inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index e68b220..5cfceac 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -115,19 +115,20 @@ public final class Configuration {
     final static int                        show_domain_architectures                              = 10;
     final static int                        show_binary_characters                                 = 11;
     final static int                        show_binary_character_counts                           = 12;
-    final static int                        show_gene_names                                        = 13;
+    final static int                        show_seq_names                                         = 13;
     final static int                        show_sequence_acc                                      = 14;
     final static int                        display_internal_data                                  = 15;
     final static int                        dynamically_hide_data                                  = 16;
     final static int                        show_taxonomy_scientific_names                         = 17;
     final static int                        show_taxonomy_common_names                             = 18;
     final static int                        color_according_to_annotation                          = 19;
-    final static int                        show_gene_symbols                                      = 20;
+    final static int                        show_seq_symbols                                       = 20;
     final static int                        node_data_popup                                        = 21;
     final static int                        show_relation_confidence                               = 22;
     final static int                        show_vector_data                                       = 23;
     final static int                        show_taxonomy_images                                   = 24;
     final static int                        show_properties                                        = 25;
+    final static int                        show_gene_names                                        = 26;
     // ------------------
     // Click-to options
     // ------------------
@@ -165,13 +166,13 @@ public final class Configuration {
             { "Use Branch Colors", "display", "no" }, { "Use Branch Widths", "display", "no" },
             { "Show Custom Nodes", "display", "yes" }, { "Protein Domains", "nodisplay", "no" },
             { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
-            { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" },
+            { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
             { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
             { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
             { "Colorize by Annotation", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
             { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
             { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
-            { "Properties", "nodisplay", "no" }                                                   };
+            { "Properties", "nodisplay", "no" }, { "Gene Name", "display", "yes" }                };
     final static String                     clickto_options[][]                                    = {
             { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
             { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" },
@@ -458,7 +459,7 @@ public final class Configuration {
     }
 
     public void setDisplaySequenceNames( final boolean b ) {
-        display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
+        display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
     }
 
     public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
@@ -466,7 +467,7 @@ public final class Configuration {
     }
 
     public void setDisplaySequenceSymbols( final boolean b ) {
-        display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
+        display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
     }
 
     public void setDisplayTaxonomyCode( final boolean b ) {
@@ -1437,6 +1438,9 @@ public final class Configuration {
             else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
                 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
             }
+            else if ( s.equalsIgnoreCase( "gene_name" ) ) {
+                setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
+            }
             else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
                 setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
             }
@@ -1486,13 +1490,8 @@ public final class Configuration {
         else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
             // yet retrieved!
             int key_index = -1;
-            if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
+            if ( key.equals( "phylogram" ) ) {
                 key_index = Configuration.display_as_phylogram;
-                if ( key.equals( "use_real_br_lengths" ) ) {
-                    ForesterUtil
-                            .printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
-                }
             }
             else if ( key.equals( "rollover" ) ) {
                 key_index = Configuration.node_data_popup;
@@ -1503,34 +1502,14 @@ public final class Configuration {
             else if ( key.equals( "show_node_names" ) ) {
                 key_index = Configuration.show_node_names;
             }
-            else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
+            else if ( key.equals( "show_taxonomy_code" ) ) {
                 key_index = Configuration.show_tax_code;
-                if ( key.equals( "show_taxonomy" ) ) {
-                    ForesterUtil
-                            .printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
-                }
             }
-            else if ( key.equals( "write_br_length_values" ) ) {
-                ForesterUtil.printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [write_br_length_values] is deprecated" );
-                key_index = DEPRECATED;
-            }
-            else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
+            else if ( key.equals( "write_confidence_values" ) ) {
                 key_index = Configuration.write_confidence_values;
-                if ( key.equals( "write_bootstrap_values" ) ) {
-                    ForesterUtil
-                            .printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
-                }
             }
-            else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
+            else if ( key.equals( "write_events" ) ) {
                 key_index = Configuration.write_events;
-                if ( key.equals( "write_dup_spec" ) ) {
-                    ForesterUtil
-                            .printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
-                }
             }
             else if ( key.equals( "color_branches" ) ) {
                 key_index = Configuration.color_branches;
@@ -1538,11 +1517,6 @@ public final class Configuration {
             else if ( key.equals( "width_branches" ) ) {
                 key_index = Configuration.width_branches;
             }
-            else if ( key.equals( "mark_nodes_with_box" ) ) {
-                ForesterUtil.printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [mark_nodes_with_box] is deprecated" );
-                key_index = DEPRECATED;
-            }
             else if ( key.equals( "show_domain_architectures" ) ) {
                 key_index = Configuration.show_domain_architectures;
             }
@@ -1555,31 +1529,24 @@ public final class Configuration {
             else if ( key.equals( "show_binary_character_counts" ) ) {
                 key_index = Configuration.show_binary_character_counts;
             }
+            else if ( key.equals( "show_seq_names" ) ) {
+                key_index = Configuration.show_seq_names;
+            }
             else if ( key.equals( "show_gene_names" ) ) {
                 key_index = Configuration.show_gene_names;
             }
-            else if ( key.equals( "show_gene_symbols" ) ) {
-                key_index = Configuration.show_gene_symbols;
+            else if ( key.equals( "show_seq_symbols" ) ) {
+                key_index = Configuration.show_seq_symbols;
             }
-            else if ( key.equals( "show_sequence_acc" ) ) {
+            else if ( key.equals( "show_seq_acc" ) ) {
                 key_index = Configuration.show_sequence_acc;
             }
-            else if ( key.equals( "show_node_ids" ) ) {
-                ForesterUtil
-                        .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
-                key_index = DEPRECATED;
-            }
             else if ( key.equals( "display_internal_data" ) ) {
                 key_index = Configuration.display_internal_data;
             }
             else if ( key.equals( "dynamically_hide_data" ) ) {
                 key_index = Configuration.dynamically_hide_data;
             }
-            else if ( key.equals( "show_taxonomy_names" ) ) {
-                ForesterUtil.printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [show_taxonomy_names] is deprecated" );
-                key_index = DEPRECATED;
-            }
             else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
                 key_index = Configuration.show_taxonomy_scientific_names;
             }

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 656cb75..7586722 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -97,8 +97,9 @@ final class ControlPanel extends JPanel implements ActionListener {
     private JCheckBox            _show_annotation;
     private JCheckBox            _show_binary_characters;
     private JCheckBox            _show_binary_character_counts;
+    private JCheckBox            _show_seq_names;
+    private JCheckBox            _show_seq_symbols;
     private JCheckBox            _show_gene_names;
-    private JCheckBox            _show_gene_symbols;
     private JCheckBox            _show_sequence_acc;
     private JCheckBox            _node_desc_popup_cb;
     private JCheckBox            _dynamically_hide_data;
@@ -237,7 +238,7 @@ final class ControlPanel extends JPanel implements ActionListener {
                 else if ( e.getSource() == _order ) {
                     DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
                     if ( ( !isShowTaxonomyScientificNames() && !isShowTaxonomyCode() && !isShowTaxonomyCommonNames() ) ) {
-                        if ( ( isShowSequenceAcc() || isShowGeneNames() || isShowGeneSymbols() ) ) {
+                        if ( ( isShowSequenceAcc() || isShowSeqNames() || isShowSeqSymbols() ) ) {
                             pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
                         }
                         else if ( isShowNodeNames() ) {
@@ -610,14 +611,19 @@ final class ControlPanel extends JPanel implements ActionListener {
                 addJCheckBox( _show_domain_architectures, ch_panel );
                 add( ch_panel );
                 break;
+            case Configuration.show_seq_names:
+                _show_seq_names = new JCheckBox( title );
+                addJCheckBox( _show_seq_names, ch_panel );
+                add( ch_panel );
+                break;
             case Configuration.show_gene_names:
                 _show_gene_names = new JCheckBox( title );
                 addJCheckBox( _show_gene_names, ch_panel );
                 add( ch_panel );
                 break;
-            case Configuration.show_gene_symbols:
-                _show_gene_symbols = new JCheckBox( title );
-                addJCheckBox( _show_gene_symbols, ch_panel );
+            case Configuration.show_seq_symbols:
+                _show_seq_symbols = new JCheckBox( title );
+                addJCheckBox( _show_seq_symbols, ch_panel );
                 add( ch_panel );
                 break;
             case Configuration.show_sequence_acc:
@@ -817,12 +823,12 @@ final class ControlPanel extends JPanel implements ActionListener {
         return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
     }
 
-    boolean isShowGeneNames() {
-        return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
+    boolean isShowSeqNames() {
+        return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
     }
 
-    boolean isShowGeneSymbols() {
-        return ( ( _show_gene_symbols != null ) && _show_gene_symbols.isSelected() );
+    boolean isShowSeqSymbols() {
+        return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
     }
 
     boolean isShowInternalData() {
@@ -837,6 +843,10 @@ final class ControlPanel extends JPanel implements ActionListener {
         return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
     }
 
+    boolean isShowGeneNames() {
+        return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
+    }
+
     boolean isShowSequenceRelationConfidence() {
         return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
     }
@@ -991,14 +1001,19 @@ final class ControlPanel extends JPanel implements ActionListener {
                     _show_domain_architectures.setSelected( state );
                 }
                 break;
+            case Configuration.show_seq_names:
+                if ( _show_seq_names != null ) {
+                    _show_seq_names.setSelected( state );
+                }
+                break;
             case Configuration.show_gene_names:
                 if ( _show_gene_names != null ) {
                     _show_gene_names.setSelected( state );
                 }
                 break;
-            case Configuration.show_gene_symbols:
-                if ( _show_gene_symbols != null ) {
-                    _show_gene_symbols.setSelected( state );
+            case Configuration.show_seq_symbols:
+                if ( _show_seq_symbols != null ) {
+                    _show_seq_symbols.setSelected( state );
                 }
                 break;
             case Configuration.show_vector_data:
@@ -1766,6 +1781,9 @@ final class ControlPanel extends JPanel implements ActionListener {
                     case SEQUENCE_NAME:
                         s = "Sequence Names";
                         break;
+                    case GENE_NAME:
+                        s = "Gene Names";
+                        break;
                     case SEQUENCE_SYMBOL:
                         s = "Sequence Symbols";
                         break;
@@ -1919,22 +1937,19 @@ final class ControlPanel extends JPanel implements ActionListener {
             setCheckbox( Configuration.show_taxonomy_common_names,
                          _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
         }
-        if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
-            addCheckbox( Configuration.show_taxonomy_images,
-                         _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
-            setCheckbox( Configuration.show_taxonomy_images,
-                         _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
-        }
-        if ( _configuration.doDisplayOption( Configuration.show_gene_symbols ) ) {
-            addCheckbox( Configuration.show_gene_symbols,
-                         _configuration.getDisplayTitle( Configuration.show_gene_symbols ) );
-            setCheckbox( Configuration.show_gene_symbols,
-                         _configuration.doCheckOption( Configuration.show_gene_symbols ) );
+        if ( _configuration.doDisplayOption( Configuration.show_seq_names ) ) {
+            addCheckbox( Configuration.show_seq_names, _configuration.getDisplayTitle( Configuration.show_seq_names ) );
+            setCheckbox( Configuration.show_seq_names, _configuration.doCheckOption( Configuration.show_seq_names ) );
         }
         if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
             addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
             setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
         }
+        if ( _configuration.doDisplayOption( Configuration.show_seq_symbols ) ) {
+            addCheckbox( Configuration.show_seq_symbols,
+                         _configuration.getDisplayTitle( Configuration.show_seq_symbols ) );
+            setCheckbox( Configuration.show_seq_symbols, _configuration.doCheckOption( Configuration.show_seq_symbols ) );
+        }
         if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
             addCheckbox( Configuration.show_sequence_acc,
                          _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
@@ -1982,6 +1997,12 @@ final class ControlPanel extends JPanel implements ActionListener {
             addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
             setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
         }
+        if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
+            addCheckbox( Configuration.show_taxonomy_images,
+                         _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
+            setCheckbox( Configuration.show_taxonomy_images,
+                         _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
+        }
     }
 
