[med-svn] r11960 - in trunk/packages/biojava3/tags: . 3.0.4-2/debian 3.0.4-2/debian/patches
Olivier Sallou
osallou at alioth.debian.org
Wed Aug 1 14:02:38 UTC 2012
Author: osallou
Date: 2012-08-01 14:02:37 +0000 (Wed, 01 Aug 2012)
New Revision: 11960
Added:
trunk/packages/biojava3/tags/3.0.4-2/
trunk/packages/biojava3/tags/3.0.4-2/debian/changelog
trunk/packages/biojava3/tags/3.0.4-2/debian/control
trunk/packages/biojava3/tags/3.0.4-2/debian/copyright
trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_ascii_character_issue
trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_code_to_support_latest_jmol
trunk/packages/biojava3/tags/3.0.4-2/debian/patches/use_simple_json
Removed:
trunk/packages/biojava3/tags/3.0.4-2/debian/changelog
trunk/packages/biojava3/tags/3.0.4-2/debian/control
trunk/packages/biojava3/tags/3.0.4-2/debian/copyright
trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_ascii_character_issue
trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_code_to_support_latest_jmol
trunk/packages/biojava3/tags/3.0.4-2/debian/patches/use_simple_json
Log:
[svn-buildpackage] Tagging biojava3-live 3.0.4-2
Deleted: trunk/packages/biojava3/tags/3.0.4-2/debian/changelog
===================================================================
--- trunk/packages/biojava3/trunk/debian/changelog 2012-08-01 13:41:15 UTC (rev 11954)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/changelog 2012-08-01 14:02:37 UTC (rev 11960)
@@ -1,5 +0,0 @@
-biojava3-live (3.0.4-1) unstable; urgency=low
-
- * Initial release (Closes: #674265)
-
- -- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Copied: trunk/packages/biojava3/tags/3.0.4-2/debian/changelog (from rev 11955, trunk/packages/biojava3/trunk/debian/changelog)
===================================================================
--- trunk/packages/biojava3/tags/3.0.4-2/debian/changelog (rev 0)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/changelog 2012-08-01 14:02:37 UTC (rev 11960)
@@ -0,0 +1,15 @@
+biojava3-live (3.0.4-2) unstable; urgency=low
+
+ [ Olivier Sallou ]
+ Patch from James Page <james.page at ubuntu.com> (Closes: #683513).
+ * Transition to use default java implementation:
+ - d/control: Use default-jdk (>= 1:1.6) instead of openjdk-6-jdk
+ for package build.
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 01 Aug 2012 15:45:32 +0200
+
+biojava3-live (3.0.4-1) unstable; urgency=low
+
+ * Initial release (Closes: #674265)
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Deleted: trunk/packages/biojava3/tags/3.0.4-2/debian/control
===================================================================
--- trunk/packages/biojava3/trunk/debian/control 2012-08-01 13:41:15 UTC (rev 11954)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/control 2012-08-01 14:02:37 UTC (rev 11960)
@@ -1,72 +0,0 @@
-Source: biojava3-live
-Section: java
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Olivier Sallou <osallou at debian.org>
-Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
- libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
- libcommons-cli-java, libguava-java (>= 11.0.1),
- openjdk-6-jdk | sun-java6-jdk, junit4,javahelper (>=0.25), libjgrapht-java,
- ant-optional, jmol-applet, icedtea-netx, libhamcrest-java, libjson-simple-java
-Build-Depends: debhelper (>= 9), ant
-Standards-Version: 3.9.3
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava3/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/biojava3/trunk/
-Homepage: http://www.biojava.org
-
-Package: libbiojava3.0-java
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends},
- libcommons-pool-java (>= 1.1),
- libcommons-collections-java (>= 2.1),
- libcommons-dbcp-java (>= 1.1),
- libhsqldb-java,
- libbytecode-java,
- jmol-applet, icedtea-netx,
- libjson-simple-java
-Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc
-Description: Java API to biological data and applications (version 3)
- 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: libbiojava3-java
-Architecture: all
-Depends: libbiojava3.0-java, ${misc:Depends}
-Provides: libbiojava3-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: libbiojava3-java-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends}
-Recommends: konqueror|html-browser
-Suggests: libbiojava3-java-demos, libbiojava3-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/biojava3/tags/3.0.4-2/debian/control (from rev 11955, trunk/packages/biojava3/trunk/debian/control)
===================================================================
