Author: osallou Date: 2015-08-18 14:20:10 +0000 (Tue, 18 Aug 2015) New Revision: 19977
Added: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/ trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/changelog trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/control trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/libbiojava4-java-doc.doc-base trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/patches/fix_ascii_characters_mapping Removed: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/changelog trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/control trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/libbiojava4-java-doc.doc-base trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/patches/fix_ascii_characters_mapping Log: [svn-buildpackage] Tagging biojava4-live 4.1.0+dfsg-3 Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/changelog =================================================================== --- trunk/packages/biojava4-live/trunk/debian/changelog 2015-08-17 12:13:53 UTC (rev 19969) +++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/changelog 2015-08-18 14:20:10 UTC (rev 19977) @@ -1,17 +0,0 @@ -biojava4-live (4.1.0+dfsg-2) unstable; urgency=medium - - * Remove some network related tests (Closes: #795685). - - -- Olivier Sallou <[email protected]> Sun, 16 Aug 2015 16:33:47 +0200 - -biojava4-live (4.1.0+dfsg-1) unstable; urgency=medium - - * New upstream release - - -- Olivier Sallou <[email protected]> Wed, 12 Aug 2015 09:32:50 +0200 - -biojava4-live (4.0.0+dfsg-1) unstable; urgency=medium - - * BioJava4 packaging (Closes: #776704). - - -- Olivier Sallou <[email protected]> Fri, 30 Jan 2015 17:24:21 +0100 Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/changelog (from rev 19971, trunk/packages/biojava4-live/trunk/debian/changelog) =================================================================== --- trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/changelog (rev 0) +++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/changelog 2015-08-18 14:20:10 UTC (rev 19977) @@ -0,0 +1,23 @@ +biojava4-live (4.1.0+dfsg-3) unstable; urgency=medium + + * Fix FTBS unmappable characters (Closes: #795849). + + -- Olivier Sallou <[email protected]> Mon, 17 Aug 2015 14:54:33 +0000 + +biojava4-live (4.1.0+dfsg-2) unstable; urgency=medium + + * Remove some network related tests (Closes: #795685). + + -- Olivier Sallou <[email protected]> Sun, 16 Aug 2015 16:33:47 +0200 + +biojava4-live (4.1.0+dfsg-1) unstable; urgency=medium + + * New upstream release + + -- Olivier Sallou <[email protected]> Wed, 12 Aug 2015 09:32:50 +0200 + +biojava4-live (4.0.0+dfsg-1) unstable; urgency=medium + + * BioJava4 packaging (Closes: #776704). + + -- Olivier Sallou <[email protected]> Fri, 30 Jan 2015 17:24:21 +0100 Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/control =================================================================== --- trunk/packages/biojava4-live/trunk/debian/control 2015-08-17 12:13:53 UTC (rev 19969) +++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/control 2015-08-18 14:20:10 UTC (rev 19977) @@ -1,84 +0,0 @@ -Source: biojava4-live -Section: java -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Olivier Sallou <[email protected]> -Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java, - libcommons-collections3-java, libcommons-pool-java (>= 1.1), - libcommons-logging-java, libcommons-math-java, - libcommons-cli-java, libguava-java (>= 17.0), - libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java, - default-jdk (>= 1:1.6), junit4,javahelper (>=0.25), - ant-optional, icedtea-netx, libhamcrest-java, - libjson-simple-java (>=1.1.1), - liblog4j2-java, libslf4j-java, - libxmlunit-java -Build-Depends: debhelper (>= 9), ant -Standards-Version: 3.9.6 -Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava4/trunk/ -Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava4/trunk/ -Homepage: http://www.biojava.org - -Package: libbiojava4.0-java -Architecture: all -Depends: ${java:Depends}, ${misc:Depends}, - libcommons-pool-java (>= 1.1), - libcommons-collections3-java, - libcommons-dbcp-java (>= 1.1), - libcommons-logging-java, - libhsqldb-java, - libbytecode-java, - icedtea-netx, - libjson-simple-java, - libcommons-codec-java, - libitext5-java (>= 5.4.1), - libjmol-java, - liblog4j2-java, - libguava-java (>= 17.0), - libslf4j-java, - libcommons-math-java -Suggests: java-virtual-machine, libjgrapht-java, libbiojava4-java, libbiojava4-java-doc -Description: Java API to biological data and applications (version 4) - This package presents the Open Source Java API to biological databases - and a series of mostly sequence-based algorithms. - . - BioJava is an open-source project dedicated to providing a Java framework - for processing biological data. It includes objects for manipulating - sequences, file parsers, server support, access to BioSQL - and Ensembl databases, and powerful analysis and statistical routines - including a dynamic programming toolkit. - -Package: libbiojava4-java -Architecture: all -Depends: libbiojava4.0-java, ${misc:Depends} -Provides: libbiojava4-java -Description: Java API to biological data and applications (default version) - BioJava is an open-source project dedicated to providing a Java framework - for processing biological data. It includes objects for manipulating - sequences, file parsers, server support, access to BioSQL - and Ensembl databases, and powerful analysis and statistical routines - including a dynamic programming toolkit. - . - BioJava is provided by a vibrant community which meets annually at - the Bioinformatics Open Source Conference (BOSC) that traditionally - accompanies the Intelligent Systems in Molecular Biology (ISMB) - meeting. Much like BioPerl, the employment of this library is valuable - for everybody active in the field because of the many tricks of the - trade one learns just by communicating on the mailing list. - . - This is a wrapper package which should enable smooth upgrades to new - versions. - -Package: libbiojava4-java-doc -Section: doc -Architecture: all -Depends: ${misc:Depends} -Recommends: konqueror|html-browser -Suggests: libbiojava4-java-demos, libbiojava4-java -Description: [Biology] Documentation for BioJava - BioJava is an open-source project dedicated to providing a Java framework - for processing biological data. - . - This package contains the HTML documentation describing the API of BioJava - which was generated automatically by JavaDoc. - Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/control (from rev 19973, trunk/packages/biojava4-live/trunk/debian/control) =================================================================== --- trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/control (rev 0) +++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/control 2015-08-18 14:20:10 UTC (rev 19977) @@ -0,0 +1,84 @@ +Source: biojava4-live +Section: java +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java, + libcommons-collections3-java, libcommons-pool-java (>= 1.1), + libcommons-logging-java, libcommons-math-java, + libcommons-cli-java, libguava-java (>= 17.0), + libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java, + default-jdk (>= 1:1.6), junit4,javahelper (>=0.25), + ant-optional, icedtea-netx, libhamcrest-java, + libjson-simple-java (>=1.1.1), + liblog4j2-java, libslf4j-java, + libxmlunit-java +Build-Depends: debhelper (>= 9), ant +Standards-Version: 3.9.6 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava4-live/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava4-live/trunk/ +Homepage: http://www.biojava.org + +Package: libbiojava4.0-java +Architecture: all +Depends: ${java:Depends}, ${misc:Depends}, + libcommons-pool-java (>= 1.1), + libcommons-collections3-java, + libcommons-dbcp-java (>= 1.1), + libcommons-logging-java, + libhsqldb-java, + libbytecode-java, + icedtea-netx, + libjson-simple-java, + libcommons-codec-java, + libitext5-java (>= 5.4.1), + libjmol-java, + liblog4j2-java, + libguava-java (>= 17.0), + libslf4j-java, + libcommons-math-java +Suggests: java-virtual-machine, libjgrapht-java, libbiojava4-java, libbiojava4-java-doc +Description: Java API to biological data and applications (version 4) + This package presents the Open Source Java API to biological databases + and a series of mostly sequence-based algorithms. + . + BioJava is an open-source project dedicated to providing a Java framework + for processing biological data. It includes objects for manipulating + sequences, file parsers, server support, access to BioSQL + and Ensembl databases, and powerful analysis and statistical routines + including a dynamic programming toolkit. + +Package: libbiojava4-java +Architecture: all +Depends: libbiojava4.0-java, ${misc:Depends} +Provides: libbiojava4-java +Description: Java API to biological data and applications (default version) + BioJava is an open-source project dedicated to providing a Java framework + for processing biological data. It includes objects for manipulating + sequences, file parsers, server support, access to BioSQL + and Ensembl databases, and powerful analysis and statistical routines + including a dynamic programming toolkit. + . + BioJava is provided by a vibrant community which meets annually at + the Bioinformatics Open Source Conference (BOSC) that traditionally + accompanies the Intelligent Systems in Molecular Biology (ISMB) + meeting. Much like BioPerl, the employment of this library is valuable + for everybody active in the field because of the many tricks of the + trade one learns just by communicating on the mailing list. + . + This is a wrapper package which should enable smooth upgrades to new + versions. + +Package: libbiojava4-java-doc +Section: doc +Architecture: all +Depends: ${misc:Depends} +Recommends: konqueror|html-browser +Suggests: libbiojava4-java-demos, libbiojava4-java +Description: [Biology] Documentation for BioJava + BioJava is an open-source project dedicated to providing a Java framework + for processing biological data. + . + This package contains the HTML documentation describing the API of BioJava + which was generated automatically by JavaDoc. + Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/libbiojava4-java-doc.doc-base =================================================================== --- trunk/packages/biojava4-live/trunk/debian/libbiojava4-java-doc.doc-base 2015-08-17 12:13:53 UTC (rev 19969) +++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/libbiojava4-java-doc.doc-base 2015-08-18 14:20:10 UTC (rev 19977) @@ -1,26 +0,0 @@ -Document: biojava4 -Title: biojava4 API -Author: BioJava developers -Abstract: Javadoc-generated API for the BioJava library. - BioJava is an open-source project dedicated to providing a Java framework - for processing biological data. It includes objects for manipulating - sequences, file parsers, DAS client and server support, access to BioSQL - and Ensembl databases, and powerful analysis and statistical routines - including a dynamic programming toolkit. - . - BioJava is provided by a vibrant community which meets annually at - the Bioinformatics Open Source Conference (BOSC) that traditionally - accompanies the Intelligent