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rio, lca, refactoring
[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 ab83ebf..6b3639f 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -372,10 +372,9 @@ public final class SurfacingUtil {
                         nodes.add( n );
                     }
                 }
-                for( int i = 0; i < nodes.size() - 1; ++i ) {
+                for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
                     for( int j = i + 1; j < nodes.size(); ++j ) {
-                        final PhylogenyNode lca = PhylogenyMethods.obtainLCA( nodes.get( i ),
-                                                                                            nodes.get( j ) );
+                        final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
                         String rank = "unknown";
                         if ( lca.getNodeData().isHasTaxonomy()
                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
@@ -1185,8 +1184,11 @@ 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 ) ) {
@@ -1198,15 +1200,34 @@ public final class SurfacingUtil {
                         out.write( separator );
                         out.write( domain_id.toString() );
                         out.write( separator );
+                        int prev_to = -1;
                         for( final Domain domain : domains ) {
-                            out.write( "/" );
-                            out.write( domain.getFrom() + "-" + domain.getTo() );
+                            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 : protein.getProteinDomains() ) {
+                        for( final Domain domain : domain_ary ) {
                             if ( first ) {
                                 first = false;
                             }
@@ -1214,6 +1235,8 @@ public final class SurfacingUtil {
                                 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()
@@ -1598,58 +1621,50 @@ public final class SurfacingUtil {
                     + all_pfams_encountered.size() );
             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
                     + pfams_without_mappings_counter + " ["
-                    + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
+                    + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
-                    + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME,
-                                         "Pfams with a mapping                    : " + pfams_with_mappings_counter
-                                                 + " ["
-                                                 + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() )
-                                                 + "%]" );
+                    + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping                    : "
+                    + pfams_with_mappings_counter + " ["
+                    + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
-                    + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME,
-                                         "Pfams with mapping to biological process: " + biological_process_counter
-                                                 + " ["
-                                                 + ( 100 * biological_process_counter / all_pfams_encountered.size() )
-                                                 + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME,
-                                         "Pfams with mapping to molecular function: " + molecular_function_counter
-                                                 + " ["
-                                                 + ( 100 * molecular_function_counter / all_pfams_encountered.size() )
-                                                 + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME,
-                                         "Pfams with mapping to cellular component: " + cellular_component_counter
-                                                 + " ["
-                                                 + ( 100 * cellular_component_counter / all_pfams_encountered.size() )
-                                                 + "%]" );
+                    + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
+                    + biological_process_counter + " ["
+                    + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
+                    + molecular_function_counter + " ["
+                    + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
+                    + cellular_component_counter + " ["
+                    + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
-                    + " [" + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
+                    + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
             summary_writer.write( "# Pfams without mapping to proc. or func. : "
                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
-                    + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
+                    + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
-                    + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
+                    + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
-                    + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
+                    + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
-                    + ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
+                    + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
-                    + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
+                    + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
-                    + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
+                    + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
             summary_writer.close();
         }
@@ -2606,4 +2621,24 @@ 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;
+        }
+    }
 }