From: cmzmasek@gmail.com Date: Sat, 14 Jul 2012 02:29:05 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=764e1546f1bcc4f6b52be283bdd801372ed2ee54;p=jalview.git in progress --- diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java index 7457b3e..5f01408 100644 --- a/forester/java/src/org/forester/application/msa_compactor.java +++ b/forester/java/src/org/forester/application/msa_compactor.java @@ -26,7 +26,7 @@ public class msa_compactor { final static private String PRG_NAME = "msa_compactor"; final static private String PRG_DESC = "multiple sequnce aligment compactor"; final static private String PRG_VERSION = "0.90"; - final static private String PRG_DATE = "2012.07.11"; + final static private String PRG_DATE = "2012.07.13"; final static private String E_MAIL = "phylosoft@gmail.com"; final static private String WWW = "www.phylosoft.org/forester/"; diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 692b699..f89d248 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -235,8 +235,8 @@ public class surfacing { final static private String INPUT_SPECIES_TREE_OPTION = "species_tree"; final static private String SEQ_EXTRACT_OPTION = "prot_extract"; final static private char SEPARATOR_FOR_INPUT_VALUES = '#'; - final static private String PRG_VERSION = "2.250"; - final static private String PRG_DATE = "2012.05.07"; + final static private String PRG_VERSION = "2.251"; + final static private String PRG_DATE = "2012.07.13"; final static private String E_MAIL = "czmasek@burnham.org"; final static private String WWW = "www.phylosoft.org/forester/applications/surfacing"; final static private boolean IGNORE_DUFS_DEFAULT = true; diff --git a/forester/java/src/org/forester/msa/MsaCompactor.java b/forester/java/src/org/forester/msa/MsaCompactor.java index 469fa31..90b2ccc 100644 --- a/forester/java/src/org/forester/msa/MsaCompactor.java +++ b/forester/java/src/org/forester/msa/MsaCompactor.java @@ -140,12 +140,13 @@ public class MsaCompactor { } final private void write( final File outfile, final double gr ) throws IOException { - writeMsa( outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_" + gr + ".aln" ); + writeMsa( outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_" + + ForesterUtil.roundToInt( gr * 100 ) + ".aln" ); } final private void writeMsa( final String outfile ) throws IOException { final Writer w = ForesterUtil.createBufferedWriter( outfile ); - _msa.write( w, MSA_FORMAT.PHYLIP ); + _msa.write( w, MSA_FORMAT.FASTA ); w.close(); } diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index a457f2c..1a0a07d 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -1192,16 +1192,30 @@ public final class SurfacingUtil { || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) { final List domains = protein.getProteinDomains( domain_id ); if ( domains.size() > 0 ) { - final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); - for( final Domain domain : domains ) { - stats.addValue( domain.getPerSequenceEvalue() ); - } out.write( protein.getSpecies().getSpeciesId() ); out.write( separator ); out.write( protein.getProteinId().getId() ); out.write( separator ); - out.write( "[" + FORMATTER.format( stats.median() ) + "]" ); + out.write( domain_id.toString() ); + out.write( separator ); + for( final Domain domain : domains ) { + out.write( "/" ); + out.write( domain.getFrom() + "-" + domain.getTo() ); + } + out.write( "/" ); out.write( separator ); + out.write( "{" ); + boolean first = true; + for( final Domain domain : protein.getProteinDomains() ) { + if ( first ) { + first = false; + } + else { + out.write( "," ); + } + out.write( domain.getDomainId().toString() ); + } + out.write( "}" ); if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription() .equals( SurfacingConstants.NONE ) ) ) { out.write( protein.getDescription() );