[med-svn] r23275 - in trunk/packages/biojava4-live/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Fri Dec 9 10:30:54 UTC 2016
Author: osallou
Date: 2016-12-09 10:30:53 +0000 (Fri, 09 Dec 2016)
New Revision: 23275
Added:
trunk/packages/biojava4-live/trunk/debian/patches/ignore_fake_tests
trunk/packages/biojava4-live/trunk/debian/patches/remove_openchart_use
Modified:
trunk/packages/biojava4-live/trunk/debian/README.source
trunk/packages/biojava4-live/trunk/debian/build.xml
trunk/packages/biojava4-live/trunk/debian/changelog
trunk/packages/biojava4-live/trunk/debian/get-orig-source
trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping
trunk/packages/biojava4-live/trunk/debian/patches/fix_import
trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates
trunk/packages/biojava4-live/trunk/debian/patches/series
trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json
trunk/packages/biojava4-live/trunk/debian/watch
Log:
new upstream release 4.2.4
Modified: trunk/packages/biojava4-live/trunk/debian/README.source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/README.source 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/README.source 2016-12-09 10:30:53 UTC (rev 23275)
@@ -2,7 +2,7 @@
------------------
Biojava uses the forester library version 0.955.
-The source version is hosted in Biojava repo only and does not
+The source version is hosted in maven/biojava repo only and does not
match any release available in forester web site. To manage,
a specific biojava4-forester library is created.
Modified: trunk/packages/biojava4-live/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/build.xml 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/build.xml 2016-12-09 10:30:53 UTC (rev 23275)
@@ -73,7 +73,7 @@
<target name="compile">
<mkdir dir="${class.dir}"/>
<mkdir dir="${dist.dir}"/>
- <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6">
+ <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.7" target="1.7">
</javac>
<copy todir="${class.dir}" failonerror="false">
<fileset dir="${resources.dir}"/>
Modified: trunk/packages/biojava4-live/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/changelog 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/changelog 2016-12-09 10:30:53 UTC (rev 23275)
@@ -1,3 +1,9 @@
+biojava4-live (4.2.4+dfsg-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 05 Dec 2016 09:37:13 +0100
+
biojava4-live (4.1.0+dfsg-4) unstable; urgency=medium
* Team upload.
@@ -18,6 +24,7 @@
-- Olivier Sallou <osallou at debian.org> Mon, 17 Aug 2015 14:54:33 +0000
+>>>>>>> .r23274
biojava4-live (4.1.0+dfsg-2) unstable; urgency=medium
* Remove some network related tests (Closes: #795685).
Modified: trunk/packages/biojava4-live/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/get-orig-source 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/get-orig-source 2016-12-09 10:30:53 UTC (rev 23275)
@@ -4,11 +4,10 @@
PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
VERSION=`uscan --verbose --force-download |
- grep "Newest version on remote site is .* local version is .*" |
+ grep "Newest version of biojava4-live on remote site is .* local version is .*" |
head -n 1 |
- sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+ sed "s/.*Newest version of biojava4-live on remote site is \([a-z0-9.]\+\),.*/\1/"`
-
mkdir -p ../tarballs
cd ../tarballs
@@ -25,12 +24,15 @@
mkdir -p biojava-forester/src/main/java
cd biojava-forester/src/main/java
#wget http://www.biojava.org/download/maven/org/forester/forester-1.005-sources/1.005/forester-1.005-sources-1.005.jar
- wget http://www.biojava.org/download/maven/org/forester/forester-lgpl/1.005/forester-lgpl-1.005-sources.jar
+ #wget http://www.biojava.org/download/maven/org/forester/forester-lgpl/1.005/forester-lgpl-1.005-sources.jar
+ wget -O forester-1.038-sources.jar "https://search.maven.org/remotecontent?filepath=org/biojava/thirdparty/forester/1.038/forester-1.038-sources.jar"
#jar xf forester-1.005-sources-1.005.jar
- jar xf forester-lgpl-1.005-sources.jar
+ #jar xf forester-lgpl-1.005-sources.jar
+ jar xf forester-1.038-sources.jar
find . -name *.class | xargs rm -f
rm -f resources/*.jar
- rm forester-lgpl-1.005-sources.jar
+ rm forester-1.038-sources.jar
+ #rm forester-lgpl-1.005-sources.jar
#rm forester-1.005-sources-1.005.jar
cd ../../../..
mkdir -p biojava-jcolorbrewer/src/main/java
Modified: trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping 2016-12-09 10:30:53 UTC (rev 23275)
@@ -6,7 +6,7 @@
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 @@
+@@ -2080,7 +2080,7 @@
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
@@ -15,91 +15,3 @@
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
-
Modified: trunk/packages/biojava4-live/trunk/debian/patches/fix_import
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_import 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_import 2016-12-09 10:30:53 UTC (rev 23275)
@@ -21,10 +21,10 @@
* structures from a FASTA file.
