import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
-import java.io.UnsupportedEncodingException;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.URI;
import java.net.URL;
-import java.net.URLEncoder;
+import java.security.KeyManagementException;
+import java.security.NoSuchAlgorithmException;
import java.text.ParseException;
import java.util.Arrays;
import java.util.HashMap;
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.imageio.ImageWriteParam;
import javax.imageio.ImageWriter;
import javax.imageio.stream.ImageOutputStream;
-import javax.swing.JApplet;
import javax.swing.JOptionPane;
import javax.swing.text.MaskFormatter;
-import org.forester.analysis.TaxonomyDataManager;
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.nhx.NHXParser.TAXONOMY_EXTRACTION;
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Accession;
-import org.forester.phylogeny.data.BranchColor;
-import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.BranchWidth;
+import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-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.ForesterConstants;
import org.forester.util.ForesterUtil;
-import org.forester.util.SequenceIdParser;
-import org.forester.ws.seqdb.UniProtTaxonomy;
+import org.forester.util.TaxonomyUtil;
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*$" );
- private final static Pattern seq_identifier_pattern_2 = Pattern
- .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
+ public static enum GraphicsExportType {
+ BMP( "bmp" ),
+ GIF( "gif" ),
+ JPG( "jpg" ),
+ PDF( "pdf" ),
+ PNG( "png" ),
+ TIFF( "tif" );
+
+ private final String _suffix;
+
+ private GraphicsExportType( final String suffix ) {
+ _suffix = suffix;
+ }
+
+ @Override
+ public String toString() {
+ return _suffix;
+ }
+ }
private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
+ .getAvailableFontFamilyNames();
static {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
- public final static String createUriForSeqWeb( final PhylogenyNode node,
- final Configuration conf,
- final TreePanel tp ) {
- String uri_str = null;
- if ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
- && conf.isHasWebLink( node.getNodeData().getSequence().getAccession().getSource().toLowerCase() ) ) {
- final Sequence seq = node.getNodeData().getSequence();
- final String source = seq.getAccession().getSource().toLowerCase();
- String url;
- if ( source.toLowerCase().equals( "ncbi" ) ) {
- url = Constants.NCBI_ALL_DATABASE_SEARCH;
+ final public static Color calculateColorFromString( final String str, final boolean is_taxonomy ) {
+ final String my_str = str.toUpperCase();
+ char first = my_str.charAt( 0 );
+ char second = ' ';
+ char third = ' ';
+ if ( my_str.length() > 1 ) {
+ if ( is_taxonomy ) {
+ second = my_str.charAt( 1 );
}
else {
- final WebLink weblink = conf.getWebLink( source );
- url = weblink.getUrl().toString();
- }
- try {
- uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- showErrorMessage( tp, e.toString() );
- e.printStackTrace();
- }
- }
- if ( ForesterUtil.isEmpty( uri_str ) ) {
- final String upkb = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
- if ( !ForesterUtil.isEmpty( upkb ) ) {
- try {
- uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- showErrorMessage( tp, e.toString() );
- e.printStackTrace();
- }
+ second = my_str.charAt( my_str.length() - 1 );
}
- }
- if ( ForesterUtil.isEmpty( uri_str ) ) {
- final String v = ForesterUtil.extractGenbankAccessor( node );
- if ( !ForesterUtil.isEmpty( v ) ) {
- try {
- if ( SequenceIdParser.isProtein( v ) ) {
- uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ if ( is_taxonomy ) {
+ if ( my_str.length() > 2 ) {
+ if ( my_str.indexOf( " " ) > 0 ) {
+ third = my_str.charAt( my_str.indexOf( " " ) + 1 );
}
else {
- uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ third = my_str.charAt( 2 );
}
}
- catch ( final UnsupportedEncodingException e ) {
- showErrorMessage( tp, e.toString() );
- e.printStackTrace();
- }
}
- }
- if ( ForesterUtil.isEmpty( uri_str ) ) {
- final String v = ForesterUtil.extractRefSeqAccessorAccessor( node );
- if ( !ForesterUtil.isEmpty( v ) ) {
- try {
- if ( SequenceIdParser.isProtein( v ) ) {
- uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
- }
- else {
- uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 );
- }
- }
- catch ( final UnsupportedEncodingException e ) {
- showErrorMessage( tp, e.toString() );
- e.printStackTrace();
- }
+ else if ( my_str.length() > 2 ) {
+ third = my_str.charAt( ( my_str.length() - 1 ) / 2 );
}
}
- return uri_str;
+ first = normalizeCharForRGB( first );
+ second = normalizeCharForRGB( second );
+ third = normalizeCharForRGB( third );
+ if ( ( first > 200 ) && ( second > 200 ) && ( third > 200 ) ) {
+ first = 0;
+ }
+ else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
+ second = 255;
+ }
+ else if ( Math.abs( first - second ) < 40 && Math.abs( second - third ) < 40 ) {
+ third = 255;
+ }
+ return new Color( first, second, third );
}
public static MaskFormatter createMaskFormatter( final String s ) {
/**
* Returns true if at least one branch has a length larger than zero.