--- trunk/packages/biojava3/tags/3.0.4-2/debian/control (rev 0)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/control 2012-08-01 14:02:37 UTC (rev 11960)
@@ -0,0 +1,72 @@
+Source: biojava3-live
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
+ libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
+ libcommons-cli-java, libguava-java (>= 11.0.1),
+ default-jdk (>= 1:1.6), junit4,javahelper (>=0.25), libjgrapht-java,
+ ant-optional, jmol-applet, icedtea-netx, libhamcrest-java, libjson-simple-java
+Build-Depends: debhelper (>= 9), ant
+Standards-Version: 3.9.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava3/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/biojava3/trunk/
+Homepage: http://www.biojava.org
+
+Package: libbiojava3.0-java
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libcommons-pool-java (>= 1.1),
+ libcommons-collections-java (>= 2.1),
+ libcommons-dbcp-java (>= 1.1),
+ libhsqldb-java,
+ libbytecode-java,
+ jmol-applet, icedtea-netx,
+ libjson-simple-java
+Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc
+Description: Java API to biological data and applications (version 3)
+ 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: libbiojava3-java
+Architecture: all
+Depends: libbiojava3.0-java, ${misc:Depends}
+Provides: libbiojava3-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: libbiojava3-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: konqueror|html-browser
+Suggests: libbiojava3-java-demos, libbiojava3-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/biojava3/tags/3.0.4-2/debian/copyright
===================================================================
--- trunk/packages/biojava3/trunk/debian/copyright 2012-08-01 13:41:15 UTC (rev 11954)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/copyright 2012-08-01 14:02:37 UTC (rev 11960)
@@ -1,73 +0,0 @@
-Format: http://dep.debian.net/deps/dep5
-Upstream-Name: biojava3
-Source: http://www.biojava.org/
-
-Files: biojava3-forester
-Copyright: 2008-2009 Christian M. Zmasek
- 2008-2009 Burnham Institute for Medical Research
-License: LGPL-2.1+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation; either version 2 .1 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU Lesser General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU Lesser General
- Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
-
-
-Files: *
-Copyright: 2008-2012 the Individual authors who contributed the code,
- as identified by the @authors tag of the respective source file.
- BioJava Developers <biojava-l at biojava.org>
- Scooter Willis <willishf at gmail dot com>, Mark Chapman, Andy Yates,
- Richard Holland, Mark Reinhold, brandstaetter, Thomas Down, Unidata Program Center,
- Ronald Tschalar, Andreas Prlic, Amr AL-Hossary, Jianjiong Gao, Spencer Bliven,
- Jules Jacobsen <jacobsen at ebi.ac.uk>, J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,
- A.TULINSKY, ap3, The MathWorks Inc. and the National Institute of Standards and Technology,
- Spencer Bliven <sbliven at ucsd.edu>, mulvaney, Peter Rose, Horvath Tamas, Peter Lackner,
- Koh Chuan Hock, Expasy4J, Benjamin Schuster-Böckle, Peter Troshin
-License: LGPL-2.1+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation; either version 2 .1 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU Lesser General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU Lesser General
- Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
-
-
-Files: debian/*
-Copyright: 2012 Olivier Sallou <osallou at debian.org>
-License: GPL-2+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
Copied: trunk/packages/biojava3/tags/3.0.4-2/debian/copyright (from rev 11956, trunk/packages/biojava3/trunk/debian/copyright)
===================================================================
--- trunk/packages/biojava3/tags/3.0.4-2/debian/copyright (rev 0)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/copyright 2012-08-01 14:02:37 UTC (rev 11960)
@@ -0,0 +1,73 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: biojava3
+Source: http://www.biojava.org/
+
+Files: biojava3-forester
+Copyright: 2008-2009 Christian M. Zmasek
+ 2008-2009 Burnham Institute for Medical Research
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; either version 2 .1 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+
+Files: *
+Copyright: 2008-2012 the Individual authors who contributed the code,
+ as identified by the @authors tag of the respective source file.
