X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FSDIR.java;h=a21fd6b6655c09764f158c34d587bdeeb808605a;hb=8aadbec1b0627ebd71e57e60e06621d4038bb79a;hp=98f1cc5c20fe95b29774332a70de34c3ae042dfe;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git diff --git a/forester/java/src/org/forester/sdi/SDIR.java b/forester/java/src/org/forester/sdi/SDIR.java index 98f1cc5..a21fd6b 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
@@ -212,6 +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
*/
public Phylogeny[] infer( final Phylogeny gene_tree,
final Phylogeny species_tree,
@@ -219,9 +220,9 @@ public class SDIR {
boolean minimize_sum_of_dup,
final boolean minimize_height,
final boolean return_trees,
- int max_trees_to_return ) {
+ int max_trees_to_return ) throws SDIException {
init();
- SDIse sdise = null;
+ SDI sdise = null;
final ArrayList