import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import javax.imageio.IIOImage;
import javax.imageio.ImageIO;
import javax.swing.JOptionPane;
import javax.swing.text.MaskFormatter;
-import org.forester.analysis.AncestralTaxonomyInference;
+import org.forester.analysis.TaxonomyDataManager;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Distribution;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.PreorderTreeIterator;
+import org.forester.util.AsciiHistogram;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
-import org.forester.ws.uniprot.UniProtTaxonomy;
+import org.forester.ws.seqdb.UniProtTaxonomy;
public final class AptxUtil {
+ private final static Pattern seq_identifier_pattern_1 = Pattern
+ .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
+ private final static Pattern seq_identifier_pattern_2 = Pattern
+ .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
.getAvailableFontFamilyNames();
static {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
+ public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) {
+ final String n = sequence_name.trim();
+ final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
+ String group1 = "";
+ String group2 = "";
+ if ( matcher1.matches() ) {
+ group1 = matcher1.group( 1 );
+ group2 = matcher1.group( 2 );
+ }
+ else {
+ final Matcher matcher2 = seq_identifier_pattern_2.matcher( n );
+ if ( matcher2.matches() ) {
+ group1 = matcher2.group( 1 );
+ group2 = matcher2.group( 2 );
+ }
+ }
+ if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) {
+ return null;
+ }
+ return new Accession( group2, group1 );
+ }
+
public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
if ( !node.getNodeData().isHasTaxonomy() ) {
node.getNodeData().setTaxonomy( new Taxonomy() );
return false;
}
- public static void writePhylogenyToGraphicsFileNonInteractive( final File intree,
- final File outfile,
- final int width,
- final int height,
- final GraphicsExportType type,
- final Configuration config ) throws IOException {
+ public static void writePhylogenyToGraphicsFile( final File intree,
+ final File outfile,
+ final int width,
+ final int height,
+ final GraphicsExportType type,
+ final Configuration config ) throws IOException {
final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
Phylogeny[] phys = null;
phys = PhylogenyMethods.readPhylogenies( parser, intree );
+ writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
+ }
+
+ public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
+ final File outfile,
+ final int width,
+ final int height,
+ final GraphicsExportType type,
+ final Configuration config ) throws IOException {
+ final Phylogeny[] phys = new Phylogeny[ 1 ];
+ phys[ 0 ] = phy;
final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
- AptxUtil.writePhylogenyToGraphicsFile( outfile, width, height, mf.getMainPanel().getCurrentTreePanel(), mf
- .getMainPanel().getControlPanel(), type, mf.getOptions() );
+ AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
+ .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
mf.end();
}
else {
UniProtTaxonomy up = null;
try {
- up = AncestralTaxonomyInference.obtainUniProtTaxonomy( temp_tax, null, null );
+ up = TaxonomyDataManager.obtainUniProtTaxonomy( temp_tax, null, null );
}
catch ( final Exception e ) {
e.printStackTrace();
}
}
- final static String crateBasicInformation( final Phylogeny phy ) {
+ final static String createBasicInformation( final Phylogeny phy ) {
final StringBuilder desc = new StringBuilder();
if ( ( phy != null ) && !phy.isEmpty() ) {
if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
desc.append( "Maximum distance to root: " );
desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
desc.append( "\n" );
- desc.append( "Descendants per node statistics: " );
- final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
- desc.append( "\n" );
- desc.append( " Median: " + ForesterUtil.round( ds.median(), 2 ) );
- desc.append( "\n" );
- desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
- desc.append( "\n" );
- desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
- desc.append( "\n" );
- desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
- desc.append( "\n" );
- desc.append( " Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
+ final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
+ if ( taxs != null ) {
+ desc.append( "Distinct external taxonomies: " );
+ desc.append( taxs.size() );
+ }
desc.append( "\n" );
- final DescriptiveStatistics cs = PhylogenyMethods.calculatConfidenceStatistics( phy );
- if ( cs.getN() > 1 ) {
- desc.append( "Support statistics: " );
+ final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
