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=95b23cb9503321843f61e21f915e92e3734b9bb7;hpb=71cc3617df51ad241c30e2eb1407c56d4df64035;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 95b23cb..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;
 
@@ -350,7 +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
@@ -1130,17 +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 or Ids 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', or Uniprot identifiers from nodes names in the form of 'xyz_1234567'" );
         _tools_menu.addSeparator();
         _tools_menu
                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
@@ -1898,7 +1900,7 @@ public final class MainFrameApplication extends MainFrame {
                             if ( counter_failed < 15 ) {
                                 sb_failed.append( name + "\n" );
                             }
-                            else if (  counter_failed == 15 ) {
+                            else if ( counter_failed == 15 ) {
                                 sb_failed.append( "...\n" );
                             }
                             counter_failed++;
@@ -1907,22 +1909,27 @@ public final class MainFrameApplication extends MainFrame {
                 }
                 if ( counter > 0 ) {
                     String failed = "";
+                    String all = "all ";
                     if ( counter_failed > 0 ) {
-                        failed = "\nDid not extract taxonomic data for "  + counter_failed + " (named) external nodes:\n" + sb_failed;
-                        
+                        all = "";
+                        failed = "\nCould not extract taxonomic data for " + counter_failed
+                                + " named external nodes:\n" + sb_failed;
                     }
                     JOptionPane.showMessageDialog( this,
-                                                   "Successfully extracted taxonomic data from " + counter
-                                                           + " external nodes:\n" + sb.toString() + failed,
-                                                   "Taxonomic Data Extraction Successfully Completed",
-                                                   JOptionPane.INFORMATION_MESSAGE );
+                                                   "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, maybe node names are empty\nor not in the form \"XYZ_CAEEL\", \"XYZ_CAEEL/12-394\", or \"XYZ_1234567\"?",
+                                                "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.WARNING_MESSAGE );
+                                                JOptionPane.ERROR_MESSAGE );
                 }
             }
         }