X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=a3781a7d09e8b2809ed8fdf7dd81fc40044a6ed8;hb=b5f2dfda36c463b93f34db95fe5bc5ff2a1516bf;hp=5caded1ec3053b177a61b686ef4c9d7edaad3812;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 5caded1..a3781a7 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,28 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.
- *
- * 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
+ * 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/>.
+ * 
+ * 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.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -32,10 +29,17 @@ 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;
@@ -99,7 +103,7 @@ public class Tree extends DatastoreItem
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
    */
   @Override
@@ -130,7 +134,7 @@ public class Tree extends DatastoreItem
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.io.vamsas.DatastoreItem#conflict()
    */
   @Override
@@ -142,7 +146,7 @@ public class Tree extends DatastoreItem
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.io.vamsas.DatastoreItem#update()
    */
   @Override
@@ -163,7 +167,7 @@ public class Tree extends DatastoreItem
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
    */
   @Override
@@ -174,7 +178,7 @@ public class Tree extends DatastoreItem
     // 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 =
@@ -201,7 +205,7 @@ public class Tree extends DatastoreItem
   /**
    * correctly creates provenance for trees calculated on an alignment by
    * jalview.
-   *
+   * 
    * @param jal
    * @param tp
    * @return
@@ -256,7 +260,7 @@ public class Tree extends DatastoreItem
 
   /**
    * look up SeqCigars in an existing alignment.
-   *
+   * 
    * @param jal
    * @param sequences
    * @return vector of alignment sequences in order of SeqCigar array (but
@@ -268,47 +272,54 @@ public class Tree extends DatastoreItem
     System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
     Vector alsq = new Vector();
     List<SequenceI> jalsqs;
-    synchronized (jalsqs=jal.getSequences())
-    {for (SequenceI asq:jalsqs)
+    synchronized (jalsqs = jal.getSequences())
     {
-      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;
   }
 
   /**
-   *
+   * 
    * Update jalview newick representation with TreeNode map
-   *
+   * 
    * @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)
     {
       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;
@@ -358,15 +369,14 @@ public class Tree extends DatastoreItem
   // / TODO: refactor to vamsas :start
   /**
    * construct treenode mappings for mapped sequences
-   *
+   * 
    * @param ntree
    * @param newick
    * @return
    */
   public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
   {
-    Vector leaves = new Vector();
-    ntree.findLeaves(ntree.getTopNode(), leaves);
+    Vector<SequenceNode> leaves = ntree.findLeaves(ntree.getTopNode());
     Vector tnv = new Vector();
     Enumeration l = leaves.elements();
     Hashtable nodespecs = new Hashtable();
@@ -416,8 +426,7 @@ public class Tree extends DatastoreItem
       tnv.copyInto(tn);
       return tn;
     }
-    return new Treenode[]
-    {};
+    return new Treenode[] {};
   }
 
   private String makeNodeSpec(Hashtable nodespecs,
@@ -435,7 +444,7 @@ public class Tree extends DatastoreItem
 
   /**
    * call to match up Treenode specs to NJTree parsed from document object.
-   *
+   * 
    * @param nodespec
    * @param leaves
    *          as returned from NJTree.findLeaves( .., ..) ..
@@ -468,7 +477,9 @@ public class Tree extends DatastoreItem
         --occurence;
       }
       else
+      {
         bn = null;
+      }
     }
     return bn;
   }
@@ -476,7 +487,7 @@ public class Tree extends DatastoreItem
   // todo: end refactor to vamsas library
   /**
    * add jalview object to vamsas document
-   *
+   * 
    */
   @Override
   public void addToDocument()
@@ -497,7 +508,7 @@ public class Tree extends DatastoreItem
   /**
    * note: this function assumes that all sequence and alignment objects
    * referenced in input data has already been associated with jalview objects.
-   *
+   * 
    * @param tp
    * @param alignFrame
    * @return Object[] { AlignmentView, AlignmentI - reference alignment for
@@ -505,7 +516,7 @@ 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++)
@@ -590,8 +601,7 @@ 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
@@ -599,7 +609,7 @@ public class Tree extends DatastoreItem
     return null;
   }
 
-  private AlignViewport getViewport(Vobject v_parent)
+  private AlignmentViewport getViewport(Vobject v_parent)
   {
     if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
     {