+ BioJava Developers <biojava-l at biojava.org>
+ Scooter Willis <willishf at gmail dot com>, Mark Chapman, Andy Yates,
+ Richard Holland, Mark Reinhold, brandstaetter, Thomas Down, Unidata Program Center,
+ Ronald Tschalar, Andreas Prlic, Amr AL-Hossary, Jianjiong Gao, Spencer Bliven,
+ Jules Jacobsen <jacobsen at ebi.ac.uk>, J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,
+ A.TULINSKY, ap3, The MathWorks Inc. and the National Institute of Standards and Technology,
+ Spencer Bliven <sbliven at ucsd.edu>, mulvaney, Peter Rose, Horvath Tamas, Peter Lackner,
+ Koh Chuan Hock, Expasy4J, Benjamin Schuster-Böckle, Peter Troshin
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; either version 2 .1 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
Deleted: trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_ascii_character_issue
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue 2012-08-01 13:41:15 UTC (rev 11954)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_ascii_character_issue 2012-08-01 14:02:37 UTC (rev 11960)
@@ -1,16 +0,0 @@
-Subject: ASCII error in pbuilder
-Description: unmappable character for encoding ASCII
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 31/05/12
-
---- a/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java
-+++ b/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java
-@@ -44,7 +44,7 @@
- /**
- * Method for access REST
- * @param query
-- * service name¡¢method name and parameter for exection rest
-+ * service name method name and parameter for exection rest
- * @return
- * execution result
- * @throws IOException
Copied: trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_ascii_character_issue (from rev 11957, trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue)
===================================================================
--- trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_ascii_character_issue (rev 0)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_ascii_character_issue 2012-08-01 14:02:37 UTC (rev 11960)
@@ -0,0 +1,16 @@
+Subject: ASCII error in pbuilder
+Description: unmappable character for encoding ASCII
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2012-05-31
+
+--- a/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java
++++ b/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java
+@@ -44,7 +44,7 @@
+ /**
+ * Method for access REST
+ * @param query
+- * service name¡¢method name and parameter for exection rest
++ * service name method name and parameter for exection rest
+ * @return
+ * execution result
+ * @throws IOException
Deleted: trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_code_to_support_latest_jmol
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol 2012-08-01 13:41:15 UTC (rev 11954)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_code_to_support_latest_jmol 2012-08-01 14:02:37 UTC (rev 11960)
@@ -1,34 +0,0 @@
-Subject: Latest JMOL library requires mode method definition
-Author: Olivier Sallou <osallou at irisa.fr>
-Description: Add required interface method from latest JMOL library definition
-Last--Updated: 29/05/12
-
---- a/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
-+++ b/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
-@@ -29,6 +29,7 @@
- import javax.swing.JTextField;
-
- import org.jmol.api.JmolStatusListener;
-+import org.jmol.constant.EnumCallback;
-
- public class MyJmolStatusListener implements JmolStatusListener {
-
-@@ -40,7 +41,17 @@
- public void setTextField (JTextField statusField) {
- status = statusField;
- }
--
-+
-+ public void resizeInnerPanel(java.lang.String arg0) {
-+ }
-+
-+ public boolean notifyEnabled(org.jmol.constant.EnumCallback callback) {
-+ return false;
-+ }
-+
-+ public void notifyCallback(EnumCallback type, Object[] data) {
-+ }
-+
- public String createImage(String arg0, String arg1, Object arg2, int arg3) {
- // TODO Auto-generated method stub
- return null;
Copied: trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_code_to_support_latest_jmol (from rev 11957, trunk/packages/biojava3/trunk/debian/patches/fix_code_to_support_latest_jmol)
===================================================================
--- trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_code_to_support_latest_jmol (rev 0)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/patches/fix_code_to_support_latest_jmol 2012-08-01 14:02:37 UTC (rev 11960)
@@ -0,0 +1,34 @@
+Subject: Latest JMOL library requires mode method definition
+Author: Olivier Sallou <osallou at irisa.fr>
+Description: Add required interface method from latest JMOL library definition
+Last--Updated: 2012-05-29
+
+--- a/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
++++ b/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java
+@@ -29,6 +29,7 @@
+ import javax.swing.JTextField;
+
+ import org.jmol.api.JmolStatusListener;
++import org.jmol.constant.EnumCallback;
+
+ public class MyJmolStatusListener implements JmolStatusListener {
+
+@@ -40,7 +41,17 @@
+ public void setTextField (JTextField statusField) {
+ status = statusField;
+ }
+-
++
++ public void resizeInnerPanel(java.lang.String arg0) {
++ }
++
++ public boolean notifyEnabled(org.jmol.constant.EnumCallback callback) {
++ return false;
++ }
++
++ public void notifyCallback(EnumCallback type, Object[] data) {
++ }
++
+ public String createImage(String arg0, String arg1, Object arg2, int arg3) {
+ // TODO Auto-generated method stub
+ return null;
Deleted: trunk/packages/biojava3/tags/3.0.4-2/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/use_simple_json 2012-08-01 13:41:15 UTC (rev 11954)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/patches/use_simple_json 2012-08-01 14:02:37 UTC (rev 11960)
@@ -1,56 +0,0 @@
-Subject: use simple_json library
-Author: Olivier Sallou <osallou at debian.org>
-Description: json.org library is not "free", use simple_json
- library and update according to API
-Last-Updated: 30/05/12
-
---- a/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
-+++ b/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
-@@ -13,8 +13,9 @@
- import java.util.TreeSet;
-
- import org.biojava3.core.sequence.ProteinSequence;
--import org.json.JSONArray;
--import org.json.JSONObject;
-+import org.json.simple.JSONArray;
-+import org.json.simple.JSONObject;
-+import org.json.simple.JSONValue;
-
-
- /** Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence.
