// Contact: phylosoft @ gmail . com
// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
-
-
package org.forester.archaeopteryx;
import java.awt.Color;
import java.text.ParseException;
import java.util.Arrays;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
public final class AptxUtil {
+ final static String UNIPROT_KB = "http://www.uniprot.org/uniprot/";
+ final static Pattern UNIPROT_KB_PATTERN_1 = Pattern
+ .compile( "\\bsp|tr.\\S([A-Z0-9]{5,6})\\b" );
+
+ final static Pattern UNIPROT_KB_PATTERN_2 = Pattern
+ .compile( "\\b[A-Z0-9]{5,6}_[A-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA\\b" );
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
}
}
+ public static Set<Taxonomy> obtainAllDistinctTaxonomies( 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() ) {
+ tax_set.add( n.getNodeData().getTaxonomy() );
+ }
+ }
+ 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 Accession obtainSequenceAccessionFromName( final String sequence_name ) {
final String n = sequence_name.trim();
final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
final ControlPanel ac,
final GraphicsExportType type,
final Options options ) throws IOException {
- tree_panel.setParametersForPainting( width, height, true );
+ tree_panel.calcParametersForPainting( width, height, true );
tree_panel.resetPreferredSize();
tree_panel.repaint();
final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
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 = PhylogenyMethods.obtainDistinctTaxonomies( n );
+ final Set<Taxonomy> taxs = obtainDistinctTaxonomies( n );
if ( ( taxs != null ) && ( taxs.size() == 1 ) ) {
AptxUtil.collapseSubtree( n, true );
if ( !n.getNodeData().isHasTaxonomy() ) {
}
if ( phy.getIdentifier() != null ) {
desc.append( "Id: " );
- desc.append( phy.getIdentifier() );
+ desc.append( phy.getIdentifier().toString() );
+ desc.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) {
+ desc.append( "Description: " );
+ desc.append( phy.getDescription() );
+ desc.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) {
+ desc.append( "Distance Unit: " );
+ desc.append( phy.getDistanceUnit() );
+ desc.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( phy.getType() ) ) {
+ desc.append( "Type: " );
+ desc.append( phy.getType() );
desc.append( "\n" );
}
desc.append( "Rooted: " );
desc.append( "Rerootable: " );
desc.append( phy.isRerootable() );
desc.append( "\n" );
- desc.append( "Node sum: " );
+ desc.append( "Nodes: " );
desc.append( phy.getNodeCount() );
desc.append( "\n" );
- desc.append( "External node sum: " );
+ desc.append( "External nodes: " );
desc.append( phy.getNumberOfExternalNodes() );
desc.append( "\n" );
- desc.append( "Internal node sum: " );
+ desc.append( "Internal nodes: " );
desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() );
desc.append( "\n" );
- desc.append( "Branche sum: " );
+ desc.append( "Internal nodes with polytomies: " );
+ desc.append( PhylogenyMethods.countNumberOfPolytomies( phy ) );
+ desc.append( "\n" );
+ desc.append( "Branches: " );
desc.append( phy.getNumberOfBranches() );
desc.append( "\n" );
desc.append( "Depth: " );
desc.append( "Maximum distance to root: " );
desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
desc.append( "\n" );
- final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
+ final Set<Taxonomy> taxs = obtainAllDistinctTaxonomies( phy.getRoot() );
if ( taxs != null ) {
desc.append( "Distinct external taxonomies: " );
desc.append( taxs.size() );
return true;
}
- final static boolean isJava15() {
- try {
- final String s = ForesterUtil.JAVA_VERSION;
- return s.startsWith( "1.5" );
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
- return false;
- }
- }
-
final static boolean isMac() {
try {
final String s = ForesterUtil.OS_NAME.toLowerCase();
}
}
+ final static void outOfMemoryError( final OutOfMemoryError e ) {
+ System.err.println();
+ System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
+ System.err.println();
+ e.printStackTrace();
+ System.err.println();
+ 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 + "]",
+ JOptionPane.ERROR_MESSAGE );
+ System.exit( -1 );
+ }
+
final static void printAppletMessage( final String applet_name, final String message ) {
System.out.println( "[" + applet_name + "] > " + message );
}
System.exit( -1 );
}
- final static void outOfMemoryError( final OutOfMemoryError e ) {
- System.err.println();
- System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
- System.err.println();
- e.printStackTrace();
- System.err.println();
- 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 + "]",
- JOptionPane.ERROR_MESSAGE );
- System.exit( -1 );
- }
-
final static void unexpectedException( final Exception e ) {
System.err.println();
e.printStackTrace( System.err );
if ( options.isGraphicsExportVisibleOnly() ) {
throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
}
- tree_panel.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
+ tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
tree_panel.resetPreferredSize();
tree_panel.repaint();
}
if ( options.isGraphicsExportVisibleOnly() ) {
throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
}
- tree_panel.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
+ tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
tree_panel.resetPreferredSize();
tree_panel.repaint();
}
git://source.jalview.org / jalview.git / blobdiff