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[jalview.git] / forester / java / src / org / forester / archaeopteryx / TreePanelUtil.java
diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
index 5d7d2fa..b58894d 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
@@ -6,6 +6,7 @@ import java.awt.Component;
 import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -25,7 +26,7 @@ import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Accession;
 import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.BranchColor;
-import org.forester.phylogeny.data.NodeData.NODE_DATA;
+import org.forester.phylogeny.data.NodeDataField;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
@@ -33,6 +34,7 @@ import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
 import org.forester.util.SequenceAccessionTools;
+import org.forester.util.StringInt;
 import org.forester.ws.seqdb.UniProtTaxonomy;
 
 public class TreePanelUtil {
@@ -148,7 +150,7 @@ public class TreePanelUtil {
         if ( cp.isShowSeqSymbols() && node.getNodeData().isHasSequence()
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
             TreePanelUtil
-                    .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
+            .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
         }
         if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
@@ -159,29 +161,29 @@ public class TreePanelUtil {
                 && ( node.getNodeData().getSequence().getAccession() != null )
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) {
             TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession()
-                    .toString(), sb );
+                                                                       .toString(), sb );
         }
         if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy()
                 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
             TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
-                    .getTaxonomyCode(), sb );
+                                                                       .getTaxonomyCode(), sb );
         }
         if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy()
                 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
             TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
-                    .getScientificName(), sb );
+                                                                       .getScientificName(), sb );
         }
         if ( cp.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy()
                 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
             TreePanelUtil
-                    .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
-        }
-        if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() )
-                && node.getNodeData().isHasSequence()
-                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
-            TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence()
-                    .getMolecularSequence(), sb );
-        }
+            .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
+        }
+        //        if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() )
+        //                && node.getNodeData().isHasSequence()
+        //                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+        //            TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence()
+        //                    .getMolecularSequence(), sb );
+        //        }
         final String s = sb.toString().trim();
         if ( !ForesterUtil.isEmpty( s ) ) {
             data.add( s );
@@ -209,7 +211,7 @@ public class TreePanelUtil {
                     TreePanelUtil.collapseSubtree( n, true );
                     if ( !n.getNodeData().isHasTaxonomy() ) {
                         n.getNodeData().setTaxonomy( ( Taxonomy ) n.getAllExternalDescendants().get( 0 ).getNodeData()
-                                .getTaxonomy().copy() );
+                                                     .getTaxonomy().copy() );
                     }
                     inferred = true;
                 }
@@ -281,7 +283,7 @@ public class TreePanelUtil {
                     final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
                     for( final PhylogenyNode desc : descs ) {
                         desc.getBranchData()
-                                .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
+                        .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
                     }
                 }
             }
@@ -296,11 +298,11 @@ public class TreePanelUtil {
             if ( n.getNodeData().isHasTaxonomy()
                     && ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() )
                             || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil
-                                .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                            .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
                 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
                         && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) {
                     final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData()
-                            .getTaxonomy() ) );
+                                                                                                   .getTaxonomy() ) );
                     TreePanelUtil.colorizeSubtree( n, c );
                     ++colorizations;
                     if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
@@ -318,7 +320,7 @@ public class TreePanelUtil {
                     for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
                         if ( true_lineage_to_color_map.containsKey( lin ) ) {
                             TreePanelUtil
-                                    .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
+                            .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
                             ++colorizations;
                             success = true;
                             break;
@@ -437,10 +439,11 @@ public class TreePanelUtil {
                 .getSynonyms().isEmpty() );
     }
 
-    static int makeSB( final List<String> data, final Options optz, final StringBuilder sb ) {
+    static final int nodeDataIntoStringBuffer( final List<String> data, final Options optz, final StringBuilder sb ) {
         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
-        if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
-                && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+        int size = 0;
+        if ( ( optz.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA )
+                && ( optz.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS ) ) {
             for( final String d : data ) {
                 if ( !ForesterUtil.isEmpty( d ) ) {
                     if ( map.containsKey( d ) ) {
@@ -451,17 +454,30 @@ public class TreePanelUtil {
                     }
                 }
             }
-        }
-        int size = 0;
-        if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
-                && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
-            for( final Entry<String, Integer> e : map.entrySet() ) {
-                final String v = e.getKey();
-                final Object c = e.getValue();
-                sb.append( v );
-                sb.append( "\t" );
-                sb.append( c );
-                sb.append( ForesterUtil.LINE_SEPARATOR );
+            if ( ( optz.getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_ALL )
+                    || ( optz.getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )
+                    || ( optz.getExtDescNodeDataToReturn() == NodeDataField.SEQ_ANNOTATIONS ) ) {
+                final ArrayList<StringInt> sis = new ArrayList<StringInt>();
+                for( final Entry<String, Integer> e : map.entrySet() ) {
+                    sis.add( new StringInt( e.getKey(), e.getValue() ) );
+                }
+                Collections.sort( sis, new StringInt.DescendingIntComparator() );
+                for( final StringInt si : sis ) {
+                    sb.append( si.getString() );
+                    sb.append( "\t" );
+                    sb.append( si.getInt() );
+                    sb.append( ForesterUtil.LINE_SEPARATOR );
+                }
+            }
+            else {
+                for( final Entry<String, Integer> e : map.entrySet() ) {
+                    final String v = e.getKey();
+                    final Object c = e.getValue();
+                    sb.append( v );
+                    sb.append( "\t" );
+                    sb.append( c );
+                    sb.append( ForesterUtil.LINE_SEPARATOR );
+                }
             }
             size = map.size();
         }