+ if ( bs.getN() > 2 ) {
desc.append( "\n" );
- desc.append( " Branches with support: " + cs.getN() );
+ desc.append( "Branch-length statistics: " );
desc.append( "\n" );
- desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) );
+ desc.append( " Number of branches with non-negative branch-lengths: " + bs.getN() );
desc.append( "\n" );
- desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
+ desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) );
desc.append( "\n" );
- if ( cs.getN() > 2 ) {
- desc.append( " SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) );
- desc.append( "\n" );
- }
- desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
+ desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) );
+ desc.append( "\n" );
+ desc.append( " SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) );
+ desc.append( "\n" );
+ desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
+ desc.append( "\n" );
+ desc.append( " Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) );
desc.append( "\n" );
- desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
desc.append( "\n" );
+ final AsciiHistogram histo = new AsciiHistogram( bs );
+ desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) );
}
- final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
- if ( taxs != null ) {
- desc.append( "Distinct external taxonomies: " );
- desc.append( taxs.size() );
+ final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
+ if ( ds.getN() > 2 ) {
+ desc.append( "\n" );
+ desc.append( "Descendants per node statistics: " );
+ desc.append( "\n" );
+ desc.append( " Median: " + ForesterUtil.round( ds.median(), 2 ) );
+ desc.append( "\n" );
+ desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
+ desc.append( "\n" );
+ desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
+ desc.append( "\n" );
+ desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
+ desc.append( "\n" );
+ desc.append( " Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
+ desc.append( "\n" );
+ }
+ List<DescriptiveStatistics> css = null;
+ try {
+ css = PhylogenyMethods.calculatConfidenceStatistics( phy );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
+ }
+ if ( ( css != null ) && ( css.size() > 0 ) ) {
+ desc.append( "\n" );
+ for( int i = 0; i < css.size(); ++i ) {
+ final DescriptiveStatistics cs = css.get( i );
+ if ( ( cs != null ) && ( cs.getN() > 1 ) ) {
+ if ( css.size() > 1 ) {
+ desc.append( "Support statistics " + ( i + 1 ) + ": " );
+ }
+ else {
+ desc.append( "Support statistics: " );
+ }
+ if ( !ForesterUtil.isEmpty( cs.getDescription() ) ) {
+ desc.append( "\n" );
+ desc.append( " Type: " + cs.getDescription() );
+ }
+ desc.append( "\n" );
+ desc.append( " Branches with support: " + cs.getN() );
+ desc.append( "\n" );
+ desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) );
+ desc.append( "\n" );
+ desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
+ desc.append( "\n" );
+ if ( cs.getN() > 2 ) {
+ desc.append( " SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) );
+ desc.append( "\n" );
+ }
+ desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
+ desc.append( "\n" );
+ desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
+ desc.append( "\n" );
+ }
+ }
}
}
return desc.toString();
}
}
- final static void launchWebBrowser( final URI uri,
- final boolean is_applet,
- final JApplet applet,
- final String frame_name ) throws IOException {
+ final public static void launchWebBrowser( final URI uri,
+ final boolean is_applet,
+ final JApplet applet,
+ final String frame_name ) throws IOException {
if ( is_applet ) {
applet.getAppletContext().showDocument( uri.toURL(), frame_name );
}
}
}
- final static void showErrorMessage( final Component parent, final String error_msg ) {
+ final public static void showErrorMessage( final Component parent, final String error_msg ) {
printAppletMessage( Constants.PRG_NAME, error_msg );
JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
+ "] Error", JOptionPane.ERROR_MESSAGE );
return msg;
}
- public final static void writePhylogenyToGraphicsFile( final File outfile,
- final int width,
- final int height,
- final TreePanel tree_panel,
- final ControlPanel ac,
- final GraphicsExportType type,
- final Options options ) throws IOException {
+ public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
+ final int width,
+ final int height,
+ final TreePanel tree_panel,
+ final ControlPanel ac,
+ final GraphicsExportType type,
+ final Options options ) throws IOException {
tree_panel.setParametersForPainting( width, height, true );
tree_panel.resetPreferredSize();
tree_panel.repaint();
git://source.jalview.org / jalview.git / blobdiff