From f3578c8bca780191d23d36d3791d2ec2c0bf38ad Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 29 Jun 2012 17:36:11 +0000 Subject: [PATCH] forester 1.005 --- .../org/forester/analysis/TaxonomyDataManager.java | 2 +- .../forester/application/gene_tree_preprocess.java | 2 + .../java/src/org/forester/application/gsdi.java | 2 +- .../forester/application/phyloxml_converter.java | 2 +- .../src/org/forester/archaeopteryx/Constants.java | 6 +- .../org/forester/archaeopteryx/ControlPanel.java | 4 +- .../archaeopteryx/MainFrameApplication.java | 71 +++++--------------- .../src/org/forester/archaeopteryx/TreePanel.java | 12 ++-- .../java/src/org/forester/phylogeny/Phylogeny.java | 51 ++++++-------- .../org/forester/phylogeny/PhylogenyMethods.java | 16 +++-- forester/java/src/org/forester/sdi/GSDI.java | 4 ++ .../java/src/org/forester/tools/SupportCount.java | 2 +- .../src/org/forester/util/ForesterConstants.java | 4 +- 13 files changed, 68 insertions(+), 110 deletions(-) diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java index 2534792..fac9f85 100644 --- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java +++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java @@ -265,7 +265,7 @@ public final class TaxonomyDataManager extends RunnableProcess { phy.deleteSubtree( node, true ); } phy.externalNodesHaveChanged(); - phy.hashIDs(); + phy.clearHashIdToNodeMap(); phy.recalculateNumberOfExternalDescendants( true ); } return not_found; diff --git a/forester/java/src/org/forester/application/gene_tree_preprocess.java b/forester/java/src/org/forester/application/gene_tree_preprocess.java index d1fd58e..f755d91 100644 --- a/forester/java/src/org/forester/application/gene_tree_preprocess.java +++ b/forester/java/src/org/forester/application/gene_tree_preprocess.java @@ -86,6 +86,8 @@ public class gene_tree_preprocess { for( final String remove_me : not_found ) { phy.deleteSubtree( phy.getNode( remove_me ), true ); } + phy.clearHashIdToNodeMap(); + phy.externalNodesHaveChanged(); if ( phy.getNumberOfExternalNodes() < 2 ) { ForesterUtil.fatalError( PRG_NAME, "after removal of unresolvable external nodes, phylogeny has " diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index c137638..1fbcf63 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -74,7 +74,7 @@ public final class gsdi { final static private String REMAPPED_SUFFIX = "_gsdi_remapped.txt"; final static private String PRG_NAME = "gsdi"; final static private String PRG_VERSION = "1.000"; - final static private String PRG_DATE = "120608"; + final static private String PRG_DATE = "120629"; final static private String PRG_DESC = "general speciation duplication inference"; final static private String E_MAIL = "phylosoft@gmail.com"; final static private String WWW = "www.phylosoft.org/forester"; diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java index 151072f..25497ec 100644 --- a/forester/java/src/org/forester/application/phyloxml_converter.java +++ b/forester/java/src/org/forester/application/phyloxml_converter.java @@ -257,7 +257,7 @@ public class phyloxml_converter { for( final Phylogeny phy : phys ) { PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.TAXONOMY ); phy.externalNodesHaveChanged(); - phy.hashIDs(); + phy.clearHashIdToNodeMap(); phy.recalculateNumberOfExternalDescendants( true ); } } diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 512df89..18a09de 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -37,13 +37,13 @@ import org.forester.util.ForesterConstants; public final class Constants { final static boolean __ALLOW_PHYLOGENETIC_INFERENCE = true; - public final static boolean __RELEASE = false; // TODO remove me + public final static boolean __RELEASE = true; // TODO remove me public final static boolean __SNAPSHOT_RELEASE = false; // TODO remove me public final static boolean __SYNTH_LF = false; // TODO remove me public final static boolean ALLOW_DDBJ_BLAST = false; public final static String PRG_NAME = "Archaeopteryx"; - final static String VERSION = "0.971 9M"; - final static String PRG_DATE = "2012.04.16"; + final static String VERSION = "0.972 9M"; + final static String PRG_DATE = "2012.06.29"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Verdana", "Tahoma", "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 5bca398..55b0314 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -254,7 +254,7 @@ final class ControlPanel extends JPanel implements ActionListener { _order_of_appearance = !