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<PhylogenyNode> 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<PhylogenyNode> 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(); ) {
}
/**
+ * 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.
*
*
final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
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 );
}
}
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.
*/
}
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,
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();
git://source.jalview.org / jalview.git / blobdiff