X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=1ac7babfa92983b6932651689f76548f094fc762;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=9c1f5ea1638d7819822b7f424d535964ae218561;hpb=3027bfb4b1b13af8686abcd419888e03141bd672;p=jalview.git

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 9c1f5ea..1ac7bab 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -22,7 +22,7 @@ package jalview.io.vamsas;
 
 import jalview.analysis.TreeBuilder;
 import jalview.analysis.TreeModel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.BinaryNode;
@@ -128,7 +128,7 @@ public class Tree extends DatastoreItem
       }
     } catch (Exception e)
     {
-      Cache.log.warn("Problems parsing treefile '"
+      Console.warn("Problems parsing treefile '"
               + tree.getNewick(0).getContent() + "'", e);
     }
   }
@@ -141,7 +141,7 @@ public class Tree extends DatastoreItem
   @Override
   public void conflict()
   {
-    Cache.log.info(
+    Console.info(
             "Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
   }
 
@@ -186,7 +186,7 @@ public class Tree extends DatastoreItem
      * 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 '" +
+     * (Exception e) { Cache.warn("Problems parsing treefile '" +
      * tree.getNewick(0).getContent() + "'", e); }
      */
     log.debug("Update the local tree in jalview from the document.");
@@ -214,7 +214,7 @@ public class Tree extends DatastoreItem
    */
   private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
   {
-    Cache.log.debug("Making Tree provenance for " + tp.getTitle());
+    Console.debug("Making Tree provenance for " + tp.getTitle());
     Provenance prov = new Provenance();
     prov.addEntry(new Entry());
     prov.getEntry(0).setAction("imported " + tp.getTitle());
@@ -259,7 +259,7 @@ public class Tree extends DatastoreItem
         vInput.addSeg(visSeg);
       }
     }
-    Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
+    Console.debug("Finished Tree provenance for " + tp.getTitle());
     return prov;
   }
 
@@ -271,14 +271,14 @@ public class Tree extends DatastoreItem
    * @return vector of alignment sequences in order of SeqCigar array (but
    *         missing unfound seqcigars)
    */
-  private Vector findAlignmentSequences(AlignmentI jal,
+  private Vector<SequenceI> findAlignmentSequences(AlignmentI jal,
           SeqCigar[] sequences)
   {
     SeqCigar[] tseqs = new SeqCigar[sequences.length];
     System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
-    Vector alsq = new Vector();
-    List<SequenceI> jalsqs;
-    synchronized (jalsqs = jal.getSequences())
+    Vector<SequenceI> alsq = new Vector<>();
+    List<SequenceI> jalsqs = jal.getSequences();
+    synchronized (jalsqs)
     {
       for (SequenceI asq : jalsqs)
       {
@@ -297,7 +297,7 @@ public class Tree extends DatastoreItem
     }
     if (alsq.size() < sequences.length)
     {
-      Cache.log.warn(
+      Console.warn(
               "Not recovered all alignment sequences for given set of input sequence CIGARS");
     }
     return alsq;
@@ -319,11 +319,10 @@ public class Tree extends DatastoreItem
 
     if (tp.getTree() == null)
     {
-      Cache.log.warn(
-              "Not updating SequenceTreeMap for " + tree.getVorbaId());
+      Console.warn("Not updating SequenceTreeMap for " + tree.getVorbaId());
       return;
     }
-    Vector<SequenceNode> leaves = tp.getTree()
+    Vector<BinaryNode> leaves = tp.getTree()
             .findLeaves(tp.getTree().getTopNode());
     Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
     // particular tree
@@ -382,7 +381,7 @@ public class Tree extends DatastoreItem
    */
   public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick)
   {
-    Vector<SequenceNode> leaves = treeModel
+    Vector<BinaryNode> leaves = treeModel
             .findLeaves(treeModel.getTopNode());
     Vector tnv = new Vector();
     Enumeration l = leaves.elements();
@@ -395,8 +394,7 @@ public class Tree extends DatastoreItem
       {
         if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
         {
-          Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
-                  .element();
+          Object assocseq = ((BinaryNode) tnode).element();
           if (assocseq instanceof SequenceI)
           {
             Vobject vobj = this.getjv2vObj(assocseq);
@@ -532,9 +530,8 @@ public class Tree extends DatastoreItem
       {
         if (tp.getEntry(pe).getInputCount() > 1)
         {
-          Cache.log.warn(
-                  "Ignoring additional input spec in provenance entry "
-                          + tp.getEntry(pe).toString());
+          Console.warn("Ignoring additional input spec in provenance entry "
+                  + tp.getEntry(pe).toString());
         }
         // LATER: deal sensibly with multiple inputs
         Input vInput = tp.getEntry(pe).getInput(0);
@@ -589,7 +586,7 @@ public class Tree extends DatastoreItem
           // bidirection alignments yet.
           if (to < se[1])
           {
-            Cache.log.warn("Ignoring invalid segment in InputData spec.");
+            Console.warn("Ignoring invalid segment in InputData spec.");
           }
           else
           {
@@ -612,7 +609,7 @@ public class Tree extends DatastoreItem
         return new Object[] { new AlignmentView(view), jal };
       }
     }
-    Cache.log.debug(
+    Console.debug(
             "Returning null for input data recovery from provenance.");
     return null;
   }
@@ -658,7 +655,7 @@ public class Tree extends DatastoreItem
       return true;
     } catch (Exception e)
     {
-      Cache.log.debug("Failed to parse newick tree string", e);
+      Console.debug("Failed to parse newick tree string", e);
     }
     return false;
   }