// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import org.forester.phylogeny.data.DomainArchitecture;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.DescriptiveStatistics;
import org.forester.util.FailedConditionCheckException;
import org.forester.util.ForesterUtil;
return max;
}
- public static int calculateMaximumNumberOfDescendantsPerNode( final Phylogeny phy ) {
- int max = 0;
+ public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.getNumberOfDescendants() > max ) {
- max = node.getNumberOfDescendants();
+ final PhylogenyNode n = iter.next();
+ if ( !n.isExternal() ) {
+ stats.addValue( n.getNumberOfDescendants() );
}
}
- return max;
+ return stats;
+ }
+
+ public static DescriptiveStatistics calculatConfidenceStatistics( final Phylogeny phy ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( !n.isExternal() ) {
+ if ( n.getBranchData().isHasConfidences() ) {
+ stats.addValue( n.getBranchData().getConfidence( 0 ).getValue() );
+ }
+ }
+ }
+ return stats;
}
/**
blue += child_color.getBlue();
}
}
- setBranchColorValue( node, new Color( ForesterUtil.roundToInt( red / n ), ForesterUtil
- .roundToInt( green / n ), ForesterUtil.roundToInt( blue / n ) ) );
+ setBranchColorValue( node,
+ new Color( ForesterUtil.roundToInt( red / n ),
+ ForesterUtil.roundToInt( green / n ),
+ ForesterUtil.roundToInt( blue / n ) ) );
}
}
}
parent.removeChildNode( remove_me );
for( final PhylogenyNode desc : descs ) {
parent.addAsChild( desc );
- desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(), desc
- .getDistanceToParent() ) );
+ desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
+ desc.getDistanceToParent() ) );
}
remove_me.setParent( null );
phylogeny.setIdHash( null );
}
}
}
- else if ( node.getNodeData().isHasSequence()
+ if ( !match && node.getNodeData().isHasSequence()
&& match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
match = true;
}
- else if ( node.getNodeData().isHasSequence()
+ if ( !match && node.getNodeData().isHasSequence()
&& match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
match = true;
}
- else if ( node.getNodeData().isHasSequence()
+ if ( !match
+ && node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getAccession() != null )
&& match( node.getNodeData().getSequence().getAccession().getValue(),
query,
partial ) ) {
match = true;
}
- else if ( node.getNodeData().isHasSequence()
+ if ( !match && node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
}
}
}
+ if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
+ Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), query, case_sensitive, partial ) ) {
+ match = true;
+ break I;
+ }
+ }
+ it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), query, case_sensitive, partial ) ) {
+ match = true;
+ break I;
+ }
+ }
+ }
if ( match ) {
nodes.add( node );
}
}
}
}
- else if ( node.getNodeData().isHasSequence()
+ if ( !match && node.getNodeData().isHasSequence()
&& match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
match = true;
}
- else if ( node.getNodeData().isHasSequence()
+ if ( !match && node.getNodeData().isHasSequence()
&& match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
match = true;
}
- else if ( node.getNodeData().isHasSequence()
+ if ( !match
+ && node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getAccession() != null )
&& match( node.getNodeData().getSequence().getAccession().getValue(),
query,
partial ) ) {
match = true;
}
- else if ( node.getNodeData().isHasSequence()
+ if ( !match && node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
}
}
}
+ if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
+ Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), query, case_sensitive, partial ) ) {
+ match = true;
+ break I;
+ }
+ }
+ it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), query, case_sensitive, partial ) ) {
+ match = true;
+ break I;
+ }
+ }
+ // final String[] bcp_ary = node.getNodeData().getBinaryCharacters()
+ // .getPresentCharactersAsStringArray();
+ // I: for( final String bc : bcp_ary ) {
+ // if ( match( bc, query, case_sensitive, partial ) ) {
+ // match = true;
+ // break I;
+ // }
+ // }
+ // final String[] bcg_ary = node.getNodeData().getBinaryCharacters()
+ // .getGainedCharactersAsStringArray();
+ // I: for( final String bc : bcg_ary ) {
+ // if ( match( bc, query, case_sensitive, partial ) ) {
+ // match = true;
+ // break I;
+ // }
+ // }
+ }
if ( !match ) {
all_matched = false;
break;