X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=e56fa3fdb299189b2953cd7c7ae19b648369430c;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=8ff825c7ce8b05fa633a8bab33c1d09b67edb59b;hpb=cfa406a916d754e600c60f7dae29b053bf045ace;p=jalview.git

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 8ff825c..e56fa3f 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,12 +1,32 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
+ *  
+ * 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/>.
+ * 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;
@@ -15,7 +35,6 @@ 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;
@@ -53,46 +72,14 @@ 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
@@ -103,30 +90,114 @@ 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.");
     }
   }
 
@@ -154,8 +225,8 @@ 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);
@@ -168,7 +239,7 @@ public class Tree extends DatastoreItem
       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
@@ -199,20 +270,22 @@ 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<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);
+          }
         }
       }
     }
@@ -227,16 +300,22 @@ 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)
   {
-    if (tp == null || tree != null)
+    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);
     Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
-                                        // particular tree
+    // particular tree
     int sz = tn.length;
     int i = 0;
 
@@ -246,7 +325,7 @@ public class Tree extends DatastoreItem
       BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);
       if (mappednode != null && mappednode instanceof SequenceNode)
       {
-        SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+        SequenceNode leaf = (SequenceNode) mappednode;
         // check if we can make the specified association
         Object jvseq = null;
         int vrf = 0, refv = 0;
@@ -275,9 +354,7 @@ public class Tree extends DatastoreItem
         else
         {
           leaf.setPlaceholder(true);
-          leaf
-                  .setElement(new Sequence(leaf.getName(),
-                          "THISISAPLACEHLDER"));
+          leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
         }
       }
     }
@@ -288,7 +365,7 @@ public class Tree extends DatastoreItem
    * construct treenode mappings for mapped sequences
    * 
    * @param ntree
-   * @param newick 
+   * @param newick
    * @return
    */
   public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
@@ -366,7 +443,7 @@ 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,
@@ -406,7 +483,8 @@ 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);
@@ -426,7 +504,7 @@ public class Tree extends DatastoreItem
    * 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 }
    */
@@ -450,7 +528,8 @@ 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();
@@ -471,7 +550,8 @@ public class Tree extends DatastoreItem
           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()];
@@ -553,6 +633,10 @@ public class Tree extends DatastoreItem
   {
     try
     {
+      if (ntree == null)
+      {
+        return false;
+      }
       ntree.parse();
       if (ntree.getTree() != null)
       {