package org.forester.archaeopteryx;
-import java.awt.Color;
import java.awt.Component;
import java.awt.Graphics2D;
import java.awt.GraphicsEnvironment;
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.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.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.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.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 {
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 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 );
+ "] 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 = my_str.charAt( ( my_str.length() - 1 ) / 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 < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
- 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 boolean show_ref_sources ) {
- 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 ( show_ref_sources && !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() );
- }
- if ( sb.charAt( sb.length() - 1 ) == ' ' ) {
- sb.deleteCharAt( sb.length() - 1 );
- }
- if ( i < ans.size() - 1 ) {
- sb.append( ", " );
- }
- }
- 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() ) {
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 ) ) ) {
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 {
String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
final static String display_options[][] = {
{ "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
- { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
+ { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
{ "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" },
{ "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" },
{ "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" },
public final static boolean __SYNTH_LF = false; // TODO remove me
public final static boolean ALLOW_DDBJ_BLAST = false;
public final static String PRG_NAME = "Archaeopteryx";
- final static String VERSION = "0.9814";
- final static String PRG_DATE = "130916";
+ final static String VERSION = "0.9815 PP";
+ final static String PRG_DATE = "130924";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica",
"Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
if ( getControlPanel().isShowAnnotation()
&& ( node.getNodeData().getSequence().getAnnotations() != null )
&& !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
- sum += getTreeFontSet()._fm_large.stringWidth( AptxUtil.createAnnotationString( node.getNodeData()
- .getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() )
+ sum += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
+ .getNodeData().getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() )
+ " " );
}
if ( getControlPanel().isShowDomainArchitectures()
}
if ( c == null ) {
if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
+ c = TreePanelUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
}
else {
- c = AptxUtil.calculateColorFromString( tax.getScientificName(), true );
+ c = TreePanelUtil.calculateColorFromString( tax.getScientificName(), true );
getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
}
}
}
if ( !node.isExternal() && !node.isRoot() ) {
final boolean collapse = !node.isCollapse();
- AptxUtil.collapseSubtree( node, collapse );
+ TreePanelUtil.collapseSubtree( node, collapse );
updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
return;
}
setWaitCursor();
- AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
+ TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
}
setWaitCursor();
AptxUtil.removeBranchColors( _phylogeny );
- final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+ final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
if ( colorizations > 0 ) {
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
}
setWaitCursor();
AptxUtil.removeBranchColors( _phylogeny );
- AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
+ TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
_sub_phylogenies[ _subtree_index ] = _phylogeny;
_sub_phylogenies_temp_roots[ _subtree_index ] = node;
++_subtree_index;
- _phylogeny = subTree( node, _phylogeny );
+ _phylogeny = TreePanelUtil.subTree( node, _phylogeny );
updateSubSuperTreeButton();
}
else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
return;
}
setWaitCursor();
- AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+ TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
if ( !ForesterUtil.isEmpty( ann_str ) ) {
c = getControlPanel().getAnnotationColors().get( ann_str );
if ( c == null ) {
- c = AptxUtil.calculateColorFromString( ann_str, false );
+ c = TreePanelUtil.calculateColorFromString( ann_str, false );
getControlPanel().getAnnotationColors().put( ann_str, c );
}
if ( c == null ) {
JOptionPane.WARNING_MESSAGE );
}
- final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot colorize subtree in unrooted display type",
- "Attempt to colorize subtree in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
+ final private void colorizeSubtree( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
}
- for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ if ( node != null ) {
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
+ }
+ if ( additional_nodes != null ) {
+ for( final PhylogenyNode n : additional_nodes ) {
+ n.getBranchData().setBranchColor( new BranchColor( c ) );
+ }
}
repaint();
}
final private void colorSubtree( final PhylogenyNode node ) {
- Color intitial_color = null;
- if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
- && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
- intitial_color = PhylogenyMethods.getBranchColorValue( node );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot colorize subtree in unrooted display type",
+ "Attempt to colorize subtree in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ _color_chooser.setPreviewPanel( new JPanel() );
+ SubtreeColorizationActionListener al;
+ if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ for( final Long id : getFoundNodes() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
- intitial_color = getTreeColorSet().getBranchColor();
+ al = new SubtreeColorizationActionListener( _color_chooser, node );
}
- _color_chooser.setColor( intitial_color );
- _color_chooser.setPreviewPanel( new JPanel() );
final JDialog dialog = JColorChooser
- .createDialog( this,
- "Subtree colorization",
- true,
- _color_chooser,
- new SubtreeColorizationActionListener( _color_chooser, node ),
- null );
