import java.util.NoSuchElementException;
import java.util.Vector;
+import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.BranchData;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.SequenceRelation;
import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.ExternalForwardIterator;
import org.forester.phylogeny.iterators.LevelOrderTreeIterator;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
/**
* Adds this Phylogeny to the list of child nodes of PhylogenyNode parent
* and sets the parent of this to parent.
- *
+ *
* @param n
* the PhylogenyNode to add
*/
/**
* This calculates the height of the subtree emanating at n for rooted,
* tree-shaped phylogenies
- *
+ *
* @param n
* the root-node of a subtree
* @return the height of the subtree emanating at n
/**
* Need to call clearHashIdToNodeMap() afterwards (not done automatically
* to allow client multiple deletions in linear time).
- * Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this
+ * Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this
* if tree is to be displayed.
- *
+ *
* @param remove_us the parent node of the subtree to be deleted
*/
public void deleteSubtree( final PhylogenyNode remove_us, final boolean collapse_resulting_node_with_one_desc ) {
final int pi = p.getChildNodeIndex();
if ( removed_node.isFirstChildNode() ) {
p.getChildNode( 1 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
- .getDistanceToParent(), p.getChildNode( 1 ).getDistanceToParent() ) );
+ .getDistanceToParent(), p.getChildNode( 1 ).getDistanceToParent() ) );
pp.setChildNode( pi, p.getChildNode( 1 ) );
}
else {
p.getChildNode( 0 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
- .getDistanceToParent(), p.getChildNode( 0 ).getDistanceToParent() ) );
+ .getDistanceToParent(), p.getChildNode( 0 ).getDistanceToParent() ) );
pp.setChildNode( pi, p.getChildNode( 0 ) );
}
}
return _distance_unit;
}
+ public final static Phylogeny createInstanceFromNhxString( final String nhx ) throws IOException {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ return factory.create( nhx, new NHXParser() )[ 0 ];
+ }
+
/**
- *
+ *
* Warning. The order of the returned nodes is random
* -- and hence cannot be relied on.
- *
+ *
* @return Unordered set of PhylogenyNode
*/
public List<PhylogenyNode> getExternalNodes() {
/**
* Sets the number of duplications of this Phylogeny (int). A value of -1
* indicates that the number of duplications is unknown.
- *
+ *
* @param clean_nh
* set to true for clean NH format
*/
* height is the longest distance from the root to an external node. Please
* note. Child nodes of collapsed nodes are ignored -- which is useful for
* display purposes but might be misleading for other applications.
- *
+ *
* @return the height for rooted, tree-shaped phylogenies
*/
public double getHeight() {
/**
* Returns a PhylogenyNode of this Phylogeny which has a matching name.
* Throws an Exception if seqname is not present in this or not unique.
- *
+ *
* @param name
* name (String) of PhylogenyNode to find
* @return PhylogenyNode with matchin name
/**
* This is time-inefficient since it runs a iterator each time it is called.
- *
+ *
*/
public int getNodeCount() {
if ( isEmpty() ) {
/**
* Returns a List with references to all Nodes of this Phylogeny which have
* a matching name.
- *
+ *
* @param name
* name (String) of Nodes to find
* @return Vector of references to Nodes of this Phylogeny with matching
return nodes;
}
+ public List<PhylogenyNode> getNodesViaGeneName( final String seq_name ) {
+ if ( isEmpty() ) {
+ return null;
+ }
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getGeneName().equals( seq_name ) ) {
+ nodes.add( n );
+ }
+ }
+ return nodes;
+ }
+
public List<PhylogenyNode> getNodesViaTaxonomyCode( final String taxonomy_code ) {
if ( isEmpty() ) {
return null;
/**
* Returns a Vector with references to all Nodes of this Phylogeny which
* have a matching species name.
- *
+ *
* @param specname
* species name (String) of Nodes to find
* @return Vector of references to Nodes of this Phylogeny with matching
* <p>
* (Last modified: 11/22/00) Olivier CHABROL :
* olivier.chabrol@univ-provence.fr
- *
+ *
* @param n
* external PhylogenyNode whose orthologs are to be returned
* @return Vector of references to all orthologous Nodes of PhylogenyNode n
if ( node.isDuplication() && isContains( taxIdList, taxonomyCodeRangeList ) ) {
if ( node.getChildNode1() == prev ) {
v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode2()
- .getAllExternalDescendants() ) );
+ .getAllExternalDescendants() ) );
}
else {
v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode1()
- .getAllExternalDescendants() ) );
+ .getAllExternalDescendants() ) );
}
}
}
/**
* Returns whether this is a completely binary tree (i.e. all internal nodes
* are bifurcations).
