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| Offset 3017, 21 lines modified | Offset 3017, 21 lines modified | ||
| 3017 | <dd> | 3017 | <dd> |
| 3018 | <div·class="block">Create·a·bean·from·an·XML·file,·then·attempt·to·enter·it.</div> | 3018 | <div·class="block">Create·a·bean·from·an·XML·file,·then·attempt·to·enter·it.</div> |
| 3019 | </dd> | 3019 | </dd> |
| 3020 | <dt><a·href="org/biojava/utils/xml/AppBeanRunner.html#%3Cinit%3E()"·class="member-name-link">AppBeanRunner()</a>·-·Constructor·for·class·org.biojava.utils.xml.<a·href="org/biojava/utils/xml/AppBeanRunner.html"·title="class·in·org.biojava.utils.xml">AppBeanRunner</a></dt> | 3020 | <dt><a·href="org/biojava/utils/xml/AppBeanRunner.html#%3Cinit%3E()"·class="member-name-link">AppBeanRunner()</a>·-·Constructor·for·class·org.biojava.utils.xml.<a·href="org/biojava/utils/xml/AppBeanRunner.html"·title="class·in·org.biojava.utils.xml">AppBeanRunner</a></dt> |
| 3021 | <dd> </dd> | 3021 | <dd> </dd> |
| 3022 | <dt><a·href="org/biojava/utils/automata/NfaSubModel.html#append(org.biojava.utils.automata.NfaSubModel)"·class="member-name-link">append(NfaSubModel)</a>·-·Method·in·class·org.biojava.utils.automata.<a·href="org/biojava/utils/automata/NfaSubModel.html"·title="class·in·org.biojava.utils.automata">NfaSubModel</a></dt> | 3022 | <dt><a·href="org/biojava/utils/automata/NfaSubModel.html#append(org.biojava.utils.automata.NfaSubModel)"·class="member-name-link">append(NfaSubModel)</a>·-·Method·in·class·org.biojava.utils.automata.<a·href="org/biojava/utils/automata/NfaSubModel.html"·title="class·in·org.biojava.utils.automata">NfaSubModel</a></dt> |
| 3023 | <dd> </dd> | 3023 | <dd> </dd> |
| 3024 | <dt><a·href="org/biojava/bio/program/fastq/ | 3024 | <dt><a·href="org/biojava/bio/program/fastq/SangerFastqWriter.html#append(T,java.lang.Iterable)"·class="member-name-link">append(T,·Iterable<Fastq>)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/SangerFastqWriter.html"·title="class·in·org.biojava.bi[·...·truncated·by·diffoscope;·len:·23,·SHA:·b850d16508fe237e228028a31d353b0c9786543866b4cfc2c135bd3245517eeb·...·]FastqWriter</a></dt> |
| 3025 | <dd> </dd> | 3025 | <dd> </dd> |
| 3026 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#append(T,java.lang.Iterable)"·class="member-name-link">append(T,·Iterable<Fastq>)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> | 3026 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#append(T,java.lang.Iterable)"·class="member-name-link">append(T,·Iterable<Fastq>)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> |
| 3027 | <dd> | 3027 | <dd> |
| 3028 | <div·class="block">Append·the·specified·FASTQ·formatted·sequences·to·the·specified·appendable.</div> | 3028 | <div·class="block">Append·the·specified·FASTQ·formatted·sequences·to·the·specified·appendable.</div> |
| 3029 | </dd> | 3029 | </dd> |
| 3030 | <dt><a·href="org/biojava/bio/program/fastq/ | 3030 | <dt><a·href="org/biojava/bio/program/fastq/SangerFastqWriter.html#append(T,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">append(T,·Fastq...)</a>·-·Method·in·class·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/SangerFastqWriter.html"·title="class·in·org.bio[·...·truncated·by·diffoscope;·len:·30,·SHA:·a624089fb2c7d8b70b42de02535ee7de650002bb71c863f002bcc035599cb4c6·...·]FastqWriter</a></dt> |
| 3031 | <dd> </dd> | 3031 | <dd> </dd> |
| 3032 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#append(T,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">append(T,·Fastq...)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> | 3032 | <dt><a·href="org/biojava/bio/program/fastq/FastqWriter.html#append(T,org.biojava.bio.program.fastq.Fastq...)"·class="member-name-link">append(T,·Fastq...)</a>·-·Method·in·interface·org.biojava.bio.program.fastq.<a·href="org/biojava/bio/program/fastq/FastqWriter.html"·title="interface·in·org.biojava.bio.program.fastq">FastqWriter</a></dt> |