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
-@@ -130,7 +130,6 @@
+@@ -131,7 +131,6 @@
}
-
+
- @Override
public Map<String, Object> getProperty(String arg0) {
// TODO Auto-generated method stub
Modified: trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates 2016-12-09 10:30:53 UTC (rev 23275)
@@ -7,7 +7,7 @@
Forwarded: no
--- a/biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java
+++ b/biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java
-@@ -39,7 +39,7 @@
+@@ -40,7 +40,7 @@
import com.itextpdf.text.DocumentException;
import com.itextpdf.text.FontFactory;
import com.itextpdf.text.Rectangle;
Added: trunk/packages/biojava4-live/trunk/debian/patches/ignore_fake_tests
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/ignore_fake_tests (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/ignore_fake_tests 2016-12-09 10:30:53 UTC (rev 23275)
@@ -0,0 +1,27 @@
+Subject: ignore some test classes
+Description: some class tests do not have tests inside, but junit tries to execute them.
+ Simple skip those classes with no real test to avoid errors during build.
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2016-12-09
+Forwarded: no
+--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
++++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
+@@ -25,7 +25,7 @@
+ import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING;
+ import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION;
+ import org.biojava.nbio.aaproperties.profeat.ProfeatProperties;
+-//import org.junit.Test;
++import org.junit.Test;
+ import org.slf4j.Logger;
+ import org.slf4j.LoggerFactory;
+
+@@ -37,6 +37,9 @@
+
+ // TODO there's no assertions here, i.e. this is not a test! must fix! For the moment removed test tags - JD 2016-03-08
+
++ at Test
++public void testFakeTest(){}
++
+ public void shortExample1() throws Exception{
+ /*
+ * Composition
Added: trunk/packages/biojava4-live/trunk/debian/patches/remove_openchart_use
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/remove_openchart_use (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/remove_openchart_use 2016-12-09 10:30:53 UTC (rev 23275)
@@ -0,0 +1,231 @@
+Subject: forester needs openchart library
+Description: biojava makes use of a limited set of forester
+ As openchart is not available in Debian, remove openchart related calls
+ to make forester compilation OK in biojava context
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2016-12-09
+Forwarded: no
+--- a/biojava-forester/src/main/java/org/forester/msa_compactor/Chart.java
++++ b/biojava-forester/src/main/java/org/forester/msa_compactor/Chart.java
+@@ -40,47 +40,22 @@
+
+ import org.forester.util.ForesterUtil;
+
+-import com.approximatrix.charting.coordsystem.BoxCoordSystem;
+-import com.approximatrix.charting.model.MultiScatterDataModel;
+-import com.approximatrix.charting.render.MultiScatterChartRenderer;
+-import com.approximatrix.charting.swing.ChartPanel;
+
+ public final class Chart extends JDialog implements ActionListener {
+
+ final private static NumberFormat NF_1 = new DecimalFormat( "0.##" );
+ private static final long serialVersionUID = -5292420246132943515L;
+- private ChartPanel _chart_panel = null;
+- private final int _initial_number_of_seqs;
++ private final int _initial_number_of_seqs=0;
+ private final JMenuItem _m_exit = new JMenuItem();
+- private final List<MsaProperties> _msa_props;
+- private final boolean _show_msa_qual;
+- private final String _title;
++ private final List<MsaProperties> _msa_props=null;
++ private final boolean _show_msa_qual=false;
++ private final String _title=null;
+
+ private Chart( final List<MsaProperties> msa_props,
+ final int initial_number_of_seqs,
+ final boolean show_msa_qual,
+ final String title ) {
+ super();
+- _msa_props = msa_props;
+- _title = title;
+- _initial_number_of_seqs = initial_number_of_seqs;
+- _show_msa_qual = show_msa_qual;
+- setTitle( "msa compactor" );
+- setSize( 600, 500 );
+- setResizable( true );
+- final JPanel content_pane = new JPanel();
+- content_pane.setLayout( new BorderLayout() );
+- setContentPane( content_pane );
+- final JMenuBar menu_bar = new JMenuBar();
+- final JMenu file_menu = new JMenu();
+- file_menu.setText( "File" );
