sorting added ...

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 064fc7d..f5532e9 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -129,7 +129,7 @@ public final class Configuration {
     final static int                        collapse_uncollapse                                    = 1;
     final static int                        reroot                                                 = 2;
     final static int                        subtree                                                = 3;
-    final static int                        swap               = 4;
+    final static int                        swap                                                   = 4;
     final static int                        color_subtree                                          = 5;
     final static int                        open_seq_web                                           = 6;
     final static int                        open_tax_web                                           = 7;
@@ -140,9 +140,7 @@ public final class Configuration {
     final static int                        add_new_node                                           = 12;
     final static int                        edit_node_data                                         = 13;
     final static int                        blast                                                  = 14;
-    final static int                        sort_descendents                                        = 15;
-    
-    
+    final static int                        sort_descendents                                       = 15;
     // ---------------------------
     // Display options for trees
     // ---------------------------
@@ -170,7 +168,8 @@ public final class Configuration {
             { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
             { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Cut Subtree", "display" },
             { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
-            { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" }, { "Sort Descendants", "display" } };
+            { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" },
+            { "Sort Descendants", "display" }                                                     };
     // This option is selected in the dropdown
     int                                     default_clickto                                        = Configuration.display_node_data;
     // --------------

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 338d2f3..451d04c 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -36,13 +36,13 @@ import org.forester.util.ForesterConstants;
 
 public final class Constants {
 
-    final static boolean        __ALLOW_PHYLOGENETIC_INFERENCE                                = true;
+    final static boolean        __ALLOW_PHYLOGENETIC_INFERENCE                                = false;
     public final static boolean __RELEASE                                                     = false;                                                    // TODO remove me
-    public final static boolean __SNAPSHOT_RELEASE                                            = false;                                                    // TODO remove me
+    public final static boolean __SNAPSHOT_RELEASE                                            = true;                                                     // TODO remove me
     public final static boolean __SYNTH_LF                                                    = false;                                                    // TODO remove me
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.969 beta BG";
-    final static String         PRG_DATE                                                      = "2012.01.11";
+    final static String         VERSION                                                       = "0.969 demo BG";
+    final static String         PRG_DATE                                                      = "2012.02.13";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Verdana", "Tahoma",
             "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 2a2ffd7..814e199 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -1321,7 +1321,8 @@ final class ControlPanel extends JPanel implements ActionListener {
         }
         if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
             _sort_descendents_item = cb_index;
-            addClickToOption( Configuration.sort_descendents, _configuration.getClickToTitle( Configuration.sort_descendents ) );
+            addClickToOption( Configuration.sort_descendents,
+                              _configuration.getClickToTitle( Configuration.sort_descendents ) );
             if ( default_option == Configuration.sort_descendents ) {
                 selected_index = cb_index;
             }

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index b561ac2..85c3d5e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -100,6 +100,7 @@ import org.forester.archaeopteryx.tools.ImageLoader;
 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.BranchColor;
@@ -4917,17 +4918,26 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         repaint();
     }
-    
-    
-    final void  sortDescendants( final PhylogenyNode node ) {
+
+    final void sortDescendants( final PhylogenyNode node ) {
         if ( !node.isExternal() ) {
-            PhylogenyMethods.sortNodeDescendents( node );
+            DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
+            if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
+                    .isShowTaxonomyCommonNames() ) ) {
+                if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
+                        .isShowGeneSymbols() ) ) {
+                    pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
+                }
+                else if ( getControlPanel().isShowNodeNames() ) {
+                    pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+                }
+            }
+            PhylogenyMethods.sortNodeDescendents( node, pri );
             setNodeInPreorderToNull();
         }
         repaint();
     }
-    
-    
+
     final private void switchDisplaygetPhylogenyGraphicsType() {
         switch ( getPhylogenyGraphicsType() ) {
             case RECTANGULAR:

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 7835d62..a042cee 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -31,6 +31,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
@@ -232,21 +233,164 @@ public class PhylogenyMethods {
             }
         }
     }
-    
-    
-    
-    final static public void sortNodeDescendents( PhylogenyNode node ) {
+
+    final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
+        class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {
+
+            @Override
+            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+                    }
+                }
+                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+                        return n1.getNodeData().getSequence().getName().toLowerCase()
+                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                        return n1.getNodeData().getSequence().getSymbol()
+                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                    }
+                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
+                            && ( n2.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+                        return n1.getNodeData().getSequence().getAccession().getValue()
+                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+                    }
+                }
+                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+                }
+                return 0;
+            }
+        }
+        class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
+
+            @Override
+            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+                        return n1.getNodeData().getSequence().getName().toLowerCase()
+                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                        return n1.getNodeData().getSequence().getSymbol()
+                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                    }
+                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
+                            && ( n2.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+                        return n1.getNodeData().getSequence().getAccession().getValue()
+                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+                    }
+                }
+                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+                    }
+                }
+                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+                }
+                return 0;
+            }
+        }
+        class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
+
+            @Override
+            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+                }
+                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+                    }
+                }
+                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+                        return n1.getNodeData().getSequence().getName().toLowerCase()
+                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                        return n1.getNodeData().getSequence().getSymbol()
+                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                    }
+                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
+                            && ( n2.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+                        return n1.getNodeData().getSequence().getAccession().getValue()
+                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+                    }
+                }
+                return 0;
+            }
+        }
+        Comparator<PhylogenyNode> c;
+        switch ( pri ) {
+            case SEQUENCE:
+                c = new PhylogenyNodeSortSequencePriority();
+                break;
+            case NODE_NAME:
+                c = new PhylogenyNodeSortNodeNamePriority();
+                break;
+            default:
+                c = new PhylogenyNodeSortTaxonomyPriority();
+        }
         final List<PhylogenyNode> descs = node.getDescendants();
-       // Collections.sort( arg0, comparator );
-        Collections.sort( descs );
-        
+        Collections.sort( descs, c );
         int i = 0;
-        for( PhylogenyNode desc : descs ) {
+        for( final PhylogenyNode desc : descs ) {
             node.setChildNode( i++, desc );
         }
-        
     }
-    
 
     final static public void transferNodeNameToField( final Phylogeny phy,
                                                       final PhylogenyMethods.PhylogenyNodeField field ) {
@@ -1430,4 +1574,8 @@ public class PhylogenyMethods {
     public static enum TAXONOMY_EXTRACTION {
         NO, YES, PFAM_STYLE_ONLY;
     }
+
+    public static enum DESCENDANT_SORT_PRIORITY {
+        TAXONOMY, SEQUENCE, NODE_NAME;
+    }
 }