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.
*
*
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,
}
private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
- final PhylogenyMethods pm = PhylogenyMethods.getInstance();
return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p1 = factory.create( "(((A:1,B:2,X:100)ab:3,C:4)abc:5,(D:7,(E:9,F:10)ef:8)def:6)r",
new NHXParser() )[ 0 ];
- final PhylogenyMethods pm = PhylogenyMethods.getInstance();
- if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
return false;
}
final Phylogeny p2 = factory.create( "((A:4,B:5,C:6)abc:1,(D:7,E:8,F:9)def:2,(G:10,H:11,I:12)ghi:3)r",
new NHXParser() )[ 0 ];
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
return false;
}
}
private static boolean testMidpointrooting() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.midpointRoot( t0 );
+ if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
+ return false;
+ }
+ if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
+ return false;
+ }
+ if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
+ 1 ) ) {
+ return false;
+ }
final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:4)CD:3[&&NHX:B=10])ABCD:0.5",
new NHXParser() )[ 0 ];
if ( !t1.isRooted() ) {
return false;
}
if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
+ System.exit( -1 );
return false;
}
if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
git://source.jalview.org / jalview.git / commitdiff