parse();
}
-
+ /**
+ * Attempt to read from the position where some other parsing process left off.
+ * @param source
+ * @throws IOException
+ */
+ public AlignFile(FileParse source) throws IOException
+ {
+ super(source);
+ initData();
+ parse();
+ }
/**
* Return the seqs Vector
*/
return seq.getDisplayId(jvSuffix);
}
/**
- * vector of String[] treeName, newickString pairs
+ * vector of String[] treeName, newickString pairs
*/
Vector newickStrings=null;
-
+
protected void addNewickTree(String treeName, String newickString)
{
if (newickStrings == null)
{
newickStrings = new Vector();
}
- newickStrings.add(new String[] { treeName, newickString});
+ newickStrings.addElement(new String[] { treeName, newickString});
}
protected int getTreeCount()