JAL-1632 remove unused check for sequences aligned

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 3b73c5a..482dff3 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -30,7 +30,6 @@ 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;
@@ -129,18 +128,6 @@ 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, scoreModel,
             params);
     PaintRefresher.Register(this, av.getSequenceSetId());
@@ -152,28 +139,6 @@ 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
    */
@@ -195,10 +160,19 @@ 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()))
@@ -264,7 +238,6 @@ 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)
@@ -313,14 +286,6 @@ 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!
    */