// 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;
_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
.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 );
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 );