cleanup

[jalview.git] / forester / java / src / org / forester / surfacing / SurfacingUtil.java

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index a22bdad..8daa322 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -58,6 +58,7 @@ import org.forester.evoinference.matrix.character.CharacterStateMatrix;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
+import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.go.GoId;
 import org.forester.go.GoNameSpace;
@@ -373,8 +374,7 @@ public final class SurfacingUtil {
                 }
                 for( int i = 0; i < nodes.size() - 1; ++i ) {
                     for( int j = i + 1; j < nodes.size(); ++j ) {
-                        final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( nodes.get( i ),
-                                                                                            nodes.get( j ) );
+                        final PhylogenyNode lca = PhylogenyMethods.obtainLCA( nodes.get( i ), nodes.get( j ) );
                         String rank = "unknown";
                         if ( lca.getNodeData().isHasTaxonomy()
                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
@@ -642,7 +642,7 @@ public final class SurfacingUtil {
     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
         checkForOutputFileWriteability( nj_tree_outfile );
         final NeighborJoining nj = NeighborJoining.createInstance();
-        final Phylogeny phylogeny = nj.execute( distance );
+        final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
         phylogeny.setName( nj_tree_outfile.getName() );
         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
         return phylogeny;
@@ -1184,23 +1184,61 @@ public final class SurfacingUtil {
                                             final DomainId domain_id,
                                             final Writer out,
                                             final String separator,
-                                            final String limit_to_species ) throws IOException {
+                                            final String limit_to_species,
+                                            final double domain_e_cutoff ) throws IOException {
+        System.out.println( "Per domain E-value: " + domain_e_cutoff );
         for( final Species species : protein_lists_per_species.keySet() ) {
+            System.out.println( species + ":" );
             for( final Protein protein : protein_lists_per_species.get( species ) ) {
                 if ( ForesterUtil.isEmpty( limit_to_species )
                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
                     final List<Domain> 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 );
+                        int prev_to = -1;
+                        for( final Domain domain : domains ) {
+                            if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
+                                out.write( "/" );
+                                out.write( domain.getFrom() + "-" + domain.getTo() );
+                                if ( prev_to >= 0 ) {
+                                    final int l = domain.getFrom() - prev_to;
+                                    System.out.println( l );
+                                }
+                                prev_to = domain.getTo();
+                            }
+                        }
+                        out.write( "/" );
                         out.write( separator );
+                        final List<Domain> domain_list = new ArrayList<Domain>();
+                        for( final Domain domain : protein.getProteinDomains() ) {
+                            if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
+                                domain_list.add( domain );
+                            }
+                        }
+                        final Domain domain_ary[] = new Domain[ domain_list.size() ];
+                        for( int i = 0; i < domain_list.size(); ++i ) {
+                            domain_ary[ i ] = domain_list.get( i );
+                        }
+                        Arrays.sort( domain_ary, new DomainComparator( true ) );
+                        out.write( "{" );
+                        boolean first = true;
+                        for( final Domain domain : domain_ary ) {
+                            if ( first ) {
+                                first = false;
+                            }
+                            else {
+                                out.write( "," );
+                            }
+                            out.write( domain.getDomainId().toString() );
+                            out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
+                            out.write( ":" + domain.getPerDomainEvalue() );
+                        }
+                        out.write( "}" );
                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
                                 .equals( SurfacingConstants.NONE ) ) ) {
                             out.write( protein.getDescription() );
@@ -2591,4 +2629,24 @@ public final class SurfacingUtil {
             e.printStackTrace();
         }
     }
+
+    final static class DomainComparator implements Comparator<Domain> {
+
+        final private boolean _ascending;
+
+        public DomainComparator( final boolean ascending ) {
+            _ascending = ascending;
+        }
+
+        @Override
+        public final int compare( final Domain d0, final Domain d1 ) {
+            if ( d0.getFrom() < d1.getFrom() ) {
+                return _ascending ? -1 : 1;
+            }
+            else if ( d0.getFrom() > d1.getFrom() ) {
+                return _ascending ? 1 : -1;
+            }
+            return 0;
+        }
+    }
 }