Systems in Molecular Biology (ISMB) - meeting. Much like BioPerl, the employment of this library is valuable - for everybody active in the field because of the many tricks of the - trade one learns just by communicating on the mailing list. - . - If using BioJava, please cite: R.C.G. Holland, T. Down, M. Pocock, - A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, - M. Heuer; M.J. Schreiber (2008) "BioJava: an Open-Source Framework - for Bioinformatics" Bioinformatics 24(18):2096-2097. -Section: Science/Biology - -Format: HTML -Index: /usr/share/doc/libbiojava4-java/api/index.html -Files: /usr/share/doc/libbiojava4-java/api/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*/*/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*/*/*/*/*.html Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/libbiojava4-java-doc.doc-base (from rev 19972, trunk/packages/biojava4-live/trunk/debian/libbiojava4-java-doc.doc-base) =================================================================== --- trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/libbiojava4-java-doc.doc-base (rev 0) +++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/libbiojava4-java-doc.doc-base 2015-08-18 14:20:10 UTC (rev 19977) @@ -0,0 +1,26 @@ +Document: biojava4 +Title: biojava4 API +Author: BioJava developers +Abstract: Javadoc-generated API for the BioJava library. + BioJava is an open-source project dedicated to providing a Java framework + for processing biological data. It includes objects for manipulating + sequences, file parsers, DAS client and server support, access to BioSQL + and Ensembl databases, and powerful analysis and statistical routines + including a dynamic programming toolkit. + . + BioJava is provided by a vibrant community which meets annually at + the Bioinformatics Open Source Conference (BOSC) that traditionally + accompanies the Intelligent Systems in Molecular Biology (ISMB) + meeting. Much like BioPerl, the employment of this library is valuable + for everybody active in the field because of the many tricks of the + trade one learns just by communicating on the mailing list. + . + If using BioJava, please cite: R.C.G. Holland, T. Down, M. Pocock, + A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, + M. Heuer; M.J. Schreiber (2008) "BioJava: an Open-Source Framework + for Bioinformatics" Bioinformatics 24(18):2096-2097. +Section: Science/Biology + +Format: HTML +Index: /usr/share/doc/libbiojava4-java/api/index-all.html +Files: /usr/share/doc/libbiojava4-java/api/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*/*/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*/*/*/*/*.html Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/patches/fix_ascii_characters_mapping =================================================================== --- trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping 2015-08-17 12:13:53 UTC (rev 19969) +++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/patches/fix_ascii_characters_mapping 2015-08-18 14:20:10 UTC (rev 19977) @@ -1,86 +0,0 @@ -Subject: ASCII error in pbuilder -Description: unmappable character for encoding ASCII -Author: Olivier Sallou <[email protected]> -Last-Updated: 2012-12-05 -Forwarded: yes -Bug: http://code.google.com/p/forester/issues/detail?id=1 ---- a/biojava-forester/src/main/java/org/forester/test/Test.java -+++ b/biojava-forester/src/main/java/org/forester/test/Test.java -@@ -1310,7 +1310,7 @@ - return false; - } - if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() -- .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) { -+ .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489-493." ) ) ) { - return false; - } - if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) { ---- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SuperPosition.java -+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SuperPosition.java -@@ -162,7 +162,6 @@ - - /** - * Returns the TM-Score for two superimposed sets of coordinates -- * Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004) - * @param x coordinate set 1 - * @param y coordinate set 2 - * @param lengthNative total length of native sequence ---- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java -+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java -@@ -36,7 +36,6 @@ - /** - * Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits - * -- * TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004) - * @param subunits subunits to be scored - * @param transformation transformation matrix - * @param permutations permutation that determines which subunits are superposed ---- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java -+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java -@@ -30,7 +30,6 @@ - /** - * A chain, a start residue, and an end residue. - * -- * Also stores a length. Because of insertion codes, this length is not necessarily {@code end − start}. - */ - public class ResidueRangeAndLength extends ResidueRange { - private static final Logger logger = LoggerFactory.getLogger(ResidueRangeAndLength.class); ---- a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java -+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java -@@ -29,13 +29,13 @@ - import java.util.List; - - /** -- * Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from -+ * Phosphosite is available under the PhosphoSitePlus is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from - * - * http://www.phosphosite.org/staticDownloads.do - * -- * Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations. -+ * Please acknowledge PhosphoSitePlus, www.phosphosite.org" at appropriate locations. - * -- * Please cite : “Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.”