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[jalview.git] / forester / java / src / org / forester / sdi / SDIR.java

diff --git a/forester/java/src/org/forester/sdi/SDIR.java b/forester/java/src/org/forester/sdi/SDIR.java
index ce7fc00..bc395c3 100644 (file)
--- 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;
  * <li>Mapping cost L <li>Phylogeny height - which is the largest distance from
  * root to external node (minimizing of which is the same as "midpoint rooting")
  * </ul>
- * 
+ *
  * @see SDIse
- * 
+ *
  * @see SDI
- * 
+ *
  * @author Christian M. Zmasek
  */
 public class SDIR {
@@ -76,7 +76,7 @@ public class SDIR {
     /**
      * Returns the number of differently rooted trees which minimize the
      * (rooting) "criterion" - as determined by method "infer".
-     * 
+     *
      * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
      * @return number of differently rooted trees which minimized the criterion
      */
@@ -97,7 +97,7 @@ public class SDIR {
      * not necessarily zero.
      * <p>
      * (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 {
      * <B>IMPORTANT </B>: 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.
      * <p>
      * (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.
      * <p>
      * (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 {
      * </ul>
      * <p>
      * (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,
@@ -222,7 +222,7 @@ public class SDIR {
                               final boolean return_trees,
                               int max_trees_to_return ) throws SDIException {
         init();
-        SDIse sdise = null;
+        SDI sdise = null;
         final ArrayList<Phylogeny> trees = new ArrayList<Phylogeny>();
         Phylogeny[] tree_array = null;
         List<PhylogenyBranch> branches = null;
@@ -282,7 +282,7 @@ public class SDIR {
         g.reRoot( g.getFirstExternalNode() );
         branches = SDIR.getBranchesInPreorder( g );
         if ( minimize_mapping_cost || minimize_sum_of_dup ) {
-            sdise = new SDIse( g, species_tree );
+            sdise = new SDI( g, species_tree );
             duplications = sdise.getDuplicationsSum();
         }
         final Set<PhylogenyBranch> used_root_placements = new HashSet<PhylogenyBranch>();
@@ -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 );
             }
@@ -418,7 +418,7 @@ public class SDIR {
                     height = height__diff[ 0 ];
                     diff = height__diff[ 1 ];
                     if ( Math.abs( diff ) < SDIR.ZERO_DIFF ) {
-                        sdise = new SDIse( g, species_tree );
+                        sdise = new SDI( g, species_tree );
                         min_duplications = sdise.getDuplicationsSum();
                         min_height = height;
                         min_diff = Math.abs( diff );
@@ -494,8 +494,8 @@ public class SDIR {
             branches.add( new PhylogenyBranch( t.getRoot().getChildNode1(), t.getRoot().getChildNode2() ) );
             return branches;
         }
-        final Set<Integer> one = new HashSet<Integer>();
-        final Set<Integer> two = new HashSet<Integer>();
+        final Set<Long> one = new HashSet<Long>();
+        final Set<Long> two = new HashSet<Long>();
         PhylogenyNode node = t.getRoot();
         while ( !node.isRoot() || !two.contains( node.getId() ) ) {
             if ( !node.isExternal() && !two.contains( node.getId() ) ) {
@@ -543,10 +543,10 @@ public class SDIR {
         double diff = 0.0;
         double height = 0.0;
         final double[] height_diff = new double[ 2 ];
-        final double l0 = t.calculateSubtreeHeight( t.getRoot().getChildNode( 0 ) );
-        final double l1 = t.calculateSubtreeHeight( t.getRoot().getChildNode( 1 ) );
+        final double l0 = t.calculateSubtreeHeight( t.getRoot().getChildNode( 0 ), false );
+        final double l1 = t.calculateSubtreeHeight( t.getRoot().getChildNode( 1 ), false );
         diff = l0 - l1;
-        height = t.getHeight();
+        height = t.calculateHeight(false);
         if ( d > 0.0 ) {
             if ( ( 2 * d ) > Math.abs( diff ) ) {
                 child0.setDistanceToParent( d - ( diff / 2.0 ) );