- *
- *
+ *
+ *
* @param phy
*/
final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
return false;
}
+ final static public boolean isHasAtLeast50PercentBranchLengthLargerThanZero( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ int positive = 0;
+ int total = 0;
+ while ( it.hasNext() ) {
+ if ( it.next().getDistanceToParent() > 0.0 ) {
+ ++positive;
+ }
+ ++total;
+ }
+ if ( total == 0 ) {
+ return false;
+ }
+ return (((( double ) positive) / total) >= 0.5 );
+ }
+
+ final static public boolean isHasNoBranchLengthSmallerThanZero( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getDistanceToParent() < 0.0 && !n.isRoot() ) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ final static public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getBranchData().isHasConfidences() ) {
+ final List<Confidence> c = n.getBranchData().getConfidences();
+ for( final Confidence confidence : c ) {
+ if ( confidence.getStandardDeviation() > 0 ) {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+ }
+
final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
return false;
}
- 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 );
- }
- else {
- // This requires Java 1.6:
- // =======================
- // boolean no_desktop = false;
- // try {
- // if ( Desktop.isDesktopSupported() ) {
- // System.out.println( "desktop supported" );
- // final Desktop dt = Desktop.getDesktop();
- // dt.browse( uri );
- // }
- // else {
- // no_desktop = true;
- // }
- // }
- // catch ( final Exception ex ) {
- // ex.printStackTrace();
- // no_desktop = true;
- // }
- // catch ( final Error er ) {
- // er.printStackTrace();
- // no_desktop = true;
- // }
- // if ( no_desktop ) {
- // System.out.println( "desktop not supported" );
- try {
- openUrlInWebBrowser( uri.toString() );
+ final static public boolean isHasAtLeastOneNodeWithScientificName( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ return true;
}
- catch ( final Exception e ) {
- throw new IOException( e );
+ }
+ return false;
+ }
+
+ final static public boolean isHasAtLeastOneNodeWithSequenceAnnotation( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAnnotations() ) ) {
+ return true;
}
- // }
}
+ return false;
+ }
+
+ final public static void launchWebBrowser( final URI uri, final String frame_name ) throws IOException {
+ // This requires Java 1.6:
+ // =======================
+ // boolean no_desktop = false;
+ // try {
+ // if ( Desktop.isDesktopSupported() ) {
+ // System.out.println( "desktop supported" );
+ // final Desktop dt = Desktop.getDesktop();
+ // dt.browse( uri );
+ // }
+ // else {
+ // no_desktop = true;
+ // }
+ // }
+ // catch ( final Exception ex ) {
+ // ex.printStackTrace();
+ // no_desktop = true;
+ // }
+ // catch ( final Error er ) {
+ // er.printStackTrace();
+ // no_desktop = true;
+ // }
+ // if ( no_desktop ) {
+ // System.out.println( "desktop not supported" );
+ try {
+ openUrlInWebBrowser( uri.toString() );
+ }
+ catch ( final Exception e ) {
+ throw new IOException( e );
+ }
+ // }
}
public static Set<Taxonomy> obtainAllDistinctTaxonomies( final PhylogenyNode node ) {
return tax_set;
}
- /**
- * Returns the set of distinct taxonomies of
- * all external nodes of node.
- * If at least one the external nodes has no taxonomy,
- * null is returned.
