/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
prov.getEntry(0).getParam(0).setName("treeType");
prov.getEntry(0).getParam(0).setType("utf8");
prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
- // general parameter
+ // general parameter
int ranges[] = tp.getTree().seqData.getVisibleContigs();
// VisibleContigs are with respect to alignment coordinates. Still need
// offsets
*
* Update jalview newick representation with TreeNode map
*
- * @param tp the treepanel that this tree is bound to.
+ * @param tp
+ * the treepanel that this tree is bound to.
*/
public void UpdateSequenceTreeMap(TreePanel tp)
{
if (tp == null || tree == null)
return;
Vector leaves = new Vector();
- if (tp.getTree()==null)
+ if (tp.getTree() == null)
{
- Cache.log.warn("Not updating SequenceTreeMap for "+tree.getVorbaId());
+ Cache.log.warn("Not updating SequenceTreeMap for "
+ + tree.getVorbaId());
return;
}
tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
- // particular tree
+ // particular tree
int sz = tn.length;
int i = 0;
* construct treenode mappings for mapped sequences
*
* @param ntree
- * @param newick
+ * @param newick
* @return
*/
public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
* referenced in input data has already been associated with jalview objects.
*
* @param tp
- * @param alignFrame
+ * @param alignFrame
* @return Object[] { AlignmentView, AlignmentI - reference alignment for
* input }
*/
// is this the whole alignment or a specific set of sequences ?
if (vInput.getObjRefCount() == 0)
{
- if (tree.getV_parent()!=null && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
+ if (tree.getV_parent() != null
+ && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
{
javport = getViewport(tree.getV_parent());
jal = javport.getAlignment();
else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
{
// recover an AlignmentView for the input data
- javport = getViewport(((Vobject) vInput.getObjRef(0)).getV_parent());
+ javport = getViewport(((Vobject) vInput.getObjRef(0))
+ .getV_parent());
jal = javport.getAlignment();
jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput
.getObjRefCount()];
{
try
{
- if (ntree==null)
+ if (ntree == null)
{
return false;
}