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=ff467b871d53bc3c8a6ab68f35dbbae9254a5bec;hpb=cec0663378230521f24a851cb1c1c9491026b70a;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index ff467b8..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
@@ -1130,10 +1132,10 @@ 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 Codes or Ids from Node Names" ) );
+                .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', or Uniprot/NCBI identifiers from nodes names in the form of 'xyz_6239'" );
+                .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 );
@@ -1923,8 +1925,8 @@ public final class MainFrameApplication extends MainFrame {
                 else {
                     JOptionPane
                             .showMessageDialog( this,
-                                                "Could not extract any taxonomic data. Maybe node names are empty\n"
-                                                        + "or not in the forms \"XYZ_CAEEL\", \"XYZ_CAEEL/12-394\", or \"XYZ_6239\",\n"
+                                                "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 );