import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.io.writers.SequenceWriter;
import org.forester.msa.Msa;
import org.forester.util.BasicTableParser;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
-import org.forester.util.ForesterUtil.PhylogenyNodeField;
-import org.forester.util.ForesterUtil.TAXONOMY_EXTRACTION;
import org.forester.util.WindowsUtils;
class DefaultFilter extends FileFilter {
public final class MainFrameApplication extends MainFrame {
- private final static int FRAME_X_SIZE = 800;
- private final static int FRAME_Y_SIZE = 800;
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
+ private final static int FRAME_X_SIZE = 800;
+ private final static int FRAME_Y_SIZE = 800;
// Filters for the file-open dialog (classes defined in this file)
- private final static NHFilter nhfilter = new NHFilter();
- private final static NHXFilter nhxfilter = new NHXFilter();
- private final static XMLFilter xmlfilter = new XMLFilter();
- private final static TolFilter tolfilter = new TolFilter();
- private final static NexusFilter nexusfilter = new NexusFilter();
- private final static PdfFilter pdffilter = new PdfFilter();
- private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
- private final static MsaFileFilter msafilter = new MsaFileFilter();
- private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
- private final static DefaultFilter defaultfilter = new DefaultFilter();
- private static final long serialVersionUID = -799735726778865234L;
+ private final static NHFilter nhfilter = new NHFilter();
+ private final static NHXFilter nhxfilter = new NHXFilter();
+ private final static XMLFilter xmlfilter = new XMLFilter();
+ private final static TolFilter tolfilter = new TolFilter();
+ private final static NexusFilter nexusfilter = new NexusFilter();
+ private final static PdfFilter pdffilter = new PdfFilter();
+ private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
+ private final static MsaFileFilter msafilter = new MsaFileFilter();
+ private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
+ private final static DefaultFilter defaultfilter = new DefaultFilter();
+ private static final long serialVersionUID = -799735726778865234L;
private final JFileChooser _values_filechooser;
private final JFileChooser _open_filechooser;
private final JFileChooser _msa_filechooser;
private File _current_dir;
private ButtonGroup _radio_group_1;
// Others:
- double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
+ double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
// Phylogeny Inference menu
private JMenu _inference_menu;
private JMenuItem _inference_from_msa_item;
private JMenuItem _inference_from_seqs_item;
// Phylogeny Inference
- private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
- private Msa _msa = null;
- private File _msa_file = null;
- private List<Sequence> _seqs = null;
- private File _seqs_file = null;
+ private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
+ private Msa _msa = null;
+ private File _msa_file = null;
+ private List<Sequence> _seqs = null;
+ private File _seqs_file = null;
// expression values menu:
JMenuItem _read_values_jmi;
MainFrameApplication.class );
UIManager.setLookAndFeel( synth );
}
- catch ( Exception ex ) {
+ catch ( final Exception ex ) {
synth_exception = true;
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"could not create synth look and feel: "
}
obtainDetailedTaxonomicInformation();
}
+ else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ obtainDetailedTaxonomicInformationDelete();
+ }
else if ( o == _obtain_uniprot_seq_information_jmi ) {
obtainUniProtSequenceInformation();
}
customizeJMenuItem( _root_min_cost_l_item );
customizeJMenuItem( _load_species_tree_item );
_analysis_menu.addSeparator();
- _analysis_menu.add( _lineage_inference = new JMenuItem( "Infer Ancestor Taxonomies" ) );
+ _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
customizeJMenuItem( _lineage_inference );
_lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
_jmenubar.add( _analysis_menu );
_tools_menu = createMenu( "Tools", getConfiguration() );
_tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
customizeJMenuItem( _confcolor_item );
+ _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
+ customizeJMenuItem( _color_rank_jmi );
+ _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
_tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
customizeJMenuItem( _taxcolor_item );
_tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
customizeJMenuItem( _infer_common_sn_names_item );
_tools_menu.addSeparator();
_tools_menu
- .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information" ) );
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
_obtain_detailed_taxonomic_information_jmi
.setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
_tools_menu
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
+ 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)" ) );
customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
_obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
JOptionPane.ERROR_MESSAGE );
return;
}
- final Phylogeny phy = _mainpanel.getCurrentPhylogeny().copy();
final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
_mainpanel.getCurrentTreePanel(),
- phy );
+ _mainpanel.getCurrentPhylogeny()
+ .copy() );
new Thread( inferrer ).start();
}
final PhylogenyNode n = it.next();
final String name = n.getName().trim();
if ( !ForesterUtil.isEmpty( name ) ) {
- final String code = ForesterUtil.extractTaxonomyCodeFromNodeName( name,
- false,
- TAXONOMY_EXTRACTION.YES );
+ final String code = ParserUtils
+ .extractTaxonomyCodeFromNodeName( name, false, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
if ( !ForesterUtil.isEmpty( code ) ) {
PhylogenyMethods.setTaxonomyCode( n, code );
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- ForesterUtil.transferNodeNameToField( phy, PhylogenyNodeField.SEQUENCE_NAME );
+ PhylogenyMethods.transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME );
}
}
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- ForesterUtil.transferNodeNameToField( phy, PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME );
+ PhylogenyMethods.transferNodeNameToField( phy,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME );
}
}
}
}
}
+ private void obtainDetailedTaxonomicInformationDelete() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ true );
+ new Thread( t ).start();
+ }
+ }
+ }
+
private void obtainUniProtSequenceInformation() {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
try {
final NHXParser nhx = new NHXParser();
setSpecialOptionsForNhxParser( nhx );
- phys = ForesterUtil.readPhylogenies( nhx, file );
+ phys = PhylogenyMethods.readPhylogenies( nhx, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
try {
final PhyloXmlParser xml_parser = createPhyloXmlParser();
- phys = ForesterUtil.readPhylogenies( xml_parser, file );
+ phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
}
catch ( final Exception e ) {
exception = true;
}
else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
- phys = ForesterUtil.readPhylogenies( new TolParser(), file );
+ phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
}
catch ( final Exception e ) {
exception = true;
try {
final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
setSpecialOptionsForNexParser( nex );
- phys = ForesterUtil.readPhylogenies( nex, file );
+ phys = PhylogenyMethods.readPhylogenies( nex, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final PhylogenyParser parser = ForesterUtil
+ final PhylogenyParser parser = ParserUtils
.createParserDependingOnFileType( file, getConfiguration()
.isValidatePhyloXmlAgainstSchema() );
if ( parser instanceof NexusPhylogeniesParser ) {
else if ( parser instanceof PhyloXmlParser ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
}
- phys = ForesterUtil.readPhylogenies( parser, file );
+ phys = PhylogenyMethods.readPhylogenies( parser, file );
}
catch ( final Exception e ) {
exception = true;
if ( nhx_or_nexus ) {
for( final Phylogeny phy : phys ) {
if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
- ForesterUtil.transferInternalNodeNamesToConfidence( phy );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
one_desc = true;
parser = new TolParser();
}
else {
- parser = ForesterUtil.createParserDependingOnUrlContents( url, getConfiguration()
+ parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
.isValidatePhyloXmlAgainstSchema() );
}
if ( parser instanceof NexusPhylogeniesParser ) {
if ( ( phys != null ) && ( phys.length > 0 ) ) {
if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
for( final Phylogeny phy : phys ) {
- ForesterUtil.transferInternalNodeNamesToConfidence( phy );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
}
Util.addPhylogeniesToTabs( phys,
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
try {
- final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
}
else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
- final Phylogeny[] trees = ForesterUtil.readPhylogenies( new TolParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
- ForesterUtil.TAXONOMY_EXTRACTION te = ForesterUtil.TAXONOMY_EXTRACTION.NO;
+ PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
if ( getOptions().isExtractPfamTaxonomyCodesInNhParsing() ) {
- te = ForesterUtil.TAXONOMY_EXTRACTION.YES;
+ te = PhylogenyMethods.TAXONOMY_EXTRACTION.YES;
}
nhx.setTaxonomyExtraction( te );
}
git://source.jalview.org / jalview.git / blobdiff