From 08bd889bc13de7415319ea7202d8afb27879c18d Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 30 Nov 2012 21:14:02 +0000 Subject: [PATCH] in progress --- .../org/forester/analysis/TaxonomyDataManager.java | 1 + .../java/src/org/forester/application/rio.java | 51 ++++++++++++-------- .../src/org/forester/archaeopteryx/TreePanel.java | 4 +- .../src/org/forester/util/ForesterConstants.java | 4 +- .../java/src/org/forester/util/ForesterUtil.java | 2 +- .../org/forester/ws/seqdb/SequenceDbWsTools.java | 12 +++-- .../src/org/forester/ws/seqdb/UniProtTaxonomy.java | 2 +- 7 files changed, 47 insertions(+), 29 deletions(-) diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java index fac9f85..50cd1cc 100644 --- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java +++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java @@ -335,6 +335,7 @@ public final class TaxonomyDataManager extends RunnableProcess { .get( lineage.size() - 1 ) ); if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) { for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) { + System.out.println( "up_taxonomy=" + up_taxonomy.getScientificName() ); boolean match = true; I: for( int i = 0; i < lineage.size(); ++i ) { if ( !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) ) ) { diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index 5564763..94e6f5c 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -47,8 +47,8 @@ import org.forester.util.ForesterUtil; public class rio { final static private String PRG_NAME = "rio"; - final static private String PRG_VERSION = "3.00 beta 1"; - final static private String PRG_DATE = "2012.11.27"; + final static private String PRG_VERSION = "3.00 beta 2"; + final static private String PRG_DATE = "2012.11.30"; final static private String E_MAIL = "czmasek@burnham.org"; final static private String WWW = "www.phylosoft.org/forester/"; final static private String HELP_OPTION_1 = "help"; @@ -103,7 +103,7 @@ public class rio { } ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, gene_trees_file ); ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, species_tree_file ); - if ( outfile.exists() ) { + if ( ( outfile != null ) && outfile.exists() ) { ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" ); } String query = null; @@ -123,16 +123,20 @@ public class rio { } double cutoff_for_orthologs = 50; double cutoff_for_ultra_paralogs = 50; - int sort = 2; + int sort = 1; try { if ( cla.isOptionSet( CUTOFF_ORTHO_OPTION ) ) { cutoff_for_orthologs = cla.getOptionValueAsDouble( CUTOFF_ORTHO_OPTION ); + if ( query == null ) { + ForesterUtil.fatalError( PRG_NAME, "missing query name, type \"rio -h\" for help" ); + } + if ( outfile == null ) { + ForesterUtil.fatalError( PRG_NAME, "missing outfile, type \"rio -h\" for help" ); + } } if ( cla.isOptionSet( CUTOFF_ULTRA_P_OPTION ) ) { cutoff_for_ultra_paralogs = cla.getOptionValueAsDouble( CUTOFF_ULTRA_P_OPTION ); - if ( !output_ultraparalogs ) { - printHelp(); - } + output_ultraparalogs = true; } if ( cla.isOptionSet( SORT_OPTION ) ) { sort = cla.getOptionValueAsInt( SORT_OPTION ); @@ -142,13 +146,13 @@ public class rio { ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getLocalizedMessage() ); } if ( ( cutoff_for_orthologs < 0 ) || ( cutoff_for_ultra_paralogs < 0 ) || ( sort < 0 ) || ( sort > 2 ) ) { - printHelp(); + ForesterUtil.fatalError( PRG_NAME, "numberical option out of range, type \"rio -h\" for help" ); } - if ( ( ( query == null ) && ( outfile != null ) ) || ( ( query != null ) && ( outfile == null ) ) ) { - printHelp(); + if ( ( ( query == null ) && ( ( outfile != null ) || output_ultraparalogs ) ) ) { + ForesterUtil.fatalError( PRG_NAME, "missing query name, type \"rio -h\" for help" ); } - if ( output_ultraparalogs && ( outfile == null ) ) { - printHelp(); + if ( ( output_ultraparalogs && ( outfile == null ) ) || ( ( query != null ) && ( outfile == null ) ) ) { + ForesterUtil.fatalError( PRG_NAME, "missing outfile, type \"rio -h\" for help" ); } long time = 0; System.out.println( "Gene trees : " + gene_trees_file ); @@ -177,12 +181,10 @@ public class rio { System.exit( -1 ); } if ( !species_tree.isRooted() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "species tree is not rooted" ); - System.exit( -1 ); + ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" ); } if ( !species_tree.isCompletelyBinary() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "species tree is not completely binary" ); - System.exit( -1 ); + ForesterUtil.fatalError( PRG_NAME, "species tree is not completely binary" ); } try { RIO rio; @@ -210,6 +212,9 @@ public class rio { tableOutput( table_outfile, rio ); } } + catch ( final IllegalArgumentException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + } catch ( final Exception e ) { ForesterUtil.printErrorMessage( PRG_NAME, e.getLocalizedMessage() ); e.printStackTrace(); @@ -267,13 +272,19 @@ public class rio { System.out.println(); System.out.println( " Options" ); System.out.println( " -" + CUTOFF_ORTHO_OPTION + " : cutoff for ortholog output (default: 50)" ); - System.out.println( " -" + TABLE_OUTPUT_OPTION + " : file-name for output table" ); - System.out.println( " -" + QUERY_OPTION + " : name for query (sequence/node)" ); - System.out.println( " -" + SORT_OPTION + " : sort (default: 2)" ); + System.out.println( " -" + TABLE_OUTPUT_OPTION + + " : file-name for output table of all vs. all ortholgy support" ); + System.out.println( " -" + QUERY_OPTION + + " : name for query (sequence/node), if this is used, [outfile] is required as well" ); + System.out.println( " -" + SORT_OPTION + " : sort (default: 1)" ); System.out.println( " -" + OUTPUT_ULTRA_P_OPTION + " : to output ultra-paralogs (species specific expansions/paralogs)" ); System.out.println( " -" + CUTOFF_ULTRA_P_OPTION + " : cutoff for ultra-paralog output (default: 50)" ); System.out.println(); + System.out.println( " Note" ); + System.out.println( " Either output of all vs. all ortholgy support with -t= and/or output for" ); + System.out.println( " one query sequence with -q= and a [outfile] are required." ); + System.out.println(); System.out.println( " Sort" ); System.out.println( RIO.getOrderHelp().toString() ); System.out.println( " Formats" ); @@ -287,6 +298,8 @@ public class rio { System.out.println( " \"rio gene_trees.nh species.xml outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60\"" ); System.out.println( " \"rio gene_trees.nh species.xml -t=outtable\"" ); System.out.println(); + System.out.println( " More information: http://code.google.com/p/forester/wiki/RIO" ); + System.out.println(); System.exit( -1 ); } } diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 1e329d3..907a20f 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -2243,7 +2243,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee Color c = getTreeColorSet().getAnnotationColor(); if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) { final StringBuilder sb = new StringBuilder(); - for( Annotation a : ann ) { + for( final Annotation a : ann ) { sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() ); } final String ann_str = sb.toString(); @@ -4038,7 +4038,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private String createAnnotationString( final SortedSet ann ) { final StringBuilder sb = new StringBuilder(); boolean first = true; - for( Annotation a : ann ) { + for( final Annotation a : ann ) { if ( !first ) { sb.append( "|" ); } diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java index 27cf706..6ff9c10 100644 --- a/forester/java/src/org/forester/util/ForesterConstants.java +++ b/forester/java/src/org/forester/util/ForesterConstants.java @@ -27,8 +27,8 @@ package org.forester.util; public final class ForesterConstants { - public final static String FORESTER_VERSION = "1.006"; - public final static String FORESTER_DATE = "121128"; + public final static String FORESTER_VERSION = "1.007"; + public final static String FORESTER_DATE = "121130"; public final static String PHYLO_XML_VERSION = "1.10"; public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org"; public final static String PHYLO_XML_XSD = "phyloxml.xsd"; diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index 043df39..ef30200 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -771,7 +771,7 @@ public final class ForesterUtil { } final public static void printErrorMessage( final String prg_name, final String message ) { - System.out.println( "[" + prg_name + "] > error: " + message ); + System.err.println( "[" + prg_name + "] > error: " + message ); } final public static void printProgramInformation( final String prg_name, final String prg_version, final String date ) { diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java index b56a633..5c1cc73 100644 --- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java +++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java @@ -121,16 +121,20 @@ public final class SequenceDbWsTools { final int max_taxonomies_return ) throws IOException { // Hack! Craniata? .. - if ( sn.equals( "Drosophila" ) ) { - return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS ); - } - else if ( sn.equals( "Xenopus" ) ) { + // if ( sn.equals( "Drosophila" ) ) { + // return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS ); + // } + /* else*/if ( sn.equals( "Xenopus" ) ) { return uniProtTaxonomyToList( UniProtTaxonomy.XENOPUS_GENUS ); } // else if ( sn.equals( "Nucleariidae and Fonticula group" ) ) { // return hack( UniProtTaxonomy.NUCLEARIIDAE_AND_FONTICULA ); // } final List result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return ); + System.out.println( "SN=" + sn ); + for( final String string : result ) { + System.out.println( "|" + string ); + } if ( result.size() > 0 ) { return parseUniProtTaxonomy( result ); } diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java index e9a2e88..145569d 100644 --- a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java +++ b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java @@ -118,7 +118,7 @@ public final class UniProtTaxonomy { } _lineage.add( _scientific_name ); if ( _lineage.isEmpty() ) { - throw new IllegalArgumentException( "lineage in a UniProt Taxonomy can not be empty\n: " + line ); + throw new IllegalArgumentException( "lineage in a UniProt taxonomy can not be empty\n: " + line ); } } -- 1.7.10.2