formatting

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 58531de..375504d 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  * PURPOSE.  See the GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.analysis;
@@ -26,7 +26,7 @@ import jalview.datamodel.*;
  * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
  * This class is used extensively in calculating alignment colourschemes that
  * depend on the amount of conservation in each alignment column.
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -172,10 +172,10 @@ public class AAFrequency
       residueHash.put(MAXCOUNT, new Integer(maxCount));
       residueHash.put(MAXRESIDUE, maxResidue);
 
-      percentage = ((float) maxCount * 100) / (float) jSize;
+      percentage = ((float) maxCount * 100) / jSize;
       residueHash.put(PID_GAPS, new Float(percentage));
 
-      percentage = ((float) maxCount * 100) / (float) nongap;
+      percentage = ((float) maxCount * 100) / nongap;
       residueHash.put(PID_NOGAPS, new Float(percentage));
       result[i] = residueHash;
     }
@@ -184,7 +184,7 @@ public class AAFrequency
   /**
    * Compute all or part of the annotation row from the given consensus
    * hashtable
-   * 
+   *
    * @param consensus
    *          - pre-allocated annotation row
    * @param hconsensus
@@ -253,9 +253,9 @@ public class AAFrequency
         {
           for (int c = 0; c < alphabet.length; c++)
           {
-            tval = ((float) profile[0][alphabet[c]])
+            tval = profile[0][alphabet[c]]
                     * 100f
-                    / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+                    / profile[1][ignoreGapsInConsensusCalculation ? 1
                             : 0];
             mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
                     + ((int) tval) + "%";
@@ -269,7 +269,7 @@ public class AAFrequency
           {
             ca[c] = new char[]
             { (char) c };
-            vl[c] = (float) profile[0][c];
+            vl[c] = profile[0][c];
           }
           ;
           jalview.util.QuickSort.sort(vl, ca);
@@ -277,9 +277,9 @@ public class AAFrequency
           {
             if (((char[]) ca[c])[0] != '-')
             {
-              tval = ((float) profile[0][((char[]) ca[c])[0]])
+              tval = profile[0][((char[]) ca[c])[0]]
                       * 100f
-                      / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+                      / profile[1][ignoreGapsInConsensusCalculation ? 1
                               : 0];
               mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
                       + " " + ((int) tval) + "%";
@@ -301,7 +301,7 @@ public class AAFrequency
 
   /**
    * get the sorted profile for the given position of the consensus
-   * 
+   *
    * @param hconsensus
    * @return
    */
@@ -318,7 +318,7 @@ public class AAFrequency
     {
       ca[c] = new char[]
       { (char) c };
-      vl[c] = (float) profile[0][c];
+      vl[c] = profile[0][c];
     }
     ;
     jalview.util.QuickSort.sort(vl, ca);
@@ -329,7 +329,7 @@ public class AAFrequency
       if (((char[]) ca[c])[0] != '-')
       {
         rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
-        rtnval[rtnval[0]] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+        rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
                 : 0]);
         rtnval[1]+=rtnval[rtnval[0]++];
       }

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 4c56e69..ca78bda 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  * PURPOSE.  See the GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.appletgui;
@@ -64,7 +64,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
   SequenceNode highlightNode;
 
-  AlignmentPanel ap; 
+  AlignmentPanel ap;
   public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
   {
     this.ap = ap;
@@ -143,7 +143,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
       if (node.element() instanceof SequenceI)
       {
-        SequenceI seq = (SequenceI) ((SequenceNode) node).element();
+        SequenceI seq = (SequenceI) node.element();
 
         if (av.getSequenceColour(seq) == Color.white)
         {
@@ -194,13 +194,13 @@ public class TreeCanvas extends Panel implements MouseListener,
       Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,
               charWidth, charHeight);
 
-      nameHash.put((SequenceI) node.element(), rect);
+      nameHash.put(node.element(), rect);
 
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
       if (selected != null
               && selected.getSequences(null).contains(
-                      (SequenceI) node.element()))
+                      node.element()))
       {
         g.setColor(Color.gray);
 
@@ -224,7 +224,7 @@ public class TreeCanvas extends Panel implements MouseListener,
       int xend = (int) (height * scale) + offx;
       int ypos = (int) (node.ycount * chunk) + offy;
 
-      g.setColor(((SequenceNode) node).color.darker());
+      g.setColor(node.color.darker());
 
       // Draw horizontal line
       g.drawLine(xstart, ypos, xend, ypos);
@@ -390,11 +390,13 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     if (tree == null)
@@ -440,7 +442,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     // for
     // scrollbar
 
-    float wscale = (float) (width - labelLength - offx * 2)
+    float wscale = (width - labelLength - offx * 2)
             / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
@@ -466,25 +468,29 @@ public class TreeCanvas extends Panel implements MouseListener,
       }
 
       int x = (int) (threshold
-              * (float) (getSize().width - labelLength - 2 * offx) + offx);
+              * (getSize().width - labelLength - 2 * offx) + offx);
 
       g.drawLine(x, 0, x, getSize().height);
     }
 
   }
 
+  @Override
   public void mouseReleased(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseEntered(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
     if (highlightNode != null)
@@ -514,10 +520,12 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseDragged(MouseEvent ect)
   {
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     av.setCurrentTree(tree);
@@ -539,6 +547,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     av.setCurrentTree(tree);
@@ -657,7 +666,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
     }
     ap.updateAnnotation();
-    
+
   }
 
   public void setShowDistances(boolean state)