Merge branch 'features/JAL-2393customMatrices' into develop

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 57a7422..e9ba1e7 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -23,13 +23,11 @@ package jalview.gui;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.ViewBasedAnalysisI;
-import jalview.bin.Cache;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
 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;
@@ -74,21 +73,39 @@ 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;
 
   /**
-   * 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())
+            .getName(), SimilarityParams.SeqSpace);
+  }
+
+  /**
+   * Constructor given sequence data, a similarity (or distance) score model
+   * name, and score calculation parameters
+   * 
+   * @param alignPanel
+   * @param modelName
+   * @param params
+   */
+  public PCAPanel(AlignmentPanel alignPanel, String modelName,
+          SimilarityParamsI params)
+  {
     super();
     this.av = alignPanel.av;
     this.ap = alignPanel;
+    boolean nucleotide = av.getAlignment().isNucleotide();
 
     progressBar = new ProgressBar(statusPanel, statusBar);
 
@@ -104,7 +121,6 @@ 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)
     {
@@ -115,20 +131,10 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
     }
 
-    // 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"),
-              MessageManager.getString("label.sequences_not_aligned"),
-              JvOptionPane.WARNING_MESSAGE);
-
-      return;
-    }
-
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
-            SimilarityParams.SeqSpace);
+    ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel(
+            modelName, ap);
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+            params);
     PaintRefresher.Register(this, av.getSequenceSetId());
 
     rc = new RotatableCanvas(alignPanel);
@@ -138,28 +144,6 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   }
 
   /**
-   * 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
    */
@@ -181,10 +165,19 @@ 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()))
@@ -196,7 +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();
@@ -250,7 +244,6 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       // rc.invalidate();
       nuclSetting.setSelected(pcaModel.isNucleotide());
       protSetting.setSelected(!pcaModel.isNucleotide());
-      jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
       top = pcaModel.getTop();
 
     } catch (OutOfMemoryError er)
@@ -268,6 +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));
     }
   }
 
@@ -299,14 +293,6 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     }
   }
 
-  @Override
-  protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
-  {
-    pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
-    Thread worker = new Thread(this);
-    worker.start();
-  }
-
   /**
    * DOCUMENT ME!
    */
@@ -797,28 +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;
-  }
 }