- *
- */
- public static Set<Taxonomy> obtainDistinctTaxonomies( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- return null;
- }
- tax_set.add( n.getNodeData().getTaxonomy() );
- }
- return tax_set;
+ public final static void printWarningMessage( final String name, final String message ) {
+ System.out.println( "[" + name + "] > " + message );
}
- 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 );
+ final public static Phylogeny[] readPhylogeniesFromUrl( final URL url,
+ final boolean phyloxml_validate_against_xsd,
+ final boolean replace_underscores,
+ final boolean internal_numbers_are_confidences,
+ final TAXONOMY_EXTRACTION taxonomy_extraction,
+ final boolean midpoint_reroot )
+ throws FileNotFoundException, IOException {
+ final PhylogenyParser parser;
+ boolean nhx_or_nexus = false;
+ if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
+ parser = new TolParser();
}
else {
- final Matcher matcher2 = seq_identifier_pattern_2.matcher( n );
- if ( matcher2.matches() ) {
- group1 = matcher2.group( 1 );
- group2 = matcher2.group( 2 );
+ parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
+ if ( parser instanceof NHXParser ) {
+ nhx_or_nexus = true;
+ final NHXParser nhx = ( NHXParser ) parser;
+ nhx.setReplaceUnderscores( replace_underscores );
+ nhx.setIgnoreQuotes( false );
+ nhx.setTaxonomyExtraction( taxonomy_extraction );
+ }
+ else if ( parser instanceof NexusPhylogeniesParser ) {
+ nhx_or_nexus = true;
+ final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
+ nex.setReplaceUnderscores( replace_underscores );
+ nex.setIgnoreQuotes( false );
}
}
- if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) {
- return null;
+ AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
+ Phylogeny[] phys = null;
+ try {
+ phys = ForesterUtil.readPhylogeniesFromUrl( url, parser );
+ }
+ catch ( final KeyManagementException e ) {
+ throw new IOException( e.getMessage() );
}
- return new Accession( group2, group1 );
- }
-
- public final static void printWarningMessage( final String name, final String message ) {
- System.out.println( "[" + name + "] > " + message );
- }
-
- 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 );
- }
-
- public final static void showExtDescNodeDataUserSelectedHelper( final ControlPanel cp,
- final PhylogenyNode node,
- final List<String> data ) {
- final StringBuilder sb = new StringBuilder();
- if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb );
- }
- if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb );
- }
- if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
- }
- if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession().toString(), sb );
- }
- if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getTaxonomyCode(), sb );
- }
- if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(), sb );
- }
- if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
- && node.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getMolecularSequence(), sb );
- }
- final String s = sb.toString().trim();
- if ( !ForesterUtil.isEmpty( s ) ) {
- data.add( s );
+ catch ( final NoSuchAlgorithmException e ) {
+ throw new IOException( e.getMessage() );
}
- }
-
- public final static void showExtDescNodeDataUserSelectedHelperHelper( final String s, final StringBuilder sb ) {
- if ( sb.length() > 0 ) {
- sb.append( "\t" );
+ if ( phys != null ) {
+ if ( nhx_or_nexus && internal_numbers_are_confidences ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
+ }
+ }
+ if ( midpoint_reroot ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.midpointRoot( phy );
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ }
+ }
}
- sb.append( s );
+ return phys;
}
- final public static void showInformationMessage( final Component parent, final String title, final String msg ) {
- JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE );
+ final public static void showErrorMessage( final Component parent, final String error_msg ) {
+ printAppletMessage( AptxConstants.PRG_NAME, error_msg );
+ JOptionPane.showMessageDialog( parent,
+ error_msg,
+ "[" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + "] Error",
+ JOptionPane.ERROR_MESSAGE );
}
public static void writePhylogenyToGraphicsFile( final File intree,
final int width,
final int height,
final GraphicsExportType type,
- final Configuration config ) throws IOException {
+ final Configuration config )
+ throws IOException {
final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
Phylogeny[] phys = null;
phys = PhylogenyMethods.readPhylogenies( parser, intree );
final int width,
final int height,
final GraphicsExportType type,
- final Configuration config ) throws IOException {
+ final Configuration config )
+ throws IOException {
final Phylogeny[] phys = new Phylogeny[ 1 ];
phys[ 0 ] = phy;
final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
- AptxUtil.writePhylogenyToGraphicsFileNonInteractive( 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();
}
final TreePanel tree_panel,
final ControlPanel ac,
final GraphicsExportType type,
- final Options options ) throws IOException {
- tree_panel.calcParametersForPainting( width, height, true );
+ final Options options )
+ throws IOException {
+ tree_panel.calcParametersForPainting( width, height );
tree_panel.resetPreferredSize();
tree_panel.repaint();
final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
g2d.dispose();
}
+ final private static char normalizeCharForRGB( char c ) {
+ c -= 65;
+ c *= 10.2;
+ c = c > 255 ? 255 : c;
+ c = c < 0 ? 0 : c;
+ return c;
+ }
+
+ final private static void openUrlInWebBrowser( final String url )
+ throws IOException, ClassNotFoundException, SecurityException, NoSuchMethodException,
