in progress

diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java
index bee52a0..6d45207 100644 (file)
--- a/forester/java/src/org/forester/application/phyloxml_converter.java
+++ b/forester/java/src/org/forester/application/phyloxml_converter.java
@@ -255,6 +255,9 @@ public class phyloxml_converter {
         if ( order_subtrees ) {
             for( final Phylogeny phy : phys ) {
                 PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.TAXONOMY );
+                phy.externalNodesHaveChanged();
+                phy.hashIDs();
+                phy.recalculateNumberOfExternalDescendants( true );
             }
         }
         try {

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 4218c4b..951ce21 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -235,7 +235,7 @@ public class surfacing {
     final static private String                               SEQ_EXTRACT_OPTION                                                     = "prot_extract";
     final static private char                                 SEPARATOR_FOR_INPUT_VALUES                                             = '#';
     final static private String                               PRG_VERSION                                                            = "2.210";
-    final static private String                               PRG_DATE                                                               = "2011.12.08";
+    final static private String                               PRG_DATE                                                               = "2012.02.21";
     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;
@@ -278,6 +278,7 @@ public class surfacing {
     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";
+    public static final String                                LIMIT_SPEC_FOR_PROT_EX                                                 = null;                                                                                                                                                                                       // e.g. "HUMAN"; set to null for not using this feature (default).
 
     private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
                                                                  final String[][] input_file_properties,
@@ -1946,7 +1947,8 @@ public class surfacing {
                         SurfacingUtil.extractProteinNames( protein_list,
                                                            query_domain_ids_array[ j ],
                                                            query_domains_writer_ary[ j ],
-                                                           "\t" );
+                                                           "\t",
+                                                           LIMIT_SPEC_FOR_PROT_EX );
                         query_domains_writer_ary[ j ].flush();
                     }
                     catch ( final IOException e ) {
@@ -2788,7 +2790,11 @@ public class surfacing {
             SurfacingUtil.checkForOutputFileWriteability( out );
             try {
                 final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
-                SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" );
+                SurfacingUtil.extractProteinNames( protein_lists_per_species,
+                                                   domain,
+                                                   proteins_file_writer,
+                                                   "\t",
+                                                   LIMIT_SPEC_FOR_PROT_EX );
                 proteins_file_writer.close();
             }
             catch ( final IOException e ) {

diff --git a/forester/java/src/org/forester/application/surfacing_hmmpfam.java b/forester/java/src/org/forester/application/surfacing_hmmpfam.java
index 476640b..dfbed8a 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing_hmmpfam.java
+++ b/forester/java/src/org/forester/application/surfacing_hmmpfam.java
@@ -1868,7 +1868,8 @@ public class surfacing_hmmpfam {
                         SurfacingUtil.extractProteinNames( protein_list,
                                                            query_domain_ids_array[ j ],
                                                            query_domains_writer_ary[ j ],
-                                                           "\t" );
+                                                           "\t",
+                                                           surfacing.LIMIT_SPEC_FOR_PROT_EX );
                         query_domains_writer_ary[ j ].flush();
                     }
                     catch ( final IOException e ) {
@@ -2576,7 +2577,7 @@ public class surfacing_hmmpfam {
             SurfacingUtil.checkForOutputFileWriteability( out );
             try {
                 final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
-                SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" );
+                SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t", null );
                 proteins_file_writer.close();
             }
             catch ( final IOException e ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 21c4891..419f2c5 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -252,6 +252,12 @@ final class ControlPanel extends JPanel implements ActionListener {
                     }
                     PhylogenyMethods.orderAppearance( tp.getPhylogeny().getRoot(), _order_of_appearance, true, pri );
                     _order_of_appearance = !_order_of_appearance;
+                    tp.setNodeInPreorderToNull();
+                    tp.getPhylogeny().externalNodesHaveChanged();
+                    tp.getPhylogeny().hashIDs();
+                    tp.getPhylogeny().recalculateNumberOfExternalDescendants( true );
+                    tp.resetNodeIdToDistToLeafMap();
+                    tp.setEdited( true );
                     displayedPhylogenyMightHaveChanged( false );
                 }
                 else if ( e.getSource() == _uncollapse_all ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index a9c154b..52d4bfb 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -4931,6 +4931,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( !node.isExternal() ) {
             node.swapChildren();
             setNodeInPreorderToNull();
+            _phylogeny.externalNodesHaveChanged();
+            _phylogeny.hashIDs();
+            _phylogeny.recalculateNumberOfExternalDescendants( true );
+            resetNodeIdToDistToLeafMap();
+            setEdited( true );
         }
         repaint();
     }
@@ -4950,6 +4955,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             PhylogenyMethods.sortNodeDescendents( node, pri );
             setNodeInPreorderToNull();
+            _phylogeny.externalNodesHaveChanged();
+            _phylogeny.hashIDs();
+            _phylogeny.recalculateNumberOfExternalDescendants( true );
+            resetNodeIdToDistToLeafMap();
+            setEdited( true );
         }
         repaint();
     }

diff --git a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
index 6996ef3..9414d39 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
+++ b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
@@ -44,6 +44,7 @@ import java.util.SortedSet;
 import java.util.TreeMap;
 import java.util.TreeSet;
 