-@@ -102,15 +103,14 @@
-
- SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
- try {
-- JSONObject json = new JSONObject(result.toString());
-+ JSONObject json= (JSONObject) JSONValue.parse(result.toString());
-+ JSONObject hmresults = (JSONObject) json.get("results");
-
-- JSONObject hmresults = json.getJSONObject("results");
-
-+ JSONArray hits = (JSONArray) hmresults.get("hits");
-
-- JSONArray hits = hmresults.getJSONArray("hits");
--
-- for(int i =0 ; i < hits.length() ; i++){
-- JSONObject hit = hits.getJSONObject(i);
-+ for(int i =0 ; i < hits.size() ; i++){
-+ JSONObject hit = (JSONObject) hits.get(i);
- //System.out.println("hit: "+ hit);
-
- HmmerResult hmmResult = new HmmerResult();
-@@ -125,11 +125,11 @@
- hmmResult.setPvalue((Double)hit.get("pvalue"));
- hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
-
-- JSONArray hmmdomains = hit.getJSONArray("domains");
-+ JSONArray hmmdomains = (JSONArray) hit.get("domains");
-
- SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
-- for ( int j= 0 ; j < hmmdomains.length() ; j++){
-- JSONObject d = hmmdomains.getJSONObject(j);
-+ for ( int j= 0 ; j < hmmdomains.size() ; j++){
-+ JSONObject d = (JSONObject) hmmdomains.get(j);
- //System.out.println(d);
- Integer is_reported = getInteger(d.get("is_reported"));
- if ( is_reported != 1) {
Copied: trunk/packages/biojava3/tags/3.0.4-2/debian/patches/use_simple_json (from rev 11957, trunk/packages/biojava3/trunk/debian/patches/use_simple_json)
===================================================================
--- trunk/packages/biojava3/tags/3.0.4-2/debian/patches/use_simple_json (rev 0)
+++ trunk/packages/biojava3/tags/3.0.4-2/debian/patches/use_simple_json 2012-08-01 14:02:37 UTC (rev 11960)
@@ -0,0 +1,56 @@
+Subject: use simple_json library
+Author: Olivier Sallou <osallou at debian.org>
+Description: json.org library is not "free", use simple_json
+ library and update according to API
+Last-Updated: 2012-05-30
+
+--- a/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
++++ b/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
+@@ -13,8 +13,9 @@
+ import java.util.TreeSet;
+
+ import org.biojava3.core.sequence.ProteinSequence;
+-import org.json.JSONArray;
+-import org.json.JSONObject;
++import org.json.simple.JSONArray;
++import org.json.simple.JSONObject;
++import org.json.simple.JSONValue;
+
+
+ /** Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence.
+@@ -102,15 +103,14 @@
+
+ SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
+ try {
+- JSONObject json = new JSONObject(result.toString());
++ JSONObject json= (JSONObject) JSONValue.parse(result.toString());
++ JSONObject hmresults = (JSONObject) json.get("results");
+
+- JSONObject hmresults = json.getJSONObject("results");
+
++ JSONArray hits = (JSONArray) hmresults.get("hits");
+
+- JSONArray hits = hmresults.getJSONArray("hits");
+-
+- for(int i =0 ; i < hits.length() ; i++){
+- JSONObject hit = hits.getJSONObject(i);
++ for(int i =0 ; i < hits.size() ; i++){
++ JSONObject hit = (JSONObject) hits.get(i);
+ //System.out.println("hit: "+ hit);
+
+ HmmerResult hmmResult = new HmmerResult();
+@@ -125,11 +125,11 @@
+ hmmResult.setPvalue((Double)hit.get("pvalue"));
+ hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
+
+- JSONArray hmmdomains = hit.getJSONArray("domains");
++ JSONArray hmmdomains = (JSONArray) hit.get("domains");
+
+ SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
+- for ( int j= 0 ; j < hmmdomains.length() ; j++){
+- JSONObject d = hmmdomains.getJSONObject(j);
++ for ( int j= 0 ; j < hmmdomains.size() ; j++){
++ JSONObject d = (JSONObject) hmmdomains.get(j);
+ //System.out.println(d);
+ Integer is_reported = getInteger(d.get("is_reported"));
+ if ( is_reported != 1) {
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