Author: chinmoy
Date: 2009-06-26 15:22:16 -0700 (Fri, 26 Jun 2009)
New Revision: 17123
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
Log:
Split parser into smaller methods
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
2009-06-26 22:01:05 UTC (rev 17122)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
2009-06-26 22:22:16 UTC (rev 17123)
@@ -64,81 +64,83 @@
}
}
-
- /*
- * parse()
- * Traverses the tree string 'treeStr'and creates appropriate nodes and
edges
- */
- private void parse()
+
+ private List<String> convertTreeStringToList(String treeString)
{
- Stack <String> stack = new Stack<String>();
- Stack<PhylipNode> parentNodeStack = new Stack<PhylipNode>();
- List<String> list = new LinkedList<String>();
- List<PhylipNode> childNodeList = new LinkedList<PhylipNode>();
- // ChildNodeList records the children of a node for the purpose
of creating edges.
- // It is cleared after the edges for each node are created.
+ List<String> returnList = new LinkedList<String>();
+ // Split the tree string into a list
+ String [] substrings =
treeString.split(":|,|;");
- List<Double> branchLengthList = new LinkedList<Double>();
- // Reflects the ChildNodeList but records the edge lengths
instead of the child nodes.
+ // Parse the input into a list ignoring ',' but
adding names, lengths and parentheses
- // Iterators for lists
- Iterator<String> iterator;
- Iterator<PhylipNode> childNodeListIterator;
- Iterator<Double> branchLengthListIterator;
+ for(int i = 0; i<substrings.length; i++)
+ {
+ substrings[i] = substrings[i].trim();
- Double branchLength = 0.0;
+ // For every parenthesis encountered,
add it to the list
+ if (substrings[i].charAt(0) == '(')
+ {
+ returnList.add("(");
+ for (int k = 1;
k<substrings[i].length(); k++)
+ {
+
if(substrings[i].charAt(k) == '(')
+ {
+
returnList.add("(");
+ }
+ else
+ {
+ // Split the
remainder of the string around the '(' if a name is encountered
+ // Add the name
to the list
+ String[]
tempSub = substrings[i].split("\\(+");
- // Split the tree string into a list
- String [] substrings = treeStr.split(":|,|;");
+
returnList.add(tempSub[1]);
+ break;
- // Parse the input into a list ignoring ',' but adding names,
lengths and parentheses
+ }
+ }
+ }
- for(int i = 0; i<substrings.length; i++)
- {
- substrings[i] = substrings[i].trim();
+ // For every name/length encountered,
splice off the ')' and add it to the list
+ else if(substrings[i].charAt(0) != '('
&& substrings[i].charAt(0) != ')')
+ {
+ String[] tempSub2 =
substrings[i].split("\\)");
+ returnList.add(tempSub2[0]);
+ }
- // For every parenthesis encountered, add it to the list
- if (substrings[i].charAt(0) == '(')
- {
- list.add("(");
- for (int k = 1; k<substrings[i].length(); k++)
- {
- if(substrings[i].charAt(k) == '(')
+ // For every ')' encountered add it to
the list
+
if(substrings[i].charAt(substrings[i].length()-1)== ')')
{
- list.add("(");
+ returnList.add(")");
}
- else
- {
- // Split the remainder of the
string around the '(' if a name is encountered
- // Add the name to the list
- String[] tempSub =
substrings[i].split("\\(+");
+ }
- list.add(tempSub[1]);
- break;
+
+ return returnList;
+ }
- }
- }
- }
+ private void readListIntoStack(List<String> list)
+ {
+
+ Stack <String> stack = new Stack<String>();
+ Stack<PhylipNode> parentNodeStack = new Stack<PhylipNode>();
+
+ List<PhylipNode> childNodeList = new LinkedList<PhylipNode>();
+ // ChildNodeList records the children of a node for the purpose
of creating edges.
+ // It is cleared after the edges for each node are created.
- // For every name/length encountered, splice off the
')' and add it to the list
- else if(substrings[i].charAt(0) != '(' &&
substrings[i].charAt(0) != ')')
- {
- String[] tempSub2 = substrings[i].split("\\)");
- list.add(tempSub2[0]);
- }
+ List<Double> branchLengthList = new LinkedList<Double>();
+ // Reflects the ChildNodeList but records the edge lengths
instead of the child nodes.
- // For every ')' encountered add it to the list
- if(substrings[i].charAt(substrings[i].length()-1)== ')')
- {
- list.add(")");
- }
- }
+ // Iterators for lists
+ Iterator<String> iterator;
+ Iterator<PhylipNode> childNodeListIterator;
+ Iterator<Double> branchLengthListIterator;
- // Traverse the list into node and edge lists using a stack
+ Double branchLength = 0.0;
iterator = list.iterator();
int parentNodeIndex = 0;
@@ -248,8 +250,22 @@
}
}
- }
+ }
+ }
+ /*
+ * parse()
+ * Traverses the tree string 'treeStr'and reads it into a list
+ * Then reads the list into a stack creating nodes and edges when
required.
+ */
+ private void parse()
+ {
+
+ // Parse the treeStr into a list of subelements
+ List<String> list = convertTreeStringToList(treeStr);
+ // Traverse the list into node and edge lists using a stack
+ readListIntoStack(list);
+
}
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