| 3033 | <dd> | 3033 | <dd> |
| 3034 | <div·class="block">Append·the·specified·FASTQ·formatted·sequences·to·the·specified·appendable.</div> | 3034 | <div·class="block">Append·the·specified·FASTQ·formatted·sequences·to·the·specified·appendable.</div> |
| 3035 | </dd> | 3035 | </dd> |
| 3036 | <dt><a·href="org/biojavax/bio/phylo/io/nexus/CharactersBlock.html#appendMatrixData(java.lang.String,java.lang.Object)"·class="member-name-link">appendMatrixData(String,·Object)</a>·-·Method·in·class·org.biojavax.bio.phylo.io.nexus.<a·href="org/biojavax/bio/phylo/io/nexus/CharactersBlock.html"·title="class·in·org.biojavax.bio.phylo.io.nexus">CharactersBlock</a></dt> | 3036 | <dt><a·href="org/biojavax/bio/phylo/io/nexus/CharactersBlock.html#appendMatrixData(java.lang.String,java.lang.Object)"·class="member-name-link">appendMatrixData(String,·Object)</a>·-·Method·in·class·org.biojavax.bio.phylo.io.nexus.<a·href="org/biojavax/bio/phylo/io/nexus/CharactersBlock.html"·title="class·in·org.biojavax.bio.phylo.io.nexus">CharactersBlock</a></dt> |
| 3037 | <dd> </dd> | 3037 | <dd> </dd> |
| Offset 2779, 22 lines modified | Offset 2779, 22 lines modified | ||
| 2779 | ··_\x8A_\x8p_\x8p_\x8B_\x8e_\x8a_\x8n_\x8R_\x8u_\x8n_\x8n_\x8e_\x8r·-·Class·in·_\x8o_\x8r_\x8g_\x8._\x8b_\x8i_\x8o_\x8j_\x8a_\x8v_\x8a_\x8._\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8x_\x8m_\x8l | 2779 | ··_\x8A_\x8p_\x8p_\x8B_\x8e_\x8a_\x8n_\x8R_\x8u_\x8n_\x8n_\x8e_\x8r·-·Class·in·_\x8o_\x8r_\x8g_\x8._\x8b_\x8i_\x8o_\x8j_\x8a_\x8v_\x8a_\x8._\x8u_\x8t_\x8i_\x8l_\x8s_\x8._\x8x_\x8m_\x8l |
| 2780 | ······Create·a·bean·from·an·XML·file,·then·attempt·to·enter·it. | 2780 | ······Create·a·bean·from·an·XML·file,·then·attempt·to·enter·it. |
| 2781 | ··_\x8A_\x8p_\x8p_\x8B_\x8e_\x8a_\x8n_\x8R_\x8u_\x8n_\x8n_\x8e_\x8r_\x8(_\x8)·-·Constructor·for·class·org.biojava.utils.xml._\x8A_\x8p_\x8p_\x8B_\x8e_\x8a_\x8n_\x8R_\x8u_\x8n_\x8n_\x8e_\x8r | 2781 | ··_\x8A_\x8p_\x8p_\x8B_\x8e_\x8a_\x8n_\x8R_\x8u_\x8n_\x8n_\x8e_\x8r_\x8(_\x8)·-·Constructor·for·class·org.biojava.utils.xml._\x8A_\x8p_\x8p_\x8B_\x8e_\x8a_\x8n_\x8R_\x8u_\x8n_\x8n_\x8e_\x8r |
| 2782 | ······ | 2782 | ······ |
| 2783 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8N_\x8f_\x8a_\x8S_\x8u_\x8b_\x8M_\x8o_\x8d_\x8e_\x8l_\x8)·-·Method·in·class·org.biojava.utils.automata._\x8N_\x8f_\x8a_\x8S_\x8u_\x8b_\x8M_\x8o_\x8d_\x8e_\x8l | 2783 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8N_\x8f_\x8a_\x8S_\x8u_\x8b_\x8M_\x8o_\x8d_\x8e_\x8l_\x8)·-·Method·in·class·org.biojava.utils.automata._\x8N_\x8f_\x8a_\x8S_\x8u_\x8b_\x8M_\x8o_\x8d_\x8e_\x8l |
| 2784 | ······ | 2784 | ······ |
| 2785 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·class | 2785 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·class |
| 2786 | ··org.biojava.bio.program.fastq._\x8 | 2786 | ··org.biojava.bio.program.fastq._\x8S_.a_.n_.g_.e_.r_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r |
| 2787 | ······ | 2787 | ······ |
| 2788 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·interface | 2788 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8I_\x8t_\x8e_\x8r_\x8a_\x8b_\x8l_\x8e_\x8<_\x8F_\x8a_\x8s_\x8t_\x8q_\x8>_\x8)·-·Method·in·interface |
| 2789 | ··org.biojava.bio.program.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r | 2789 | ··org.biojava.bio.program.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r |
| 2790 | ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified | 2790 | ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified |
| 2791 | ······appendable. | 2791 | ······appendable. |