     private void setVisibilityOfDomainStrucureControls() {

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 248a5a4..8f65e7b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -1473,6 +1473,9 @@ public final class MainFrameApplication extends MainFrame {
                         nodes = phy.getNodesViaSequenceSymbol( seq_name );
                     }
                     if ( nodes.isEmpty() ) {
+                        nodes = phy.getNodesViaGeneName( seq_name );
+                    }
+                    if ( nodes.isEmpty() ) {
                         nodes = phy.getNodes( seq_name );
                     }
                     if ( nodes.size() > 1 ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
index 1892411..f593a78 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
@@ -337,6 +337,7 @@ class NodeEditPanel extends JPanel {
         }
         addSubelementEditable( category, NodePanel.SEQ_NAME, seq.getName(), PHYLOXML_TAG.SEQ_NAME );
         addSubelementEditable( category, NodePanel.SEQ_SYMBOL, seq.getSymbol(), PHYLOXML_TAG.SEQ_SYMBOL );
+        addSubelementEditable( category, NodePanel.SEQ_GENE_NAME, seq.getGeneName(), PHYLOXML_TAG.SEQ_GENE_NAME );
         addSubelementEditable( category,
                                NodePanel.SEQ_ACCESSION,
                                acc.getValue(),
@@ -841,6 +842,10 @@ class NodeEditPanel extends JPanel {
                     break;
                 }
                 break;
+            case SEQ_GENE_NAME:
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                getMyNode().getNodeData().getSequence().setGeneName( value );
+                break;
             case SEQ_TYPE:
                 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 try {
@@ -1062,6 +1067,7 @@ class NodeEditPanel extends JPanel {
         TAXONOMY_URI,
         SEQ_SYMBOL,
         SEQ_NAME,
+        SEQ_GENE_NAME,
         SEQ_LOCATION,
         SEQ_TYPE,
         SEQ_MOL_SEQ,

diff --git a/forester/java/src/org/forester/archaeopteryx/NodePanel.java b/forester/java/src/org/forester/archaeopteryx/NodePanel.java
index 90c7010..c861354 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/NodePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/NodePanel.java
@@ -63,57 +63,57 @@ import org.forester.util.ForesterUtil;
 
 class NodePanel extends JPanel implements TreeSelectionListener {
 
-    static final String         BASIC                    = "Basic";
-    static final String         BINARY_CHARACTERS        = "Binary characters";
-    static final String         CONFIDENCE               = "Confidence";
-    static final String         CONFIDENCE_TYPE          = "type";
-    static final String         DATE                     = "Date";
-    static final String         DATE_DESCRIPTION         = "Description";
-    static final String         DATE_MAX                 = "Max";
-    static final String         DATE_MIN                 = "Min";
-    static final String         DATE_UNIT                = "Unit";
-    static final String         DATE_VALUE               = "Value";
-    static final String         DIST_ALT_UNIT            = "Altitude unit";
-    static final String         DIST_ALTITUDE            = "Altitude";
-    static final String         DIST_DESCRIPTION         = "Description";
-    static final String         DIST_GEODETIC_DATUM      = "Geodetic datum";
-    static final String         DIST_LATITUDE            = "Latitude";
-    static final String         DIST_LONGITUDE           = "Longitude";
-    static final String         DISTRIBUTION             = "Distribution";
-    static final String         EVENTS                   = "Events";
-    static final String         EVENTS_DUPLICATIONS      = "Duplications";
-    static final String         EVENTS_GENE_LOSSES       = "Gene losses";
-    static final String         EVENTS_SPECIATIONS       = "Speciations";
-    static final String         LIT_REFERENCE            = "Reference";
-    static final String         LIT_REFERENCE_DESC       = "Description";
-    static final String         LIT_REFERENCE_DOI        = "DOI";
-    static final String         NODE_BRANCH_COLOR        = "Branch color";
-    static final String         NODE_BRANCH_LENGTH       = "Branch length";
-    static final String         NODE_BRANCH_WIDTH        = "Branch width";
-    static final String         NODE_NAME                = "Name";
-    static final String         PROP                     = "Properties";
-    static final String         REFERENCE                = "Reference";
-    static final String         SEQ_ACCESSION            = "Accession";
-    static final String         SEQ_LOCATION             = "Location";
-    static final String         SEQ_MOL_SEQ              = "Mol seq";
-    static final String         SEQ_NAME                 = "Name";
-    static final String         SEQ_SYMBOL               = "Symbol";
-    static final String         SEQ_TYPE                 = "Type";
-    static final String         SEQ_URI                  = "URI";
-    static final String         SEQUENCE                 = "Sequence";
-    static final String         TAXONOMY                 = "Taxonomy";
-    static final String         TAXONOMY_AUTHORITY       = "Authority";
-    static final String         TAXONOMY_CODE            = "Code";
-    static final String         TAXONOMY_COMMON_NAME     = "Common name";
-    static final String         TAXONOMY_IDENTIFIER      = "Identifier";
-    static final String         TAXONOMY_RANK            = "Rank";
-    static final String         TAXONOMY_SCIENTIFIC_NAME = "Scientific name";
-    static final String         TAXONOMY_SYNONYM         = "Synonym";
-    static final String         TAXONOMY_URI             = "URI";
-    private static final String SEQ_GENE_NAME            = "Gene name";
-    private static final long   serialVersionUID         = 5120159904388100771L;
-    private final JEditorPane   _pane;
-    private final JTree         _tree;
+    static final String       BASIC                    = "Basic";
+    static final String       BINARY_CHARACTERS        = "Binary characters";
+    static final String       CONFIDENCE               = "Confidence";
+    static final String       CONFIDENCE_TYPE          = "type";
+    static final String       DATE                     = "Date";
+    static final String       DATE_DESCRIPTION         = "Description";
+    static final String       DATE_MAX                 = "Max";
+    static final String       DATE_MIN                 = "Min";
+    static final String       DATE_UNIT                = "Unit";
+    static final String       DATE_VALUE               = "Value";
+    static final String       DIST_ALT_UNIT            = "Altitude unit";
+    static final String       DIST_ALTITUDE            = "Altitude";
+    static final String       DIST_DESCRIPTION         = "Description";
+    static final String       DIST_GEODETIC_DATUM      = "Geodetic datum";
+    static final String       DIST_LATITUDE            = "Latitude";
+    static final String       DIST_LONGITUDE           = "Longitude";
+    static final String       DISTRIBUTION             = "Distribution";
+    static final String       EVENTS                   = "Events";
+    static final String       EVENTS_DUPLICATIONS      = "Duplications";
+    static final String       EVENTS_GENE_LOSSES       = "Gene losses";
+    static final String       EVENTS_SPECIATIONS       = "Speciations";
+    static final String       LIT_REFERENCE            = "Reference";
+    static final String       LIT_REFERENCE_DESC       = "Description";
+    static final String       LIT_REFERENCE_DOI        = "DOI";
+    static final String       NODE_BRANCH_COLOR        = "Branch color";
+    static final String       NODE_BRANCH_LENGTH       = "Branch length";
+    static final String       NODE_BRANCH_WIDTH        = "Branch width";
+    static final String       NODE_NAME                = "Name";
+    static final String       PROP                     = "Properties";
+    static final String       REFERENCE                = "Reference";
+    static final String       SEQ_ACCESSION            = "Accession";
+    static final String       SEQ_LOCATION             = "Location";
+    static final String       SEQ_MOL_SEQ              = "Mol seq";
+    static final String       SEQ_NAME                 = "Name";
+    static final String       SEQ_SYMBOL               = "Symbol";
+    static final String       SEQ_GENE_NAME            = "Gene name";
+    static final String       SEQ_TYPE                 = "Type";
+    static final String       SEQ_URI                  = "URI";
+    static final String       SEQUENCE                 = "Sequence";
+    static final String       TAXONOMY                 = "Taxonomy";
+    static final String       TAXONOMY_AUTHORITY       = "Authority";
+    static final String       TAXONOMY_CODE            = "Code";
+    static final String       TAXONOMY_COMMON_NAME     = "Common name";
+    static final String       TAXONOMY_IDENTIFIER      = "Identifier";
+    static final String       TAXONOMY_RANK            = "Rank";
+    static final String       TAXONOMY_SCIENTIFIC_NAME = "Scientific name";
+    static final String       TAXONOMY_SYNONYM         = "Synonym";
+    static final String       TAXONOMY_URI             = "URI";
+    private static final long serialVersionUID         = 5120159904388100771L;
+    private final JEditorPane _pane;
+    private final JTree       _tree;
 
