X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=43febb451c8c4e6f2194c07591bf469b414e5317;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=fd9294b739b07e1388e4f5b413b8705b87e61fc9;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index fd9294b..43febb4 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,30 +1,30 @@
/*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * 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.List;
import java.util.Vector;
import jalview.analysis.NJTree;
-import jalview.analysis.SequenceIdMatcher;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
@@ -33,7 +33,6 @@ import jalview.datamodel.SeqCigar;
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;
@@ -71,46 +70,14 @@ public class Tree extends DatastoreItem
uk.ac.vamsas.objects.core.Tree vtree)
{
Tree toTree = new Tree(datastore, alignFrame, vtree);
-
}
public Tree(VamsasAppDatastore datastore,
jalview.gui.AlignFrame alignFrame,
uk.ac.vamsas.objects.core.Tree vtree)
{
- super(datastore);
- tree = vtree;
- TreePanel tp = (TreePanel) getvObj2jv(tree);
- if (tp != null)
- {
- if (tree.isUpdated())
- {
- Cache.log
- .info("Update from vamsas document to alignment associated tree not implemented yet.");
- }
- }
- else
- {
- // make a new tree
- Object[] idata = recoverInputData(tree.getProvenance());
- try
- {
- if (idata != null && idata[0] != null)
- {
- inputData = (AlignmentView) idata[0];
- }
- ntree = getNtree();
- title = tree.getNewick(0).getTitle();
- if (title == null || title.length() == 0)
- {
- title = tree.getTitle(); // hack!!!!
- }
- } catch (Exception e)
- {
- Cache.log.warn("Problems parsing treefile '"
- + tree.getNewick(0).getContent() + "'", e);
- }
- }
+ super(datastore, vtree, TreePanel.class);
+ doJvUpdate();
}
private NewickFile getNtree() throws IOException
@@ -121,30 +88,114 @@ public class Tree extends DatastoreItem
public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
uk.ac.vamsas.objects.core.Alignment alignment2)
{
- super(datastore);
+ super(datastore, tp2, uk.ac.vamsas.objects.core.Tree.class);
jal = jal2;
- tp = tp2;
+ tp = (TreePanel) jvobj;
alignment = alignment2;
- tree = (uk.ac.vamsas.objects.core.Tree) getjv2vObj(tp);
- if (tree == null)
- {
- add();
- }
- else
+ tree = (uk.ac.vamsas.objects.core.Tree) vobj;
+ doSync();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
+ */
+ @Override
+ public void addFromDocument()
+ {
+ tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
+ TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
+ // make a new tree
+ Object[] idata = recoverInputData(tree.getProvenance());
+ try
{
- if (isModifiable(tree.getModifiable()))
+ if (idata != null && idata[0] != null)
{
- // synchronize(); // update();
- // verify any changes.
- System.out.println("Update tree in document.");
+ inputData = (AlignmentView) idata[0];
}
- else
+ ntree = getNtree();
+ title = tree.getNewick(0).getTitle();
+ if (title == null || title.length() == 0)
{
- // handle conflict
- System.out.println("Add modified tree as new tree in document.");
+ title = tree.getTitle(); // hack!!!!
}
+ } catch (Exception e)
+ {
+ Cache.log.warn("Problems parsing treefile '"
+ + tree.getNewick(0).getContent() + "'", e);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.vamsas.DatastoreItem#conflict()
+ */
+ @Override
+ public void conflict()
+ {
+ Cache.log
+ .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.vamsas.DatastoreItem#update()
+ */
+ @Override
+ public void updateToDoc()
+ {
+ if (isModifiable(tree.getModifiable()))
+ {
+ // synchronize(); // update();
+ // verify any changes.
+ log.info("TODO: Update tree in document from jalview.");
+ }
+ else
+ {
+ // handle conflict
+ log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @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
+ // one
+ // TODO: Tree.updateFromDoc
+ /*
+ * TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
+ *
+ * // make a new tree Object[] idata =
+ * recoverInputData(tree.getProvenance()); try { if (idata != null &&
+ * idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
+ * getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
+ * title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
+ * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
+ * tree.getNewick(0).getContent() + "'", e); }
+ */
+ log.debug("Update the local tree in jalview from the document.");
+
+ if (isModifiable(tree.getModifiable()))
+ {
+ // synchronize(); // update();
+ // verify any changes.
+ log.debug("Update tree in document from jalview.");
+ }
+ else
+ {
+ // handle conflict
+ log.debug("Add modified jalview tree as new tree in document.");
}
}
@@ -172,8 +223,8 @@ public class Tree extends DatastoreItem
// or just correctly resolve the tree's seqData to the correct alignment
// in
// the document.
- Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp
- .getTree().seqData.getSequences()));
+ Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
+ tp.getTree().seqData.getSequences()));
Object[] alsqs = new Object[alsqrefs.size()];
alsqrefs.copyInto(alsqs);
vInput.setObjRef(alsqs);
@@ -217,20 +268,22 @@ public class Tree extends DatastoreItem
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 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);
+ }
}
}
}
@@ -245,7 +298,7 @@ public class Tree extends DatastoreItem
* Update jalview newick representation with TreeNode map
*
* @param tp
- * the treepanel that this tree is bound to.
+ * the treepanel that this tree is bound to.
*/
public void UpdateSequenceTreeMap(TreePanel tp)
{
@@ -299,9 +352,7 @@ public class Tree extends DatastoreItem
else
{
leaf.setPlaceholder(true);
- leaf
- .setElement(new Sequence(leaf.getName(),
- "THISISAPLACEHLDER"));
+ leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
}
}
}
@@ -390,7 +441,7 @@ public class Tree extends DatastoreItem
*
* @param nodespec
* @param leaves
- * as returned from NJTree.findLeaves( .., ..) ..
+ * as returned from NJTree.findLeaves( .., ..) ..
* @return
*/
private jalview.datamodel.BinaryNode findNodeSpec(String nodespec,
@@ -430,7 +481,8 @@ public class Tree extends DatastoreItem
* add jalview object to vamsas document
*
*/
- public void add()
+ @Override
+ public void addToDocument()
{
tree = new uk.ac.vamsas.objects.core.Tree();
bindjvvobj(tp, tree);