X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogeny.java;h=038ea8bf8199f510b9528beb97c82f2b10db0f4b;hb=45081fca2f4b6ba45ebc5026450980afb8340911;hp=a4102d20377f63f79e92bc4233374664724d4273;hpb=f3578c8bca780191d23d36d3791d2ec2c0bf38ad;p=jalview.git
diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index a4102d2..038ea8b 100644
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -39,7 +39,7 @@ import java.util.NoSuchElementException;
import java.util.Vector;
import org.forester.io.writers.PhylogenyWriter;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.BranchData;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Identifier;
@@ -144,6 +144,10 @@ public class Phylogeny {
}
}
+ public void clearHashIdToNodeMap() {
+ setIdToNodeMap( null );
+ }
+
/**
* Returns a deep copy of this Phylogeny.
*
@@ -155,60 +159,60 @@ public class Phylogeny {
}
/**
- * Returns a shallow copy of this Phylogeny.
+ * Returns a deep copy of this Phylogeny.
*
* (The resulting Phylogeny has its references in the external nodes
* corrected, if they are lacking/obsolete in this.)
*/
- public Phylogeny copyShallow() {
- return copyShallow( _root );
- }
-
- public Phylogeny copyShallow( final PhylogenyNode source ) {
+ public Phylogeny copy( final PhylogenyNode source ) {
final Phylogeny tree = new Phylogeny();
if ( isEmpty() ) {
tree.init();
return tree;
}
tree._rooted = _rooted;
- tree._name = _name;
- tree._description = _description;
- tree._type = _type;
+ tree._name = new String( _name );
+ tree._description = new String( _description );
+ tree._type = new String( _type );
tree._rerootable = _rerootable;
- tree._distance_unit = _distance_unit;
- tree._confidence = _confidence;
- tree._identifier = _identifier;
+ tree._distance_unit = new String( _distance_unit );
+ if ( _confidence != null ) {
+ tree._confidence = ( Confidence ) _confidence.copy();
+ }
+ if ( _identifier != null ) {
+ tree._identifier = ( Identifier ) _identifier.copy();
+ }
tree.setAllowMultipleParents( isAllowMultipleParents() );
- tree._root = PhylogenyMethods.copySubTreeShallow( source );
+ tree._root = PhylogenyMethods.copySubTree( source );
return tree;
}
/**
- * Returns a deep copy of this Phylogeny.
+ * Returns a shallow copy of this Phylogeny.
*
* (The resulting Phylogeny has its references in the external nodes
* corrected, if they are lacking/obsolete in this.)
*/
- public Phylogeny copy( final PhylogenyNode source ) {
+ public Phylogeny copyShallow() {
+ return copyShallow( _root );
+ }
+
+ public Phylogeny copyShallow( final PhylogenyNode source ) {
final Phylogeny tree = new Phylogeny();
if ( isEmpty() ) {
tree.init();
return tree;
}
tree._rooted = _rooted;
- tree._name = new String( _name );
- tree._description = new String( _description );
- tree._type = new String( _type );
+ tree._name = _name;
+ tree._description = _description;
+ tree._type = _type;
tree._rerootable = _rerootable;
- tree._distance_unit = new String( _distance_unit );
- if ( _confidence != null ) {
- tree._confidence = ( Confidence ) _confidence.copy();
- }
- if ( _identifier != null ) {
- tree._identifier = ( Identifier ) _identifier.copy();
- }
+ tree._distance_unit = _distance_unit;
+ tree._confidence = _confidence;
+ tree._identifier = _identifier;
tree.setAllowMultipleParents( isAllowMultipleParents() );
- tree._root = PhylogenyMethods.copySubTree( source );
+ tree._root = PhylogenyMethods.copySubTreeShallow( source );
return tree;
}
@@ -375,10 +379,6 @@ public class Phylogeny {
return _identifier;
}
- private HashMap getIdToNodeMap() {
- return _id_to_node_map;
- }
-
/**
* Returns the name of this Phylogeny.
*/
@@ -414,32 +414,27 @@ public class Phylogeny {
}
final List nodes = getNodes( name );
if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
- throw new IllegalArgumentException( "node named [" + name + "] not found" );
+ throw new IllegalArgumentException( "node named \"" + name + "\" not found" );
}
if ( nodes.size() > 1 ) {
- throw new IllegalArgumentException( "node named [" + name + "] not unique" );
+ throw new IllegalArgumentException( "node named \"" + name + "\" not unique" );
}
return nodes.get( 0 );
}
/**
- * Return Node by TaxonomyId Olivier CHABROL :
- * olivier.chabrol@univ-provence.fr
+ * This is time-inefficient since it runs a iterator each time it is called.
