}\r
}\r
\r
+ public Hashtable getHiddenSequences()\r
+ {\r
+ return hiddenSequences;\r
+ }\r
+\r
public SequenceI getHiddenSequence(int alignmentIndex)\r
{\r
return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));\r
\r
return alignmentIndex ;\r
}\r
+\r
+ public AlignmentI getFullAlignment()\r
+ {\r
+ int isize = alignment.getHeight()+hiddenSequences.size();\r
+ SequenceI [] seq = new Sequence[isize];\r
+\r
+ Enumeration en = hiddenSequences.keys();\r
+ while(en.hasMoreElements())\r
+ {\r
+ Integer key = (Integer)en.nextElement();\r
+ seq[key.intValue()] = (SequenceI)hiddenSequences.get(key);\r
+ }\r
+\r
+ int index = 0;\r
+ for(int i=0; i<isize; i++)\r
+ {\r
+ if(seq[i]!=null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ seq[i] = alignment.getSequenceAt(index);\r
+ index++;\r
+ }\r
+\r
+ return new Alignment(seq);\r
+ }\r
+\r
+ public boolean isHidden(SequenceI seq)\r
+ {\r
+ return hiddenSequences.containsValue(seq);\r
+ }\r
}\r