+ IllegalArgumentException, IllegalAccessException, InvocationTargetException, InterruptedException {
+ final String os = System.getProperty( "os.name" );
+ final Runtime runtime = Runtime.getRuntime();
+ if ( os.toLowerCase().startsWith( "win" ) ) {
+ Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
+ }
+ else if ( ForesterUtil.isMac() ) {
+ final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
+ final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
+ open_url.invoke( null, new Object[] { url } );
+ }
+ else {
+ final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
+ String browser = null;
+ for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
+ if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
+ browser = browsers[ i ];
+ }
+ }
+ if ( browser == null ) {
+ throw new IOException( "could not find a web browser to open [" + url + "] in" );
+ }
+ else {
+ runtime.exec( new String[] { browser, url } );
+ }
+ }
+ }
+
final static void addPhylogeniesToTabs( final Phylogeny[] phys,
final String default_name,
final String full_path,
final Configuration configuration,
final MainPanel main_panel ) {
- if ( phys.length > Constants.MAX_TREES_TO_LOAD ) {
- JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
- + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
- + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
+ if ( phys.length > AptxConstants.MAX_TREES_TO_LOAD ) {
+ JOptionPane.showMessageDialog( main_panel,
+ "Attempt to load " + phys.length
+ + " phylogenies,\ngoing to load only the first "
+ + AptxConstants.MAX_TREES_TO_LOAD,
+ AptxConstants.PRG_NAME + " more than " + AptxConstants.MAX_TREES_TO_LOAD
+ + " phylogenies",
+ JOptionPane.WARNING_MESSAGE );
}
int i = 1;
for( final Phylogeny phy : phys ) {
if ( !phy.isEmpty() ) {
- if ( i <= Constants.MAX_TREES_TO_LOAD ) {
+ if ( i <= AptxConstants.MAX_TREES_TO_LOAD ) {
String my_name = "";
String my_name_for_file = "";
if ( phys.length > 1 ) {
lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
}
- final static Color calculateColorFromString( final String str ) {
- final String species_uc = str.toUpperCase();
- char first = species_uc.charAt( 0 );
- char second = ' ';
- char third = ' ';
- if ( species_uc.length() > 1 ) {
- second = species_uc.charAt( 1 );
- if ( species_uc.length() > 2 ) {
- if ( species_uc.indexOf( " " ) > 0 ) {
- third = species_uc.charAt( species_uc.indexOf( " " ) + 1 );
- }
- else {
- third = species_uc.charAt( 2 );
- }
- }
- }
- first = AptxUtil.normalizeCharForRGB( first );
- second = AptxUtil.normalizeCharForRGB( second );
- third = AptxUtil.normalizeCharForRGB( third );
- if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
- first = 0;
- }
- else if ( ( first < 80 ) && ( second < 80 ) && ( third < 80 ) ) {
- second = 255;
- }
- return new Color( first, second, third );
- }
-
// Returns true if the specified format name can be written
final static boolean canWriteFormat( final String format_name ) {
final Iterator<ImageWriter> iter = ImageIO.getImageWritersByFormatName( format_name );
return iter.hasNext();
}
- final static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) {
- boolean inferred = false;
- for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( !n.isExternal() && !n.isCollapse() && ( n.getNumberOfDescendants() > 1 ) ) {
- final Set<Taxonomy> taxs = obtainDistinctTaxonomies( n );
- if ( ( taxs != null ) && ( taxs.size() == 1 ) ) {
- AptxUtil.collapseSubtree( n, true );
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( ( Taxonomy ) n.getAllExternalDescendants().get( 0 ).getNodeData()
- .getTaxonomy().copy() );
- }
- inferred = true;
- }
- else {
- n.setCollapse( false );
- }
- }
- }
- if ( inferred ) {
- phy.setRerootable( false );
- }
- }
-
- final static void collapseSubtree( final PhylogenyNode node, final boolean collapse ) {
- node.setCollapse( collapse );
- if ( node.isExternal() ) {
- return;
- }
- final PhylogenyNodeIterator it = new PreorderTreeIterator( node );
- while ( it.hasNext() ) {
- it.next().setCollapse( collapse );
- }
- }
-
- final static void colorPhylogenyAccordingToConfidenceValues( final Phylogeny tree, final TreePanel tree_panel ) {
- double max_conf = 0.0;
- for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- n.getBranchData().setBranchColor( null );
- if ( n.getBranchData().isHasConfidences() ) {
- final double conf = PhylogenyMethods.getConfidenceValue( n );
- if ( conf > max_conf ) {
- max_conf = conf;
- }
- }
- }
- if ( max_conf > 0.0 ) {
- final Color bg = tree_panel.getTreeColorSet().getBackgroundColor();
- final Color br = tree_panel.getTreeColorSet().getBranchColor();
- for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( n.getBranchData().isHasConfidences() ) {
- final double conf = PhylogenyMethods.getConfidenceValue( n );
- final BranchColor c = new BranchColor( ForesterUtil.calcColor( conf, 0.0, max_conf, bg, br ) );
- colorizeSubtree( n, c );
- }
- }
- }
- }
-
- final static void colorPhylogenyAccordingToExternalTaxonomy( final Phylogeny tree, final TreePanel tree_panel ) {
- for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( null );
- }
- for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( !n.getBranchData().isHasBranchColor() ) {
- final Taxonomy tax = PhylogenyMethods.getExternalDescendantsTaxonomy( n );
- if ( tax != null ) {
- n.getBranchData().setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
- final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
- for( final PhylogenyNode desc : descs ) {
- desc.getBranchData()
- .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
- }
- }
- }
- }
- }
-
- final static int colorPhylogenyAccordingToRanks( final Phylogeny tree, final String rank, final TreePanel tree_panel ) {