_order_of_appearance; tp.setNodeInPreorderToNull(); tp.getPhylogeny().externalNodesHaveChanged(); - tp.getPhylogeny().hashIDs(); + tp.getPhylogeny().clearHashIdToNodeMap(); tp.getPhylogeny().recalculateNumberOfExternalDescendants( true ); tp.resetNodeIdToDistToLeafMap(); tp.setEdited( true ); @@ -1820,7 +1820,7 @@ final class ControlPanel extends JPanel implements ActionListener { tp.updateSetOfCollapsedExternalNodes(); t.recalculateNumberOfExternalDescendants( false ); tp.setNodeInPreorderToNull(); - t.hashIDs(); + t.clearHashIdToNodeMap(); showWhole(); } } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 96febec..655383c 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -97,9 +97,7 @@ import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.sdi.GSDI; -import org.forester.sdi.SDI; import org.forester.sdi.SDIR; -import org.forester.sdi.SDIse; import org.forester.sequence.Sequence; import org.forester.util.BasicDescriptiveStatistics; import org.forester.util.BasicTable; @@ -203,7 +201,6 @@ public final class MainFrameApplication extends MainFrame { // Analysis menu private JMenu _analysis_menu; private JMenuItem _load_species_tree_item; - private JMenuItem _sdi_item; private JMenuItem _gsdi_item; private JMenuItem _root_min_dups_item; private JMenuItem _root_min_cost_l_item; @@ -531,12 +528,6 @@ public final class MainFrameApplication extends MainFrame { else if ( o == _load_species_tree_item ) { readSpeciesTreeFromFile(); } - else if ( o == _sdi_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - executeSDI(); - } else if ( o == _lineage_inference ) { if ( isSubtreeDisplayed() ) { JOptionPane.showMessageDialog( this, @@ -658,16 +649,12 @@ public final class MainFrameApplication extends MainFrame { void buildAnalysisMenu() { _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); - _analysis_menu.add( _sdi_item = new JMenuItem( "SDI (Speciation Duplication Inference)" ) ); - if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) { - _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); - } + _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); _analysis_menu.addSeparator(); _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) ); _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) ); _analysis_menu.addSeparator(); _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) ); - customizeJMenuItem( _sdi_item ); customizeJMenuItem( _gsdi_item ); customizeJMenuItem( _root_min_dups_item ); customizeJMenuItem( _root_min_cost_l_item ); @@ -1111,7 +1098,7 @@ public final class MainFrameApplication extends MainFrame { } if ( to_be_removed.size() > 0 ) { phy.externalNodesHaveChanged(); - phy.hashIDs(); + phy.clearHashIdToNodeMap(); phy.recalculateNumberOfExternalDescendants( true ); getCurrentTreePanel().resetNodeIdToDistToLeafMap(); getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); @@ -1210,23 +1197,29 @@ public final class MainFrameApplication extends MainFrame { gene_tree.setAllNodesToNotCollapse(); gene_tree.recalculateNumberOfExternalDescendants( false ); GSDI gsdi = null; - int duplications = -1; try { - gsdi = new GSDI( gene_tree, _species_tree.copy(), true, true, false ); - duplications = gsdi.getDuplicationsSum(); + gsdi = new GSDI( gene_tree, _species_tree.copy(), false, true, true ); } catch ( final Exception e ) { JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE ); } gene_tree.setRerootable( false ); _mainpanel.getCurrentTreePanel().setTree( gene_tree ); + _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap(); + _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true ); + _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + _mainpanel.getCurrentTreePanel().setEdited( true ); getControlPanel().setShowEvents( true ); showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( gsdi.getSpeciesTree(), getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); _mainpanel.getCurrentTreePanel().setEdited( true ); - JOptionPane.showMessageDialog( this, - "Number of duplications: " + duplications, - "GSDI successfully completed", - JOptionPane.INFORMATION_MESSAGE ); + JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: " + + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE ); } void executeFunctionAnalysis() { @@ -1294,40 +1287,6 @@ public final class MainFrameApplication extends MainFrame { } } - void executeSDI() { - if ( !isOKforSDI( true, true ) ) { - return; - } - if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { - JOptionPane.showMessageDialog( this, - "Gene tree is not rooted", - "Cannot execute SDI", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); - gene_tree.setAllNodesToNotCollapse(); - gene_tree.recalculateNumberOfExternalDescendants( false ); - SDI sdi = null; - int duplications = -1; - try { - sdi = new SDIse( gene_tree, _species_tree.copy() ); - duplications = sdi.getDuplicationsSum(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, e.toString(), "Error during SDI", JOptionPane.ERROR_MESSAGE ); - } - gene_tree.setRerootable( false ); - _mainpanel.getCurrentTreePanel().setTree( gene_tree ); - getControlPanel().setShowEvents( true ); - showWhole(); - _mainpanel.getCurrentTreePanel().setEdited( true ); - JOptionPane.showMessageDialog( this, - "Number of duplications: " + duplications, - "SDI successfully completed", - JOptionPane.INFORMATION_MESSAGE ); - } - void executeSDIR( final boolean minimize_cost ) { if ( !isOKforSDI( true, true ) ) { return; diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index e857426..befe375 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -411,7 +411,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } setNodeInPreorderToNull(); _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -882,7 +882,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee setCopiedAndPastedNodes( null ); setCutOrCopiedTree( _phylogeny.copy( node ) ); _phylogeny.deleteSubtree( node, true ); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -948,7 +948,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _phylogeny.deleteSubtree( node, true ); } _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -4243,7 +4243,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getCopiedAndPastedNodes().addAll( node_ids ); setNodeInPreorderToNull(); _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -4956,7 +4956,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee node.swapChildren(); setNodeInPreorderToNull(); _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -4980,7 +4980,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee PhylogenyMethods.sortNodeDescendents( node, pri ); setNodeInPreorderToNull(); _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java index b1677b1..a4102d2 100644 --- a/forester/java/src/org/forester/phylogeny/Phylogeny.java +++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java @@ -68,7 +68,7 @@ public class Phylogeny { private Confidence _confidence; private Identifier _identifier; private boolean _rerootable; - private HashMap _idhash; + private HashMap _id_to_node_map; private List _external_nodes_set; private Collection _sequenceRelationQueries; private Collection _relevant_sequence_relation_types; @@ -213,7 +213,7 @@ public class Phylogeny { } /** - * Need the delete and/or rehash _idhash (not done automatically + * Need to call clearHashIdToNodeMap() afterwards (not done automatically * to allow client multiple deletions in linear time). * Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this * if tree is to be displayed. @@ -269,7 +269,6 @@ public class Phylogeny { } } remove_us.removeConnections(); - setIdHash( null ); externalNodesHaveChanged(); } @@ -376,11 +375,8 @@ public class Phylogeny { return _identifier; } - // --------------------------------------------------------- - // Modification of Phylogeny topology and Phylogeny appearance - // --------------------------------------------------------- - private HashMap getIdHash() { - return _idhash; + private HashMap getIdToNodeMap() { + return _id_to_node_map; } /** @@ -392,29 +388,16 @@ public class Phylogeny { /** * Finds the PhylogenyNode of this Phylogeny which has a matching ID number. - * Takes O(n) time. After method hashIDs() has been called it runs in - * constant time. - * - * @param id - * ID number (int) of the PhylogenyNode to find * @return PhylogenyNode with matching ID, null if not found */ public PhylogenyNode getNode( final int id ) throws NoSuchElementException { if ( isEmpty() ) { throw new NoSuchElementException( "attempt to get node in an empty phylogeny" ); } - if ( _idhash != null ) { - return _idhash.get( id ); - } - else { - for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); - if ( node.getId() == id ) { - return node; - } - } + if ( ( getIdToNodeMap() == null ) || getIdToNodeMap().isEmpty() ) { + reHashIdToNodeMap(); } - return null; + return getIdToNodeMap().get( id ); } /** @@ -724,17 +707,21 @@ public class Phylogeny { * constant time. Important: The user is responsible for calling this method * (again) after this Phylogeny has been changed/created/renumbered. */ - public void hashIDs() { + private void reHashIdToNodeMap() { if ( isEmpty() ) { return; } - setIdHash( new HashMap() ); + setIdToNodeMap( new HashMap() ); for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) { final PhylogenyNode node = iter.next(); - getIdHash().put( node.getId(), node ); + getIdToNodeMap().put( node.getId(), node ); } } + public void clearHashIdToNodeMap() { + setIdToNodeMap( null ); + } + /** * Deletes this Phylogeny. */ @@ -745,7 +732,7 @@ public class Phylogeny { _description = ""; _type = ""; _distance_unit = ""; - _idhash = null; + _id_to_node_map = null; _confidence = null; _identifier = null; _rerootable = true; @@ -849,7 +836,7 @@ public class Phylogeny { if ( isEmpty() ) { return; } - _idhash = null; + _id_to_node_map = null; int max = 0; for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); ) { final PhylogenyNode node = it.next(); @@ -870,7 +857,7 @@ public class Phylogeny { if ( isEmpty() ) { return; } - setIdHash( null ); + setIdToNodeMap( null ); int i = PhylogenyNode.getNodeCount(); for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); ) { it.next().setId( i++ ); @@ -1165,8 +1152,8 @@ public class Phylogeny { _identifier = identifier; } - void setIdHash( final HashMap idhash ) { - _idhash = idhash; + private void setIdToNodeMap( final HashMap idhash ) { + _id_to_node_map = idhash; } /** diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java index 1a1a19d..b154b48 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java @@ -751,11 +751,12 @@ public class PhylogenyMethods { } public static void deleteExternalNodesNegativeSelection( final Set to_delete, final Phylogeny phy ) { - phy.hashIDs(); + phy.clearHashIdToNodeMap(); for( final Integer id : to_delete ) { phy.deleteSubtree( phy.getNode( id ), true ); } - phy.hashIDs(); + phy.clearHashIdToNodeMap(); + phy.externalNodesHaveChanged(); } public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p ) @@ -776,6 +777,8 @@ public class PhylogenyMethods { p.deleteSubtree( n, true ); } } + p.clearHashIdToNodeMap(); + p.externalNodesHaveChanged(); } public static void deleteExternalNodesPositiveSelection( final Set species_to_keep, final Phylogeny phy ) { @@ -792,9 +795,8 @@ public class PhylogenyMethods { throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" ); } } - phy.hashIDs(); + phy.clearHashIdToNodeMap(); phy.externalNodesHaveChanged(); - // deleteExternalNodesNegativeSelection( to_delete, phy ); } public static List deleteExternalNodesPositiveSelection( final String[] node_names_to_keep, @@ -1286,6 +1288,8 @@ public class PhylogenyMethods { } if ( remove_me.isExternal() ) { phylogeny.deleteSubtree( remove_me, false ); + phylogeny.clearHashIdToNodeMap(); + phylogeny.externalNodesHaveChanged(); } else { final PhylogenyNode parent = remove_me.getParent(); @@ -1297,7 +1301,7 @@ public class PhylogenyMethods { desc.getDistanceToParent() ) ); } remove_me.setParent( null ); - phylogeny.setIdHash( null ); + phylogeny.clearHashIdToNodeMap(); phylogeny.externalNodesHaveChanged(); } } @@ -1613,6 +1617,8 @@ public class PhylogenyMethods { for( final PhylogenyNode phylogenyNode : nodes_to_delete ) { to_be_stripped.deleteSubtree( phylogenyNode, true ); } + to_be_stripped.clearHashIdToNodeMap(); + to_be_stripped.externalNodesHaveChanged(); return nodes_to_delete.size(); } diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java index 1639bbe..8629acb 100644 --- a/forester/java/src/org/forester/sdi/GSDI.java +++ b/forester/java/src/org/forester/sdi/GSDI.java @@ -354,6 +354,8 @@ public final class GSDI extends SDI { _stripped_species_tree_nodes.add( s ); } } + _species_tree.clearHashIdToNodeMap(); + _species_tree.externalNodesHaveChanged(); } public List getStrippedSpeciesTreeNodes() { @@ -364,6 +366,8 @@ public final class GSDI extends SDI { for( final PhylogenyNode g : _stripped_gene_tree_nodes ) { _gene_tree.deleteSubtree( g, true ); } + _gene_tree.clearHashIdToNodeMap(); + _gene_tree.externalNodesHaveChanged(); } public Set getMappedExternalSpeciesTreeNodes() { diff --git a/forester/java/src/org/forester/tools/SupportCount.java b/forester/java/src/org/forester/tools/SupportCount.java index e542c5e..5c8e924 100644 --- a/forester/java/src/org/forester/tools/SupportCount.java +++ b/forester/java/src/org/forester/tools/SupportCount.java @@ -205,7 +205,7 @@ public final class SupportCount { // phylos are saved // to file. evaluator_phylogeny.externalNodesHaveChanged(); - evaluator_phylogeny.hashIDs(); + evaluator_phylogeny.clearHashIdToNodeMap(); evaluator_phylogeny.recalculateNumberOfExternalDescendants( true ); } final double s = SupportCount.compare( phylogeny, diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java index cb21569..4cfd40a 100644 --- a/forester/java/src/org/forester/util/ForesterConstants.java +++ b/forester/java/src/org/forester/util/ForesterConstants.java @@ -27,8 +27,8 @@ package org.forester.util; public final class ForesterConstants { - public final static String FORESTER_VERSION = "1.004"; - public final static String FORESTER_DATE = "120619"; + public final static String FORESTER_VERSION = "1.005"; + public final static String FORESTER_DATE = "120629"; public final static String PHYLO_XML_VERSION = "1.10"; public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org"; public final static String PHYLO_XML_XSD = "phyloxml.xsd"; -- 1.7.10.2