- public void UpdateSequenceTreeMap(TreePanel tp)\r
- {\r
- if (tp==null || tree!=null)\r
- return;\r
- Vector leaves = new Vector();\r
- tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);\r
- Treenode[] tn = tree.getTreenode(); // todo: select nodes for this particular tree\r
- int sz = tn.length;\r
- int i = 0;\r
- \r
- while (i < sz)\r
- {\r
- Treenode node = tn[i++];\r
- BinaryNode mappednode = findNodeSpec(node.getNodespec(),leaves);\r
- if (mappednode!=null && mappednode instanceof SequenceNode) {\r
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
- // check if we can make the specified association\r
- Object jvseq = null;\r
- int vrf=0,refv=0;\r
- while (jvseq==null && vrf<node.getVrefCount())\r
- {\r
- if (refv<node.getVref(vrf).getRefsCount())\r
- {\r
- Object noderef = node.getVref(vrf).getRefs(refv++);\r
- if (noderef instanceof AlignmentSequence)\r
- {\r
- // we only make these kind of associations\r
- jvseq = getvObj2jv((Vobject) noderef);\r
- }\r
- } else {\r
- refv=0;\r
- vrf++;\r
- }\r
- }\r
- if (jvseq instanceof SequenceI)\r
- {\r
- leaf.setElement(jvseq);\r
- leaf.setPlaceholder(false);\r
- } else {\r
- leaf.setPlaceholder(true);\r
- leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));\r
- }\r
- }\r
- }\r
- }\r
-\r
- /// TODO: refactor to vamsas :start \r
+ public void UpdateSequenceTreeMap(TreePanel tp)\r
+ {\r
+ if (tp == null || tree != null)\r
+ return;\r
+ Vector leaves = new Vector();\r
+ tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);\r
+ Treenode[] tn = tree.getTreenode(); // todo: select nodes for this\r
+ // particular tree\r
+ int sz = tn.length;\r
+ int i = 0;\r
+\r
+ while (i < sz)\r
+ {\r
+ Treenode node = tn[i++];\r
+ BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);\r
+ if (mappednode != null && mappednode instanceof SequenceNode)\r
+ {\r
+ SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
+ // check if we can make the specified association\r
+ Object jvseq = null;\r
+ int vrf = 0, refv = 0;\r
+ while (jvseq == null && vrf < node.getVrefCount())\r
+ {\r
+ if (refv < node.getVref(vrf).getRefsCount())\r
+ {\r
+ Object noderef = node.getVref(vrf).getRefs(refv++);\r
+ if (noderef instanceof AlignmentSequence)\r
+ {\r
+ // we only make these kind of associations\r
+ jvseq = getvObj2jv((Vobject) noderef);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ refv = 0;\r
+ vrf++;\r
+ }\r
+ }\r
+ if (jvseq instanceof SequenceI)\r
+ {\r
+ leaf.setElement(jvseq);\r
+ leaf.setPlaceholder(false);\r
+ }\r
+ else\r
+ {\r
+ leaf.setPlaceholder(true);\r
+ leaf\r
+ .setElement(new Sequence(leaf.getName(),\r
+ "THISISAPLACEHLDER"));\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ // / TODO: refactor to vamsas :start\r