// 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 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 ) );
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++;
}
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 );
}
}
}