- final Map<String, Color> true_lineage_to_color_map = new HashMap<String, Color>();
- int colorizations = 0;
- for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( n.getNodeData().isHasTaxonomy()
- && ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() )
- || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil
- .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
- if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
- && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) {
- final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData()
- .getTaxonomy() ) );
- colorizeSubtree( n, c );
- ++colorizations;
- if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- true_lineage_to_color_map.put( n.getNodeData().getTaxonomy().getScientificName(), c.getValue() );
- }
+ final static String createBasicInformation( final Phylogeny phy, final File treefile ) {
+ final StringBuilder desc = new StringBuilder();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ String f = null;
+ if ( treefile != null ) {
+ try {
+ f = treefile.getCanonicalPath();
}
- }
- }
- for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
- final PhylogenyNode node = it.next();
- if ( ( node.getBranchData().getBranchColor() == null ) && node.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getLineage() ) ) {
- boolean success = false;
- if ( !true_lineage_to_color_map.isEmpty() ) {
- for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
- if ( true_lineage_to_color_map.containsKey( lin ) ) {
- colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
- ++colorizations;
- success = true;
- break;
- }
- }
+ catch ( final IOException e ) {
+ //Not important, ignore.
}
- if ( !success ) {
- final Map<String, String> lineage_to_rank_map = MainPanel.getLineageToRankMap();
- for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
- final Taxonomy temp_tax = new Taxonomy();
- temp_tax.setScientificName( lin );
- if ( lineage_to_rank_map.containsKey( lin )
- && !ForesterUtil.isEmpty( lineage_to_rank_map.get( lin ) )
- && lineage_to_rank_map.get( lin ).equalsIgnoreCase( rank ) ) {
- final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) );
- colorizeSubtree( node, c );
- ++colorizations;
- true_lineage_to_color_map.put( lin, c.getValue() );
- break;
- }
- else {
- UniProtTaxonomy up = null;
- try {
- up = TaxonomyDataManager.obtainUniProtTaxonomy( temp_tax, null, null );
- }
- catch ( final Exception e ) {
- e.printStackTrace();
- }
- if ( ( up != null ) && !ForesterUtil.isEmpty( up.getRank() ) ) {
- lineage_to_rank_map.put( lin, up.getRank() );
- if ( up.getRank().equalsIgnoreCase( rank ) ) {
- final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) );
- colorizeSubtree( node, c );
- ++colorizations;
- true_lineage_to_color_map.put( lin, c.getValue() );
- break;
- }
- }
- }
- }
+ if ( !ForesterUtil.isEmpty( f ) ) {
+ desc.append( "Path: " );
+ desc.append( f );
+ desc.append( "\n" );
}
}
- }
- return colorizations;
- }
-
- final static String createBasicInformation( final Phylogeny phy ) {
- final StringBuilder desc = new StringBuilder();
- if ( ( phy != null ) && !phy.isEmpty() ) {
if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
desc.append( "Name: " );
desc.append( phy.getName() );
desc.append( "Distinct external taxonomies: " );
desc.append( taxs.size() );
}
+ for( final Taxonomy t : taxs ) {
+ System.out.println( t.toString() );
+ }
desc.append( "\n" );
- final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
+ final DescriptiveStatistics bs = PhylogenyMethods.calculateBranchLengthStatistics( phy );
if ( bs.getN() > 3 ) {
desc.append( "\n" );
desc.append( "Branch-length statistics: " );
desc.append( "\n" );
desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) );
desc.append( "\n" );
- desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) );
- desc.append( "\n" );
- desc.append( " SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) );
+ desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
+ + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
desc.append( "\n" );
desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
desc.append( "\n" );
desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) );
}
}
- final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
+ final DescriptiveStatistics ds = PhylogenyMethods.calculateNumberOfDescendantsPerNodeStatistics( 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( " Median: " + ForesterUtil.round( ds.median(), 6 ) );
desc.append( "\n" );
- desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
- desc.append( "\n" );
- desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
+ desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 6 ) + " (stdev: "
+ + ForesterUtil.round( ds.sampleStandardDeviation(), 6 ) + ")" );
desc.append( "\n" );
desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
desc.append( "\n" );
}
List<DescriptiveStatistics> css = null;
try {
- css = PhylogenyMethods.calculatConfidenceStatistics( phy );
+ css = PhylogenyMethods.calculateConfidenceStatistics( phy );
}
catch ( final IllegalArgumentException e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, e.getMessage() );
}
if ( ( css != null ) && ( css.size() > 0 ) ) {
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( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
}
- desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
desc.append( "\n" );
- desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
+ desc.append( " Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) );
+ desc.append( "\n" );
+ desc.append( " Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) );
desc.append( "\n" );
}
}
/**
* Exits with -1.
