Menu
▾
▴
[Obo-svn-commit] SF.net SVN: obo:[2695] OBD-WS/trunk/src/org/obd/ws/util/TaxonTree.java
|
From: <car...@us...> - 2009-06-25 13:25:14
|
Revision: 2695
http://obo.svn.sourceforge.net/obo/?rev=2695&view=rev
Author: cartik73
Date: 2009-06-25 13:25:07 +0000 (Thu, 25 Jun 2009)
Log Message:
-----------
Cleaned up some code and changed some parameter names
Modified Paths:
--------------
OBD-WS/trunk/src/org/obd/ws/util/TaxonTree.java
Modified: OBD-WS/trunk/src/org/obd/ws/util/TaxonTree.java
===================================================================
--- OBD-WS/trunk/src/org/obd/ws/util/TaxonTree.java 2009-06-24 23:07:35 UTC (rev 2694)
+++ OBD-WS/trunk/src/org/obd/ws/util/TaxonTree.java 2009-06-25 13:25:07 UTC (rev 2695)
@@ -4,13 +4,14 @@
import java.io.IOException;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.List;
import java.util.Map;
import java.util.Set;
import org.obd.ws.util.dto.NodeDTO;
/**
- * This is a tree order for a group on taxa, with a root
+ * This is a tree order for a group of taxa, with a root
* (the MRCA of all the taxa), branches and leaves. At each node
* in the tree, the grouping of qualities exhibited by the taxa
* at and below that node are stored. So are the numbers of
@@ -21,13 +22,18 @@
public class TaxonTree {
private NodeDTO root;
- private Map<NodeDTO, Set<NodeDTO>> branchingPointsAndChildren;
private Set<NodeDTO> leaves;
+ /** This structure keeps track of branching points and their children.
+ * NOTE: The root */
+ private Map<NodeDTO, Set<NodeDTO>> parentToChildrenMap;
+
+ /**This structure keeps track of all the EQs exhibited by a node and its descendants */
private Map<NodeDTO, Map<NodeDTO, Set<NodeDTO>>> nodeToEQMap;
+ /** This structure keeps track of annotation counts for the node and its descendants **/
private Map<NodeDTO, Integer> nodeToAnnotationCountMap;
/** This has been added tp keep track of reif link ids - Cartik 061909*/
- private Map<NodeDTO, String[]> nodeToAnnotationMap;
+ private Map<NodeDTO, List<String>> nodeToReifIdsMap;
/*
* GETTERs and SETTERs
@@ -40,14 +46,6 @@
this.root = root;
}
- public Map<NodeDTO, Set<NodeDTO>> getBranchingPointsAndChildren() {
- return branchingPointsAndChildren;
- }
- public void setBranchingPointsAndChildren(
- Map<NodeDTO, Set<NodeDTO>> branchingPointsAndChidren) {
- this.branchingPointsAndChildren = branchingPointsAndChidren;
- }
-
public Set<NodeDTO> getLeaves() {
return leaves;
}
@@ -55,6 +53,15 @@
this.leaves = leaves;
}
+ public Map<NodeDTO, Set<NodeDTO>> getParentToChildrenMap() {
+ return parentToChildrenMap;
+ }
+ public void setParentToChildrenMap(
+ Map<NodeDTO, Set<NodeDTO>> parentToChildrenMap) {
+ this.parentToChildrenMap = parentToChildrenMap;
+ }
+
+
public Map<NodeDTO, Map<NodeDTO, Set<NodeDTO>>> getNodeToEQMap() {
return nodeToEQMap;
}
@@ -71,20 +78,22 @@
this.nodeToAnnotationCountMap = nodeToAnnotationCountMap;
}
- public Map<NodeDTO, String[]> getNodeToAnnotationMap() {
- return nodeToAnnotationMap;
+ public Map<NodeDTO, List<String>> getNodeToReifIdsMap() {
+ return nodeToReifIdsMap;
}
- public void setNodeToAnnotationMap(Map<NodeDTO, String[]> nodeToAnnotationMap) {
- this.nodeToAnnotationMap = nodeToAnnotationMap;
+ public void setNodeToReifIdsMap(Map<NodeDTO, List<String>> nodeToReifIdsMap) {
+ this.nodeToReifIdsMap = nodeToReifIdsMap;
}
+
/**
* The constructor simply initializes the branches, the leaves, the qualities to node
- * map and the node to annotation count map
+ * map, node to reif ids map and the node to annotation count map
*/
public TaxonTree(){
- branchingPointsAndChildren = new HashMap<NodeDTO, Set<NodeDTO>>();
+ parentToChildrenMap = new HashMap<NodeDTO, Set<NodeDTO>>();
leaves = new HashSet<NodeDTO>();
nodeToEQMap = new HashMap<NodeDTO, Map<NodeDTO, Set<NodeDTO>>>();
+ nodeToReifIdsMap = new HashMap<NodeDTO, List<String>>();
nodeToAnnotationCountMap = new HashMap<NodeDTO, Integer>();
}
@@ -94,11 +103,11 @@
* @CAUTION Hardcoded file path for writing out the taxonomy
* @param node - the node whose children are to printed along with the node
* itself
- * @param tabCt - the number of indents
- * @param bw - buffered reader which contains a pointer to a text file
+ * @param tabCt - the number of indents. used for formatting the output text
+ * @param writer - buffered writer which contains a pointer to a text file
* @throws IOException
*/
- public void printTaxonomy(NodeDTO node, int tabCt, BufferedWriter bw)
+ public void printTaxonomy(NodeDTO node, int tabCt, BufferedWriter writer)
throws IOException{
String tabs = "";
@@ -106,22 +115,22 @@
tabs += " ";
}
if(!this.getLeaves().contains(node)){//this is not a leaf node
- if(this.getBranchingPointsAndChildren().get(node) != null ){
- for(NodeDTO child : this.getBranchingPointsAndChildren().get(node)){
- bw.write(tabs + child.getId() + "\t" + child.getName() + "\n");
- bw.write(tabs + "Annotation Count: " + this.getNodeToAnnotationCountMap().get(child) + "\n");
+ if(this.getParentToChildrenMap().get(node) != null ){
+ for(NodeDTO child : this.getParentToChildrenMap().get(node)){
+ writer.write(tabs + child.getId() + "\t" + child.getName() + "\n");
+ writer.write(tabs + "Annotation Count: " + this.getNodeToAnnotationCountMap().get(child) + "\n");
if(this.getNodeToEQMap().containsKey(child)){
- Map<NodeDTO, Set<NodeDTO>> e2qMap = this.getNodeToEQMap().get(child);
- for(NodeDTO e : e2qMap.keySet()){
- bw.write(tabs + "Exhibits " + e.getName() + " that are: ");
- for(NodeDTO q : e2qMap.get(e)){
- bw.write(q.getName() + " ");
+ Map<NodeDTO, Set<NodeDTO>> eToQMap = this.getNodeToEQMap().get(child);
+ for(NodeDTO e : eToQMap.keySet()){
+ writer.write(tabs + "Exhibits " + e.getName() + " that are: ");
+ for(NodeDTO q : eToQMap.get(e)){
+ writer.write(q.getName() + " ");
}
- bw.write("\n");
+ writer.write("\n");
}
}
- printTaxonomy(child, tabCt + 1, bw);
+ printTaxonomy(child, tabCt + 1, writer);
}
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|