
-[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.959 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
+[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.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.007 s - in org.biojava.nbio.structure.TestEntityHeuristics
-[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.027 s - in org.biojava.nbio.structure.TestParsingCalcium
-[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.029 s - in org.biojava.nbio.structure.TestStructureCrossReferences
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.848 s - in org.biojava.nbio.structure.SourceCompoundTest
+[INFO] Running org.biojava.nbio.structure.PDBStatusTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.009 s - in org.biojava.nbio.structure.PDBStatusTest
+[INFO] Running org.biojava.nbio.structure.TestCloning
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.032 s - in org.biojava.nbio.structure.TestCloning
 [INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[INFO] Running org.biojava.nbio.structure.TestKeywords
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.016 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
+[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.048 s - in org.biojava.nbio.structure.contact.TestContactCalc
+[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.332 s - in org.biojava.nbio.structure.TestKeywords
-[INFO] Running org.biojava.nbio.structure.TestBond
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.069 s - in org.biojava.nbio.structure.TestBond
-[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
+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: 0.381 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
+[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.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 2.18 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
-[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.038 s - in org.biojava.nbio.structure.TestDNAAlignment
-[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.427 s - in org.biojava.nbio.structure.TestCalc
+[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.
-[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.378 s - in org.biojava.nbio.structure.ResidueRangeTest
-[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[INFO] Running org.biojava.nbio.structure.PDBStatusTest
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.012 s - in org.biojava.nbio.structure.PDBStatusTest
-[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.063 s - in org.biojava.nbio.structure.AtomPositionMapTest
-[INFO] Running org.biojava.nbio.structure.Test2JA5
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 2.386 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: 0.066 s - in org.biojava.nbio.structure.ResidueNumberTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.352 s - in org.biojava.nbio.structure.TestStructureImpl
+[INFO] Running org.biojava.nbio.structure.ElementTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 s - in org.biojava.nbio.structure.ElementTest
+[INFO] Running org.biojava.nbio.structure.TestNucleotides
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.06 s - in org.biojava.nbio.structure.TestNucleotides
+[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.036 s - in org.biojava.nbio.structure.TestExperimentalTechniques
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6317,20 +6353,20 @@
 [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: 0.275 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: 0.293 s - in org.biojava.nbio.structure.gui.RenderStyleTest
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.38 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
+[INFO] Running org.biojava.nbio.structure.gui.ViewerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.636 s - in org.biojava.nbio.structure.gui.ViewerTest
 [INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.439 s - in org.biojava.nbio.structure.gui.StructureViewerTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.517 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: 0.225 s - in org.biojava.nbio.structure.gui.TestAtomInfo
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.556 s - in org.biojava.nbio.structure.gui.TestAtomInfo
+[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 s - in org.biojava.nbio.structure.gui.RenderStyleTest
 [INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.294 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
-[INFO] Running org.biojava.nbio.structure.gui.ViewerTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.399 s - in org.biojava.nbio.structure.gui.ViewerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.472 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6359,51 +6395,51 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.genome.TestIssue355
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.31 s - in org.biojava.nbio.genome.TestIssue355
-[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.552 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.437 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: 0.084 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 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: 0.081 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.938 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.604 s - in org.biojava.nbio.genome.io.fastq.FastqTest
+[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: 3.134 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
+[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.586 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.356 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.401 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.247 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.189 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.TestIssue355
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.genome.TestIssue355
+[INFO] Running org.biojava.nbio.genome.TestLocation
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 s - in org.biojava.nbio.genome.TestLocation
+[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.076 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: 0.237 s - in org.biojava.nbio.genome.FeatureListTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.nbio.genome.FeatureListTest
 [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: 0.207 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
-[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.474 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
+[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: 0.424 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.624 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.188 s - in org.biojava.nbio.genome.io.fastq.FastqTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.682 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
-[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.438 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 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: 4.884 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.095 s - in org.biojava.nbio.genome.TestGenomeMapping
-[INFO] Running org.biojava.nbio.genome.TestLocation
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 s - in org.biojava.nbio.genome.TestLocation
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.071 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6432,20 +6468,20 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running 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] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.114 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: 4.288 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.415 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
 [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: 5.066 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.641 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
+[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.08 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
+[INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.269 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6475,7 +6511,7 @@
 [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: 0.127 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.438 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6508,9 +6544,9 @@
 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: 21.986 s - in org.biojava.nbio.ronn.JronnTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.46 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: 13.419 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.507 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6539,42 +6575,32 @@
 [INFO] -------------------------------------------------------
 [INFO]  T E S T S
 [INFO] -------------------------------------------------------
-[INFO] Running 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.
-SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
-NP_000257                133 aa            linear   PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715
-SequenceName,A,N,MolecularWeight
-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: 4.955 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.816 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.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.457 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.386 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
 [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: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.259 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
-[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.086 s - in org.biojava.nbio.aaproperties.xml.ElementTest
-[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.188 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
+[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.432 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
+[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest
 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.aaproperties.xml.GenerateJavaCodesFromTextTest
+SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
+NP_000257                133 aa            linear   PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715
+SequenceName,A,N,MolecularWeight
+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: 2.093 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
 [INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
 SLF4J: Defaulting to no-operation (NOP) logger implementation
@@ -6591,12 +6617,22 @@
 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: 11.323 s - in org.biojava.nbio.aaproperties.CommandPromptTest
-[INFO] Running org.biojava.nbio.aaproperties.CookBookTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.696 s - in org.biojava.nbio.aaproperties.CommandPromptTest
+[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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.009 s - in org.biojava.nbio.aaproperties.CookBookTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.388 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
+[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.934 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
+[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.13 s - in org.biojava.nbio.aaproperties.xml.ElementTest
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6649,17 +6685,17 @@
 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: 0.802 s - in org.biojava.nbio.ontology.TestParseSBO
-[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.967 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: 1.337 s - in org.biojava.nbio.ontology.TestOboFileParsing
-[INFO] Running org.biojava.nbio.ontology.TestParseOBO
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.576 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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.281 s - in org.biojava.nbio.ontology.TestParseOBO
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.086 s - in org.biojava.nbio.ontology.TestOboFileParsing
 [INFO] 
 [INFO] Results:
 [INFO] 
@@ -6688,26 +6724,26 @@
 [INFO] ------------------------------------------------------------------------
 [INFO] Reactor Summary for biojava 6.1.0:
 [INFO] 
-[INFO] biojava ............................................ SUCCESS [  0.009 s]
-[INFO] biojava-core ....................................... SUCCESS [30:59 min]
-[INFO] biojava-forester ................................... SUCCESS [  0.046 s]
-[INFO] biojava-alignment .................................. SUCCESS [09:12 min]
-[INFO] biojava-structure .................................. SUCCESS [53:28 min]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.574 s]
+[INFO] biojava ............................................ SUCCESS [  0.004 s]
+[INFO] biojava-core ....................................... SUCCESS [31:51 min]
+[INFO] biojava-forester ................................... SUCCESS [  0.213 s]
+[INFO] biojava-alignment .................................. SUCCESS [09:41 min]
+[INFO] biojava-structure .................................. SUCCESS [57:46 min]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.113 s]
 [INFO] biojava-structure-gui .............................. SUCCESS [03:19 min]
-[INFO] biojava-genome ..................................... SUCCESS [09:51 min]
-[INFO] biojava-modfinder .................................. SUCCESS [02:18 min]
-[INFO] biojava-ws ......................................... SUCCESS [ 33.738 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [01:39 min]
-[INFO] biojava-aa-prop .................................... SUCCESS [05:29 min]
-[INFO] biojava-survival ................................... SUCCESS [  1.103 s]
-[INFO] biojava-ontology ................................... SUCCESS [01:48 min]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [  6.850 s]
+[INFO] biojava-genome ..................................... SUCCESS [09:36 min]
+[INFO] biojava-modfinder .................................. SUCCESS [02:06 min]
+[INFO] biojava-ws ......................................... SUCCESS [ 32.792 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [01:20 min]
+[INFO] biojava-aa-prop .................................... SUCCESS [04:32 min]
