private final static DefaultFilter defaultfilter = new DefaultFilter();
private static final long serialVersionUID = -799735726778865234L;
private final JFileChooser _values_filechooser;
+ private final JFileChooser _sequences_filechooser;
private final JFileChooser _open_filechooser;
private final JFileChooser _msa_filechooser;
- private final JFileChooser _seqs_filechooser;
+ private final JFileChooser _seqs_pi_filechooser;
private final JFileChooser _open_filechooser_for_species_tree;
private final JFileChooser _save_filechooser;
private final JFileChooser _writetopdf_filechooser;
private File _msa_file = null;
private List<Sequence> _seqs = null;
private File _seqs_file = null;
- // expression values menu:
JMenuItem _read_values_jmi;
+ JMenuItem _read_seqs_jmi;
private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
_configuration = config;
_writetopdf_filechooser = null;
_writetographics_filechooser = null;
_msa_filechooser = null;
- _seqs_filechooser = null;
+ _seqs_pi_filechooser = null;
_values_filechooser = null;
+ _sequences_filechooser = null;
_jmenubar = new JMenuBar();
buildFileMenu();
buildTypeMenu();
_msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
_msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );
// Seqs:
- _seqs_filechooser = new JFileChooser();
- _seqs_filechooser.setName( "Read Sequences File" );
- _seqs_filechooser.setCurrentDirectory( new File( "." ) );
- _seqs_filechooser.setMultiSelectionEnabled( false );
- _seqs_filechooser.addChoosableFileFilter( _seqs_filechooser.getAcceptAllFileFilter() );
- _seqs_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
+ _seqs_pi_filechooser = new JFileChooser();
+ _seqs_pi_filechooser.setName( "Read Sequences File" );
+ _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );
+ _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
+ _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );
// Expression
_values_filechooser = new JFileChooser();
_values_filechooser.setCurrentDirectory( new File( "." ) );
_values_filechooser.setMultiSelectionEnabled( false );
+ // Sequences
+ _sequences_filechooser = new JFileChooser();
+ _sequences_filechooser.setCurrentDirectory( new File( "." ) );
+ _sequences_filechooser.setMultiSelectionEnabled( false );
// build the menu bar
_jmenubar = new JMenuBar();
if ( !_configuration.isUseNativeUI() ) {
}
addExpressionValuesFromFile();
}
+ else if ( o == _read_seqs_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ addSequencesFromFile();
+ }
else if ( o == _move_node_names_to_tax_sn_jmi ) {
moveNodeNamesToTaxSn();
}
}
}
catch ( final MsaFormatException e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
"Multiple sequence alignment format error",
return;
}
catch ( final IOException e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
"Failed to read multiple sequence alignment",
return;
}
catch ( final IllegalArgumentException e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
"Unexpected error during reading of multiple sequence alignment",
return;
}
catch ( final Exception e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
e.printStackTrace();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
}
}
- public void readSeqsFromFile() {
+ public void readSeqsFromFileforPI() {
// Set an initial directory if none set yet
final File my_dir = getCurrentDir();
- _seqs_filechooser.setMultiSelectionEnabled( false );
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );
// Open file-open dialog and set current directory
if ( my_dir != null ) {
- _seqs_filechooser.setCurrentDirectory( my_dir );
+ _seqs_pi_filechooser.setCurrentDirectory( my_dir );
}
- final int result = _seqs_filechooser.showOpenDialog( _contentpane );
+ final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
// All done: get the seqs
- final File file = _seqs_filechooser.getSelectedFile();
- setCurrentDir( _seqs_filechooser.getCurrentDirectory() );
+ final File file = _seqs_pi_filechooser.getSelectedFile();
+ setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
setSeqsFile( null );
setSeqs( null );
}
}
catch ( final MsaFormatException e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
"Multiple sequence file format error",
return;
}
catch ( final IOException e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
"Failed to read multiple sequence file",
return;
}
catch ( final IllegalArgumentException e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
"Unexpected error during reading of multiple sequence file",
return;
}
catch ( final Exception e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
e.printStackTrace();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
// return;
// }
System.gc();
- setSeqsFile( _seqs_filechooser.getSelectedFile() );
+ setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
setSeqs( seqs );
}
}
.setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
_tools_menu.addSeparator();
}
- _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) );
