JAL-2428 simplify TreeModel constructors, add getOriginalData

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 2f8d788..62b0594 100644 (file)
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -46,7 +46,7 @@ public class TreeModel
    * SequenceData is a string representation of what the user
    * sees. The display may contain hidden columns.
    */
-  public AlignmentView seqData;
+  private AlignmentView seqData;
 
   int noseqs;
 
@@ -68,7 +68,7 @@ public class TreeModel
 
   /**
    * Create a new TreeModel object with leaves associated with sequences in
-   * seqs, and original alignment data represented by Cigar strings
+   * seqs, and (optionally) original alignment data represented by Cigar strings
    * 
    * @param seqs
    *          SequenceI[]
@@ -79,22 +79,9 @@ public class TreeModel
    */
   public TreeModel(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
   {
-    this(seqs, treefile);
-    seqData = odata;
-  }
-
-  /**
-   * Creates a new TreeModel object from a tree from an external source
-   * 
-   * @param seqs
-   *          SequenceI which should be associated with leafs of treefile
-   * @param treefile
-   *          A parsed tree
-   */
-  public TreeModel(SequenceI[] seqs, NewickFile treefile)
-  {
     this(seqs, treefile.getTree(), treefile.HasDistances(), treefile
             .HasBootstrap(), treefile.HasRootDistance());
+    seqData = odata;
 
     associateLeavesToSequences(seqs);
   }
@@ -468,15 +455,6 @@ public class TreeModel
   }
 
   /**
-   * 
-   * @return true if original sequence data can be recovered
-   */
-  public boolean hasOriginalSequenceData()
-  {
-    return seqData != null;
-  }
-
-  /**
    * Returns original alignment data used for calculation - or null where not
    * available.
    * 
@@ -710,4 +688,9 @@ public class TreeModel
       ;
     }
   }
+
+  public AlignmentView getOriginalData()
+  {
+    return seqData;
+  }
 }

diff --git a/src/jalview/api/analysis/ScoreModelI.java b/src/jalview/api/analysis/ScoreModelI.java
index 9a633f0..4433cea 100644 (file)
--- a/src/jalview/api/analysis/ScoreModelI.java
+++ b/src/jalview/api/analysis/ScoreModelI.java
@@ -27,4 +27,5 @@ public interface ScoreModelI
    */
   boolean isProtein();
 
+  // TODO getName, isDNA, isProtein can be static methods in Java 8
 }

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index a9e11a7..905a54a 100644 (file)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -164,7 +164,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     // yields unaligned seqs)
     // or create a selection box around columns in alignment view
     // test Alignment(SeqCigar[])
-    if (tree.seqData != null)
+    if (tree.getOriginalData() != null)
     {
       char gc = '-';
       try
@@ -175,8 +175,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       } catch (Exception ex)
       {
       }
-      ;
-      Object[] alAndColsel = tree.seqData
+
+      Object[] alAndColsel = tree.getOriginalData()
               .getAlignmentAndColumnSelection(gc);
 
       if (alAndColsel != null && alAndColsel[0] != null)
@@ -210,17 +210,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     {
       if (newtree != null)
       {
-        if (odata == null)
-        {
-          tree = new TreeModel(av.getAlignment().getSequencesArray(),
-                  newtree);
-        }
-        else
-        {
-          tree = new TreeModel(av.getAlignment().getSequencesArray(),
-                  odata, newtree);
-        }
-
+        tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+                newtree);
       }
       else
       {

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 1e98535..d4c6009 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -170,11 +170,7 @@ public class TreePanel extends GTreePanel
       }
     });
 
-    TreeLoader tl = new TreeLoader(newTree);
-    if (inputData != null)
-    {
-      tl.odata = inputData;
-    }
+    TreeLoader tl = new TreeLoader(newTree, inputData);
     tl.start();
 
   }
@@ -246,13 +242,15 @@ public class TreePanel extends GTreePanel
 
   class TreeLoader extends Thread
   {
-    NewickFile newtree;
+    private NewickFile newtree;
 
-    AlignmentView odata = null;
+    private AlignmentView odata = null;
 