. -+ * Please cite : "Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261-70.". - * - ( - * -@@ -111,7 +111,7 @@ - public void download(){ - - System.out.println("Downloading data from www.phosposite.org. Data is under CC-BY-NC-SA license. Please link to site and cite: "); -- System.out.println("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70."); -+ System.out.println("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261-70."); - - File dir = getLocalDir(); - ---- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java -+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java -@@ -74,7 +74,7 @@ - * immutable Annotation instances that are built from scratch each time. - * @author Matthew Pocock - * @author <a href="mailto:[email protected]";>Keith James</a> (docs). -- * @author Kalle N�slund (docs) -+ * @author Kalle Nslund (docs) - * @see org.biojavax.RichAnnotatable - * @since 1.0 - */ Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/patches/fix_ascii_characters_mapping (from rev 19971, trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping) =================================================================== --- trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/patches/fix_ascii_characters_mapping (rev 0) +++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-3/debian/patches/fix_ascii_characters_mapping 2015-08-18 14:20:10 UTC (rev 19977) @@ -0,0 +1,105 @@ +Subject: ASCII error in pbuilder +Description: unmappable character for encoding ASCII +Author: Olivier Sallou <[email protected]> +Last-Updated: 2012-12-05 +Forwarded: yes +Bug: http://code.google.com/p/forester/issues/detail?id=1 +--- a/biojava-forester/src/main/java/org/forester/test/Test.java ++++ b/biojava-forester/src/main/java/org/forester/test/Test.java +@@ -1310,7 +1310,7 @@ + return false; + } + if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() +- .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) { ++ .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489-493." ) ) ) { + return false; + } + if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) { +--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SuperPosition.java ++++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SuperPosition.java +@@ -162,7 +162,6 @@ + + /** + * Returns the TM-Score for two superimposed sets of coordinates +- * Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004) + * @param x coordinate set 1 + * @param y coordinate set 2 + * @param lengthNative total length of native sequence +--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java ++++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java +@@ -36,7 +36,6 @@ + /** + * Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits + * +- * TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004) + * @param subunits subunits to be scored + * @param transformation transformation matrix + * @param permutations permutation that determines which subunits are superposed +--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java ++++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java +@@ -30,7 +30,6 @@ + /** + * A chain, a start residue, and an end residue. + * +- * Also stores a length. Because of insertion codes, this length is not necessarily {@code end − start}. + */ + public class ResidueRangeAndLength extends ResidueRange { + private static final Logger logger = LoggerFactory.getLogger(ResidueRangeAndLength.class); +--- a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java ++++ b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java +@@ -29,13 +29,13 @@ + import java.util.List; + + /** +- * Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from ++ * Phosphosite is available under the PhosphoSitePlus is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from + * + * http://www.phosphosite.org/staticDownloads.do + * +- * Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations. ++ * Please acknowledge PhosphoSitePlus, www.phosphosite.org" at appropriate locations. + * +- * Please cite : “Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.”. ++ * Please cite : "Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261-70.". + * + ( + * +@@ -111,7 +111,7 @@ + public void download(){ + + System.out.println("Downloading data from www.phosposite.org. Data is under CC-BY-NC-SA license. Please link to site and cite: "); +- System.out.println("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70."); ++ System.out.println("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261-70."); + + File dir = getLocalDir(); + +--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java ++++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java +@@ -74,7 +74,7 @@ + * immutable Annotation instances that are built from scratch each time. + * @author Matthew Pocock + * @author <a href="mailto:[email protected]";>Keith James</a> (docs). +- * @author Kalle N�slund (docs) ++ * @author Kalle Nslund (docs) + * @see org.biojavax.RichAnnotatable + * @since 1.0 + */ +--- a/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java ++++ b/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java +@@ -57,11 +57,11 @@ + 2WPD has 2 local symmetries. + + Other examples with a single local symmetry are: +- 4F88 – local C8 +- 1LTI – local C5 +- 2W6E – local C3 +- 2LXC – local C2 +- 3OE7 – local C3 ++ 4F88 - local C8 ++ 1LTI - local C5 ++ 2W6E - local C3 ++ 2LXC - local C2 ++ 3OE7 - local C3 + + Local Pseudosymmetry, structure only + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
