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 <[email protected]> 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 <[email protected]> (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 <[email protected]> Wed, 01 Aug 2012 15:45:32 +0200 + +biojava3-live (3.0.4-1) unstable; urgency=low + + * Initial release (Closes: #674265) + + -- Olivier Sallou <[email protected]> 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 <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Olivier Sallou <[email protected]> -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 <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Olivier Sallou <[email protected]> +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 <[email protected]> - 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 <[email protected]>, 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 <[email protected]>, 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 <[email protected]> -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 <[email protected]> + 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 <[email protected]>, 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 <[email protected]>, 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 <[email protected]> +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 <[email protected]> -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 <[email protected]> +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 <[email protected]> -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 <[email protected]> +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 <[email protected]> -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 <[email protected]> +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) { _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