     public NodePanel( final PhylogenyNode phylogeny_node ) {
         String node_name = "";

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 32dd030..6d793c8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -607,13 +607,18 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                             .getValue()
                             + " " );
                 }
-                if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+                if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
                     sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
                 }
-                if ( getControlPanel().isShowGeneSymbols()
+                if ( getControlPanel().isShowSeqSymbols()
                         && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
                     sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
                 }
+                if ( getControlPanel().isShowGeneNames()
+                        && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+                    sum += getTreeFontSet()._fm_large
+                            .stringWidth( node.getNodeData().getSequence().getGeneName() + " " );
+                }
                 if ( getControlPanel().isShowAnnotation()
                         && ( node.getNodeData().getSequence().getAnnotations() != null )
                         && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
@@ -1925,8 +1930,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
             if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
                     .isShowTaxonomyCommonNames() ) ) {
-                if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
-                        .isShowGeneSymbols() ) ) {
+                if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowSeqNames() || getControlPanel()
+                        .isShowSeqSymbols() ) ) {
                     pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
                 }
                 else if ( getControlPanel().isShowNodeNames() ) {
@@ -3224,6 +3229,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         switch ( getOptions().getExtDescNodeDataToReturn() ) {
             case NODE_NAME:
                 return "Node Names";
+            case GENE_NAME:
+                return "Gene Names";
             case SEQUENCE_NAME:
                 return "Sequence Names";
             case SEQUENCE_SYMBOL:
@@ -3984,13 +3991,19 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             _sb.append( node.getName() );
         }
         if ( node.getNodeData().isHasSequence() ) {
-            if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
+            if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
                 if ( _sb.length() > 0 ) {
                     _sb.append( " " );
                 }
                 _sb.append( node.getNodeData().getSequence().getSymbol() );
             }
-            if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+            if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+                if ( _sb.length() > 0 ) {
+                    _sb.append( " " );
+                }
+                _sb.append( node.getNodeData().getSequence().getGeneName() );
+            }
+            if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
                 if ( _sb.length() > 0 ) {
                     _sb.append( " " );
                 }
@@ -4234,7 +4247,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 }
                 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
             }
-            if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+            if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
                 if ( _sb.length() > 0 ) {
                     _sb.append( " " );
                 }
@@ -4477,16 +4490,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         }
                     }
                     if ( node.getNodeData().isHasSequence() ) {
-                        if ( getControlPanel().isShowGeneNames()
+                        if ( getControlPanel().isShowSeqNames()
                                 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
                             x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
                                     + " " );
                         }
-                        if ( getControlPanel().isShowGeneSymbols()
+                        if ( getControlPanel().isShowSeqSymbols()
                                 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
                             x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
                                     + " " );
                         }
+                        if ( getControlPanel().isShowGeneNames()
+                                && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) ) {
+                            x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getGeneName()
+                                    + " " );
+                        }
                         if ( getControlPanel().isShowSequenceAcc()
                                 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
                             x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
@@ -5093,6 +5111,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         data.add( n.getNodeData().getSequence().getName() );
                     }
                     break;
+                case GENE_NAME:
+                    if ( n.getNodeData().isHasSequence()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+                        data.add( n.getNodeData().getSequence().getGeneName() );
+                    }
+                    break;
                 case SEQUENCE_SYMBOL:
                     if ( n.getNodeData().isHasSequence()
                             && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
@@ -5124,6 +5148,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                             ann.append( n.getNodeData().getSequence().getName() );
                             ann.append( "|" );
                         }
+                        if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+                            ann.append( "GN=" );
+                            ann.append( n.getNodeData().getSequence().getGeneName() );
+                            ann.append( "|" );
+                        }
                         if ( n.getNodeData().getSequence().getAccession() != null ) {
                             ann.append( "ACC=" );
                             ann.append( n.getNodeData().getSequence().getAccession().asText() );
@@ -5366,6 +5395,17 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         _popup_buffer.append( "]" );
                         enc_data = true;
                     }
+                    if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
+                        if ( enc_data ) {
+                            _popup_buffer.append( " [" );
+                        }
+                        else {
+                            _popup_buffer.append( "[" );
+                        }
+                        _popup_buffer.append( seq.getGeneName() );
+                        _popup_buffer.append( "]" );
+                        enc_data = true;
+                    }
                     if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
                         if ( enc_data ) {
                             _popup_buffer.append( " " );