+ .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
dialog.setVisible( true );
}
cannotOpenBrowserWarningMessage( "sequence" );
return;
}
- final String uri_str = AptxUtil.createUriForSeqWeb( node, getConfiguration(), this );
+ final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
AptxUtil.launchWebBrowser( new URI( uri_str ),
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
outline_color = Color.BLACK;
}
- else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
+ else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
outline_color = getTreeColorSet().getDuplicationBoxColor();
else if ( getControlPanel().isColorAccordingToAnnotation() ) {
g.setColor( calculateColorForAnnotation( ann ) );
}
- final String ann_str = AptxUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
+ final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
_sb.setLength( 0 );
if ( getControlPanel().isShowAnnotation()
&& ( node.getNodeData().getSequence().getAnnotations() != null )
&& ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( AptxUtil.createAnnotationString( node
+ x += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
.getNodeData().getSequence().getAnnotations(), getOptions()
.isShowAnnotationRefSource() )
+ " " );
sb.append( " " );
}
final Property p = properties.getProperty( ref );
- sb.append( getPartAfterColon( p.getRef() ) );
+ sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
sb.append( "=" );
sb.append( p.getValue() );
if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- sb.append( getPartAfterColon( p.getUnit() ) );
+ sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
}
}
return sb;
}
break;
case UNKNOWN:
- AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
break;
default:
throw new IllegalArgumentException( "unknown data element: "
}
else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
if ( sb.length() < 1 ) {
- AptxUtil.showInformationMessage( this,
- "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
- "Descendants of selected node do not contain selected data" );
+ TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
+ + ")", "Descendants of selected node do not contain selected data" );
clearCurrentExternalNodesDataBuffer();
}
else {
final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
try {
if ( ( node.getName().length() > 0 )
- || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
- || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
- || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
- || node.getBranchData().isHasConfidences() ) {
+ || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData()
+ .getTaxonomy() ) )
+ || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
+ .getSequence() ) ) || ( node.getNodeData().isHasDate() )
+ || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
_popup_buffer.setLength( 0 );
short lines = 0;
if ( node.getName().length() > 0 ) {
lines++;
_popup_buffer.append( node.getName() );
}
- if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
+ if ( node.getNodeData().isHasTaxonomy()
+ && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
lines++;
boolean enc_data = false;
final Taxonomy tax = node.getNodeData().getTaxonomy();
}
}
}
- if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
+ if ( node.getNodeData().isHasSequence()
+ && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
lines++;
boolean enc_data = false;
if ( _popup_buffer.length() > 0 ) {
for( final String ref : properties.getPropertyRefs() ) {
_popup_buffer.append( "\n" );
final Property p = properties.getProperty( ref );
- _popup_buffer.append( getPartAfterColon( p.getRef() ) );
+ _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
_popup_buffer.append( "=" );
_popup_buffer.append( p.getValue() );
if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
+ _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
}
}
}
}
}
- final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
- g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
- }
-
final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
}
- final private static String getPartAfterColon( final String s ) {
- final int i = s.indexOf( ':' );
- if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
- return s;
- }
- return s.substring( i + 1, s.length() );
- }
-
- final private static boolean isSequenceEmpty( final Sequence seq ) {
- return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
- && ForesterUtil.isEmpty( seq.getSymbol() );
- }
-
- final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
- return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
- && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
- .getSynonyms().isEmpty() );
- }
-
final private static boolean plusPressed( final int key_code ) {
return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
|| ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
}
- final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
- final Phylogeny new_phy = new Phylogeny();
- new_phy.setRooted( true );
- new_phy.setName( source_phy.getName() );
- new_phy.setDescription( source_phy.getDescription() );
- new_phy.setType( source_phy.getType() );
- new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
- new_phy.setConfidence( source_phy.getConfidence() );
- new_phy.setIdentifier( source_phy.getIdentifier() );
- new_phy.setRoot( new_root.copyNodeDataShallow() );
- int i = 0;
- for( final PhylogenyNode n : new_root.getDescendants() ) {
- new_phy.getRoot().setChildNode( i++, n );
- }
- return new_phy;
- }
-
final private class SubtreeColorizationActionListener implements ActionListener {
- JColorChooser _chooser;
- PhylogenyNode _node;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
+ List<PhylogenyNode> _additional_nodes = null;
SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
_chooser = chooser;
_node = node;
}
+ SubtreeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _chooser = chooser;
+ _node = node;
+ _additional_nodes = additional_nodes;
+ }
+
@Override
public void actionPerformed( final ActionEvent e ) {
final Color c = _chooser.getColor();
if ( c != null ) {
- colorizeSubtree( c, _node );
+ colorizeSubtree( c, _node, _additional_nodes );
}
}
}
--- /dev/null
+
+package org.forester.archaeopteryx;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+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 javax.swing.JOptionPane;
+
+import org.forester.analysis.TaxonomyDataManager;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Annotation;
