import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
+import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import javax.swing.filechooser.FileFilter;
import javax.swing.plaf.synth.SynthLookAndFeel;
-import org.forester.analysis.TaxonomyDataObtainer;
+import org.forester.analysis.TaxonomyDataManager;
import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.sdi.GSDI;
-import org.forester.sdi.SDI;
import org.forester.sdi.SDIR;
-import org.forester.sdi.SDIse;
import org.forester.sequence.Sequence;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
// Analysis menu
private JMenu _analysis_menu;
private JMenuItem _load_species_tree_item;
- private JMenuItem _sdi_item;
private JMenuItem _gsdi_item;
private JMenuItem _root_min_dups_item;
private JMenuItem _root_min_cost_l_item;
// hide until everything is ready
setVisible( false );
setOptions( Options.createInstance( _configuration ) );
+ setInferenceManager( InferenceManager.createInstance( _configuration ) );
setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
- _textframe = null;
+ // _textframe = null; #~~~~
_species_tree = null;
// set title
setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
else if ( o == _load_species_tree_item ) {
readSpeciesTreeFromFile();
}
- else if ( o == _sdi_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- executeSDI();
- }
else if ( o == _lineage_inference ) {
if ( isSubtreeDisplayed() ) {
JOptionPane.showMessageDialog( this,
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
- _analysis_menu.add( _sdi_item = new JMenuItem( "SDI (Speciation Duplication Inference)" ) );
- if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
- _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
- }
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
_analysis_menu.addSeparator();
_analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
_analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
_analysis_menu.addSeparator();
_analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
- customizeJMenuItem( _sdi_item );
customizeJMenuItem( _gsdi_item );
customizeJMenuItem( _root_min_dups_item );
customizeJMenuItem( _root_min_cost_l_item );
}
void buildPhylogeneticInferenceMenu() {
- final InferenceManager inference_manager = InferenceManager.getInstance();
+ final InferenceManager im = getInferenceManager();
_inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
_inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
customizeJMenuItem( _inference_from_msa_item );
_inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
- _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
- customizeJMenuItem( _inference_from_seqs_item );
- _inference_from_seqs_item.setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
+ if ( im.canDoMsa() ) {
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
+ customizeJMenuItem( _inference_from_seqs_item );
+ _inference_from_seqs_item
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
+ }
+ else {
+ _inference_menu
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
+ customizeJMenuItem( _inference_from_seqs_item );
+ _inference_from_seqs_item.setEnabled( false );
+ }
_jmenubar.add( _inference_menu );
}
customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
_obtain_detailed_taxonomic_information_deleting_jmi
.setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
- _tools_menu
- .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
+ _tools_menu.add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
- _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
+ _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu.addSeparator();
if ( !Constants.__RELEASE ) {
_tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
}
if ( to_be_removed.size() > 0 ) {
phy.externalNodesHaveChanged();
- phy.hashIDs();
+ phy.clearHashIdToNodeMap();
phy.recalculateNumberOfExternalDescendants( true );
getCurrentTreePanel().resetNodeIdToDistToLeafMap();
getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
gene_tree.setAllNodesToNotCollapse();
gene_tree.recalculateNumberOfExternalDescendants( false );
GSDI gsdi = null;
- int duplications = -1;
try {
- gsdi = new GSDI( gene_tree, _species_tree.copy(), true );
- duplications = gsdi.getDuplicationsSum();
+ gsdi = new GSDI( gene_tree, _species_tree.copy(), false, true, true );
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
}
gene_tree.setRerootable( false );
_mainpanel.getCurrentTreePanel().setTree( gene_tree );
+ _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap();
+ _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true );
+ _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
getControlPanel().setShowEvents( true );
showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( gsdi.getSpeciesTree(), getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
_mainpanel.getCurrentTreePanel().setEdited( true );
- JOptionPane.showMessageDialog( this,
- "Number of duplications: " + duplications,
- "GSDI successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
+ JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
+ + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
}
void executeFunctionAnalysis() {
}
}
- void executeSDI() {
- if ( !isOKforSDI( true, true ) ) {
- return;
- }
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not rooted",
- "Cannot execute SDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
- gene_tree.setAllNodesToNotCollapse();
- gene_tree.recalculateNumberOfExternalDescendants( false );
- SDI sdi = null;
- int duplications = -1;
- try {
- sdi = new SDIse( gene_tree, _species_tree.copy() );
- duplications = sdi.getDuplicationsSum();
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this, e.toString(), "Error during SDI", JOptionPane.ERROR_MESSAGE );
- }
- gene_tree.setRerootable( false );
- _mainpanel.getCurrentTreePanel().setTree( gene_tree );
- getControlPanel().setShowEvents( true );
- showWhole();
- _mainpanel.getCurrentTreePanel().setEdited( true );
- JOptionPane.showMessageDialog( this,
- "Number of duplications: " + duplications,
- "SDI successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
-
void executeSDIR( final boolean minimize_cost ) {
if ( !isOKforSDI( true, true ) ) {
return;
}
void exit() {
- removeTextFrame();
+ removeAllTextFrames();
_mainpanel.terminate();
_contentpane.removeAll();
setVisible( false );
dispose();
}
- private void extractTaxCodeFromNodeNames() {
+ private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
final String name = n.getName().trim();
if ( !ForesterUtil.isEmpty( name ) ) {
final String code = ParserUtils
- .extractTaxonomyCodeFromNodeName( name, false, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+ .extractTaxonomyCodeFromNodeName( name, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
if ( !ForesterUtil.isEmpty( code ) ) {
PhylogenyMethods.setTaxonomyCode( n, code );
}
private File getCurrentDir() {
if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
- if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1 ) {
+ if ( ForesterUtil.isWindowns() ) {
try {
_current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
}
return false;
}
- private void moveNodeNamesToSeqNames() {
+ private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- PhylogenyMethods.transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME );
+ PhylogenyMethods
+ .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
}
}
}
- private void moveNodeNamesToTaxSn() {
+ private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
PhylogenyMethods.transferNodeNameToField( phy,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME );
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ false );
}
}
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
- _mainpanel.getCurrentTreePanel(),
- phy.copy() );
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ false,
+ true );
new Thread( t ).start();
}
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
- _mainpanel.getCurrentTreePanel(),
- phy.copy(),
- true );
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ true,
+ true );
new Thread( t ).start();
}
}
setMsa( null );
Msa msa = null;
try {
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
- msa = FastaParser.parseMsa( new FileInputStream( file ) );
- System.out.println( msa.toString() );
+ final InputStream is = new FileInputStream( file );
+ if ( FastaParser.isLikelyFasta( file ) ) {
+ msa = FastaParser.parseMsa( is );
}
else {
- msa = GeneralMsaParser.parse( new FileInputStream( file ) );
+ msa = GeneralMsaParser.parse( is );
}
}
catch ( final MsaFormatException e ) {
git://source.jalview.org / jalview.git / blobdiff