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
index 322199e..7c1cbaf 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
@@ -165,15 +165,20 @@ public class TreePanelUtil {
         if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
             TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb );
         }
-        if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
+        if ( cp.isShowSeqNames() && node.getNodeData().isHasSequence()
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
             TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb );
         }
-        if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence()
+        if ( cp.isShowSeqSymbols() && node.getNodeData().isHasSequence()
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
             TreePanelUtil
                     .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
         }
+        if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
+                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
+            TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getGeneName(),
+                                                                       sb );
+        }
         if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence()
                 && ( node.getNodeData().getSequence().getAccession() != null )
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) {
@@ -195,7 +200,7 @@ public class TreePanelUtil {
             TreePanelUtil
                     .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
         }
-        if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
+        if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() )
                 && node.getNodeData().isHasSequence()
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
             TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence()
@@ -485,7 +490,7 @@ public class TreePanelUtil {
 
     final static boolean isSequenceEmpty( final Sequence seq ) {
         return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
-                && ForesterUtil.isEmpty( seq.getSymbol() );
+                && ForesterUtil.isEmpty( seq.getGeneName() ) && ForesterUtil.isEmpty( seq.getSymbol() );
     }
 
     final static boolean isTaxonomyEmpty( final Taxonomy tax ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java
index 839a328..49e2841 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java
@@ -99,6 +99,13 @@ public final class Blast {
                     query = id.getValue();
                 }
             }
+            if ( ForesterUtil.isEmpty( query )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
+                final Identifier id = SequenceIdParser.parse( node.getNodeData().getSequence().getGeneName() );
+                if ( id != null ) {
+                    query = id.getValue();
+                }
+            }
         }
         if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getName() ) ) {
             final Identifier id = SequenceIdParser.parse( node.getName() );

diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index 723fab8..3679cd5 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -489,6 +489,20 @@ public class Phylogeny {
         return nodes;
     }
 
+    public List<PhylogenyNode> getNodesViaGeneName( final String seq_name ) {
+        if ( isEmpty() ) {
+            return null;
+        }
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+        for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getGeneName().equals( seq_name ) ) {
+                nodes.add( n );
+            }
+        }
+        return nodes;
+    }
+
     public List<PhylogenyNode> getNodesViaTaxonomyCode( final String taxonomy_code ) {
         if ( isEmpty() ) {
             return null;

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 9c83603..08fe7f0 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -1245,6 +1245,11 @@ public class PhylogenyMethods {
                         return n1.getNodeData().getSequence().getSymbol()
                                 .compareTo( n2.getNodeData().getSequence().getSymbol() );
                     }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+                        return n1.getNodeData().getSequence().getGeneName()
+                                .compareTo( n2.getNodeData().getSequence().getGeneName() );
+                    }
                     if ( ( n1.getNodeData().getSequence().getAccession() != null )
                             && ( n2.getNodeData().getSequence().getAccession() != null )
                             && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
@@ -1274,6 +1279,11 @@ public class PhylogenyMethods {
                         return n1.getNodeData().getSequence().getSymbol()
                                 .compareTo( n2.getNodeData().getSequence().getSymbol() );
                     }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+                        return n1.getNodeData().getSequence().getGeneName()
+                                .compareTo( n2.getNodeData().getSequence().getGeneName() );
+                    }
                     if ( ( n1.getNodeData().getSequence().getAccession() != null )
                             && ( n2.getNodeData().getSequence().getAccession() != null )
                             && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
@@ -1340,6 +1350,11 @@ public class PhylogenyMethods {
                         return n1.getNodeData().getSequence().getSymbol()
                                 .compareTo( n2.getNodeData().getSequence().getSymbol() );
                     }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+                        return n1.getNodeData().getSequence().getGeneName()
+                                .compareTo( n2.getNodeData().getSequence().getGeneName() );
+                    }
                     if ( ( n1.getNodeData().getSequence().getAccession() != null )
                             && ( n2.getNodeData().getSequence().getAccession() != null )
                             && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 3994605..05876e7 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -1097,6 +1097,10 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
                 sb.append( getNodeData().getSequence().getSymbol() );
                 sb.append( " " );
             }
+            if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getGeneName() ) ) {
+                sb.append( getNodeData().getSequence().getGeneName() );
+                sb.append( " " );
+            }
             if ( getNodeData().getSequence().getAccession() != null ) {
                 sb.append( getNodeData().getSequence().getAccession().toString() );
                 sb.append( " " );

diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java
index 4591155..da6d557 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/NodeData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java
@@ -42,6 +42,7 @@ public class NodeData implements PhylogenyData {
         NODE_NAME,
         EVENT,
         SEQUENCE_NAME,
+        GENE_NAME,
         SEQUENCE_SYMBOL,
         SEQUENCE_MOL_SEQ,
         SEQUENCE_MOL_SEQ_FASTA,

diff --git a/forester/java/src/org/forester/phylogeny/data/Sequence.java b/forester/java/src/org/forester/phylogeny/data/Sequence.java
index 25f7e70..afc342b 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Sequence.java
+++ b/forester/java/src/org/forester/phylogeny/data/Sequence.java
@@ -39,36 +39,27 @@ import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.util.ForesterUtil;
 
-public class Sequence implements PhylogenyData, MultipleUris {
+public class Sequence implements PhylogenyData, MultipleUris, Comparable<Sequence> {
 