+- _m_exit.setText( "Exit" );
+- file_menu.add( _m_exit );
+- menu_bar.add( file_menu );
+- setJMenuBar( menu_bar );
+- setDefaultCloseOperation( WindowConstants.DISPOSE_ON_CLOSE );
+- _m_exit.addActionListener( this );
+- content_pane.add( obtainChartPanel(), BorderLayout.CENTER );
+ }
+
+ @Override
+@@ -90,150 +65,4 @@
+ }
+ }
+
+- private ChartPanel obtainChartPanel() {
+- if ( _chart_panel == null ) {
+- final MultiScatterDataModel model = new MultiScatterDataModel();
+- final double[][] seqs_length = new double[ _msa_props.size() ][ 2 ];
+- int max_length = -1;
+- int min_length = Integer.MAX_VALUE;
+- double max_gap_ratio = -1;
+- double min_gap_ratio = Double.MAX_VALUE;
+- double max_avg_gap_count = -1;
+- double min_avg_gap_count = Double.MAX_VALUE;
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- seqs_length[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- //
+- final int length = _msa_props.get( i ).getLength();
+- seqs_length[ i ][ 1 ] = length;
+- if ( length > max_length ) {
+- max_length = length;
+- }
+- if ( length < min_length ) {
+- min_length = length;
+- }
+- //
+- final double gap_ratio = _msa_props.get( i ).getGapRatio();
+- if ( gap_ratio > max_gap_ratio ) {
+- max_gap_ratio = gap_ratio;
+- }
+- if ( gap_ratio < min_gap_ratio ) {
+- min_gap_ratio = gap_ratio;
+- }
+- //
+- final double avg_gap_count = _msa_props.get( i ).getAvgNumberOfGaps();
+- if ( avg_gap_count > max_avg_gap_count ) {
+- max_avg_gap_count = avg_gap_count;
+- }
+- if ( avg_gap_count < min_avg_gap_count ) {
+- min_avg_gap_count = avg_gap_count;
+- }
+- }
+- model.addData( seqs_length, "Length" + " (" + minMaxToString( min_length, max_length ) + ")" );
+- model.setSeriesLine( "Series " + "Length", true );
+- model.setSeriesMarker( "Series " + "Length", false );
+- final double[][] seqs_gaps = new double[ _msa_props.size() ][ 2 ];
+- double max_ent7 = -1;
+- double max_ent21 = -1;
+- double min_ent7 = Double.MAX_VALUE;
+- double min_ent21 = Double.MAX_VALUE;
+- if ( _show_msa_qual ) {
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- final double ent7 = _msa_props.get( i ).getEntropy7();
+- if ( ent7 > max_ent7 ) {
+- max_ent7 = ent7;
+- }
+- if ( ent7 < max_ent7 ) {
+- min_ent7 = ent7;
+- }
+- final double ent21 = _msa_props.get( i ).getEntropy21();
+- if ( ent21 > min_ent21 ) {
+- max_ent21 = ent21;
+- }
+- if ( ent21 < min_ent21 ) {
+- min_ent21 = ent21;
+- }
+- }
+- }
+- final double gap_ratio_factor = ( max_length / 2.0 ) / max_gap_ratio;
+- final double avg_gaps_counts_factor = ( max_length / 2.0 ) / max_avg_gap_count;
+- final double ent7_factor = ( max_length / 2.0 ) / max_ent7;
+- final double ent21_factor = ( max_length / 2.0 ) / max_ent21;
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- seqs_gaps[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- seqs_gaps[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getGapRatio() * gap_ratio_factor );
+- }
+- model.addData( seqs_gaps, "Gap Ratio" + " (" + minMaxToString( min_gap_ratio, max_gap_ratio ) + ")" );
+- model.setSeriesLine( "Series " + "Gap Ratio", true );
+- model.setSeriesMarker( "Series " + "Gap Ratio", false );
+- final double[][] gap_counts = new double[ _msa_props.size() ][ 2 ];
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- gap_counts[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- gap_counts[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getAvgNumberOfGaps()
+- * avg_gaps_counts_factor );
+- }
+- model.addData( gap_counts, "Mean Gap Count" + " (" + minMaxToString( min_avg_gap_count, max_avg_gap_count )
+- + ")" );
+- model.setSeriesLine( "Series " + "Mean Gap Count", true );
+- model.setSeriesMarker( "Series " + "Mean Gap Count", false );
+- if ( _show_msa_qual ) {
+- final double[][] entropy7 = new double[ _msa_props.size() ][ 2 ];
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- entropy7[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- entropy7[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy7() * ent7_factor );
+- }
+- model.addData( entropy7, "Entropy norm 7" + " (" + minMaxToString( min_ent7, max_ent7 ) + ")" );
+- model.setSeriesLine( "Series " + "Entropy norm 7", true );
+- model.setSeriesMarker( "Series " + "Entropy norm 7", false );