- *
+ *
*/
public boolean isCompletelyBinary() {
if ( isEmpty() ) {
/**
* Checks whether a Phylogeny object is deleted (or empty).
- *
+ *
* @return true if the tree is deleted (or empty), false otherwise
*/
public boolean isEmpty() {
* Resets the ID numbers of the nodes of this Phylogeny in level order,
* starting with start_label (for the root). <br>
* WARNING. After this method has been called, node IDs are no longer
- * unique.
+ * unique.
*/
public void levelOrderReID() {
if ( isEmpty() ) {
* (Re)counts the number of children for each PhylogenyNode of this
* Phylogeny. As an example, this method needs to be called after a
* Phylogeny has been reRooted and it is to be displayed.
- *
+ *
* @param consider_collapsed_nodes
* set to true to take into account collapsed nodes (collapsed
* nodes have 1 child).
* <p>
* <li>recalculateNumberOfExternalDescendants(boolean)
* <li>recalculateAndReset()
- *
+ *
* @param id
* ID (int) of PhylogenyNode of this Phylogeny
*/
}
/**
- * Places the root of this Phylogeny on Branch b. The new root is always
- * placed on the middle of the branch b.
- *
- */
- public void reRoot( final PhylogenyBranch b ) {
- final PhylogenyNode n1 = b.getFirstNode();
- final PhylogenyNode n2 = b.getSecondNode();
- if ( n1.isExternal() ) {
- reRoot( n1 );
- }
- else if ( n2.isExternal() ) {
- reRoot( n2 );
- }
- else if ( ( n2 == n1.getChildNode1() ) || ( n2 == n1.getChildNode2() ) ) {
- reRoot( n2 );
- }
- else if ( ( n1 == n2.getChildNode1() ) || ( n1 == n2.getChildNode2() ) ) {
- reRoot( n1 );
- }
- else if ( ( n1.getParent() != null ) && n1.getParent().isRoot()
- && ( ( n1.getParent().getChildNode1() == n2 ) || ( n1.getParent().getChildNode2() == n2 ) ) ) {
- reRoot( n1 );
- }
- else {
- throw new IllegalArgumentException( "reRoot( Branch b ): b is not a branch." );
- }
- }
-
- /**
* Places the root of this Phylogeny on the parent branch PhylogenyNode n.
* The new root is always placed on the middle of the branch.
* <p>
* </ul>
* <p>
* (Last modified: 10/01/01)
- *
+ *
* @param n
* PhylogenyNode of this Phylogeny\
*/
}
else {
node.setDistanceToParent( ( c.getDistanceToParent() >= 0.0 ? c.getDistanceToParent() : 0.0 )
- + ( node.getDistanceToParent() >= 0.0 ? node.getDistanceToParent() : 0.0 ) );
+ + ( node.getDistanceToParent() >= 0.0 ? node.getDistanceToParent() : 0.0 ) );
}
if ( c.getBranchDataDirectly() != null ) {
node.setBranchData( ( BranchData ) c.getBranchDataDirectly().copy() );
}
public String toNewHampshire() {
- return toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+ return toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
}
- public String toNewHampshire( final boolean simple_nh,
- final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
+ public String toNewHampshire( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
try {
- return new PhylogenyWriter().toNewHampshire( this, simple_nh, true, nh_conversion_support_style )
- .toString();
+ return new PhylogenyWriter().toNewHampshire( this, true, nh_conversion_support_style ).toString();
}
catch ( final IOException e ) {
throw new Error( "this should not have happend: " + e.getMessage() );
// ---------------------------------------------------------
/**
* Converts this Phylogeny to a New Hampshire X (String) representation.
- *
+ *
* @return New Hampshire X (String) representation of this
* @see #toNewHampshireX()
*/
/**
* Return Node by TaxonomyId Olivier CHABROL :
* olivier.chabrol@univ-provence.fr
- *
+ *
* @param taxonomyID
* search taxonomy identifier
* @param nodes
/**
* 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
* Create a map [<PhylogenyNode, List<String>], 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
/**
* 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
git://source.jalview.org / jalview.git / blobdiff