- *
- *
+ *
+ *
* @param message
* to message to be printed
*/
final static void dieWithSystemError( final String message ) {
System.out.println();
- System.out.println( Constants.PRG_NAME + " encountered the following system error: " + message );
+ System.out.println( AptxConstants.PRG_NAME + " encountered the following system error: " + message );
System.out.println( "Please contact the authors." );
- System.out.println( Constants.PRG_NAME + " needs to close." );
+ System.out.println( AptxConstants.PRG_NAME + " needs to close." );
System.out.println();
System.exit( -1 );
}
final static String[] getAllPossibleRanks() {
- final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
+ final String[] str_array = new String[ TaxonomyUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
int i = 0;
- for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
- if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
+ for( final String e : TaxonomyUtil.TAXONOMY_RANKS_LIST ) {
+ if ( !e.equals( TaxonomyUtil.UNKNOWN ) && !e.equals( TaxonomyUtil.OTHER ) ) {
str_array[ i++ ] = e;
}
}
return str_array;
}
+ final static String[] getAllPossibleRanks( final Map<String, Integer> present_ranks ) {
+ final String[] str_array = new String[ TaxonomyUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
+ int i = 0;
+ for( final String e : TaxonomyUtil.TAXONOMY_RANKS_LIST ) {
+ if ( !e.equals( TaxonomyUtil.UNKNOWN ) && !e.equals( TaxonomyUtil.OTHER ) ) {
+ if ( present_ranks != null && present_ranks.containsKey( e ) ) {
+ str_array[ i++ ] = e + " (" + present_ranks.get( e ) + ")";
+ }
+ else {
+ str_array[ i++ ] = e;
+ }
+ }
+ }
+ return str_array;
+ }
+
final static String[] getAllRanks( final Phylogeny tree ) {
final SortedSet<String> ranks = new TreeSet<String>();
for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
return AVAILABLE_FONT_FAMILIES_SORTED;
}
- final static boolean isHasAssignedEvent( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasEvent() ) {
- return false;
- }
- if ( ( node.getNodeData().getEvent() ).isUnassigned() ) {
- return false;
- }
- return true;
- }
-
- final static boolean isMac() {
- try {
- final String s = ForesterUtil.OS_NAME.toLowerCase();
- return s.startsWith( "mac" );
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
- return false;
- }
- }
-
final static boolean isUsOrCanada() {
try {
if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
return false;
}
- final static boolean isWindows() {
- try {
- final String s = ForesterUtil.OS_NAME.toLowerCase();
- return s.indexOf( "win" ) > -1;
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
- return false;
+ final static void lookAtRealBranchLengthsForAptxControlSettings( final Phylogeny t, final ControlPanel cp ) {
+ if ( ( t != null ) && !t.isEmpty() ) {
+ final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t );
+ if ( !has_bl ) {
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM );
+ cp.setDrawPhylogramEnabled( false );
+ }
+ else {
+ final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t );
+ if ( has_all_bl ) {
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM );
+ }
+ if ( cp.getDisplayAsUnalignedPhylogramRb() != null ) {
+ cp.setDrawPhylogramEnabled( true );
+ }
+ }
}
}
- final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
- final ControlPanel atv_control,
+ public final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
+ final ControlPanel cp,
final Configuration configuration ) {
if ( ( t != null ) && !t.isEmpty() ) {
- if ( !AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
- atv_control.setDrawPhylogram( false );
- atv_control.setDrawPhylogramEnabled( false );
+ final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t );
+ if ( !has_bl ) {
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM );
+ cp.setDrawPhylogramEnabled( false );
+ }
+ if ( t.getFirstExternalNode().getBranchData().getBranchColor() != null
+ && cp.getUseVisualStylesCb() != null ) {
+ cp.getUseVisualStylesCb().setSelected( true );
+ }
+ if ( t.getFirstExternalNode().getBranchData().getBranchWidth() != null
+ && t.getFirstExternalNode().getBranchData().getBranchWidth()
+ .getValue() != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE
+ && cp.getUseBranchWidthsCb() != null ) {
+ cp.getUseBranchWidthsCb().setSelected( true );
}
if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
- if ( atv_control.getDisplayAsPhylogramCb() != null ) {
- if ( AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
- atv_control.setDrawPhylogram( true );
- atv_control.setDrawPhylogramEnabled( true );
+ if ( cp.getDisplayAsAlignedPhylogramRb() != null ) {
+ if ( has_bl ) {
+ final boolean has_mostly_bl = AptxUtil.isHasAtLeast50PercentBranchLengthLargerThanZero( t );
+ if ( has_mostly_bl ) {
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM );
+ }
+ cp.setDrawPhylogramEnabled( true );
}
else {
- atv_control.setDrawPhylogram( false );
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM );
}
}
}