+- //
+- final double[][] entropy21 = new double[ _msa_props.size() ][ 2 ];
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- entropy21[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- entropy21[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy21() * ent21_factor );
+- }
+- model.addData( entropy21, "Entropy norm 21" + " (" + minMaxToString( min_ent21, max_ent21 ) + ")" );
+- model.setSeriesLine( "Series " + "Entropy norm 21", true );
+- model.setSeriesMarker( "Series " + "Entropy norm 21", false );
+- }
+- final BoxCoordSystem coord = new BoxCoordSystem( model );
+- coord.setUnitFont( coord.getUnitFont().deriveFont( 16.0f ) );
+- coord.setXAxisUnit( "Number of Removed Sequences" );
+- coord.setPaintGrid( true );
+- coord.setYAxisUnit( "MSA Length" );
+- _chart_panel = new ChartPanel( model, _title );
+- _chart_panel.setCoordSystem( coord );
+- final MultiScatterChartRenderer renderer = new MultiScatterChartRenderer( coord, model );
+- renderer.setAllowBuffer( false );
+- _chart_panel.addChartRenderer( renderer, 0 );
+- }
+- return _chart_panel;
+- }
+-
+- private final static String minMaxToString( final double min, final double max ) {
+- return NF_1.format( min ) + "-" + NF_1.format( max );
+- }
+-
+- public static void display( final List<MsaProperties> msa_props,
+- final int initial_number_of_seqs,
+- final boolean show_msa_qual,
+- final String title ) {
+- try {
+- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+- }
+- catch ( final Exception e ) {
+- e.printStackTrace();
+- }
+- final Chart chart = new Chart( msa_props, initial_number_of_seqs, show_msa_qual, title );
+- chart.setVisible( true );
+- }
+-
+- public static void main( final String[] args ) {
+- try {
+- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+- }
+- catch ( final Exception e ) {
+- e.printStackTrace();
+- }
+- final Chart temp = new Chart( null, 0, true, "title" );
+- temp.setVisible( true );
+- }
+ }
+--- a/biojava-forester/src/main/java/org/forester/application/msa_compactor.java
++++ b/biojava-forester/src/main/java/org/forester/application/msa_compactor.java
+@@ -39,7 +39,6 @@
+ import org.forester.msa.Msa.MSA_FORMAT;
+ import org.forester.msa.MsaInferrer;
+ import org.forester.msa.MsaMethods;
+-import org.forester.msa_compactor.Chart;
+ import org.forester.msa_compactor.MsaCompactor;
+ import org.forester.msa_compactor.MsaProperties;
+ import org.forester.util.CommandLineArguments;
+@@ -396,7 +395,7 @@
+ else {
+ msa_props = mc.chart( step, realign, normalize_for_effective_seq_length );
+ }
+- Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
++ //Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
+ System.out.println();
+ System.out.println( "Final MSA properties" );
+ printMsaInfo( msa, MsaMethods.calculateEffectiveLengthStatistics( msa ));
Modified: trunk/packages/biojava4-live/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/series 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/patches/series 2016-12-09 10:30:53 UTC (rev 23275)
@@ -4,3 +4,5 @@
faketest
fix_ascii_characters_mapping
skip_network_related_tests
+remove_openchart_use
+ignore_fake_tests
Modified: trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests 2016-12-09 10:30:53 UTC (rev 23275)
@@ -1,143 +1,139 @@
-Author: Olivier Sallou <osallou at debian/org>
-Last-Updated: 2015-01-31
-Subject: Some tests use network access
-Description: Remove tests requiring external
- network access
-Forwarded: yes
-Bug: https://redmine.open-bio.org/issues/3402
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
-@@ -75,18 +75,7 @@
- /*
- * Method 1: With the GenbankProxySequenceReader
- */
-- //Try with the GenbankProxySequenceReader
-- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
-- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
-- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
-- logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
--
-- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
-- = new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet());
-- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
-- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
-- logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
-+
- /*