+ _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
customizeJMenuItem( _read_values_jmi );
- _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" );
+ _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
+ _jmenubar.add( _tools_menu );
+ _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
+ customizeJMenuItem( _read_seqs_jmi );
+ _read_seqs_jmi
+ .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
_jmenubar.add( _tools_menu );
}
_contentpane.repaint();
}
+ private void addSequencesFromFile() {
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Need to load evolutionary tree first",
+ "Can Not Read Sequences",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ final File my_dir = getCurrentDir();
+ if ( my_dir != null ) {
+ _sequences_filechooser.setCurrentDirectory( my_dir );
+ }
+ final int result = _sequences_filechooser.showOpenDialog( _contentpane );
+ final File file = _sequences_filechooser.getSelectedFile();
+ List<Sequence> seqs = null;
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
+ try {
+ if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
+ seqs = FastaParser.parse( new FileInputStream( file ) );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Format does not appear to be Fasta",
+ "Multiple sequence file format error",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ }
+ catch ( final MsaFormatException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Multiple sequence file format error",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final IOException e ) {
+ setArrowCursor();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Failed to read multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ setArrowCursor();
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Unexpected error during reading of multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Multiple sequence file is empty",
+ "Empty multiple sequence file",
+ JOptionPane.ERROR_MESSAGE );
+ setArrowCursor();
+ return;
+ }
+ }
+ if ( seqs != null ) {
+ for( final Sequence seq : seqs ) {
+ System.out.println( seq.getIdentifier() );
+ }
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ int total_counter = 0;
+ int attached_counter = 0;
+ for( final Sequence seq : seqs ) {
+ ++total_counter;
+ final String seq_name = seq.getIdentifier();
+ if ( !ForesterUtil.isEmpty( seq_name ) ) {
+ List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
+ if ( nodes.isEmpty() ) {
+ nodes = phy.getNodesViaSequenceSymbol( seq_name );
+ }
+ if ( nodes.isEmpty() ) {
+ nodes = phy.getNodes( seq_name );
+ }
+ if ( nodes.size() > 1 ) {
+ JOptionPane.showMessageDialog( this,
+ "Sequence name \"" + seq_name + "\" is not unique",
+ "Sequence name not unique",
+ JOptionPane.ERROR_MESSAGE );
+ setArrowCursor();
+ return;
+ }
+ final String[] a = seq_name.split( "\\s" );
+ if ( nodes.isEmpty() && ( a.length > 1 ) ) {
+ final String seq_name_split = a[ 0 ];
+ nodes = phy.getNodesViaSequenceName( seq_name_split );
+ if ( nodes.isEmpty() ) {
+ nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
+ }
+ if ( nodes.isEmpty() ) {
+ nodes = phy.getNodes( seq_name_split );
+ }
+ if ( nodes.size() > 1 ) {
+ JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
+ + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
+ setArrowCursor();
+ return;
+ }
+ }
+ if ( nodes.size() == 1 ) {
+ ++attached_counter;
+ final PhylogenyNode n = nodes.get( 0 );
+ if ( !n.getNodeData().isHasSequence() ) {
+ n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
+ }
+ n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
+ if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+ n.getNodeData().getSequence().setName( seq_name );
+ }
+ }
+ }
+ }
+ if ( attached_counter > 0 ) {
+ int ext_nodes = 0;
+ int ext_nodes_with_seq = 0;
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+ ++ext_nodes;
+ final PhylogenyNode n = iter.next();
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+ ++ext_nodes_with_seq;
+ }
+ }
+ final String s;
+ if ( ext_nodes == ext_nodes_with_seq ) {
+ s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
+ }
+ else {
+ s = ext_nodes_with_seq + " out of " + ext_nodes
+ + " external nodes now have a molecular sequence attached to them.";
+ }
+ if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
+ "All sequences attached",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this, "Attached " + attached_counter
+ + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
+ + " sequences attached", JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ else {
+ JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
+ + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
+ }
+ }
+ }
+
+ private void setArrowCursor() {
+ try {
+ _mainpanel.getCurrentTreePanel().setArrowCursor();
+ }
+ catch ( final Exception ex ) {
+ // Do nothing.
+ }
+ }
+
private void addExpressionValuesFromFile() {
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
JOptionPane.showMessageDialog( this,
git://source.jalview.org / jalview.git / commitdiff