+    private Accession              _accession;
+    private SortedSet<Annotation>  _annotations;
+    private DomainArchitecture     _da;
+    private String                 _gene_name;
+    private String                 _location;
     private String                 _mol_sequence;
     private boolean                _mol_sequence_is_aligned;
     private String                 _name;
-    private String                 _gene_name;
+    private List<SequenceRelation> _seq_relations;
     private String                 _source_id;
-    private Accession              _accession;
     private String                 _symbol;
-    private String                 _location;
     private String                 _type;
-    private SortedSet<Annotation>  _annotations;
-    private DomainArchitecture     _da;
     private List<Uri>              _uris;
-    private List<SequenceRelation> _seq_relations;
     private SortedSet<Accession>   _xrefs;
 
     public Sequence() {
         init();
     }
 
-    public boolean isEmpty() {
-        return ( getAccession() == null ) && ForesterUtil.isEmpty( getName() ) && ForesterUtil.isEmpty( getSymbol() )
-                && ForesterUtil.isEmpty( getType() ) && ForesterUtil.isEmpty( getLocation() )
-                && ForesterUtil.isEmpty( getSourceId() ) && ForesterUtil.isEmpty( getMolecularSequence() )
-                && ( getDomainArchitecture() == null ) && ForesterUtil.isEmpty( _annotations )
-                && ForesterUtil.isEmpty( _uris ) && ForesterUtil.isEmpty( _seq_relations )
-                && ( ( getCrossReferences() == null ) || getCrossReferences().isEmpty() );
-    }
-
     public void addAnnotation( final Annotation annotation ) {
         getAnnotations().add( annotation );
     }
@@ -80,12 +71,8 @@ public class Sequence implements PhylogenyData, MultipleUris {
         getCrossReferences().add( cross_reference );
     }
 
-    public SortedSet<Accession> getCrossReferences() {
-        return _xrefs;
-    }
-
-    private void setCrossReferences( final TreeSet<Accession> cross_references ) {
-        _xrefs = cross_references;
+    public void addSequenceRelation( final SequenceRelation sr ) {
+        getSequenceRelations().add( sr );
     }
 
     @Override
@@ -96,10 +83,6 @@ public class Sequence implements PhylogenyData, MultipleUris {
         getUris().add( uri );
     }
 
-    public void addSequenceRelation( final SequenceRelation sr ) {
-        _seq_relations.add( sr );
-    }
-
     @Override
     public StringBuffer asSimpleText() {
         final StringBuffer sb = new StringBuffer();
@@ -123,6 +106,29 @@ public class Sequence implements PhylogenyData, MultipleUris {
         return asSimpleText();
     }
 
+    @Override
+    public int compareTo( final Sequence o ) {
+        if ( ( !ForesterUtil.isEmpty( getName() ) ) && ( !ForesterUtil.isEmpty( o.getName() ) ) ) {
+            return getName().compareTo( o.getName() );
+        }
+        if ( ( !ForesterUtil.isEmpty( getSymbol() ) ) && ( !ForesterUtil.isEmpty( o.getSymbol() ) ) ) {
+            return getSymbol().compareTo( o.getSymbol() );
+        }
+        if ( ( !ForesterUtil.isEmpty( getGeneName() ) ) && ( !ForesterUtil.isEmpty( o.getGeneName() ) ) ) {
+            return getGeneName().compareTo( o.getGeneName() );
+        }
+        if ( ( getAccession() != null ) && ( o.getAccession() != null )
+                && !ForesterUtil.isEmpty( getAccession().getValue() )
+                && !ForesterUtil.isEmpty( o.getAccession().getValue() ) ) {
+            return getAccession().getValue().compareTo( o.getAccession().getValue() );
+        }
+        if ( ( !ForesterUtil.isEmpty( getMolecularSequence() ) )
+                && ( !ForesterUtil.isEmpty( o.getMolecularSequence() ) ) ) {
+            return getMolecularSequence().compareTo( o.getMolecularSequence() );
+        }
+        return 0;
+    }
+
     /**
      * Not a deep copy.
      * 
@@ -211,10 +217,18 @@ public class Sequence implements PhylogenyData, MultipleUris {
         return _annotations;
     }
 
+    public SortedSet<Accession> getCrossReferences() {
+        return _xrefs;
+    }
+
     public DomainArchitecture getDomainArchitecture() {
         return _da;
     }
 
+    public String getGeneName() {
+        return _gene_name;
+    }
+
     public String getLocation() {
         return _location;
     }
@@ -223,18 +237,10 @@ public class Sequence implements PhylogenyData, MultipleUris {
         return _mol_sequence;
     }
 
-    public boolean isMolecularSequenceAligned() {
-        return _mol_sequence_is_aligned;
-    }
-
     public String getName() {
         return _name;
     }
 
-    public String getGeneName() {
-        return _gene_name;
-    }
-
     public List<SequenceRelation> getSequenceRelations() {
         if ( _seq_relations == null ) {
             _seq_relations = new ArrayList<SequenceRelation>();
@@ -242,10 +248,6 @@ public class Sequence implements PhylogenyData, MultipleUris {
         return _seq_relations;
     }
 
-    private void setSequenceRelations( final List<SequenceRelation> seq_relations ) {
-        _seq_relations = seq_relations;
-    }
-
     public String getSourceId() {
         return _source_id;
     }
@@ -259,13 +261,13 @@ public class Sequence implements PhylogenyData, MultipleUris {
     }
 
     @Override
-    public List<Uri> getUris() {
-        return _uris;
+    public Uri getUri( final int index ) {
+        return getUris().get( index );
     }
 
     @Override
-    public Uri getUri( final int index ) {
-        return getUris().get( index );
+    public List<Uri> getUris() {
+        return _uris;
     }
 
     @Override
@@ -273,10 +275,13 @@ public class Sequence implements PhylogenyData, MultipleUris {
         if ( getAccession() != null ) {
             return getAccession().hashCode();
         }
-        int result = getSymbol().hashCode();
-        if ( getName().length() > 0 ) {
+        int result = getName().hashCode();
+        if ( getSymbol().length() > 0 ) {
             result ^= getName().hashCode();
         }
+        if ( getGeneName().length() > 0 ) {
+            result ^= getGeneName().hashCode();
+        }
         if ( getMolecularSequence().length() > 0 ) {
             result ^= getMolecularSequence().hashCode();
         }
@@ -314,6 +319,16 @@ public class Sequence implements PhylogenyData, MultipleUris {
         setAnnotations( null );
     }
 
