X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FGSDI.java;h=fa7a52c8baa3db2ab8cbb8fd08d0e88967cd533c;hb=41ea5973f93687513d29e5b7cad1abff8f3adb4b;hp=63c6215253b89bc58f5ef013d91167a220504bbf;hpb=cec0663378230521f24a851cb1c1c9491026b70a;p=jalview.git diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java index 63c6215..fa7a52c 100644 --- a/forester/java/src/org/forester/sdi/GSDI.java +++ b/forester/java/src/org/forester/sdi/GSDI.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.sdi; @@ -58,6 +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 ) ); @@ -74,7 +83,8 @@ public final class GSDI implements GSDII { _tax_comp_base = nodes_linking_result.getTaxCompBase(); PhylogenyMethods.preOrderReId( species_tree ); final GSDIsummaryResult gsdi_summary_result = geneTreePostOrderTraversal( gene_tree, - _most_parsimonious_duplication_model ); + _most_parsimonious_duplication_model, + transfer_taxonomy ); _speciation_or_duplication_events_sum = gsdi_summary_result.getSpeciationOrDuplicationEventsSum(); _speciations_sum = gsdi_summary_result.getSpeciationsSum(); _duplications_sum = gsdi_summary_result.getDuplicationsSum(); @@ -142,13 +152,14 @@ 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
*
*/
final static GSDIsummaryResult geneTreePostOrderTraversal( final Phylogeny gene_tree,
- final boolean most_parsimonious_duplication_model )
- throws SDIException {
+ final boolean most_parsimonious_duplication_model,
+ final boolean transfer_taxonomy ) throws SDIException {
final GSDIsummaryResult res = new GSDIsummaryResult();
for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {
final PhylogenyNode g = it.next();
@@ -170,6 +181,40 @@ public final class GSDI implements GSDII {
g.setLink( s1 );
determineEvent( s1, g, most_parsimonious_duplication_model, res );
}
+ if ( transfer_taxonomy ) {
+ transferTaxonomy( g );
+ }
+ }
+ return res;
+ }
+
+ final static GSDIsummaryResult geneTreePostOrderTraversal( final Phylogeny gene_tree,
+ final boolean most_parsimonious_duplication_model,
+ final int min_duplications ) throws SDIException {
+ final GSDIsummaryResult res = new GSDIsummaryResult();
+ for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode g = it.next();
+ if ( g.isInternal() ) {
+ if ( g.getNumberOfDescendants() != 2 ) {
+ throw new SDIException( "gene tree contains internal node with " + g.getNumberOfDescendants()
+ + " descendents" );
+ }
+ PhylogenyNode s1 = g.getChildNode1().getLink();
+ PhylogenyNode s2 = g.getChildNode2().getLink();
+ while ( s1 != s2 ) {
+ if ( s1.getId() > s2.getId() ) {
+ s1 = s1.getParent();
+ }
+ else {
+ s2 = s2.getParent();
+ }
+ }
+ g.setLink( s1 );
+ determineEvent( s1, g, most_parsimonious_duplication_model, res );
+ if ( res.getDuplicationsSum() > min_duplications ) {
+ return null;
+ }
+ }
}
return res;
}
@@ -277,6 +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