X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=aa130cc48138233020856b71b352fad3322a1f3d;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=02ce4346ac1fcdd7ea329f5ebcc568e3a3f421a4;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 02ce434..aa130cc 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,30 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 .
+ * 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.TreeBuilder;
+import jalview.analysis.TreeModel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
@@ -33,10 +30,17 @@ import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
-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;
@@ -137,8 +141,8 @@ public class Tree extends DatastoreItem
@Override
public void conflict()
{
- Cache.log
- .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
+ Cache.log.info(
+ "Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
}
/*
@@ -158,7 +162,8 @@ public class Tree extends DatastoreItem
else
{
// handle conflict
- log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
+ log.info(
+ "TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
}
}
@@ -216,7 +221,9 @@ public class Tree extends DatastoreItem
prov.getEntry(0).setUser(provEntry.getUser());
prov.getEntry(0).setApp(provEntry.getApp());
prov.getEntry(0).setDate(provEntry.getDate());
- if (tp.getTree().hasOriginalSequenceData())
+
+ AlignmentView originalData = tp.getTree().getOriginalData();
+ if (originalData != null)
{
Input vInput = new Input();
// LATER: check to see if tree input data is contained in this alignment -
@@ -224,7 +231,7 @@ public class Tree extends DatastoreItem
// in
// the document.
Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
- tp.getTree().seqData.getSequences()));
+ tp.getTree().getOriginalData().getSequences()));
Object[] alsqs = new Object[alsqrefs.size()];
alsqrefs.copyInto(alsqs);
vInput.setObjRef(alsqs);
@@ -236,12 +243,13 @@ public class Tree extends DatastoreItem
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
- int ranges[] = tp.getTree().seqData.getVisibleContigs();
+ prov.getEntry(0).getParam(0)
+ .setContent(TreeBuilder.NEIGHBOUR_JOINING);
+ // TODO: type of tree is a general parameter
+ int ranges[] = originalData.getVisibleContigs();
// VisibleContigs are with respect to alignment coordinates. Still need
// offsets
- int start = tp.getTree().seqData.getAlignmentOrigin();
+ int start = tp.getTree().getOriginalData().getAlignmentOrigin();
for (int r = 0; r < ranges.length; r += 2)
{
Seg visSeg = new Seg();
@@ -263,7 +271,8 @@ public class Tree extends DatastoreItem
* @return vector of alignment sequences in order of SeqCigar array (but
* missing unfound seqcigars)
*/
- private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
+ private Vector findAlignmentSequences(AlignmentI jal,
+ SeqCigar[] sequences)
{
SeqCigar[] tseqs = new SeqCigar[sequences.length];
System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
@@ -275,9 +284,8 @@ public class Tree extends DatastoreItem
{
for (int t = 0; t < sequences.length; t++)
{
- if (tseqs[t] != null
- && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
- .getDatasetSequence()))
+ if (tseqs[t] != null && (tseqs[t].getRefSeq() == asq
+ || tseqs[t].getRefSeq() == asq.getDatasetSequence()))
// && tseqs[t].getStart()>=asq.getStart() &&
// tseqs[t].getEnd()<=asq.getEnd())
{
@@ -288,8 +296,10 @@ public class Tree extends DatastoreItem
}
}
if (alsq.size() < sequences.length)
- Cache.log
- .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+ {
+ Cache.log.warn(
+ "Not recovered all alignment sequences for given set of input sequence CIGARS");
+ }
return alsq;
}
@@ -303,15 +313,18 @@ public class Tree extends DatastoreItem
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());
+ Cache.log.warn(
+ "Not updating SequenceTreeMap for " + tree.getVorbaId());
return;
}
- tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
+ Vector leaves = tp.getTree()
+ .findLeaves(tp.getTree().getTopNode());
Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
// particular tree
int sz = tn.length;
@@ -352,7 +365,8 @@ public class Tree extends DatastoreItem
else
{
leaf.setPlaceholder(true);
- leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
+ leaf.setElement(
+ new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
}
}
}
@@ -362,14 +376,14 @@ public class Tree extends DatastoreItem
/**
* 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 leaves = treeModel
+ .findLeaves(treeModel.getTopNode());
Vector tnv = new Vector();
Enumeration l = leaves.elements();
Hashtable nodespecs = new Hashtable();
@@ -404,10 +418,10 @@ public class Tree extends DatastoreItem
else
{
System.err.println("WARNING: Unassociated treeNode "
- + tnode.element().toString()
- + " "
- + ((tnode.getName() != null) ? " label "
- + tnode.getName() : ""));
+ + tnode.element().toString() + " "
+ + ((tnode.getName() != null)
+ ? " label " + tnode.getName()
+ : ""));
}
}
}
@@ -419,8 +433,7 @@ public class Tree extends DatastoreItem
tnv.copyInto(tn);
return tn;
}
- return new Treenode[]
- {};
+ return new Treenode[] {};
}
private String makeNodeSpec(Hashtable nodespecs,
@@ -471,7 +484,9 @@ public class Tree extends DatastoreItem
--occurence;
}
else
+ {
bn = null;
+ }
}
return bn;
}
@@ -488,7 +503,7 @@ public class Tree extends DatastoreItem
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));
@@ -508,7 +523,7 @@ public class Tree extends DatastoreItem
*/
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++)
@@ -517,8 +532,8 @@ public class Tree extends DatastoreItem
{
if (tp.getEntry(pe).getInputCount() > 1)
{
- Cache.log
- .warn("Ignoring additional input spec in provenance entry "
+ Cache.log.warn(
+ "Ignoring additional input spec in provenance entry "
+ tp.getEntry(pe).toString());
}
// LATER: deal sensibly with multiple inputs
@@ -526,8 +541,8 @@ public class Tree extends DatastoreItem
// 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();
@@ -537,26 +552,27 @@ public class Tree extends DatastoreItem
else
{
// Explicit reference - to alignment, sequences or what.
- if (vInput.getObjRefCount() == 1
- && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
+ if (vInput.getObjRefCount() == 1 && vInput.getObjRef(
+ 0) instanceof uk.ac.vamsas.objects.core.Alignment)
{
// recover an AlignmentView for the input data
javport = getViewport((Vobject) vInput.getObjRef(0));
jal = javport.getAlignment();
view = javport.getAlignment().getCompactAlignment();
}
- else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
+ 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()];
for (int i = 0, iSize = vInput.getObjRefCount(); i < iSize; i++)
{
- SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput
- .getObjRef(i));
+ SequenceI seq = (SequenceI) getvObj2jv(
+ (Vobject) vInput.getObjRef(i));
seqs[i] = seq;
}
view = new jalview.datamodel.Alignment(seqs)
@@ -593,16 +609,15 @@ public class Tree extends DatastoreItem
// off by
// one for to
}
- return new Object[]
- { new AlignmentView(view), jal };
+ return new Object[] { new AlignmentView(view), jal };
}
}
- Cache.log
- .debug("Returning null for input data recovery from provenance.");
+ Cache.log.debug(
+ "Returning null for input data recovery from provenance.");
return null;
}
- private AlignViewport getViewport(Vobject v_parent)
+ private AlignmentViewport getViewport(Vobject v_parent)
{
if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
{