*
- * @param taxonomyID
- * search taxonomy identifier
- * @param nodes
- * sublist node to search
- * @return List node with the same taxonomy identifier
*/
- private List getNodeByTaxonomyID( final String taxonomyID, final List nodes ) {
- final List retour = new ArrayList();
- for( final PhylogenyNode node : nodes ) {
- if ( taxonomyID.equals( PhylogenyMethods.getTaxonomyIdentifier( node ) ) ) {
- retour.add( node );
- }
+ public int getNodeCount() {
+ if ( isEmpty() ) {
+ return 0;
}
- return retour;
+ int c = 0;
+ for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); it.next() ) {
+ ++c;
+ }
+ return c;
}
/**
@@ -547,21 +542,6 @@ public class Phylogeny {
return nodes.get( 0 );
}
- /**
- * This is time-inefficient since it runs a iterator each time it is called.
- *
- */
- public int getNodeCount() {
- if ( isEmpty() ) {
- return 0;
- }
- int c = 0;
- for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); it.next() ) {
- ++c;
- }
- return c;
- }
-
public int getNumberOfBranches() {
if ( isEmpty() ) {
return 0;
@@ -655,74 +635,11 @@ public class Phylogeny {
return _sequenceRelationQueries;
}
- /**
- * List all species contains in all leaf under a node Olivier CHABROL :
- * olivier.chabrol@univ-provence.fr
- *
- * @param node
- * PhylogenyNode whose sub node species are returned
- * @return species contains in all leaf under the param node
- */
- private List getSubNodeTaxonomy( final PhylogenyNode node ) {
- final List taxonomyList = new ArrayList();
- final List childs = node.getAllExternalDescendants();
- String speciesId = null;
- for( final PhylogenyNode phylogenyNode : childs ) {
- // taxId = new Long(phylogenyNode.getTaxonomyID());
- speciesId = PhylogenyMethods.getTaxonomyIdentifier( phylogenyNode );
- if ( !taxonomyList.contains( speciesId ) ) {
- taxonomyList.add( speciesId );
- }
- }
- return taxonomyList;
- }
-
- /**
- * Create a map [], the list contains the
- * species contains in all leaf under phylogeny node Olivier CHABROL :
- * olivier.chabrol@univ-provence.fr
- *
- * @param node
- * the tree root node
- * @param map
- * map to fill
- */
- private void getTaxonomyMap( final PhylogenyNode node, final Map> map ) {
- // node is leaf
- if ( node.isExternal() ) {
- return;
- }
- map.put( node, getSubNodeTaxonomy( node ) );
- getTaxonomyMap( node.getChildNode1(), map );
- getTaxonomyMap( node.getChildNode2(), map );
- }
-
public String getType() {
return _type;
}
/**
- * Hashes the ID number of each PhylogenyNode of this Phylogeny to its
- * corresponding PhylogenyNode, in order to make method getNode( id ) run in
- * constant time. Important: The user is responsible for calling this method
- * (again) after this Phylogeny has been changed/created/renumbered.
- */
- private void reHashIdToNodeMap() {
- if ( isEmpty() ) {
- return;
- }
- setIdToNodeMap( new HashMap() );
- for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- getIdToNodeMap().put( node.getId(), node );
- }
- }
-
- public void clearHashIdToNodeMap() {
- setIdToNodeMap( null );
- }
-
- /**
* Deletes this Phylogeny.
*/
public void init() {
@@ -739,10 +656,6 @@ public class Phylogeny {
setAllowMultipleParents( Phylogeny.ALLOW_MULTIPLE_PARENTS_DEFAULT );
}
- private boolean isAllowMultipleParents() {
- return _allow_multiple_parents;
- }
-
/**
* Returns whether this is a completely binary tree (i.e. all internal nodes
* are bifurcations).
@@ -762,31 +675,6 @@ public class Phylogeny {
}
/**
- * Util method to check if all element of a list is contains in the
- * rangeList. Olivier CHABROL : olivier.chabrol@univ-provence.fr
- *
- * @param list
- * list to be check
- * @param rangeList
- * the range list to compare
- * @return true if all param list element are contains in param
- * rangeList, false otherwise.
- */
- private boolean isContains( final List list, final List rangeList ) {
- if ( list.size() > rangeList.size() ) {
- return false;
- }
- String l = null;
- for( final Iterator iterator = list.iterator(); iterator.hasNext(); ) {
- l = iterator.next();
- if ( !rangeList.contains( l ) ) {
- return false;
- }
- }
- return true;
- }
-
- /**
* Checks whether a Phylogeny object is deleted (or empty).
*
* @return true if the tree is deleted (or empty), false otherwise
@@ -853,18 +741,6 @@ public class Phylogeny {
PhylogenyNode.setNodeCount( max + 1 );
}
- public void preOrderReId() {
- if ( isEmpty() ) {
- return;
- }
- setIdToNodeMap( null );
- int i = PhylogenyNode.getNodeCount();
- for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); ) {
- it.next().setId( i++ );
- }
- PhylogenyNode.setNodeCount( i );
- }
-
/**
* Prints descriptions of all external Nodes of this Phylogeny to
* System.out.
