X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FSDIR.java;h=bc395c345b6a7dc49b85422dc1a0d28b91f43f11;hb=fbb7c0a322111e5221773fed19591da29296efb5;hp=7af2359389b62a1a822c1385bcc605d3a4fc9e2c;hpb=9bad57b1ba0f75075ab8c6bda1dedb906f8c6280;p=jalview.git diff --git a/forester/java/src/org/forester/sdi/SDIR.java b/forester/java/src/org/forester/sdi/SDIR.java index 7af2359..bc395c3 100644 --- a/forester/java/src/org/forester/sdi/SDIR.java +++ b/forester/java/src/org/forester/sdi/SDIR.java @@ -23,7 +23,7 @@ // 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; @@ -45,11 +45,11 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator; *
* (Last modified: 01/22/00) - * + * * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) * @return the minimal difference in tree heights -- IF calculated by * "infer" @@ -113,7 +113,7 @@ public class SDIR { * IMPORTANT : If the tree is not rooted by minimizing the sum of * duplications or the mapping cost L, then this number is NOT NECESSARILY * the MINIMAL number of duplications. - * + * * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) * @return (minimal) number of duplications */ @@ -126,7 +126,7 @@ public class SDIR { * minimize_mapping_cost is set to true. *
* (Last modified: 11/07/00) - * + * * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) * @return the minimal mapping cost "L" -- IF calculated by "infer" */ @@ -142,7 +142,7 @@ public class SDIR { * first criterion. *
* (Last modified: 01/12/00) - * + * * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) * @return the minimal tree height -- IF calculated by "infer" */ @@ -153,7 +153,7 @@ public class SDIR { /** * Returns the sum of times (in ms) needed to run method infer of class SDI. * Final variable TIME needs to be set to true. - * + * * @return sum of times (in ms) needed to run method infer of class SDI */ public long getTimeSumSDI() { @@ -188,7 +188,7 @@ public class SDIR { * *
* (Last modified: 10/01/01)
- *
+ *
* @param gene_tree
* a binary (except deepest node) gene Phylogeny
* @param species_tree
@@ -212,7 +212,7 @@ public class SDIR {
* Array) must be no lower than 1
* @return array of rooted Trees with duplication vs. speciation assigned if
* return_trees is set to true, null otherwise
- * @throws SDIException
+ * @throws SDIException
*/
public Phylogeny[] infer( final Phylogeny gene_tree,
final Phylogeny species_tree,
@@ -292,7 +292,7 @@ public class SDIR {
prev_root_c2 = prev_root.getChildNode2();
prev_root_was_dup = prev_root.isDuplication();
final PhylogenyBranch current_branch = branches.get( j );
- g.reRoot( current_branch );
+ GSDIR.reRoot( current_branch, g );
if ( minimize_mapping_cost || minimize_sum_of_dup ) {
duplications = sdise.updateM( prev_root_was_dup, prev_root_c1, prev_root_c2 );
}
@@ -494,8 +494,8 @@ public class SDIR {
branches.add( new PhylogenyBranch( t.getRoot().getChildNode1(), t.getRoot().getChildNode2() ) );
return branches;
}
- final Set