From: cmzmasek@gmail.com Date: Sat, 18 Jun 2011 01:01:15 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=91af2d9f4f8b3e1f0ac624aea14f2625934fbbbd;p=jalview.git in progress --- diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 9d2c987..feb122d 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -272,6 +272,7 @@ public class surfacing { public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt"; public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt"; public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt"; private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option, final String[][] input_file_properties, diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index 0e200dc..60cf2f4 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -34,6 +34,7 @@ import java.io.Writer; import java.text.DecimalFormat; import java.text.NumberFormat; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collections; import java.util.Comparator; import java.util.HashMap; @@ -164,11 +165,13 @@ public final class SurfacingUtil { private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l, final String outfilename_for_counts, final String outfilename_for_dc, - final String outfilename_for_dc_for_go_mapping ) { + final String outfilename_for_dc_for_go_mapping, + final String outfilename_for_dc_for_go_mapping_unique ) { try { final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) ); final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) ); final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) ); + final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) ); final SortedMap dc_gain_counts = new TreeMap(); for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) { final PhylogenyNode n = it.next(); @@ -185,20 +188,25 @@ public final class SurfacingUtil { final SortedMap histogram = new TreeMap(); final SortedMap domain_lists = new TreeMap(); final SortedMap> domain_lists_go = new TreeMap>(); + final SortedMap> domain_lists_go_unique = new TreeMap>(); final Set dcs = dc_gain_counts.keySet(); for( final String dc : dcs ) { final int count = dc_gain_counts.get( dc ); if ( histogram.containsKey( count ) ) { histogram.put( count, histogram.get( count ) + 1 ); - domain_lists.put( count, domain_lists.get( count ).append( ", " + dc ) ); - domain_lists_go.get( count ).add( dc ); + domain_lists.get( count ).append( ", " + dc ); + domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) ); + domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) ); } else { histogram.put( count, 1 ); domain_lists.put( count, new StringBuilder( dc ) ); final PriorityQueue q = new PriorityQueue(); - q.add( dc ); + q.addAll( splitDomainCombination( dc ) ); domain_lists_go.put( count, q ); + final SortedSet set = new TreeSet(); + set.addAll( splitDomainCombination( dc ) ); + domain_lists_go_unique.put( count, set ); } } final Set histogram_keys = histogram.keySet(); @@ -207,10 +215,21 @@ public final class SurfacingUtil { final StringBuilder dc = domain_lists.get( histogram_key ); out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR ); out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR ); + out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR ); + final Object[] sorted = domain_lists_go.get( histogram_key ).toArray(); + Arrays.sort( sorted ); + for( final Object domain : sorted ) { + out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR ); + } + out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR ); + for( final String domain : domain_lists_go_unique.get( histogram_key ) ) { + out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR ); + } } out_counts.close(); out_dc.close(); out_dc_for_go_mapping.close(); + out_dc_for_go_mapping_unique.close(); } catch ( final IOException e ) { ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e ); @@ -222,6 +241,9 @@ public final class SurfacingUtil { ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to (for GO mapping) [" + outfilename_for_dc_for_go_mapping + "]" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, + "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) [" + + outfilename_for_dc_for_go_mapping_unique + "]" ); } public static int calculateOverlap( final Domain domain, final List covered_positions ) { @@ -701,7 +723,8 @@ public final class SurfacingUtil { calculateIndependentDomainCombinationGains( local_phylogeny_l, outfile_name + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX, outfile_name + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX, outfile_name - + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX ); + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX, outfile_name + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX ); } } @@ -1066,6 +1089,19 @@ public final class SurfacingUtil { return domains; } + private static List splitDomainCombination( final String dc ) { + final String[] s = dc.split( "=" ); + if ( s.length != 2 ) { + ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: " + + dc ); + System.exit( -1 ); + } + final List l = new ArrayList( 2 ); + l.add( s[ 0 ] ); + l.add( s[ 1 ] ); + return l; + } + public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p, final boolean get_gains, final String outdir,