inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index b09e7b9..689fde7 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -139,17 +139,18 @@ public final class Configuration {
     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;
-    final static int                        blast                                                  = 8;
-    final static int                        cut_subtree                                            = 9;
-    final static int                        copy_subtree                                           = 10;
-    final static int                        paste_subtree                                          = 11;
-    final static int                        delete_subtree_or_node                                 = 12;
-    final static int                        add_new_node                                           = 13;
-    final static int                        edit_node_data                                         = 14;
-    final static int                        sort_descendents                                       = 15;
-    final static int                        get_ext_desc_data                                      = 16;
-    final static int                        select_nodes                                           = 17;
+    final static int                        open_pdb_web                                           = 7;
+    final static int                        open_tax_web                                           = 8;
+    final static int                        blast                                                  = 9;
+    final static int                        cut_subtree                                            = 10;
+    final static int                        copy_subtree                                           = 11;
+    final static int                        paste_subtree                                          = 12;
+    final static int                        delete_subtree_or_node                                 = 13;
+    final static int                        add_new_node                                           = 14;
+    final static int                        edit_node_data                                         = 15;
+    final static int                        sort_descendents                                       = 16;
+    final static int                        get_ext_desc_data                                      = 17;
+    final static int                        select_nodes                                           = 18;
     // ---------------------------
     // Display options for trees
     // ---------------------------
@@ -176,7 +177,7 @@ public final class Configuration {
     final static String                     clickto_options[][]                                    = {
             { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
             { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" },
-            { "Colorize Subtree/Node(s)", "display" }, { "Open Sequence DB", "display" },
+            { "Colorize Subtree/Node(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
             { "Open Taxonomy DB", "display" }, { "Blast", "display" }, { "Cut Subtree", "display" },
             { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
             { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
@@ -834,6 +835,9 @@ public final class Configuration {
         else if ( name.equals( "open_seq_web" ) ) {
             index = Configuration.open_seq_web;
         }
+        else if ( name.equals( "open_pdb_web" ) ) {
+            index = Configuration.open_pdb_web;
+        }
         else if ( name.equals( "open_tax_web" ) ) {
             index = Configuration.open_tax_web;
         }

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 7586722..4c65e2a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -137,6 +137,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     private int                  _edit_node_data_item;
     private int                  _select_nodes_item;
     private int                  _get_ext_desc_data;
+    private int                  _open_pdb_item;
     private int                  _blast_item;
     // zooming and quick tree manipulation buttons:
     private JButton              _zoom_in_x;
@@ -1119,6 +1120,9 @@ final class ControlPanel extends JPanel implements ActionListener {
         else if ( action == _get_ext_desc_data ) {
             setActionWhenNodeClicked( NodeClickAction.GET_EXT_DESC_DATA );
         }
+        else if ( action == _open_pdb_item ) {
+            setActionWhenNodeClicked( NodeClickAction.OPEN_PDB_WEB );
+        }
         else {
             throw new RuntimeException( "unknown action: " + action );
         }
@@ -1733,6 +1737,14 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             cb_index++;
         }
+        if ( _configuration.doDisplayClickToOption( Configuration.open_pdb_web ) ) {
+            _open_pdb_item = cb_index;
+            addClickToOption( Configuration.open_pdb_web, _configuration.getClickToTitle( Configuration.open_pdb_web ) );
+            if ( default_option == Configuration.open_pdb_web ) {
+                selected_index = cb_index;
+            }
+            cb_index++;
+        }
         if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
             _open_tax_web_item = cb_index;
             addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
@@ -2053,6 +2065,7 @@ final class ControlPanel extends JPanel implements ActionListener {
         SELECT_NODES,
         SORT_DESCENDENTS,
         GET_EXT_DESC_DATA,
-        BLAST;
+        BLAST,
+        OPEN_PDB_WEB;
     }
 }

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 9f7dd65..2833f8e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -2850,6 +2850,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             case OPEN_TAX_WEB:
                 openTaxWeb( node );
                 break;
+            case OPEN_PDB_WEB:
+                openPdbWeb( node );
+                break;
             case CUT_SUBTREE:
                 cutSubtree( node );
                 break;
@@ -2942,6 +2945,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         return null;
     }
 
