X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyMethods.java;h=d48db8d446ec877376f673c2da84fcdfbdfeca12;hb=7d44b232d0b61c02ef01d96d3db1d68744015bd7;hp=1dbcfa3ba002b5c6c74870c5962f138aa0213ed2;hpb=89f36e42fb462f8d7b59def3ead995fb16a87b59;p=jalview.git diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java index 1dbcfa3..d48db8d 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java @@ -58,76 +58,56 @@ import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.util.BasicDescriptiveStatistics; import org.forester.util.DescriptiveStatistics; -import org.forester.util.FailedConditionCheckException; import org.forester.util.ForesterUtil; public class PhylogenyMethods { - private static PhylogenyMethods _instance = null; - private PhylogenyNode _farthest_1 = null; - private PhylogenyNode _farthest_2 = null; - + //private static PhylogenyMethods _instance = null; + //private final PhylogenyNode _farthest_1 = null; + //private final PhylogenyNode _farthest_2 = null; private PhylogenyMethods() { // Hidden constructor. } - /** - * Calculates the distance between PhylogenyNodes node1 and node2. - * - * - * @param node1 - * @param node2 - * @return distance between node1 and node2 - */ - public double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) { - final PhylogenyNode lca = calculateLCA( node1, node2 ); - final PhylogenyNode n1 = node1; - final PhylogenyNode n2 = node2; - return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) ); - } - - public double calculateFurthestDistance( final Phylogeny phylogeny ) { - if ( phylogeny.getNumberOfExternalNodes() < 2 ) { - return 0.0; - } - _farthest_1 = null; - _farthest_2 = null; - PhylogenyNode node_1 = null; - PhylogenyNode node_2 = null; - double farthest_d = -Double.MAX_VALUE; - final PhylogenyMethods methods = PhylogenyMethods.getInstance(); - final List ext_nodes = phylogeny.getRoot().getAllExternalDescendants(); - for( int i = 1; i < ext_nodes.size(); ++i ) { - for( int j = 0; j < i; ++j ) { - final double d = methods.calculateDistance( ext_nodes.get( i ), ext_nodes.get( j ) ); - if ( d < 0.0 ) { - throw new RuntimeException( "distance cannot be negative" ); - } - if ( d > farthest_d ) { - farthest_d = d; - node_1 = ext_nodes.get( i ); - node_2 = ext_nodes.get( j ); - } - } - } - _farthest_1 = node_1; - _farthest_2 = node_2; - return farthest_d; - } - + // public double calculateFurthestDistance( final Phylogeny phylogeny ) { + // if ( phylogeny.getNumberOfExternalNodes() < 2 ) { + // return 0.0; + // } + // _farthest_1 = null; + // _farthest_2 = null; + // PhylogenyNode node_1 = null; + // PhylogenyNode node_2 = null; + // double farthest_d = -Double.MAX_VALUE; + // final PhylogenyMethods methods = PhylogenyMethods.getInstance(); + // final List ext_nodes = phylogeny.getRoot().getAllExternalDescendants(); + // for( int i = 1; i < ext_nodes.size(); ++i ) { + // for( int j = 0; j < i; ++j ) { + // final double d = methods.calculateDistance( ext_nodes.get( i ), ext_nodes.get( j ) ); + // if ( d < 0.0 ) { + // throw new RuntimeException( "distance cannot be negative" ); + // } + // if ( d > farthest_d ) { + // farthest_d = d; + // node_1 = ext_nodes.get( i ); + // node_2 = ext_nodes.get( j ); + // } + // } + // } + // _farthest_1 = node_1; + // _farthest_2 = node_2; + // return farthest_d; + // } @Override public Object clone() throws CloneNotSupportedException { throw new CloneNotSupportedException(); } - public PhylogenyNode getFarthestNode1() { - return _farthest_1; - } - - public PhylogenyNode getFarthestNode2() { - return _farthest_2; - } - + // public PhylogenyNode getFarthestNode1() { + // return _farthest_1; + // } + // public PhylogenyNode getFarthestNode2() { + // return _farthest_2; + // } public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) { final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { @@ -168,6 +148,21 @@ public class PhylogenyMethods { } /** + * Calculates the distance between PhylogenyNodes node1 and node2. + * + * + * @param node1 + * @param node2 + * @return distance between node1 and node2 + */ + public static double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) { + final PhylogenyNode lca = calculateLCA( node1, node2 ); + final PhylogenyNode n1 = node1; + final PhylogenyNode n2 = node2; + return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) ); + } + + /** * Returns the LCA of PhylogenyNodes node1 and node2. * * @@ -413,7 +408,7 @@ public class PhylogenyMethods { final ArrayList to_delete = new ArrayList(); for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) { final PhylogenyNode n = iter.next(); - if ( !n.isExternal() && ( n.getNumberOfDescendants() == 1 ) ) { + if ( ( !n.isExternal() ) && ( !n.isRoot() ) && ( n.getNumberOfDescendants() == 1 ) ) { to_delete.add( n ); } } @@ -550,13 +545,12 @@ public class PhylogenyMethods { return farthest; } - public static PhylogenyMethods getInstance() { - if ( PhylogenyMethods._instance == null ) { - PhylogenyMethods._instance = new PhylogenyMethods(); - } - return PhylogenyMethods._instance; - } - + // public