import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
-import java.io.UnsupportedEncodingException;
+import java.io.InputStream;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.URI;
import java.net.URL;
-import java.net.URLEncoder;
+import java.net.URLConnection;
import java.text.ParseException;
-import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
-import java.util.Map;
-import java.util.Map.Entry;
import java.util.Set;
-import java.util.SortedMap;
import java.util.SortedSet;
-import java.util.TreeMap;
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.TaxonomyDataManager;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
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.Annotation;
-import org.forester.phylogeny.data.BranchColor;
+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;
public final class AptxUtil {
private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
.getAvailableFontFamilyNames();
- private final static Pattern seq_identifier_pattern_1 = Pattern
- .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
- private final static Pattern seq_identifier_pattern_2 = Pattern
- .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
static {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
return formatter;
}
- public final static String createUriForSeqWeb( final PhylogenyNode node,
- final Configuration conf,
- final TreePanel tp ) {
- String uri_str = null;
- 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();
- }
- }
- 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 );
- }
- else {
- uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 );
- }
- }
- 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();
- }
- }
- }
- if ( ForesterUtil.isEmpty( uri_str ) ) {
- final String v = ForesterUtil.extractGInumber( node );
- if ( !ForesterUtil.isEmpty( v ) ) {
- try {
- uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- showErrorMessage( tp, e.toString() );
- e.printStackTrace();
- }
- }
- }
- return uri_str;
- }
-
final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
return false;
}
+ 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 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;
+ }
+ }
+ 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 boolean is_applet,
final JApplet applet,
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 );
- 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 final static void printWarningMessage( final String name, final String message ) {
System.out.println( "[" + name + "] > " + message );
}
+ "] 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.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), 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 );
- }
- }
-
- public final static void showExtDescNodeDataUserSelectedHelperHelper( final String s, final StringBuilder sb ) {
- if ( sb.length() > 0 ) {
- sb.append( "\t" );
- }
- sb.append( s );
- }
-
- final public static void showInformationMessage( final Component parent, final String title, final String msg ) {
- JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE );
- }
-
public static void writePhylogenyToGraphicsFile( final File intree,
final File outfile,
final int width,
lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
}
- final 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 {
- second = my_str.charAt( my_str.length() - 1 );
- }
- if ( is_taxonomy ) {
- if ( my_str.length() > 2 ) {
- if ( my_str.indexOf( " " ) > 0 ) {
- third = my_str.charAt( my_str.indexOf( " " ) + 1 );
- }
- else {
- third = my_str.charAt( 2 );
- }
- }
- }
- else if ( my_str.length() > 2 ) {
- third = ( char ) ( Math.abs( str.hashCode() / 16909320 ) );
- System.out.println( str.hashCode() );
- }
- }
- first = AptxUtil.normalizeCharForRGB( first );
- second = AptxUtil.normalizeCharForRGB( second );
- if ( is_taxonomy ) {
- third = AptxUtil.normalizeCharForRGB( third );
- }
- else {
- third = third > 255 ? 255 : 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() );
- }
- }
- }
- }
- 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;
- }
- }
- }
- 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;
- }
- }
- }
- }
- }
- }
- }
- return colorizations;
- }
-
- final static String createAnnotationString( final SortedSet<Annotation> annotations ) {
- final SortedMap<String, List<Annotation>> m = new TreeMap<String, List<Annotation>>();
- for( final Annotation an : annotations ) {
- final String ref_source = ForesterUtil.isEmpty( an.getRefSource() ) ? "?" : an.getRefSource();
- if ( !m.containsKey( ref_source ) ) {
- m.put( ref_source, new ArrayList<Annotation>() );
- }
- m.get( ref_source ).add( an );
- }
- final StringBuilder sb = new StringBuilder();
- for( final Entry<String, List<Annotation>> e : m.entrySet() ) {
- final String ref_source = e.getKey();
- final List<Annotation> ans = e.getValue();
- if ( m.size() > 1 ) {
- sb.append( "[" );
- }
- if ( !ref_source.equals( "?" ) ) {
- sb.append( ref_source );
- sb.append( ": " );
- }
- for( int i = 0; i < ans.size(); ++i ) {
- final Annotation an = ans.get( i );
- if ( !ForesterUtil.isEmpty( an.getRefValue() ) ) {
- sb.append( an.getRefValue() );
- sb.append( " " );
- }
- if ( !ForesterUtil.isEmpty( an.getDesc() ) ) {
- sb.append( an.getDesc() );
+ 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();
}
- if ( sb.charAt( sb.length() - 1 ) == ' ' ) {
- sb.deleteCharAt( sb.length() - 1 );
+ catch ( final IOException e ) {
+ //Not important, ignore.
}
- if ( i < ans.size() - 1 ) {
- sb.append( ", " );
+ if ( !ForesterUtil.isEmpty( f ) ) {
+ desc.append( "Path: " );
+ desc.append( f );
+ desc.append( "\n" );
}
}
- if ( m.size() > 1 ) {
- sb.append( "] " );
- }
- }
- return sb.toString();
- }
-
- 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( "\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 ) + " (stdev: "
- + 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" );
desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
}
desc.append( "\n" );
- desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
+ desc.append( " Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) );
desc.append( "\n" );
- desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
+ desc.append( " Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) );
desc.append( "\n" );
}
}
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 isUsOrCanada() {
try {
if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
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,
- final boolean midpoint_reroot ) throws FileNotFoundException,
- IOException {
+ 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 PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser parser;
boolean nhx_or_nexus = false;
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 );
+ AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
+ final URLConnection url_connection = url.openConnection();
+ url_connection.setDefaultUseCaches( false );
+ final InputStream i = url_connection.getInputStream();
+ final Phylogeny[] phys = factory.create( i, parser );
+ i.close();
+ 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 );
+ if ( midpoint_reroot ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.midpointRoot( phy );
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ }
}
}
return phys;
}
}
+ final static void removeVisualStyles( final Phylogeny phy ) {
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+ it.next().getNodeData().setNodeVisualData( null );
+ }
+ }
+
final static void unexpectedError( final Error e ) {
System.err.println();
e.printStackTrace( System.err );
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 {
}
}
- // 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 {
BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
return _suffix;
}
}
+
+ 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 {
+ second = my_str.charAt( my_str.length() - 1 );
+ }
+ if ( is_taxonomy ) {
+ if ( my_str.length() > 2 ) {
+ if ( my_str.indexOf( " " ) > 0 ) {
+ third = my_str.charAt( my_str.indexOf( " " ) + 1 );
+ }
+ else {
+ third = my_str.charAt( 2 );
+ }
+ }
+ }
+ else if ( my_str.length() > 2 ) {
+ third = my_str.charAt( ( my_str.length() - 1 ) / 2 );
+ }
+ }
+ first = normalizeCharForRGB( first );
+ second = normalizeCharForRGB( second );
+ third = normalizeCharForRGB( third );
+ if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
+ first = 0;
+ }
+ else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
+ second = 255;
+ }
+ return new Color( first, second, third );
+ }
+
+ final private static char normalizeCharForRGB( char c ) {
+ c -= 65;
+ c *= 10.2;
+ c = c > 255 ? 255 : c;
+ c = c < 0 ? 0 : c;
+ return c;
+ }
}
git://source.jalview.org / jalview.git / blobdiff