| 2792 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·class | 2792 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·class |
| 2793 | ··org.biojava.bio.program.fastq._\x8 | 2793 | ··org.biojava.bio.program.fastq._\x8S_.a_.n_.g_.e_.r_\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r |
| 2794 | ······ | 2794 | ······ |
| 2795 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·interface | 2795 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8(_\x8T_\x8,_\x8·_\x8F_\x8a_\x8s_\x8t_\x8q_\x8._\x8._\x8._\x8)·-·Method·in·interface |
| 2796 | ··org.biojava.bio.program.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r | 2796 | ··org.biojava.bio.program.fastq._\x8F_\x8a_\x8s_\x8t_\x8q_\x8W_\x8r_\x8i_\x8t_\x8e_\x8r |
| 2797 | ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified | 2797 | ······Append·the·specified·FASTQ·formatted·sequences·to·the·specified |
| 2798 | ······appendable. | 2798 | ······appendable. |
| 2799 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8M_\x8a_\x8t_\x8r_\x8i_\x8x_\x8D_\x8a_\x8t_\x8a_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8O_\x8b_\x8j_\x8e_\x8c_\x8t_\x8)·-·Method·in·class | 2799 | ··_\x8a_\x8p_\x8p_\x8e_\x8n_\x8d_\x8M_\x8a_\x8t_\x8r_\x8i_\x8x_\x8D_\x8a_\x8t_\x8a_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8O_\x8b_\x8j_\x8e_\x8c_\x8t_\x8)·-·Method·in·class |
| 2800 | ··org.biojavax.bio.phylo.io.nexus._\x8C_\x8h_\x8a_\x8r_\x8a_\x8c_\x8t_\x8e_\x8r_\x8s_\x8B_\x8l_\x8o_\x8c_\x8k | 2800 | ··org.biojavax.bio.phylo.io.nexus._\x8C_\x8h_\x8a_\x8r_\x8a_\x8c_\x8t_\x8e_\x8r_\x8s_\x8B_\x8l_\x8o_\x8c_\x8k |
| Offset 3994, 25 lines modified | Offset 3994, 25 lines modified | ||
| 3994 | },·{ | 3994 | },·{ |
| 3995 | ····"p":·"org.biojava.utils.automata", | 3995 | ····"p":·"org.biojava.utils.automata", |
| 3996 | ····"c":·"NfaSubModel", | 3996 | ····"c":·"NfaSubModel", |
| 3997 | ····"l":·"append(NfaSubModel)", | 3997 | ····"l":·"append(NfaSubModel)", |
| 3998 | ····"u":·"append(org.biojava.utils.automata.NfaSubModel)" | 3998 | ····"u":·"append(org.biojava.utils.automata.NfaSubModel)" |
| 3999 | },·{ | 3999 | },·{ |
| 4000 | ····"p":·"org.biojava.bio.program.fastq", | 4000 | ····"p":·"org.biojava.bio.program.fastq", |
| 4001 | ····"c":·" | 4001 | ····"c":·"SangerFastqWriter", |
| 4002 | ····"l":·"append(T,·Fastq...)", | 4002 | ····"l":·"append(T,·Fastq...)", |
| 4003 | ····"u":·"append(T,org.biojava.bio.program.fastq.Fastq...)" | 4003 | ····"u":·"append(T,org.biojava.bio.program.fastq.Fastq...)" |
| 4004 | },·{ | 4004 | },·{ |
| 4005 | ····"p":·"org.biojava.bio.program.fastq", | 4005 | ····"p":·"org.biojava.bio.program.fastq", |
| 4006 | ····"c":·"FastqWriter", | 4006 | ····"c":·"FastqWriter", |
| 4007 | ····"l":·"append(T,·Fastq...)", | 4007 | ····"l":·"append(T,·Fastq...)", |
| 4008 | ····"u":·"append(T,org.biojava.bio.program.fastq.Fastq...)" | 4008 | ····"u":·"append(T,org.biojava.bio.program.fastq.Fastq...)" |
| 4009 | },·{ | 4009 | },·{ |
| 4010 | ····"p":·"org.biojava.bio.program.fastq", | 4010 | ····"p":·"org.biojava.bio.program.fastq", |
| 4011 | ····"c":·" | 4011 | ····"c":·"SangerFastqWriter", |
| 4012 | ····"l":·"append(T,·Iterable<Fastq>)", | 4012 | ····"l":·"append(T,·Iterable<Fastq>)", |
| 4013 | ····"u":·"append(T,java.lang.Iterable)" | 4013 | ····"u":·"append(T,java.lang.Iterable)" |
| 4014 | },·{ | 4014 | },·{ |
| 4015 | ····"p":·"org.biojava.bio.program.fastq", | 4015 | ····"p":·"org.biojava.bio.program.fastq", |
| 4016 | ····"c":·"FastqWriter", | 4016 | ····"c":·"FastqWriter", |
| 4017 | ····"l":·"append(T,·Iterable<Fastq>)", | 4017 | ····"l":·"append(T,·Iterable<Fastq>)", |
| 4018 | ····"u":·"append(T,java.lang.Iterable)" | 4018 | ····"u":·"append(T,java.lang.Iterable)" |