JAL-2393 code tidying for review comments

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 6bf812c..07f43da 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -116,7 +116,7 @@ public class AlignSeq
 
   String type; // AlignSeq.PEP or AlignSeq.DNA
 
-  private ScoreMatrix scoreModel;
+  private ScoreMatrix scoreMatrix;
 
   private static final int GAP_INDEX = -1;
 
@@ -343,7 +343,7 @@ public class AlignSeq
     }
 
     type = moleculeType;
-    scoreModel = ScoreModels.getInstance().getDefaultModel(
+    scoreMatrix = ScoreModels.getInstance().getDefaultModel(
             PEP.equals(type));
   }
 
@@ -589,7 +589,7 @@ public class AlignSeq
   {
     int t = 0;
     // float pairwiseScore = lookup[seq1[i]][seq2[j]];
-    float pairwiseScore = scoreModel.getPairwiseScore(s1str.charAt(i),
+    float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
             s2str.charAt(j));
     float max = score[i - 1][j - 1] + (pairwiseScore * 10);
 
@@ -635,7 +635,7 @@ public class AlignSeq
     int m = seq2.length;
 
     // top left hand element
-    score[0][0] = scoreModel.getPairwiseScore(s1str.charAt(0),
+    score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0),
             s2str.charAt(0)) * 10;
     E[0][0] = -gapExtend;
     F[0][0] = 0;
@@ -647,7 +647,7 @@ public class AlignSeq
       E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);
       F[0][j] = -gapExtend;
 
-      float pairwiseScore = scoreModel.getPairwiseScore(s1str.charAt(0),
+      float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
               s2str.charAt(j));
       score[0][j] = max(pairwiseScore * 10, -gapOpen, -gapExtend);
 
@@ -660,7 +660,7 @@ public class AlignSeq
       E[i][0] = -gapOpen;
       F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
 
-      float pairwiseScore = scoreModel.getPairwiseScore(s1str.charAt(i),
+      float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
               s2str.charAt(0));
       score[i][0] = max(pairwiseScore * 10, E[i][0], F[i][0]);
       traceback[i][0] = -1;
@@ -674,7 +674,7 @@ public class AlignSeq
         E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] - gapExtend);
         F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] - gapExtend);
 
-        float pairwiseScore = scoreModel.getPairwiseScore(s1str.charAt(i),
+        float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
                 s2str.charAt(j));
         score[i][j] = max(score[i - 1][j - 1]
                 + (pairwiseScore * 10), E[i][j], F[i][j]);
@@ -776,7 +776,7 @@ public class AlignSeq
     for (int i = 0; i < s.length(); i++)
     {
       char c = s.charAt(i);
-      encoded[i] = scoreModel.getMatrixIndex(c);
+      encoded[i] = scoreMatrix.getMatrixIndex(c);
     }
 
     return encoded;

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 885c3bf..f75c756 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -273,7 +273,6 @@ 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)
@@ -322,14 +321,6 @@ 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!
    */

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 24961c0..3715acc 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -66,8 +66,6 @@ public class GPCAPanel extends JInternalFrame
 
   protected JCheckBoxMenuItem protSetting = new JCheckBoxMenuItem();
 
-  protected JCheckBoxMenuItem jvVersionSetting = new JCheckBoxMenuItem();
-
   protected JLabel statusBar = new JLabel();
 
   protected JPanel statusPanel = new JPanel();
@@ -299,17 +297,7 @@ public class GPCAPanel extends JInternalFrame
         protSetting_actionPerfomed(arg0);
       }
     });
-    jvVersionSetting.setText(MessageManager
-            .getString("label.jalview_pca_calculation"));
-    jvVersionSetting.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent arg0)
-      {
-        jvVersionSetting_actionPerfomed(arg0);
-      }
-    });
-    // calcSettings.add(jvVersionSetting); // todo remove? JAL-2416
+
     calcSettings.add(nuclSetting);
     calcSettings.add(protSetting);
     calcSettings.add(scoreModelMenu);
@@ -435,10 +423,4 @@ public class GPCAPanel extends JInternalFrame
   {
 
   }
-
-  protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
-  {
-    // TODO Auto-generated method stub
-
-  }
 }