static PhylogenyMethods getInstance() { + // if ( PhylogenyMethods._instance == null ) { + // PhylogenyMethods._instance = new PhylogenyMethods(); + // } + // return PhylogenyMethods._instance; + // } /** * Returns the largest confidence value found on phy. */ @@ -666,36 +660,77 @@ public class PhylogenyMethods { } public static void midpointRoot( final Phylogeny phylogeny ) { - if ( phylogeny.getNumberOfExternalNodes() < 2 ) { + if ( ( phylogeny.getNumberOfExternalNodes() < 2 ) || ( calculateMaxDistanceToRoot( phylogeny ) <= 0 ) ) { return; } - final PhylogenyMethods methods = getInstance(); - final double farthest_d = methods.calculateFurthestDistance( phylogeny ); - final PhylogenyNode f1 = methods.getFarthestNode1(); - final PhylogenyNode f2 = methods.getFarthestNode2(); - if ( farthest_d <= 0.0 ) { - return; - } - double x = farthest_d / 2.0; - PhylogenyNode n = f1; - if ( PhylogenyMethods.getDistance( f1, phylogeny.getRoot() ) < PhylogenyMethods.getDistance( f2, phylogeny - .getRoot() ) ) { - n = f2; - } - while ( ( x > n.getDistanceToParent() ) && !n.isRoot() ) { - x -= ( n.getDistanceToParent() > 0 ? n.getDistanceToParent() : 0 ); - n = n.getParent(); + int counter = 0; + final int total_nodes = phylogeny.getNodeCount(); + while ( true ) { + if ( ++counter > total_nodes ) { + throw new RuntimeException( "this should not have happened: midpoint rooting does not converge" ); + } + PhylogenyNode a = null; + double da = 0; + double db = 0; + for( int i = 0; i < phylogeny.getRoot().getNumberOfDescendants(); ++i ) { + final PhylogenyNode f = getFurthestDescendant( phylogeny.getRoot().getChildNode( i ) ); + final double df = getDistance( f, phylogeny.getRoot() ); + if ( df > 0 ) { + if ( df > da ) { + db = da; + da = df; + a = f; + } + else if ( df > db ) { + db = df; + } + } + } + final double diff = da - db; + if ( diff < 0.000001 ) { + break; + } + double x = da - ( diff / 2.0 ); + while ( ( x > a.getDistanceToParent() ) && !a.isRoot() ) { + x -= ( a.getDistanceToParent() > 0 ? a.getDistanceToParent() : 0 ); + a = a.getParent(); + } + phylogeny.reRoot( a, x ); } - phylogeny.reRoot( n, x ); phylogeny.recalculateNumberOfExternalDescendants( true ); - final PhylogenyNode a = getFurthestDescendant( phylogeny.getRoot().getChildNode1() ); - final PhylogenyNode b = getFurthestDescendant( phylogeny.getRoot().getChildNode2() ); - final double da = getDistance( a, phylogeny.getRoot() ); - final double db = getDistance( b, phylogeny.getRoot() ); - if ( Math.abs( da - db ) > 0.000001 ) { - throw new FailedConditionCheckException( "this should not have happened: midpoint rooting failed: da=" - + da + ", db=" + db + ", diff=" + Math.abs( da - db ) ); - } + } + + public static void midpointRootOLD( final Phylogeny phylogeny ) { + // if ( phylogeny.getNumberOfExternalNodes() < 2 ) { + // return; + // } + // final PhylogenyMethods methods = getInstance(); + //final double farthest_d = methods.calculateFurthestDistance( phylogeny ); + // final PhylogenyNode f1 = methods.getFarthestNode1(); + // final PhylogenyNode f2 = methods.getFarthestNode2(); + // if ( farthest_d <= 0.0 ) { + // return; + // } + // double x = farthest_d / 2.0; + // PhylogenyNode n = f1; + // if ( PhylogenyMethods.getDistance( f1, phylogeny.getRoot() ) < PhylogenyMethods.getDistance( f2, phylogeny + // .getRoot() ) ) { + // n = f2; + // } + // while ( ( x > n.getDistanceToParent() ) && !n.isRoot() ) { + // x -= ( n.getDistanceToParent() > 0 ? n.getDistanceToParent() : 0 ); + // n = n.getParent(); + // } + // phylogeny.reRoot( n, x ); + // phylogeny.recalculateNumberOfExternalDescendants( true ); + // final PhylogenyNode a = getFurthestDescendant( phylogeny.getRoot().getChildNode1() ); + // final PhylogenyNode b = getFurthestDescendant( phylogeny.getRoot().getChildNode2() ); + // final double da = getDistance( a, phylogeny.getRoot() ); + // final double db = getDistance( b, phylogeny.getRoot() ); + // if ( Math.abs( da - db ) > 0.000001 ) { + // throw new FailedConditionCheckException( "this should not have happened: midpoint rooting failed: da=" + // + da + ", db=" + db + ", diff=" + Math.abs( da - db ) ); + // } } public static void normalizeBootstrapValues( final Phylogeny phylogeny, @@ -879,9 +914,19 @@ public class PhylogenyMethods { public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) { if ( remove_me.isRoot() ) { - throw new IllegalArgumentException( "ill advised attempt to remove root node" ); + if ( remove_me.getNumberOfDescendants() == 1 ) { + final PhylogenyNode desc = remove_me.getDescendants().get( 0 ); + desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(), + desc.getDistanceToParent() ) ); + desc.setParent( null ); + phylogeny.setRoot( desc ); + phylogeny.clearHashIdToNodeMap(); + } + else { + throw new IllegalArgumentException( "attempt to remove a root node with more than one descendants" ); + } } - if ( remove_me.isExternal() ) { + else if ( remove_me.isExternal() ) { phylogeny.deleteSubtree( remove_me, false ); phylogeny.clearHashIdToNodeMap(); phylogeny.externalNodesHaveChanged();