/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import jalview.analysis.NJTree;
-import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.gui.TreePanel;
import jalview.io.NewickFile;
import jalview.io.VamsasAppDatastore;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.AlignmentSequence;
import uk.ac.vamsas.objects.core.Entry;
*
* @see jalview.io.vamsas.DatastoreItem#addFromDocument()
*/
+ @Override
public void addFromDocument()
{
tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
*
* @see jalview.io.vamsas.DatastoreItem#conflict()
*/
+ @Override
public void conflict()
{
Cache.log
*
* @see jalview.io.vamsas.DatastoreItem#update()
*/
+ @Override
public void updateToDoc()
{
if (isModifiable(tree.getModifiable()))
*
* @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
*/
+ @Override
public void updateFromDoc()
{
// should probably just open a new tree panel in the same place as the old
prov.getEntry(0).addParam(new Param());
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
+ prov.getEntry(0).getParam(0)
+ .setContent(TreeBuilder.NEIGHBOUR_JOINING);
+ // TODO: type of tree is a general parameter
int ranges[] = tp.getTree().seqData.getVisibleContigs();
// VisibleContigs are with respect to alignment coordinates. Still need
// offsets
SeqCigar[] tseqs = new SeqCigar[sequences.length];
System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
Vector alsq = new Vector();
- Enumeration as = jal.getSequences().elements();
- while (as.hasMoreElements())
+ List<SequenceI> jalsqs;
+ synchronized (jalsqs = jal.getSequences())
{
- SequenceI asq = (SequenceI) as.nextElement();
- for (int t = 0; t < sequences.length; t++)
+ for (SequenceI asq : jalsqs)
{
- if (tseqs[t] != null
- && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
- .getDatasetSequence()))
- // && tseqs[t].getStart()>=asq.getStart() &&
- // tseqs[t].getEnd()<=asq.getEnd())
+ for (int t = 0; t < sequences.length; t++)
{
- tseqs[t] = null;
- alsq.add(asq);
+ if (tseqs[t] != null
+ && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
+ .getDatasetSequence()))
+ // && tseqs[t].getStart()>=asq.getStart() &&
+ // tseqs[t].getEnd()<=asq.getEnd())
+ {
+ tseqs[t] = null;
+ alsq.add(asq);
+ }
}
}
}
if (alsq.size() < sequences.length)
+ {
Cache.log
.warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+ }
return alsq;
}
public void UpdateSequenceTreeMap(TreePanel tp)
{
if (tp == null || tree == null)
+ {
return;
- Vector leaves = new Vector();
+ }
+
if (tp.getTree() == null)
{
Cache.log.warn("Not updating SequenceTreeMap for "
+ tree.getVorbaId());
return;
}
- tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
+ Vector<SequenceNode> leaves = tp.getTree().findLeaves(
+ tp.getTree().getTopNode());
Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
// particular tree
int sz = tn.length;
/**
* construct treenode mappings for mapped sequences
*
- * @param ntree
+ * @param treeModel
* @param newick
* @return
*/
- public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
+ public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick)
{
- Vector leaves = new Vector();
- ntree.findLeaves(ntree.getTopNode(), leaves);
+ Vector<SequenceNode> leaves = treeModel.findLeaves(treeModel
+ .getTopNode());
Vector tnv = new Vector();
Enumeration l = leaves.elements();
Hashtable nodespecs = new Hashtable();
tnv.copyInto(tn);
return tn;
}
- return new Treenode[]
- {};
+ return new Treenode[] {};
}
private String makeNodeSpec(Hashtable nodespecs,
--occurence;
}
else
+ {
bn = null;
+ }
}
return bn;
}
* add jalview object to vamsas document
*
*/
+ @Override
public void addToDocument()
{
tree = new uk.ac.vamsas.objects.core.Tree();
bindjvvobj(tp, tree);
tree.setTitle(tp.getTitle());
Newick newick = new Newick();
- newick.setContent(tp.getTree().toString());
+ newick.setContent(tp.getTree().print());
newick.setTitle(tp.getTitle());
tree.addNewick(newick);
tree.setProvenance(makeTreeProvenance(jal, tp));
*/
public Object[] recoverInputData(Provenance tp)
{
- AlignViewport javport = null;
+ AlignmentViewport javport = null;
jalview.datamodel.AlignmentI jal = null;
jalview.datamodel.CigarArray view = null;
for (int pe = 0; pe < tp.getEntryCount(); pe++)
// off by
// one for to
}
- return new Object[]
- { new AlignmentView(view), jal };
+ return new Object[] { new AlignmentView(view), jal };
}
}
Cache.log
return null;
}
- private AlignViewport getViewport(Vobject v_parent)
+ private AlignmentViewport getViewport(Vobject v_parent)
{
if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
{
git://source.jalview.org / jalview.git / blobdiff