X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogeny.java;h=3d94dd72ab5061be72b9b7e310919d7e6f0c8108;hb=3b40e07c1b3964dee89b5d24209946ac54a5e21f;hp=115e88512c60745e05b464c1193695de332419ec;hpb=c956545c704f53df5c8711ede20e786641bfc7be;p=jalview.git diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java index 115e885..3d94dd7 100644 --- a/forester/java/src/org/forester/phylogeny/Phylogeny.java +++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java @@ -86,7 +86,7 @@ public class Phylogeny { /** * 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 */ @@ -126,7 +126,7 @@ public class Phylogeny { /** * 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 @@ -222,9 +222,9 @@ public class Phylogeny { /** * 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 ) { @@ -261,12 +261,12 @@ public class Phylogeny { 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 ) ); } } @@ -313,10 +313,10 @@ public class Phylogeny { } /** - * + * * Warning. The order of the returned nodes is random * -- and hence cannot be relied on. - * + * * @return Unordered set of PhylogenyNode */ public List getExternalNodes() { @@ -342,7 +342,7 @@ public class Phylogeny { /** * 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 */ @@ -373,7 +373,7 @@ public class Phylogeny { * 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() { @@ -411,7 +411,7 @@ public class Phylogeny { /** * 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 @@ -432,7 +432,7 @@ public class Phylogeny { /** * This is time-inefficient since it runs a iterator each time it is called. - * + * */ public int getNodeCount() { if ( isEmpty() ) { @@ -448,7 +448,7 @@ public class Phylogeny { /** * 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 @@ -529,7 +529,7 @@ public class Phylogeny { /** * 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 @@ -629,7 +629,7 @@ public class Phylogeny { *

* (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 @@ -658,11 +658,11 @@ public class Phylogeny { 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() ) ); } } } @@ -711,7 +711,7 @@ public class Phylogeny { /** * Returns whether this is a completely binary tree (i.e. all internal nodes * are bifurcations). - * + * */ public boolean isCompletelyBinary() { if ( isEmpty() ) { @@ -728,7 +728,7 @@ public class Phylogeny { /** * Checks whether a Phylogeny object is deleted (or empty). - * + * * @return true if the tree is deleted (or empty), false otherwise */ public boolean isEmpty() { @@ -770,7 +770,7 @@ public class Phylogeny { * Resets the ID numbers of the nodes of this Phylogeny in level order, * starting with start_label (for the root).
* WARNING. After this method has been called, node IDs are no longer - * unique. + * unique. */ public void levelOrderReID() { if ( isEmpty() ) { @@ -810,7 +810,7 @@ public class Phylogeny { * (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). @@ -843,7 +843,7 @@ public class Phylogeny { *

*

  • recalculateNumberOfExternalDescendants(boolean) *
  • recalculateAndReset() - * + * * @param id * ID (int) of PhylogenyNode of this Phylogeny */ @@ -863,7 +863,7 @@ public class Phylogeny { * *

    * (Last modified: 10/01/01) - * + * * @param n * PhylogenyNode of this Phylogeny\ */ @@ -995,7 +995,7 @@ public class 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() ); @@ -1146,7 +1146,7 @@ public class Phylogeny { // --------------------------------------------------------- /** * Converts this Phylogeny to a New Hampshire X (String) representation. - * + * * @return New Hampshire X (String) representation of this * @see #toNewHampshireX() */ @@ -1180,7 +1180,7 @@ public class Phylogeny { /** * Return Node by TaxonomyId Olivier CHABROL : * olivier.chabrol@univ-provence.fr - * + * * @param taxonomyID * search taxonomy identifier * @param nodes @@ -1200,7 +1200,7 @@ public class Phylogeny { /** * 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 @@ -1223,7 +1223,7 @@ public class Phylogeny { * 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 @@ -1246,7 +1246,7 @@ 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