-    public TreeLoader(NewickFile newickFile)
+    public TreeLoader(NewickFile newickFile, AlignmentView inputData)
     {
       this.newtree = newickFile;
+      this.odata = inputData;
+
       if (newickFile != null)
       {
         // Must be outside run(), as Jalview2XML tries to
@@ -268,19 +266,11 @@ public class TreePanel extends GTreePanel
 
       if (newtree != null)
       {
-        if (odata == null)
+        tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+                newtree);
+        if (tree.getOriginalData() == null)
         {
-          tree = new TreeModel(av.getAlignment().getSequencesArray(),
-                  newtree);
-        }
-        else
-        {
-          tree = new TreeModel(av.getAlignment().getSequencesArray(),
-                  odata, newtree);
-        }
-        if (!tree.hasOriginalSequenceData())
-        {
-          allowOriginalSeqData(false);
+          originalSeqData.setVisible(false);
         }
       }
       else
@@ -323,11 +313,6 @@ public class TreePanel extends GTreePanel
     treeCanvas.setMarkPlaceholders(b);
   }
 
-  private void allowOriginalSeqData(boolean b)
-  {
-    originalSeqData.setVisible(b);
-  }
-
   /**
    * DOCUMENT ME!
    * 
@@ -422,7 +407,8 @@ public class TreePanel extends GTreePanel
   @Override
   public void originalSeqData_actionPerformed(ActionEvent e)
   {
-    if (!tree.hasOriginalSequenceData())
+    AlignmentView originalData = tree.getOriginalData();
+    if (originalData == null)
     {
       jalview.bin.Cache.log
               .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
@@ -444,8 +430,9 @@ public class TreePanel extends GTreePanel
     } catch (Exception ex)
     {
     }
-    ;
-    Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
+
+    Object[] alAndColsel = originalData
+            .getAlignmentAndColumnSelection(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {

diff --git a/src/jalview/io/packed/JalviewDataset.java b/src/jalview/io/packed/JalviewDataset.java
index 736591b..9f84c16 100644 (file)
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -20,6 +20,7 @@
  */
 package jalview.io.packed;
 
+import jalview.analysis.TreeModel;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -151,8 +152,7 @@ public class JalviewDataset
       {
         // the following works because all trees are already had node/SequenceI
         // associations created.
-        jalview.analysis.TreeModel njt = new jalview.analysis.TreeModel(
-                al.getSequencesArray(), nf);
+        TreeModel njt = new TreeModel(al.getSequencesArray(), null, nf);
         // this just updates the displayed leaf name on the tree according to
         // the SequenceIs.
         njt.renameAssociatedNodes();

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index f676347..d800d20 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -220,15 +220,17 @@ 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 -
       // 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().getOriginalData().getSequences()));
       Object[] alsqs = new Object[alsqrefs.size()];
       alsqrefs.copyInto(alsqs);
       vInput.setObjRef(alsqs);
@@ -243,10 +245,10 @@ public class Tree extends DatastoreItem
       prov.getEntry(0).getParam(0)
               .setContent(TreeBuilder.NEIGHBOUR_JOINING);
       // TODO: type of tree is a general parameter
-      int ranges[] = tp.getTree().seqData.getVisibleContigs();
+      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();

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index 4a32790..a92f5fb 100644 (file)
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.java
@@ -125,7 +125,8 @@ public class NewickFileTests
       stage = "Compare original and generated tree" + treename;
 
       Vector<SequenceNode> oseqs, nseqs;
-      oseqs = new TreeModel(new SequenceI[0], nf).findLeaves(nf.getTree());
+      oseqs = new TreeModel(new SequenceI[0], null, nf).findLeaves(nf
+              .getTree());
       AssertJUnit.assertTrue(stage + "No nodes in original tree.",
               oseqs.size() > 0);
       SequenceI[] olsqs = new SequenceI[oseqs.size()];
@@ -133,7 +134,8 @@ public class NewickFileTests
       {
         olsqs[i] = (SequenceI) oseqs.get(i).element();
       }
-      nseqs = new TreeModel(new SequenceI[0], nf_regen).findLeaves(nf_regen
+      nseqs = new TreeModel(new SequenceI[0], null, nf_regen)
+              .findLeaves(nf_regen
               .getTree());
       AssertJUnit.assertTrue(stage + "No nodes in regerated tree.",
               nseqs.size() > 0);