+    final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
+        final List<Accession> pdb_ids = new ArrayList<Accession>();
+        if ( node.getNodeData().isHasSequence() ) {
+            final Sequence seq = node.getNodeData().getSequence();
+            if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
+                final SortedSet<Accession> cross_refs = seq.getCrossReferences();
+                for( final Accession acc : cross_refs ) {
+                    if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
+                        pdb_ids.add( acc );
+                    }
+                }
+            }
+        }
+        return pdb_ids;
+    }
+
     final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
         if ( node.getNodeData().isHasTaxonomy()
                 && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
@@ -3177,6 +3196,41 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     _node_popup_menu_items[ i ].setEnabled( false );
                 }
             }
+            else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
+                final List<Accession> accs = getPdbAccs( node );
+                _node_popup_menu_items[ i ] = new JMenuItem( title );
+                if ( !ForesterUtil.isEmpty( accs ) ) {
+                    if ( accs.size() == 1 ) {
+                        _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+                                + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
+                        _node_popup_menu_items[ i ].setEnabled( true );
+                    }
+                    else if ( accs.size() == 2 ) {
+                        _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+                                + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+                                + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
+                        _node_popup_menu_items[ i ].setEnabled( true );
+                    }
+                    else if ( accs.size() == 3 ) {
+                        _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+                                + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+                                + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+                                + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
+                        _node_popup_menu_items[ i ].setEnabled( true );
+                    }
+                    else {
+                        _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+                                + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+                                + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+                                + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
+                        _node_popup_menu_items[ i ].setEnabled( true );
+                    }
+                }
+                else {
+                    _node_popup_menu_items[ i ].setEnabled( false );
+                }
+                //
+            }
             else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
                 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
             }
@@ -3297,6 +3351,36 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
+    final private void openPdbWeb( final PhylogenyNode node ) {
+        final List<Accession> pdb_ids = getPdbAccs( node );
+        if ( ForesterUtil.isEmpty( pdb_ids ) ) {
+            cannotOpenBrowserWarningMessage( "PDB" );
+            return;
+        }
+        final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
+        if ( !ForesterUtil.isEmpty( uri_strs ) ) {
+            for( final String uri_str : uri_strs ) {
+                try {
+                    AptxUtil.launchWebBrowser( new URI( uri_str ),
+                                               isApplet(),
+                                               isApplet() ? obtainApplet() : null,
+                                               "_aptx_seq" );
+                }
+                catch ( final IOException e ) {
+                    AptxUtil.showErrorMessage( this, e.toString() );
+                    e.printStackTrace();
+                }
+                catch ( final URISyntaxException e ) {
+                    AptxUtil.showErrorMessage( this, e.toString() );
+                    e.printStackTrace();
+                }
+            }
+        }
+        else {
+            cannotOpenBrowserWarningMessage( "PDB" );
+        }
+    }
+
     final private void openTaxWeb( final PhylogenyNode node ) {
         if ( !isCanOpenTaxWeb( node ) ) {
             cannotOpenBrowserWarningMessage( "taxonomic" );

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
index 61db054..5b5537c 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
@@ -22,6 +22,7 @@ import org.forester.analysis.TaxonomyDataManager;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 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;
@@ -36,46 +37,6 @@ import org.forester.ws.seqdb.UniProtTaxonomy;
 
 public class TreePanelUtil {
 
-    static int makeSB( 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 ) ) {
-            for( final String d : data ) {
-                if ( !ForesterUtil.isEmpty( d ) ) {
-                    if ( map.containsKey( d ) ) {
-                        map.put( d, map.get( d ) + 1 );
-                    }
-                    else {
-                        map.put( d, 1 );
-                    }
-                }
-            }
-        }
-        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 );
-            }
-            size = map.size();
-        }
-        else {
-            for( final String d : data ) {
-                if ( !ForesterUtil.isEmpty( d ) ) {
-                    sb.append( d );
-                    sb.append( ForesterUtil.LINE_SEPARATOR );
-                }
-            }
-            size = data.size();
-        }
-        return size;
-    }
-
     public final static String createUriForSeqWeb( final PhylogenyNode node,
                                                    final Configuration conf,
                                                    final TreePanel tp ) {
@@ -139,6 +100,21 @@ public class TreePanelUtil {
         return uri_str;
     }
 
+    public static List<String> createUrisForPdbWeb( final PhylogenyNode node,
+                                                    final List<Accession> pdb_accs,
+                                                    final Configuration configuration,
+                                                    final TreePanel treePanel ) {
+        final List<String> uris = new ArrayList<String>();
+        if ( !ForesterUtil.isEmpty( pdb_accs ) ) {
+            for( final Accession pdb_acc : pdb_accs ) {
+                if ( !ForesterUtil.isEmpty( pdb_acc.getValue() ) ) {
+                    uris.add( ForesterUtil.PDB + pdb_acc.getValue() );
+                }
+            }
+        }
+        return uris;
+    }
+
     /**
      * Returns the set of distinct taxonomies of
      * all external nodes of node.
@@ -499,6 +475,46 @@ public class TreePanelUtil {
                 .getSynonyms().isEmpty() );
     }
 
+    static int makeSB( 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 ) ) {
+            for( final String d : data ) {
+                if ( !ForesterUtil.isEmpty( d ) ) {
+                    if ( map.containsKey( d ) ) {
+                        map.put( d, map.get( d ) + 1 );
+                    }
+                    else {
+                        map.put( d, 1 );
+                    }
+                }
+            }
+        }
+        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 );
+            }
+            size = map.size();
+        }
+        else {
+            for( final String d : data ) {
+                if ( !ForesterUtil.isEmpty( d ) ) {
+                    sb.append( d );
+                    sb.append( ForesterUtil.LINE_SEPARATOR );
+                }
+            }
+            size = data.size();
+        }
+        return size;
+    }
+
     final static char normalizeCharForRGB( char c ) {
         c -= 65;
         c *= 10.2;
@@ -507,6 +523,13 @@ public class TreePanelUtil {
         return c;
     }
 
+    final static String pdbAccToString( final List<Accession> accs, final int i ) {
+        if ( ForesterUtil.isEmpty( accs.get( i ).getComment() ) ) {
+            return accs.get( i ).getValue();
+        }
+        return accs.get( i ).getValue() + " (" + accs.get( i ).getComment().toLowerCase() + ")";
+    }
+
     final static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
         final Phylogeny new_phy = new Phylogeny();
         new_phy.setRooted( true );

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 1908f8f..7492f1e 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -91,6 +91,7 @@ public final class ForesterUtil {
     public static final String       NCBI_NUCCORE                     = "http://www.ncbi.nlm.nih.gov/nuccore/";
     public final static String       UNIPROT_KB                       = "http://www.uniprot.org/uniprot/";
     public static final String       NCBI_GI                          = "http://www.ncbi.nlm.nih.gov/protein/gi:";
+    public static final String       PDB                              = "http://www.pdb.org/pdb/explore/explore.do?pdbId=";
     static {
         final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
         dfs.setDecimalSeparator( '.' );