[med-svn] r19977 - in trunk/packages/biojava4-live/tags: . 4.1.0+dfsg-3/debian 4.1.0+dfsg-3/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Tue Aug 18 14:20:10 UTC 2015
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 <osallou at debian.org> Sun, 16 Aug 2015 16:33:47 +0200
-
-biojava4-live (4.1.0+dfsg-1) unstable; urgency=medium
-
- * New upstream release
-
- -- Olivier Sallou <osallou at debian.org> Wed, 12 Aug 2015 09:32:50 +0200
-
-biojava4-live (4.0.0+dfsg-1) unstable; urgency=medium
-
- * BioJava4 packaging (Closes: #776704).
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> Sun, 16 Aug 2015 16:33:47 +0200
+
+biojava4-live (4.1.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 12 Aug 2015 09:32:50 +0200
+
+biojava4-live (4.0.0+dfsg-1) unstable; urgency=medium
+
+ * BioJava4 packaging (Closes: #776704).
+
+ -- Olivier Sallou <osallou at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>
-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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+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 <osallou at debian.org>
-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:kdj at sanger.ac.uk">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 <osallou at debian.org>
+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:kdj at sanger.ac.uk">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
+
More information about the debian-med-commit
mailing list