- * Method 2: With the GenbankReaderHelper
- */
+@@ -67,21 +67,6 @@
+ @Test
+ public void testProcess() throws Throwable {
+ /*
+- * Method 1: With the GenbankProxySequenceReader
+- */
+- //Try with the GenbankProxySequenceReader
+- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
+- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
+- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
+- logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
+-
+- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
+- = new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet());
+- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
+- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
+- logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
+- /*
+ * Method 2: With the GenbankReaderHelper
+ */
+ //Try with the GenbankReaderHelper
--- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
+++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
@@ -67,20 +67,6 @@
-
+
private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException {
-
+
- ProteinSequence seq = getUniprot(uniprotID);
--
+-
- AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
--
+-
-/* for (AminoAcidCompound compound : seq) {
- System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
-- }
+- }
- */
- assertTrue(compoundSet.isValidSequence(seq));
--
--
--
+-
+-
+-
- Jronn.getDisorderScores(seq);
--
-
+-
+
}
-
+
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
-@@ -75,88 +75,10 @@
+@@ -75,89 +75,9 @@
- @Test
- public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
-- logger.info("run test for protein: {}", gi);
-- GenbankProxySequenceReader<AminoAcidCompound> genbankReader
-- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
-- this.gi,
-- AminoAcidCompoundSet.getAminoAcidCompoundSet());
+ @Test
+ public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
+- logger.info("run test for protein: {}", gi);
+- GenbankProxySequenceReader<AminoAcidCompound> genbankReader
+- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
+- this.gi,
+- AminoAcidCompoundSet.getAminoAcidCompoundSet());
-
-- // why only tests on protein sequences?
-- ProteinSequence seq = new ProteinSequence(genbankReader);
+- // why only tests on protein sequences?
+- ProteinSequence seq = new ProteinSequence(genbankReader);
-
-- Assert.assertNotNull("protein sequence is null", seq);
+- Assert.assertNotNull("protein sequence is null", seq);
-
-- /*
-- parse description from header. There is no separate interface/abstract class for method getHeader()
-- so it should be done here (manualy).
-- */
-- genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);
+- /*
+- parse description from header. There is no separate interface/abstract class for method getHeader()
+- so it should be done here (manualy).
+- */
+- genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);
-
-- // test description
-- Assert.assertTrue(seq.getDescription() != null);
+- // test description
+- Assert.assertTrue(seq.getDescription() != null);
-
-- // test accession Id
-- logger.info("accession id: {}", seq.getAccession().getID());
-- Assert.assertNotNull(seq.getAccession().getID());
-- // test GID number
-- Assert.assertEquals(gi, seq.getAccession().getIdentifier());
-- logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
+- // test accession Id
+- logger.info("accession id: {}", seq.getAccession().getID());
+- Assert.assertNotNull(seq.getAccession().getID());
+- // test GID number
+- Assert.assertEquals(gi, seq.getAccession().getIdentifier());
+- logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
-
-- // test taxonomy id
-- logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
-- Assert.assertNotNull(seq.getTaxonomy().getID());
-- Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1]));
+- // test taxonomy id
+- logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
+- Assert.assertNotNull(seq.getTaxonomy().getID());
+- Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1]));
-
-- // test taxonomy name
-- String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").getValue();
-- logger.info("taxonomy name '{}'", taxonName);
-- Assert.assertNotNull(taxonName);
+- // test taxonomy name
+- String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").get(0).getValue();