+[INFO] biojava-survival ................................... SUCCESS [  0.075 s]
+[INFO] biojava-ontology ................................... SUCCESS [01:38 min]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.154 s]
 [INFO] ------------------------------------------------------------------------
 [INFO] BUILD SUCCESS
 [INFO] ------------------------------------------------------------------------
-[INFO] Total time:  01:58 h
-[INFO] Finished at: 2026-02-25T00:47:51-12:00
+[INFO] Total time:  02:02 h
+[INFO] Finished at: 2025-01-23T22:46:13+14:00
 [INFO] ------------------------------------------------------------------------
    create-stamp debian/debhelper-build-stamp
    dh_prep
@@ -6939,26 +6975,26 @@
 [INFO] ------------------------------------------------------------------------
 [INFO] Reactor Summary for biojava 6.1.0:
 [INFO] 
-[INFO] biojava ............................................ SUCCESS [ 20.373 s]
-[INFO] biojava-core ....................................... SUCCESS [  0.153 s]
-[INFO] biojava-forester ................................... SUCCESS [  0.085 s]
-[INFO] biojava-alignment .................................. SUCCESS [  0.154 s]
-[INFO] biojava-structure .................................. SUCCESS [  0.192 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.044 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [  0.085 s]
-[INFO] biojava-genome ..................................... SUCCESS [  0.058 s]
-[INFO] biojava-modfinder .................................. SUCCESS [  0.181 s]
-[INFO] biojava-ws ......................................... SUCCESS [  0.068 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [  0.054 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [  0.042 s]
-[INFO] biojava-survival ................................... SUCCESS [  0.053 s]
-[INFO] biojava-ontology ................................... SUCCESS [  0.072 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.075 s]
+[INFO] biojava ............................................ SUCCESS [  2.005 s]
+[INFO] biojava-core ....................................... SUCCESS [  0.368 s]
+[INFO] biojava-forester ................................... SUCCESS [  0.426 s]
+[INFO] biojava-alignment .................................. SUCCESS [  0.484 s]
+[INFO] biojava-structure .................................. SUCCESS [  0.188 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [  0.453 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [  0.316 s]
+[INFO] biojava-genome ..................................... SUCCESS [  0.123 s]
+[INFO] biojava-modfinder .................................. SUCCESS [  0.262 s]
+[INFO] biojava-ws ......................................... SUCCESS [  0.347 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [  0.456 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [  0.203 s]
+[INFO] biojava-survival ................................... SUCCESS [  0.240 s]
+[INFO] biojava-ontology ................................... SUCCESS [  0.250 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [  0.126 s]
 [INFO] ------------------------------------------------------------------------
 [INFO] BUILD SUCCESS
 [INFO] ------------------------------------------------------------------------
-[INFO] Total time:  23.543 s
-[INFO] Finished at: 2026-02-25T00:48:46-12:00
+[INFO] Total time:  7.493 s
+[INFO] Finished at: 2025-01-23T22:46:29+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...
@@ -7180,16 +7216,16 @@
    jh_classpath
 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"
 Duplicate specification "V:s" 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 "version|V" for option "V"
 Duplicate specification "V:s" for option "V"
 Duplicate specification "version|V" for option "V"
+Duplicate specification "V:s" for option "V"
+Duplicate specification "V:s" for option "V"
    jh_manifest
    jh_depends
    dh_strip_nondeterminism
@@ -7198,12 +7234,12 @@
    dh_missing
    dh_installdeb
    dh_gencontrol
-dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined
-dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:Depends} unused, but is defined
-dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:DocDepends} unused, but is defined
 dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:CompileDepends} unused, but is defined
 dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:Depends} unused, but is defined
 dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:DocDepends} unused, but is defined
+dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined
+dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:Depends} unused, but is defined
+dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:DocDepends} unused, but is defined
    dh_md5sums
    dh_builddeb
 dpkg-deb: building package 'libbiojava6-java-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-5_all.deb'.
@@ -7215,12 +7251,14 @@
 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/770555/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/770555/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/640563 and its subdirectories
-I: Current time: Wed Feb 25 00:59:22 -12 2026
-I: pbuilder-time-stamp: 1772024362
+I: removing directory /srv/workspace/pbuilder/770555 and its subdirectories
+I: Current time: Thu Jan 23 22:57:46 +14 2025
+I: pbuilder-time-stamp: 1737622666