JAL-2491 Tidies

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 769dc86..0d53172 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -401,9 +401,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       int start = r[0];
       int end = r[1];
-      // DEBUG
-      // System.err.println(this.av.viewName + " Seq : " + seqIndex
-      // + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -442,9 +439,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       seqIndex = Math.max(0, seqIndex - verticalOffset);
 
-      // System.out.println("start=" + start + ", end=" + end + ", startv="
-      // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
-      // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
         if ((startv = vpRanges.getStartRes()) >= start)
@@ -452,7 +446,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
           /*
            * Scroll left to make start of search results visible
            */
-          // setScrollValues(start - 1, seqIndex); // plus one residue
           setScrollValues(start, seqIndex);
         }
         else if ((endv = vpRanges.getEndRes()) <= end)
@@ -460,7 +453,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
           /*
            * Scroll right to make end of search results visible
            */
-          // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
           setScrollValues(startv + end - endv, seqIndex);
         }
         else if ((starts = vpRanges.getStartSeq()) > seqIndex)
@@ -659,8 +651,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          visible row to scroll to
    * 
    */
-  public void setScrollValues(int x, int y)
+  public void setScrollValues(int xpos, int ypos)
   {
+    int x = xpos;
+    int y = ypos;
+
     if (av == null || av.getAlignment() == null)
     {
       return;
@@ -672,7 +667,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-
       int width = av.getAlignment().getWidth();
       int height = av.getAlignment().getHeight();
 
@@ -722,10 +716,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Respond to adjustment event when horizontal or vertical scrollbar is
+   * changed
    * 
    * @param evt
-   *          DOCUMENT ME!
+   *          adjustment event encoding whether hscroll or vscroll changed
    */
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -1841,6 +1836,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
     this.scrollComplementaryPanel = b;
   }
 
+  /**
+   * Get whether to scroll complement panel
+   * 
+   * @return true if cDNA/protein complement panels should be scrolled
+   */
   protected boolean isSetToScrollComplementPanel()
   {
     return this.scrollComplementaryPanel;