X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FGSDI.java;h=4ab6395af79a9f6928d9863cf88723acbf5770e5;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=44fb8561b394eb192579ab01889fb8d7eef56c5c;hpb=6fbecc5890472ea8419c338c278cb4e0b3dd7cc7;p=jalview.git diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java index 44fb856..4ab6395 100644 --- a/forester/java/src/org/forester/sdi/GSDI.java +++ b/forester/java/src/org/forester/sdi/GSDI.java @@ -37,7 +37,6 @@ import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.data.Event; -import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.sdi.SDIutil.TaxonomyComparisonBase; import org.forester.util.ForesterUtil; @@ -59,6 +58,15 @@ public final class GSDI implements GSDII { final boolean most_parsimonious_duplication_model, final boolean strip_gene_tree, final boolean strip_species_tree ) throws SDIException { + this( gene_tree, species_tree, most_parsimonious_duplication_model, strip_gene_tree, strip_species_tree, true ); + } + + public GSDI( final Phylogeny gene_tree, + final Phylogeny species_tree, + final boolean most_parsimonious_duplication_model, + final boolean strip_gene_tree, + final boolean strip_species_tree, + final boolean transfer_taxonomy ) throws SDIException { _most_parsimonious_duplication_model = most_parsimonious_duplication_model; if ( gene_tree.getRoot().getNumberOfDescendants() == 3 ) { gene_tree.reRoot( gene_tree.getRoot().getChildNode( 2 ) ); @@ -76,7 +84,7 @@ public final class GSDI implements GSDII { PhylogenyMethods.preOrderReId( species_tree ); final GSDIsummaryResult gsdi_summary_result = geneTreePostOrderTraversal( gene_tree, _most_parsimonious_duplication_model, - true ); + transfer_taxonomy ); _speciation_or_duplication_events_sum = gsdi_summary_result.getSpeciationOrDuplicationEventsSum(); _speciations_sum = gsdi_summary_result.getSpeciationsSum(); _duplications_sum = gsdi_summary_result.getDuplicationsSum(); @@ -144,10 +152,10 @@ public final class GSDI implements GSDII { * Preconditions: Mapping M for external nodes must have been calculated and * the species tree must be labeled in preorder. *
- * @param transfer_taxonomy
- * @return
- * @throws SDIException
- *
+ * @param transfer_taxonomy
+ * @return
+ * @throws SDIException
+ *
*/
final static GSDIsummaryResult geneTreePostOrderTraversal( final Phylogeny gene_tree,
final boolean most_parsimonious_duplication_model,
@@ -158,7 +166,7 @@ public final class GSDI implements GSDII {
if ( g.isInternal() ) {
if ( g.getNumberOfDescendants() != 2 ) {
throw new SDIException( "gene tree contains internal node with " + g.getNumberOfDescendants()
- + " descendents" );
+ + " descendents" );
}
PhylogenyNode s1 = g.getChildNode1().getLink();
PhylogenyNode s2 = g.getChildNode2().getLink();
@@ -171,46 +179,13 @@ public final class GSDI implements GSDII {
}
}
g.setLink( s1 );
- if ( transfer_taxonomy ) {
- transferTaxonomy( g, s1 );
- }
determineEvent( s1, g, most_parsimonious_duplication_model, res );
}
- }
- return res;
- }
-
- private static final void transferTaxonomy( final PhylogenyNode g, final PhylogenyNode s ) {
- if ( s.getNodeData().isHasTaxonomy() ) {
- g.getNodeData().setTaxonomy( s.getNodeData().getTaxonomy() );
- if ( g.isInternal() ) {
- if ( g.getChildNode1().isInternal() ) {
- if ( g.getChildNode1().getNodeData().isHasTaxonomy() && g.getChildNode1().getNodeData().getTaxonomy() == s.getNodeData().getTaxonomy() ) {