if ( configuration.doGuessCheckOption( Configuration.write_confidence_values ) ) {
- if ( atv_control.getWriteConfidenceCb() != null ) {
+ if ( cp.getWriteConfidenceCb() != null ) {
if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( t ) ) {
- atv_control.setCheckbox( Configuration.write_confidence_values, true );
+ cp.setCheckbox( Configuration.write_confidence_values, true );
}
else {
- atv_control.setCheckbox( Configuration.write_confidence_values, false );
+ cp.setCheckbox( Configuration.write_confidence_values, false );
}
}
}
if ( configuration.doGuessCheckOption( Configuration.write_events ) ) {
- if ( atv_control.getShowEventsCb() != null ) {
+ if ( cp.getShowEventsCb() != null ) {
if ( AptxUtil.isHasAtLeastNodeWithEvent( t ) ) {
- atv_control.setCheckbox( Configuration.write_events, true );
+ cp.setCheckbox( Configuration.write_events, true );
}
else {
- atv_control.setCheckbox( Configuration.write_events, false );
+ cp.setCheckbox( Configuration.write_events, false );
}
}
}
}
}
- final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException {
+ final static void openWebsite( final String url ) throws IOException {
try {
- AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME );
+ AptxUtil.launchWebBrowser( new URI( url ), AptxConstants.PRG_NAME );
}
catch ( final Exception e ) {
throw new IOException( e );
JOptionPane.showMessageDialog( null,
"Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
+ "\n\nError: " + e.getLocalizedMessage(),
- "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
+ "Out of Memory Error [" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION
+ + "]",
JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
}
System.out.println( "[" + applet_name + "] > " + message );
}
- final static Phylogeny[] readPhylogeniesFromUrl( final URL url,
- final boolean phyloxml_validate_against_xsd,
- final boolean replace_underscores,
- final boolean internal_numbers_are_confidences,
- final TAXONOMY_EXTRACTION taxonomy_extraction )
- throws FileNotFoundException, IOException {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser parser;
- boolean nhx_or_nexus = false;
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
- parser = new TolParser();
- }
- else {
- parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
- if ( parser instanceof NHXParser ) {
- nhx_or_nexus = true;
- final NHXParser nhx = ( NHXParser ) parser;
- nhx.setReplaceUnderscores( replace_underscores );
- nhx.setIgnoreQuotes( false );
- nhx.setTaxonomyExtraction( taxonomy_extraction );
- }
- else if ( parser instanceof NexusPhylogeniesParser ) {
- nhx_or_nexus = true;
- final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
- nex.setReplaceUnderscores( replace_underscores );
- nex.setIgnoreQuotes( false );
- }
- }
- final Phylogeny[] phys = factory.create( url.openStream(), parser );
- if ( nhx_or_nexus && internal_numbers_are_confidences ) {
- for( final Phylogeny phy : phys ) {
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
- }
+ final static void removeBranchColors( final Phylogeny phy ) {
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( null );
}
- return phys;
}
- final static void removeBranchColors( final Phylogeny phy ) {
+ final static void removeVisualStyles( final Phylogeny phy ) {
for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( null );
+ it.next().getNodeData().setNodeVisualData( null );
}
}
for( final StackTraceElement s : e.getStackTrace() ) {
sb.append( s + "\n" );
}
- JOptionPane
- .showMessageDialog( null,
- "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
- + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
- + sb,
- "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( null,
+ "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
+ + AptxConstants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage()
+ + "\n" + sb,
+ "Unexpected Severe Error [" + AptxConstants.PRG_NAME + " "
+ + AptxConstants.VERSION + "]",
+ JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
}
}
JOptionPane.showMessageDialog( null,
"An unexpected exception has occured. \nPlease contact: "
- + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+ + AptxConstants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+ "\n" + sb,
- "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
+ "Unexpected Exception [" + AptxConstants.PRG_NAME + AptxConstants.VERSION + "]",
JOptionPane.ERROR_MESSAGE );
}
final TreePanel tree_panel,
final ControlPanel ac,
final GraphicsExportType type,
- final Options options ) throws IOException {
- if ( !options.isGraphicsExportUsingActualSize() ) {
- if ( options.isGraphicsExportVisibleOnly() ) {
- throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
- }
- tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
- tree_panel.resetPreferredSize();
- tree_panel.repaint();
- }
+ final Options options )
+ throws IOException {
final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
RenderingHints.VALUE_RENDER_QUALITY );
rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
return "";
}
Rectangle visible = null;
- if ( !options.isGraphicsExportUsingActualSize() ) {
- width = options.getPrintSizeX();
- height = options.getPrintSizeY();
- }
- else if ( options.isGraphicsExportVisibleOnly() ) {
+ // if ( !options.isGraphicsExportUsingActualSize() ) {
+ // width = options.getPrintSizeX();
+ // height = options.getPrintSizeY();
+ // }
+ /* else*/ if ( options.isGraphicsExportVisibleOnly() ) {
visible = tree_panel.getVisibleRect();
width = visible.width;
height = visible.height;
final TreePanel tree_panel,
final ControlPanel ac,
final GraphicsExportType type,
- final Options options ) throws IOException {
- if ( !options.isGraphicsExportUsingActualSize() ) {
- if ( options.isGraphicsExportVisibleOnly() ) {
- throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
- }
- tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
- tree_panel.resetPreferredSize();
- tree_panel.repaint();
- }
+ final Options options )
+ throws IOException {
final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
RenderingHints.VALUE_RENDER_QUALITY );
rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
throw new IOException( "\"" + file_name + "\" is a directory" );
}
Rectangle visible = null;
- if ( !options.isGraphicsExportUsingActualSize() ) {
- width = options.getPrintSizeX();
- height = options.getPrintSizeY();
- }
- else if ( options.isGraphicsExportVisibleOnly() ) {
+ // if ( !options.isGraphicsExportUsingActualSize() ) {
+ // width = options.getPrintSizeX();
+ // height = options.getPrintSizeY();
+ // }
+ /*else*/ if ( options.isGraphicsExportVisibleOnly() ) {
visible = tree_panel.getVisibleRect();
width = visible.width;
height = visible.height;
writer.write( null, iio_image, image_write_param );
}
- private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
- node.getBranchData().setBranchColor( c );
- final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
- for( final PhylogenyNode desc : descs ) {
- desc.getBranchData().setBranchColor( c );
- }
- }
-
- final private static char normalizeCharForRGB( char c ) {
- c -= 65;
- c *= 10.2;
- c = c > 255 ? 255 : c;
- c = c < 0 ? 0 : c;
- return c;
- }
-
- final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
- SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
- InvocationTargetException, InterruptedException {
- final String os = System.getProperty( "os.name" );
- final Runtime runtime = Runtime.getRuntime();
- if ( os.toLowerCase().startsWith( "win" ) ) {
- Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
- }
- else if ( isMac() ) {
- final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
- final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
- open_url.invoke( null, new Object[] { url } );
- }
- else {
- final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
- String browser = null;
- for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
- if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
- browser = browsers[ i ];
+ final static Map<String, Integer> getRankCounts( final Phylogeny tree ) {
+ final Map<String, Integer> present_ranks = new HashMap<String, Integer>();
+ if ( ( tree != null ) && !tree.isEmpty() ) {
+ for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() && n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) && !n.isRoot() ) {
+ final String rank = n.getNodeData().getTaxonomy().getRank().toLowerCase();
+ if ( present_ranks.containsKey( rank ) ) {
+ present_ranks.put( rank, present_ranks.get( rank ) + 1 );
+ }
+ else {
+ present_ranks.put( rank, 1 );
+ }
}
}
- if ( browser == null ) {
- throw new IOException( "could not find a web browser to open [" + url + "] in" );
- }
- else {
- runtime.exec( new String[] { browser, url } );
- }
- }
- }
-
- // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
- // static void openDDBJRest() throws IOException {
- // //set URL
- // URL url = new URL( "http://xml.nig.ac.jp/rest/Invoke" );
- // //set parameter
- // String query = "service=GetEntry&method=getDDBJEntry&accession=AB000100";
- // //make connection
- // URLConnection urlc = url.openConnection();
- // //use post mode
- // urlc.setDoOutput( true );
- // urlc.setAllowUserInteraction( false );
- // //send query
- // PrintStream ps = new PrintStream( urlc.getOutputStream() );
- // ps.print( query );
- // ps.close();
- // //get result
- // BufferedReader br = new BufferedReader( new InputStreamReader(
- // urlc.getInputStream() ) );
- // String l = null;
- // while ( ( l = br.readLine() ) != null ) {
- // System.out.println( l );
- // }
- // br.close();
- // }
- public static enum GraphicsExportType {
- GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" ), BMP( "bmp" );
-
- private final String _suffix;
-
- private GraphicsExportType( final String suffix ) {
- _suffix = suffix;
- }
-
- @Override
- public String toString() {
- return _suffix;
}
+ return present_ranks;
}
}
git://source.jalview.org / jalview.git / blobdiff