+import org.forester.application.surfacing;
 import org.forester.go.GoId;
 import org.forester.go.GoTerm;
 import org.forester.util.BasicDescriptiveStatistics;
@@ -820,7 +821,11 @@ public final class DomainCountsDifferenceUtil {
                 + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
         SurfacingUtil.checkForOutputFileWriteability( my_proteins_file );
         final Writer proteins_file_writer = new BufferedWriter( new FileWriter( my_proteins_file ) );
-        SurfacingUtil.extractProteinNames( protein_lists_per_species, domain_id, proteins_file_writer, "\t" );
+        SurfacingUtil.extractProteinNames( protein_lists_per_species,
+                                           domain_id,
+                                           proteins_file_writer,
+                                           "\t",
+                                           surfacing.LIMIT_SPEC_FOR_PROT_EX );
         proteins_file_writer.close();
         System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
     }

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index c6df0b2..f979897 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -845,65 +845,35 @@ public final class SurfacingUtil {
     public static void extractProteinNames( final List<Protein> proteins,
                                             final List<DomainId> query_domain_ids_nc_order,
                                             final Writer out,
-                                            final String separator ) throws IOException {
+                                            final String separator,
+                                            final String limit_to_species ) throws IOException {
         for( final Protein protein : proteins ) {
-            if ( protein.contains( query_domain_ids_nc_order, true ) ) {
-                out.write( protein.getSpecies().getSpeciesId() );
-                out.write( separator );
-                out.write( protein.getProteinId().getId() );
-                out.write( separator );
-                out.write( "[" );
-                final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
-                boolean first = true;
-                for( final Domain domain : protein.getProteinDomains() ) {
-                    if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
-                        visited_domain_ids.add( domain.getDomainId() );
-                        if ( first ) {
-                            first = false;
-                        }
-                        else {
-                            out.write( " " );
-                        }
-                        out.write( domain.getDomainId().getId() );
-                        out.write( " {" );
-                        out.write( "" + domain.getTotalCount() );
-                        out.write( "}" );
-                    }
-                }
-                out.write( "]" );
-                out.write( separator );
-                if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
-                        .equals( SurfacingConstants.NONE ) ) ) {
-                    out.write( protein.getDescription() );
-                }
-                out.write( separator );
-                if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
-                        .equals( SurfacingConstants.NONE ) ) ) {
-                    out.write( protein.getAccession() );
-                }
-                out.write( SurfacingConstants.NL );
-            }
-        }
-        out.flush();
-    }
-
-    public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
-                                            final DomainId domain_id,
-                                            final Writer out,
-                                            final String separator ) throws IOException {
-        for( final Species species : protein_lists_per_species.keySet() ) {
-            for( final Protein protein : protein_lists_per_species.get( 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() );
-                    }
+            if ( ForesterUtil.isEmpty( limit_to_species )
+                    || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
+                if ( protein.contains( query_domain_ids_nc_order, true ) ) {
                     out.write( protein.getSpecies().getSpeciesId() );
                     out.write( separator );
                     out.write( protein.getProteinId().getId() );
                     out.write( separator );
-                    out.write( "[" + FORMATTER.format( stats.median() ) + "]" );
+                    out.write( "[" );
+                    final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
+                    boolean first = true;
+                    for( final Domain domain : protein.getProteinDomains() ) {
+                        if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
+                            visited_domain_ids.add( domain.getDomainId() );
+                            if ( first ) {
+                                first = false;
+                            }
+                            else {
+                                out.write( " " );
+                            }
+                            out.write( domain.getDomainId().getId() );
+                            out.write( " {" );
+                            out.write( "" + domain.getTotalCount() );
+                            out.write( "}" );
+                        }
+                    }
+                    out.write( "]" );
                     out.write( separator );
                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
                             .equals( SurfacingConstants.NONE ) ) ) {
@@ -921,6 +891,44 @@ public final class SurfacingUtil {
         out.flush();
     }
 
+    public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
+                                            final DomainId domain_id,
+                                            final Writer out,
+                                            final String separator,
+                                            final String limit_to_species ) throws IOException {
+        for( final Species species : protein_lists_per_species.keySet() ) {
+            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( separator );
+                        if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
+                                .equals( SurfacingConstants.NONE ) ) ) {
+                            out.write( protein.getDescription() );
+                        }
+                        out.write( separator );
+                        if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
+                                .equals( SurfacingConstants.NONE ) ) ) {
+                            out.write( protein.getAccession() );
+                        }
+                        out.write( SurfacingConstants.NL );
+                    }
+                }
+            }
+        }
+        out.flush();
+    }
+
     public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
         final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {

diff --git a/forester/java/src/org/forester/tools/SupportCount.java b/forester/java/src/org/forester/tools/SupportCount.java
index e554d4e..e542c5e 100644 (file)
--- a/forester/java/src/org/forester/tools/SupportCount.java
+++ b/forester/java/src/org/forester/tools/SupportCount.java
@@ -204,6 +204,9 @@ public final class SupportCount {
                 // comparison if
                 // phylos are saved
                 // to file.
+                evaluator_phylogeny.externalNodesHaveChanged();
+                evaluator_phylogeny.hashIDs();
+                evaluator_phylogeny.recalculateNumberOfExternalDescendants( true );
             }
             final double s = SupportCount.compare( phylogeny,
                                                    evaluator_phylogenies[ i ],