- g.getChildNode1().getNodeData().setTaxonomy( null );
- }
- }
- if ( g.getChildNode2().isInternal() ) {
- if ( g.getChildNode2().getNodeData().isHasTaxonomy() && g.getChildNode2().getNodeData().getTaxonomy() == s.getNodeData().getTaxonomy() ) {
- g.getChildNode2().getNodeData().setTaxonomy( null );
- }
- }
- }
- }
- else if ( ForesterUtil.isEmpty( g.getName() ) && !ForesterUtil.isEmpty( s.getName() ) ) {
- g.setName( s.getName() );
- if ( g.isInternal() ) {
- if ( g.getChildNode1().isInternal() ) {
- if ( g.getChildNode1().getName() == s.getName() ) {
- g.getChildNode1().setName( "" );
- }
- }
- if ( g.getChildNode2().isInternal() ) {
- if ( g.getChildNode2().getName() == s.getName() ) {
- g.getChildNode2().setName( "" );
- }
- }
+ if ( transfer_taxonomy ) {
+ transferTaxonomy( g );
}
}
+ return res;
}
final static GSDIsummaryResult geneTreePostOrderTraversal( final Phylogeny gene_tree,
@@ -222,7 +197,7 @@ public final class GSDI implements GSDII {
if ( g.isInternal() ) {
if ( g.getNumberOfDescendants() != 2 ) {
throw new SDIException( "gene tree contains internal node with " + g.getNumberOfDescendants()
- + " descendents" );
+ + " descendents" );
}
PhylogenyNode s1 = g.getChildNode1().getLink();
PhylogenyNode s2 = g.getChildNode2().getLink();
@@ -259,8 +234,8 @@ public final class GSDI implements GSDII {
* This allows for linking of internal nodes of the species tree (as opposed
* to just external nodes, as in the method it overrides.
* If TaxonomyComparisonBase is null, it will try to determine it.
- * @throws SDIException
- *
+ * @throws SDIException
+ *
*/
final static NodesLinkingResult linkNodesOfG( final Phylogeny gene_tree,
final Phylogeny species_tree,
@@ -324,7 +299,7 @@ public final class GSDI implements GSDII {
}
else {
throw new SDIException( "taxonomy \"" + g.getNodeData().getTaxonomy()
- + "\" not present in species tree" );
+ + "\" not present in species tree" );
}
}
else {
@@ -347,6 +322,40 @@ public final class GSDI implements GSDII {
return res;
}
+ static final void transferTaxonomy( final PhylogenyNode g ) {
+ if ( g == null ) {
+ throw new IllegalArgumentException( "gene tree node is null" );
+ }
+ final PhylogenyNode s = g.getLink();
+ if ( s == null ) {
+ throw new IllegalArgumentException( "mapped species tree node is null" );
+ }
+ if ( s.getNodeData().isHasTaxonomy() ) {
+ g.getNodeData().setTaxonomy( s.getNodeData().getTaxonomy() );
+ if ( g.isInternal() ) {
+ if ( g.getChildNode1().isInternal() && g.getChildNode1().getNodeData().isHasTaxonomy()
+ && ( g.getChildNode1().getNodeData().getTaxonomy() == s.getNodeData().getTaxonomy() ) ) {
+ g.getChildNode1().getNodeData().setTaxonomy( null );
+ }
+ if ( g.getChildNode2().isInternal() && g.getChildNode2().getNodeData().isHasTaxonomy()
+ && ( g.getChildNode2().getNodeData().getTaxonomy() == s.getNodeData().getTaxonomy() ) ) {
+ g.getChildNode2().getNodeData().setTaxonomy( null );
+ }
+ }
+ }
+ else if ( ForesterUtil.isEmpty( g.getName() ) && !ForesterUtil.isEmpty( s.getName() ) ) {
+ g.setName( s.getName() );
+ if ( g.isInternal() ) {
+ if ( g.getChildNode1().isInternal() && ( g.getChildNode1().getName() == s.getName() ) ) {
+ g.getChildNode1().setName( "" );
+ }
+ if ( g.getChildNode2().isInternal() && ( g.getChildNode2().getName() == s.getName() ) ) {
+ g.getChildNode2().setName( "" );
+ }
+ }
+ }
+ }
+
private final static void addScientificNamesMappedToReducedSpecificity( final String s1,
final String s2,
final SortedSet