@@ -1132,10 +1008,6 @@ public class Phylogeny {
}
}
- private void setAllowMultipleParents( final boolean allow_multiple_parents ) {
- _allow_multiple_parents = allow_multiple_parents;
- }
-
public void setConfidence( final Confidence confidence ) {
_confidence = confidence;
}
@@ -1152,7 +1024,7 @@ public class Phylogeny {
_identifier = identifier;
}
- private void setIdToNodeMap( final HashMap idhash ) {
+ public void setIdToNodeMap( final HashMap idhash ) {
_id_to_node_map = idhash;
}
@@ -1226,6 +1098,10 @@ public class Phylogeny {
}
}
+ public String toNexus() {
+ return toNexus( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+ }
+
public String toNexus( final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) {
try {
return new PhylogenyWriter().toNexus( this, svs ).toString();
@@ -1235,10 +1111,6 @@ public class Phylogeny {
}
}
- public String toNexus() {
- return toNexus( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
- }
-
public String toPhyloXML( final int phyloxml_level ) {
try {
return new PhylogenyWriter().toPhyloXML( this, phyloxml_level ).toString();
@@ -1279,4 +1151,120 @@ public class Phylogeny {
setRooted( false );
return;
} // unRoot()
+
+ private HashMap getIdToNodeMap() {
+ return _id_to_node_map;
+ }
+
+ /**
+ * Return Node by TaxonomyId Olivier CHABROL :
+ * olivier.chabrol@univ-provence.fr
+ *
+ * @param taxonomyID
+ * search taxonomy identifier
+ * @param nodes
+ * sublist node to search
+ * @return List node with the same taxonomy identifier
+ */
+ private List getNodeByTaxonomyID( final String taxonomyID, final List nodes ) {
+ final List retour = new ArrayList();
+ for( final PhylogenyNode node : nodes ) {
+ if ( taxonomyID.equals( PhylogenyMethods.getTaxonomyIdentifier( node ) ) ) {
+ retour.add( node );
+ }
+ }
+ return retour;
+ }
+
+ /**
+ * List all species contains in all leaf under a node Olivier CHABROL :
+ * olivier.chabrol@univ-provence.fr
+ *
+ * @param node
+ * PhylogenyNode whose sub node species are returned
+ * @return species contains in all leaf under the param node
+ */
+ private List getSubNodeTaxonomy( final PhylogenyNode node ) {
+ final List taxonomyList = new ArrayList();
+ final List childs = node.getAllExternalDescendants();
+ String speciesId = null;
+ for( final PhylogenyNode phylogenyNode : childs ) {
+ // taxId = new Long(phylogenyNode.getTaxonomyID());
+ speciesId = PhylogenyMethods.getTaxonomyIdentifier( phylogenyNode );
+ if ( !taxonomyList.contains( speciesId ) ) {
+ taxonomyList.add( speciesId );
+ }
+ }
+ return taxonomyList;
+ }
+
+ /**
+ * Create a map [], the list contains the
+ * species contains in all leaf under phylogeny node Olivier CHABROL :
+ * olivier.chabrol@univ-provence.fr
+ *
+ * @param node
+ * the tree root node
+ * @param map
+ * map to fill
+ */
+ private void getTaxonomyMap( final PhylogenyNode node, final Map> map ) {
+ // node is leaf
+ if ( node.isExternal() ) {
+ return;
+ }
+ map.put( node, getSubNodeTaxonomy( node ) );
+ getTaxonomyMap( node.getChildNode1(), map );
+ getTaxonomyMap( node.getChildNode2(), map );
+ }
+
+ private boolean isAllowMultipleParents() {
+ return _allow_multiple_parents;
+ }
+
+ /**
+ * Util method to check if all element of a list is contains in the
+ * rangeList. Olivier CHABROL : olivier.chabrol@univ-provence.fr
+ *
+ * @param list
+ * list to be check
+ * @param rangeList
+ * the range list to compare
+ * @return true if all param list element are contains in param
+ * rangeList, false otherwise.
+ */
+ private boolean isContains( final List list, final List rangeList ) {
+ if ( list.size() > rangeList.size() ) {
+ return false;
+ }
+ String l = null;
+ for( final Iterator iterator = list.iterator(); iterator.hasNext(); ) {
+ l = iterator.next();
+ if ( !rangeList.contains( l ) ) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Hashes the ID number of each PhylogenyNode of this Phylogeny to its
+ * corresponding PhylogenyNode, in order to make method getNode( id ) run in
+ * constant time. Important: The user is responsible for calling this method
+ * (again) after this Phylogeny has been changed/created/renumbered.
+ */
+ private void reHashIdToNodeMap() {
+ if ( isEmpty() ) {
+ return;
+ }
+ setIdToNodeMap( new HashMap() );
+ for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ getIdToNodeMap().put( node.getId(), node );
+ }
+ }
+
+ private void setAllowMultipleParents( final boolean allow_multiple_parents ) {
+ _allow_multiple_parents = allow_multiple_parents;
+ }
}