// Copyright (C) 2000-2001 Washington University School of Medicine
// and Howard Hughes Medical Institute
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// 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;
* <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 {
/**
* 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
*/
* 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"
* <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
*/
* 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"
*/
* 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"
*/
/**
* 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() {
* </ul>
* <p>
* (Last modified: 10/01/01)
- *
+ *
* @param gene_tree
* a binary (except deepest node) gene Phylogeny
* @param species_tree
* 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,
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<Phylogeny> trees = new ArrayList<Phylogeny>();
Phylogeny[] tree_array = null;
List<PhylogenyBranch> branches = null;
final PhylogenyNode n = iter.next();
if ( n.isRoot() ) {
if ( ( n.getNumberOfDescendants() != 2 ) && ( n.getNumberOfDescendants() != 3 ) ) {
- throw new IllegalArgumentException( "attempt to run SDI on gene tree with "
- + n.getNumberOfDescendants() + " child nodes at its root" );
+ throw new SDIException( "gene tree has " + n.getNumberOfDescendants() + " descendents at its root" );
}
}
else if ( !n.isExternal() && ( n.getNumberOfDescendants() != 2 ) ) {
- throw new IllegalArgumentException( "attempt to run SDI on gene tree which is not completely binary [found node with "
- + n.getNumberOfDescendants() + " child nodes]" );
+ throw new SDIException( "gene tree is not completely binary" );
}
}
for( final PhylogenyNodeIterator iter = species_tree.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode n = iter.next();
if ( !n.isExternal() && ( n.getNumberOfDescendants() != 2 ) ) {
- throw new IllegalArgumentException( "attempt to run SDI with a species tree which is not completely binary (after stripping) [found node with "
- + n.getNumberOfDescendants() + " child nodes]" );
+ throw new SDIException( "species tree (after stripping) is not completely binary" );
}
}
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>();
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 );
}
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 );
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() ) ) {
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 ) );
git://source.jalview.org / jalview.git / blobdiff