+import org.forester.phylogeny.data.BranchColor;
+import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.phylogeny.iterators.PreorderTreeIterator;
+import org.forester.util.ForesterConstants;
+import org.forester.util.ForesterUtil;
+import org.forester.util.SequenceIdParser;
+import org.forester.ws.seqdb.UniProtTaxonomy;
+
+public class TreePanelUtil {
+
+ 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 ) {
+ AptxUtil.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 ) {
+ AptxUtil.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 ) {
+ AptxUtil.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 ) {
+ AptxUtil.showErrorMessage( tp, e.toString() );
+ e.printStackTrace();
+ }
+ }
+ }
+ return uri_str;
+ }
+
+ /**
+ * 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 showExtDescNodeDataUserSelectedHelper( final ControlPanel cp,
+ final PhylogenyNode node,
+ final List<String> data ) {
+ final StringBuilder sb = new StringBuilder();
+ if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb );
+ }
+ if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb );
+ }
+ if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
+ TreePanelUtil
+ .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
+ }
+ if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) {
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession()
+ .toString(), sb );
+ }
+ if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
+ .getTaxonomyCode(), sb );
+ }
+ if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
+ .getScientificName(), sb );
+ }
+ if ( cp.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
+ TreePanelUtil
+ .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
+ }
+ if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
+ && node.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ TreePanelUtil.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 );
+ }
+
+ 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 = my_str.charAt( ( my_str.length() - 1 ) / 2 );
+ }
+ }
+ first = TreePanelUtil.normalizeCharForRGB( first );
+ second = TreePanelUtil.normalizeCharForRGB( second );
+ third = TreePanelUtil.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 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 = TreePanelUtil.obtainDistinctTaxonomies( n );
+ if ( ( taxs != null ) && ( taxs.size() == 1 ) ) {
+ TreePanelUtil.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 );
+ }
+ }
+
+ 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 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 ) );
+ TreePanelUtil.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() ) );
+ TreePanelUtil.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 ) ) {
+ TreePanelUtil
+ .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 ) );
+ TreePanelUtil.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 ) );
+ TreePanelUtil.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 boolean show_ref_sources ) {
+ 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 ( show_ref_sources && !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() );
+ }
+ if ( sb.charAt( sb.length() - 1 ) == ' ' ) {
+ sb.deleteCharAt( sb.length() - 1 );
+ }
+ if ( i < ans.size() - 1 ) {
+ sb.append( ", " );
+ }
+ }
+ if ( m.size() > 1 ) {
+ sb.append( "] " );
+ }
+ }
+ return sb.toString();
+ }
+
+ final static String getPartAfterColon( final String s ) {
+ final int i = s.indexOf( ':' );
+ if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
+ return s;
+ }
+ return s.substring( i + 1, s.length() );
+ }
+
+ 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 isSequenceEmpty( final Sequence seq ) {
+ return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
+ && ForesterUtil.isEmpty( seq.getSymbol() );
+ }
+
+ final static boolean isTaxonomyEmpty( final Taxonomy tax ) {
+ return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
+ && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
+ .getSynonyms().isEmpty() );
+ }
+
+ final static char normalizeCharForRGB( char c ) {
+ c -= 65;
+ c *= 10.2;
+ c = c > 255 ? 255 : c;
+ c = c < 0 ? 0 : c;
+ return c;
+ }
+
+ final static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
+ final Phylogeny new_phy = new Phylogeny();
+ new_phy.setRooted( true );
+ new_phy.setName( source_phy.getName() );
+ new_phy.setDescription( source_phy.getDescription() );
+ new_phy.setType( source_phy.getType() );
+ new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
+ new_phy.setConfidence( source_phy.getConfidence() );
+ new_phy.setIdentifier( source_phy.getIdentifier() );
+ new_phy.setRoot( new_root.copyNodeDataShallow() );
+ int i = 0;
+ for( final PhylogenyNode n : new_root.getDescendants() ) {
+ new_phy.getRoot().setChildNode( i++, n );
+ }
+ return new_phy;
+ }
+}
import java.util.Set;
import org.forester.application.support_transfer;
-import org.forester.archaeopteryx.AptxUtil;
+import org.forester.archaeopteryx.TreePanelUtil;
import org.forester.development.DevelopmentTools;
import org.forester.evoinference.TestPhylogenyReconstruction;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
try {
final PhylogenyNode n = new PhylogenyNode();
n.setName( "tr|B3RJ64" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
return false;
}
n.setName( "B0LM41_HUMAN" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
return false;
}
n.setName( "NP_001025424" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
return false;
}
n.setName( "_NM_001030253-" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
return false;
}
n.setName( "XM_002122186" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
return false;
}
n.setName( "dgh_AAA34956_gdg" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
return false;
}
n.setName( "j40f4_Q06891.1_fndn2 fnr3" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "Q06891.1" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "Q06891.1" ) ) {
return false;
}
n.setName( "GI:394892" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
- System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
return false;
}
n.setName( "gi_394892" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
- System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
return false;
}
n.setName( "gi6335_gi_394892_56635_Gi_43" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
- System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
return false;
}
}
git://source.jalview.org / jalview.git / commitdiff