+    public boolean isEmpty() {
+        return ( getAccession() == null ) && ForesterUtil.isEmpty( getName() ) && ForesterUtil.isEmpty( getSymbol() )
+                && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getType() )
+                && ForesterUtil.isEmpty( getLocation() ) && ForesterUtil.isEmpty( getSourceId() )
+                && ForesterUtil.isEmpty( getMolecularSequence() ) && ( getDomainArchitecture() == null )
+                && ForesterUtil.isEmpty( _annotations ) && ForesterUtil.isEmpty( _uris )
+                && ForesterUtil.isEmpty( _seq_relations )
+                && ( ( getCrossReferences() == null ) || getCrossReferences().isEmpty() );
+    }
+
     @Override
     public boolean isEqual( final PhylogenyData data ) {
         if ( this == data ) {
@@ -327,18 +342,22 @@ public class Sequence implements PhylogenyData, MultipleUris {
                 && s.getSymbol().equals( getSymbol() ) && s.getGeneName().equals( getGeneName() );
     }
 
-    public void setAccession( final Accession accession ) {
-        _accession = accession;
+    public boolean isMolecularSequenceAligned() {
+        return _mol_sequence_is_aligned;
     }
 
-    private void setAnnotations( final SortedSet<Annotation> annotations ) {
-        _annotations = annotations;
+    public void setAccession( final Accession accession ) {
+        _accession = accession;
     }
 
     public void setDomainArchitecture( final DomainArchitecture ds ) {
         _da = ds;
     }
 
+    public void setGeneName( final String gene_name ) {
+        _gene_name = gene_name;
+    }
+
     public void setLocation( final String description ) {
         _location = description;
     }
@@ -355,10 +374,6 @@ public class Sequence implements PhylogenyData, MultipleUris {
         _name = name;
     }
 
-    public void setGeneName( final String gene_name ) {
-        _gene_name = gene_name;
-    }
-
     public void setSourceId( final String source_id ) {
         _source_id = source_id;
     }
@@ -463,4 +478,16 @@ public class Sequence implements PhylogenyData, MultipleUris {
     public String toString() {
         return asText().toString();
     }
+
+    private void setAnnotations( final SortedSet<Annotation> annotations ) {
+        _annotations = annotations;
+    }
+
+    private void setCrossReferences( final TreeSet<Accession> cross_references ) {
+        _xrefs = cross_references;
+    }
+
+    private void setSequenceRelations( final List<SequenceRelation> seq_relations ) {
+        _seq_relations = seq_relations;
+    }
 }

diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java
index aca0f7a..0de8e9a 100644 (file)
--- a/forester/java/src/org/forester/rio/RIO.java
+++ b/forester/java/src/org/forester/rio/RIO.java
@@ -881,6 +881,10 @@ public final class RIO {
         else if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
             label = n.getNodeData().getSequence().getSymbol();
         }
+        else if ( n.getNodeData().isHasSequence()
+                && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+            label = n.getNodeData().getSequence().getGeneName();
+        }
         else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
             label = n.getName();
         }

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 46eceac..aed217b 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -112,6 +112,9 @@ public final class ForesterUtil {
             if ( !isEmpty( seq.getSymbol() ) ) {
                 v = SequenceIdParser.parseRefSeqAccessor( seq.getSymbol() );
             }
+            if ( !isEmpty( seq.getGeneName() ) ) {
+                v = SequenceIdParser.parseRefSeqAccessor( seq.getGeneName() );
+            }
             if ( isEmpty( v ) && !isEmpty( seq.getName() ) ) {
                 v = SequenceIdParser.parseRefSeqAccessor( seq.getName() );
             }
@@ -133,6 +136,9 @@ public final class ForesterUtil {
             if ( !isEmpty( seq.getSymbol() ) ) {
                 v = SequenceIdParser.parseGenbankAccessor( seq.getSymbol() );
             }
+            if ( !isEmpty( seq.getGeneName() ) ) {
+                v = SequenceIdParser.parseGenbankAccessor( seq.getGeneName() );
+            }
             if ( isEmpty( v ) && !isEmpty( seq.getName() ) ) {
                 v = SequenceIdParser.parseGenbankAccessor( seq.getName() );
             }
@@ -209,6 +215,18 @@ public final class ForesterUtil {
                     }
                 }
             }
+            if ( isEmpty( upkb ) && !isEmpty( seq.getGeneName() ) ) {
+                m = UNIPROT_KB_PATTERN_1.matcher( seq.getGeneName() );
+                if ( m.find() ) {
+                    upkb = m.group( 1 );
+                }
+                else {
+                    m = UNIPROT_KB_PATTERN_2.matcher( seq.getGeneName() );
+                    if ( m.find() ) {
+                        upkb = m.group();
+                    }
+                }
+            }
             if ( isEmpty( upkb ) && ( node.getNodeData().getSequence().getAccession() != null )
                     && !isEmpty( seq.getAccession().getValue() ) ) {
                 m = UNIPROT_KB_PATTERN_1.matcher( seq.getAccession().getValue() );

diff --git a/forester/java/src/org/forester/util/SequenceIdParser.java b/forester/java/src/org/forester/util/SequenceIdParser.java
index 7b400d2..8fcf6ee 100644 (file)
--- a/forester/java/src/org/forester/util/SequenceIdParser.java
+++ b/forester/java/src/org/forester/util/SequenceIdParser.java
@@ -70,17 +70,19 @@ public final class SequenceIdParser {
      * \r
      */\r
     public final static Identifier parse( final String s ) {\r
-        String v = parseGenbankAccessor( s );\r
-        if ( !ForesterUtil.isEmpty( v ) ) {\r
-            return new Identifier( v, Identifier.NCBI );\r
-        }\r
-        v = parseRefSeqAccessor( s );\r
-        if ( !ForesterUtil.isEmpty( v ) ) {\r
-            return new Identifier( v, Identifier.REFSEQ );\r
-        }\r
-        v = parseTrEMBLAccessor( s );\r
-        if ( !ForesterUtil.isEmpty( v ) ) {\r
-            return new Identifier( v, Identifier.SP );\r
+        if ( !ForesterUtil.isEmpty( s ) ) {\r
+            String v = parseGenbankAccessor( s );\r
+            if ( !ForesterUtil.isEmpty( v ) ) {\r
+                return new Identifier( v, Identifier.NCBI );\r
+            }\r
+            v = parseRefSeqAccessor( s );\r
+            if ( !ForesterUtil.isEmpty( v ) ) {\r
+                return new Identifier( v, Identifier.REFSEQ );\r
+            }\r
+            v = parseTrEMBLAccessor( s );\r
+            if ( !ForesterUtil.isEmpty( v ) ) {\r
+                return new Identifier( v, Identifier.SP );\r
+            }\r
         }\r
         return null;\r
     }\r

diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
index 111fa68..f5f83e4 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -162,10 +162,19 @@ public final class SequenceDbWsTools {
             String query = null;
             Identifier id = null;
             Db db = Db.NONE;
-            if ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null )
+            if ( node.getNodeData().isHasSequence()
+                    && ( node.getNodeData().getSequence().getAccession() != null )
                     && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
                     && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
-                    && node.getNodeData().getSequence().getAccession().getValue().toLowerCase().startsWith( "uniprot" ) ) {
+                    && ( node.getNodeData().getSequence().getAccession().getValue().toLowerCase()
+                            .startsWith( "uniprot" )
+                            || node.getNodeData().getSequence().getAccession().getValue().toLowerCase()
+                                    .startsWith( "swissprot" )
+                            || node.getNodeData().getSequence().getAccession().getValue().toLowerCase()
+                                    .startsWith( "trembl" )
+                            || node.getNodeData().getSequence().getAccession().getValue().toLowerCase()
+                                    .startsWith( "sp" ) || node.getNodeData().getSequence().getAccession().getValue()
+                            .toLowerCase().startsWith( "uniprotkb" ) ) ) {
                 query = node.getNodeData().getSequence().getAccession().getValue();
                 db = Db.UNIPROT;
             }
@@ -178,21 +187,63 @@ public final class SequenceDbWsTools {
                 query = node.getNodeData().getSequence().getAccession().getValue();
                 db = Db.EMBL;
             }
-            else if ( !ForesterUtil.isEmpty( node.getName() ) ) {
+            else if ( node.getNodeData().isHasSequence()
+                    && ( node.getNodeData().getSequence().getAccession() != null )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
+                    && ( node.getNodeData().getSequence().getAccession().getValue().toLowerCase().startsWith( "ncbi" ) || node
+                            .getNodeData().getSequence().getAccession().getValue().toLowerCase().startsWith( "genbank" ) ) ) {
+                query = node.getNodeData().getSequence().getAccession().getValue();
+                // db = Db.NCBI;
+            }
+            else if ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
+                    && node.getNodeData().getSequence().getAccession().getValue().toLowerCase().startsWith( "refseq" ) ) {
+                query = node.getNodeData().getSequence().getAccession().getValue();
+                db = Db.REFSEQ;
+            }
+            else {
                 if ( ( query = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node ) ) != null ) {
                     db = Db.UNIPROT;
                 }
-                else if ( ( id = SequenceIdParser.parse( node.getName() ) ) != null ) {
-                    if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
-                        db = Db.NCBI;
+                else if ( node.getNodeData().isHasSequence() ) {
+                    if ( ( id = SequenceIdParser.parse( node.getName() ) ) != null ) {
+                        if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+                            //  db = Db.NCBI;
+                        }
+                        else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+                            db = Db.REFSEQ;
+                        }
+                    }
+                    else if ( ( id = SequenceIdParser.parse( node.getNodeData().getSequence().getName() ) ) != null ) {
+                        if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+                            // = Db.NCBI;
+                        }
+                        else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+                            db = Db.REFSEQ;
+                        }
                     }
-                    else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
-                        db = Db.REFSEQ;
+                    else if ( ( id = SequenceIdParser.parse( node.getNodeData().getSequence().getGeneName() ) ) != null ) {
+                        if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+                            // db = Db.NCBI;
+                        }
+                        else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+                            db = Db.REFSEQ;
+                        }
+                    }
+                    else if ( ( id = SequenceIdParser.parse( node.getNodeData().getSequence().getSymbol() ) ) != null ) {
+                        if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+                            // db = Db.NCBI;
+                        }
+                        else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+                            db = Db.REFSEQ;
+                        }
                     }
                 }
             }
             if ( db == Db.NONE ) {
-                not_found.add( node.getName() );
+                not_found.add( node.toString() );
             }
             SequenceDatabaseEntry db_entry = null;
             if ( !ForesterUtil.isEmpty( query ) ) {
@@ -202,22 +253,31 @@ public final class SequenceDbWsTools {
                     }
                     db_entry = obtainUniProtEntry( query, lines_to_return );
                 }
-                if ( ( db == Db.EMBL ) || ( ( db == Db.UNIPROT ) && ( db_entry == null ) ) ) {
+                else if ( db == Db.EMBL ) {
                     if ( DEBUG ) {
                         System.out.println( "embl: " + query );
                     }
                     db_entry = obtainEmblEntry( new Identifier( query ), lines_to_return );
-                    if ( ( db == Db.UNIPROT ) && ( db_entry != null ) ) {
-                        db = Db.EMBL;
+                }
+                else if ( db == Db.REFSEQ ) {
+                    if ( DEBUG ) {
+                        System.out.println( "refseq: " + query );
                     }
+                    db_entry = obtainRefSeqEntryFromEmbl( new Identifier( query ), lines_to_return );
                 }
+                //   else if ( db == Db.NCBI ) {
+                //       if ( DEBUG ) {
+                //           System.out.println( "ncbi: " + query );
+                //       }
+                //       db_entry = obtainNcbiEntry( new Identifier( query ), lines_to_return );
+                //  }
             }
             else if ( ( db == Db.REFSEQ ) && ( id != null ) ) {
                 db_entry = obtainRefSeqEntryFromEmbl( id, lines_to_return );
             }
-            else if ( ( db == Db.NCBI ) && ( id != null ) ) {
-                db_entry = obtainEmblEntry( id, lines_to_return ); //TODO ?
-            }
+            //else if ( ( db == Db.NCBI ) && ( id != null ) ) {
+            //    db_entry = obtainNcbiEntry( id, lines_to_return );
+            //}
             if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
                 final Sequence seq = node.getNodeData().isHasSequence() ? node.getNodeData().getSequence()
                         : new Sequence();
@@ -229,9 +289,9 @@ public final class SequenceDbWsTools {
                     else if ( db == Db.UNIPROT ) {
                         type = "uniprot";
                     }
-                    else if ( db == Db.NCBI ) {
-                        type = "ncbi";
-                    }
+                    //   else if ( db == Db.NCBI ) {
+                    //       type = "ncbi";
+                    //   }
                     else if ( db == Db.REFSEQ ) {
                         type = "refseq";
                     }