X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=d8e6b06247b2d3a7f357a5efc6ac08151847023a;hb=478b462be553125d574fd2f96f7c234b74f9f61b;hp=482dff37d946c67bb10c44b79cadfc281a7edad6;hpb=8a62c90cab2506fc5c52126fa5ddb84af917befc;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 482dff3..d8e6b06 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -24,12 +24,10 @@ 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;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPCAPanel;
 import jalview.util.MessageManager;
@@ -38,6 +36,7 @@ import jalview.viewmodel.PCAModel;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -74,6 +73,10 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
   PCAModel pcaModel;
 
+  private static final int MIN_WIDTH = 470;
+
+  private static final int MIN_HEIGHT = 250;
+
   int top = 0;
 
   /**
@@ -83,20 +86,20 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public PCAPanel(AlignmentPanel alignPanel)
   {
-    this(alignPanel, ScoreModels.getInstance().getDefaultModel(
-            !alignPanel.av.getAlignment().isNucleotide()),
-            SimilarityParams.SeqSpace);
+    this(alignPanel, ScoreModels.getInstance()
+            .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide())
+            .getName(), SimilarityParams.SeqSpace);
   }
 
   /**
-   * Constructor given sequence data, a similarity (or distance) score model,
-   * and score calculation parameters
+   * Constructor given sequence data, a similarity (or distance) score model
+   * name, and score calculation parameters
    * 
    * @param alignPanel
-   * @param scoreModel
+   * @param modelName
    * @param params
    */
-  public PCAPanel(AlignmentPanel alignPanel, ScoreModelI scoreModel,
+  public PCAPanel(AlignmentPanel alignPanel, String modelName,
           SimilarityParamsI params)
   {
     super();
@@ -128,6 +131,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
     }
 
+    ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel(
+            modelName, ap);
     pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
             params);
     PaintRefresher.Register(this, av.getSequenceSetId());
@@ -184,7 +189,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
           {
             if (!pcaModel.getScoreModelName().equals(name))
             {
-              ScoreModelI sm2 = configureScoreModel(sm);
+              ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel(
+                      name, ap);
               pcaModel.setScoreModel(sm2);
               Thread worker = new Thread(PCAPanel.this);
               worker.start();
@@ -255,6 +261,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       addKeyListener(rc);
       Desktop.addInternalFrame(this, MessageManager
               .getString("label.principal_component_analysis"), 475, 450);
+      this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
     }
   }
 
@@ -399,7 +406,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     }
     ;
     Object[] alAndColsel = pcaModel.getSeqtrings()
-            .getAlignmentAndColumnSelection(gc);
+            .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
@@ -416,8 +423,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       if (true)
       {
         // make a new frame!
-        AlignFrame af = new AlignFrame(al,
-                (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+        AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
+                AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
 
         // >>>This is a fix for the moment, until a better solution is
@@ -776,28 +783,4 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     top = t;
     zCombobox.setSelectedIndex(2);
   }
-
-  /**
-   * If the score model is one that requires to get state data from the current
-   * view, allow it to do so
-   * 
-   * @param sm
-   * @return
-   */
-  protected ScoreModelI configureScoreModel(ScoreModelI sm)
-  {
-    if (sm instanceof ViewBasedAnalysisI)
-    {
-      try
-      {
-        sm = sm.getClass().newInstance();
-        ((ViewBasedAnalysisI) sm).configureFromAlignmentView(ap);
-      } catch (Exception q)
-      {
-        Cache.log.error("Couldn't create a scoremodel instance for "
-                + sm.getName());
-      }
-    }
-    return sm;
-  }
 }