X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=7c136947dfcf8d1370fb2bcc6c8d5406f7b4702c;hb=713d694ab9ab4e0701fd756af1ea2a892f96ade9;hp=7b3f4113c564857e3aeb6f1c675616b8aeb9c1c6;hpb=89f36e42fb462f8d7b59def3ead995fb16a87b59;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 7b3f411..7c13694 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -22,7 +22,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -268,9 +268,6 @@ public final class MainFrameApplication extends MainFrame {
         catch ( final IllegalAccessException e ) {
             AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
         }
-        catch ( final Exception e ) {
-            AptxUtil.dieWithSystemError( e.toString() );
-        }
         if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
             setCurrentDir( current_dir );
         }
@@ -353,7 +350,9 @@ public final class MainFrameApplication extends MainFrame {
         _contentpane.setLayout( new BorderLayout() );
         _contentpane.add( _mainpanel, BorderLayout.CENTER );
         // App is this big
-        setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
+        setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : FRAME_X_SIZE,
+                 getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : FRAME_Y_SIZE );
+       
         //        addWindowFocusListener( new WindowAdapter() {
         //
         //            @Override
@@ -510,7 +509,7 @@ public final class MainFrameApplication extends MainFrame {
                 moveNodeNamesToSeqNames();
             }
             else if ( o == _extract_tax_code_from_node_names_jmi ) {
-                extractTaxCodeFromNodeNames();
+                extractTaxDataFromNodeNames();
             }
             else if ( o == _gsdi_item ) {
                 if ( isSubtreeDisplayed() ) {
@@ -1133,17 +1132,17 @@ public final class MainFrameApplication extends MainFrame {
                 .setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
         _tools_menu.addSeparator();
         _tools_menu
+                .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
+        customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
+        _extract_tax_code_from_node_names_jmi
+                .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
+        _tools_menu
                 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
         customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
         _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
         _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
         customizeJMenuItem( _move_node_names_to_seq_names_jmi );
         _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
-        _tools_menu
-                .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes from Node Names" ) );
-        customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
-        _extract_tax_code_from_node_names_jmi
-                .setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI'" );
         _tools_menu.addSeparator();
         _tools_menu
                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
@@ -1874,22 +1873,64 @@ public final class MainFrameApplication extends MainFrame {
         }
     }
 
-    private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException {
+    private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
+        final StringBuilder sb = new StringBuilder();
+        final StringBuilder sb_failed = new StringBuilder();
+        int counter = 0;
+        int counter_failed = 0;
         if ( getCurrentTreePanel() != null ) {
             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
             if ( ( phy != null ) && !phy.isEmpty() ) {
-                final PhylogenyNodeIterator it = phy.iteratorPostorder();
+                final PhylogenyNodeIterator it = phy.iteratorExternalForward();
                 while ( it.hasNext() ) {
                     final PhylogenyNode n = it.next();
                     final String name = n.getName().trim();
                     if ( !ForesterUtil.isEmpty( name ) ) {
-                        final String code = ParserUtils
-                                .extractTaxonomyCodeFromNodeName( name, NHXParser.TAXONOMY_EXTRACTION.YES );
-                        if ( !ForesterUtil.isEmpty( code ) ) {
-                            PhylogenyMethods.setTaxonomyCode( n, code );
+                        final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.YES );
+                        if ( !ForesterUtil.isEmpty( nt ) ) {
+                            if ( counter < 15 ) {
+                                sb.append( name + ": " + nt + "\n" );
+                            }
+                            else if ( counter == 15 ) {
+                                sb.append( "...\n" );
+                            }
+                            counter++;
+                        }
+                        else {
+                            if ( counter_failed < 15 ) {
+                                sb_failed.append( name + "\n" );
+                            }
+                            else if ( counter_failed == 15 ) {
+                                sb_failed.append( "...\n" );
+                            }
+                            counter_failed++;
                         }
                     }
                 }
+                if ( counter > 0 ) {
+                    String failed = "";
+                    String all = "all ";
+                    if ( counter_failed > 0 ) {
+                        all = "";
+                        failed = "\nCould not extract taxonomic data for " + counter_failed
+                                + " named external nodes:\n" + sb_failed;
+                    }
+                    JOptionPane.showMessageDialog( this,
+                                                   "Extracted taxonomic data from " + all + counter
+                                                           + " named external nodes:\n" + sb.toString() + failed,
+                                                   "Taxonomic Data Extraction Completed",
+                                                   counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
+                                                           : JOptionPane.INFORMATION_MESSAGE );
+                }
+                else {
+                    JOptionPane
+                            .showMessageDialog( this,
+                                                "Could not extract any taxonomic data.\nMaybe node names are empty\n"
+                                                        + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
+                                                        + "or nodes already have taxonomic data?\n",
+                                                "No Taxonomic Data Extracted",
+                                                JOptionPane.ERROR_MESSAGE );
+                }
             }
         }
     }
@@ -2350,6 +2391,7 @@ public final class MainFrameApplication extends MainFrame {
 
     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
+        nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
     }
 
     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {