X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=885c3bf8a2026a9c05418479999d03e5103bf171;hb=5c45059a31d5f2ed14a8898d700ead9b3431bccf;hp=3f0c37f04988ad1a1811c501121044499190c887;hpb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 3f0c37f..885c3bf 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -21,7 +21,9 @@
 package jalview.gui;
 
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -76,26 +78,47 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   int top = 0;
 
   /**
-   * Creates a new PCAPanel object.
+   * Creates a new PCAPanel object using default score model and parameters
    * 
-   * @param av
-   *          DOCUMENT ME!
-   * @param s
-   *          DOCUMENT ME!
+   * @param alignPanel
+   */
+  public PCAPanel(AlignmentPanel alignPanel)
+  {
+    this(alignPanel, ScoreModels.getInstance().getDefaultModel(
+            !alignPanel.av.getAlignment().isNucleotide()),
+            SimilarityParams.SeqSpace);
+  }
+
+  /**
+   * Constructor given sequence data, a similarity (or distance) score model,
+   * and score calculation parameters
+   * 
+   * @param alignPanel
+   * @param scoreModel
+   * @param params
    */
-  public PCAPanel(AlignmentPanel ap)
+  public PCAPanel(AlignmentPanel alignPanel, ScoreModelI scoreModel,
+          SimilarityParamsI params)
   {
     super();
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alignPanel.av;
+    this.ap = alignPanel;
+    boolean nucleotide = av.getAlignment().isNucleotide();
 
     progressBar = new ProgressBar(statusPanel, statusBar);
 
-    boolean sameLength = true;
+    addInternalFrameListener(new InternalFrameAdapter()
+    {
+      @Override
+      public void internalFrameClosed(InternalFrameEvent e)
+      {
+        close_actionPerformed();
+      }
+    });
+
     boolean selected = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 0;
     AlignmentView seqstrings = av.getAlignmentView(selected);
-    boolean nucleotide = av.getAlignment().isNucleotide();
     SequenceI[] seqs;
     if (!selected)
     {
@@ -105,19 +128,10 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     {
       seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
     }
-    SeqCigar sq[] = seqstrings.getSequences();
-    int length = sq[0].getWidth();
-
-    for (int i = 0; i < seqs.length; i++)
-    {
-      if (sq[i].getWidth() != length)
-      {
-        sameLength = false;
-        break;
-      }
-    }
 
-    if (!sameLength)
+    // TODO can we allow PCA on unaligned data given choice of
+    // similarity measure parameters?
+    if (!checkAligned(seqstrings))
     {
       JvOptionPane.showMessageDialog(Desktop.desktop,
               MessageManager.getString("label.pca_sequences_not_aligned"),
@@ -127,25 +141,39 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       return;
     }
 
-    addInternalFrameListener(new InternalFrameAdapter()
-    {
-      @Override
-      public void internalFrameClosed(InternalFrameEvent e)
-      {
-        close_actionPerformed();
-      }
-    });
-
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+            params);
     PaintRefresher.Register(this, av.getSequenceSetId());
 
-    rc = new RotatableCanvas(ap);
+    rc = new RotatableCanvas(alignPanel);
     this.getContentPane().add(rc, BorderLayout.CENTER);
     Thread worker = new Thread(this);
     worker.start();
   }
 
   /**
+   * Answers true if all sequences have the same aligned length, else false
+   * 
+   * @param seqstrings
+   * @return
+   */
+  protected boolean checkAligned(AlignmentView seqstrings)
+  {
+    SeqCigar sq[] = seqstrings.getSequences();
+    int length = sq[0].getWidth();
+    boolean sameLength = true;
+    for (int i = 0; i < sq.length; i++)
+    {
+      if (sq[i].getWidth() != length)
+      {
+        sameLength = false;
+        break;
+      }
+    }
+    return sameLength;
+  }
+
+  /**
    * Ensure references to potentially very large objects (the PCA matrices) are
    * nulled when the frame is closed
    */
@@ -167,10 +195,19 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
     {
       final String name = sm.getName();
-      // create an entry for this score matrix for use in PCA
-      JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
-      jm.setText(MessageManager.getStringOrReturn("label.score_model_",
-              name));
+      JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
+
+      /*
+       * if the score model doesn't provide a description, try to look one
+       * up in the text bundle, falling back on its name
+       */
+      String tooltip = sm.getDescription();
+      if (tooltip == null)
+      {
+        tooltip = MessageManager.getStringOrReturn("label.score_model_",
+                name);
+      }
+      jm.setToolTipText(tooltip);
       jm.setSelected(pcaModel.getScoreModelName().equals(name));
       if ((pcaModel.isNucleotide() && sm.isDNA())
               || (!pcaModel.isNucleotide() && sm.isProtein()))