JAL-1632 dialog to calculate either Tree or PCA

[jalview.git] / src / jalview / gui / PCAPanel.java

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 57a7422..3b73c5a 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -23,6 +23,7 @@ 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;
@@ -77,18 +78,32 @@ 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 alignPanel, ScoreModelI scoreModel,
+          SimilarityParamsI params)
+  {
     super();
     this.av = alignPanel.av;
     this.ap = alignPanel;
+    boolean nucleotide = av.getAlignment().isNucleotide();
 
     progressBar = new ProgressBar(statusPanel, statusBar);
 
@@ -104,7 +119,6 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     boolean selected = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 0;
     AlignmentView seqstrings = av.getAlignmentView(selected);
-    boolean nucleotide = av.getAlignment().isNucleotide();
     SequenceI[] seqs;
     if (!selected)
     {
@@ -127,8 +141,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       return;
     }
 
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
-            SimilarityParams.SeqSpace);
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+            params);
     PaintRefresher.Register(this, av.getSequenceSetId());
 
     rc = new RotatableCanvas(alignPanel);