+- logger.info("taxonomy name '{}'", taxonName);
+- Assert.assertNotNull(taxonName);
-
-- if (seq.getFeaturesByType("CDS").size() > 0) {
-- FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
-- logger.info("CDS: {}", CDS);
-- String codedBy = CDS.getQualifiers().get("coded_by").getValue();
-- Assert.assertNotNull(codedBy);
-- Assert.assertTrue(!codedBy.isEmpty());
-- logger.info("\t\tcoded_by: {}", codedBy);
-- }
- }
+- if (seq.getFeaturesByType("CDS").size() > 0) {
+- FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
+- logger.info("CDS: {}", CDS);
+- String codedBy = CDS.getQualifiers().get("coded_by").get(0).getValue();
+- Assert.assertNotNull(codedBy);
+- Assert.assertTrue(!codedBy.isEmpty());
+- logger.info("\t\tcoded_by: {}", codedBy);
+- }
+ }
- @Test
- public void testProteinSequenceFactoring() throws Exception {
- logger.info("create protein sequence test for target {}", gi);
+ @Test
+ public void testProteinSequenceFactoring() throws Exception {
+- logger.info("create protein sequence test for target {}", gi);
-
-- GenbankProxySequenceReader<AminoAcidCompound> genbankReader
-- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
-- this.gi,
-- AminoAcidCompoundSet.getAminoAcidCompoundSet());
+- GenbankProxySequenceReader<AminoAcidCompound> genbankReader
+- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
+- this.gi,
+- AminoAcidCompoundSet.getAminoAcidCompoundSet());
-
-- ProteinSequence seq = new ProteinSequence(genbankReader);
+- ProteinSequence seq = new ProteinSequence(genbankReader);
-
-- // if target protein contain CDS/coded_by than it should contain parent nucleotide seq
-- ArrayList<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");
+- // if target protein contain CDS/coded_by than it should contain parent nucleotide seq
+- ArrayList<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");
-
-- if (CDSs != null) {
-- if (CDSs.size() == 1) {
-- Qualifier codedBy = (Qualifier) CDSs.get(0).getQualifiers().get("coded_by");
-- if (codedBy != null) {
+- if (CDSs != null) {
+- if (CDSs.size() == 1) {
+- ArrayList<Qualifier> qualifiers = (ArrayList)CDSs.get(0).getQualifiers().get("coded_by");
+- Qualifier codedBy = qualifiers.get(0);
+- if (codedBy != null) {
-
-- AbstractSequence<?> parentSeq = seq.getParentSequence();
-- Assert.assertNotNull(parentSeq);
+- AbstractSequence<?> parentSeq = seq.getParentSequence();
+- Assert.assertNotNull(parentSeq);
-
-- /*
-- Sometimes protein might have many 'parents' with different accessions
-- so accession is not set.
--
-- That test is always failed
-- */
-- //Assert.assertTrue(parentSeq.getAccession());
-- Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty());
-- }
-- }
-- } else {
-- logger.info("target {} has no CDS", gi);
-- }
+- /*
+- Sometimes protein might have many 'parents' with different accessions
+- so accession is not set.
-
- }
+- That test is always failed
+- */
+- //Assert.assertTrue(parentSeq.getAccession());
+- Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty());
+- }
+- }
+- } else {
+- logger.info("target {} has no CDS", gi);
+- }
+-
+ }
}
Modified: trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json 2016-12-09 10:30:53 UTC (rev 23275)
@@ -19,7 +19,7 @@
import org.biojava.nbio.core.sequence.ProteinSequence;
import java.io.*;
-@@ -133,15 +135,13 @@
+@@ -132,15 +134,13 @@
SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
try {
@@ -39,7 +39,7 @@
//System.out.println("hit: "+ hit);
HmmerResult hmmResult = new HmmerResult();
-@@ -166,11 +166,11 @@
+@@ -165,11 +165,11 @@
hmmResult.setPvalue((Double)hit.get("pvalue"));
hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
Modified: trunk/packages/biojava4-live/trunk/debian/watch
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/watch 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/trunk/debian/watch 2016-12-09 10:30:53 UTC (rev 23275)
@@ -2,5 +2,5 @@
#opts=filenamemangle=s/.+\/biojava-?(\d\S*)\.tar\.gz/biojava-$1.tar.gz/ \
opts=dversionmangle=s/\+(repack|dfsg)// \
- https://github.com/biojava/biojava/tags .*/biojava-?([.\d]+)\.tar\.gz
+ https://github.com/biojava/biojava/tags .*/biojava-?(4\S*)\.tar\.gz
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