JAL-1551 spotlessApply

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 2177a26..ae8fdbc 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -605,7 +605,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
     else
     {
-      // no row (or row that can be adjusted) was pressed. Simulate a ruler click
+      // no row (or row that can be adjusted) was pressed. Simulate a ruler
+      // click
       ap.getScalePanel().mousePressed(evt);
     }
   }
@@ -739,27 +740,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
             }
             c--;
           }
-            c = to;
-            while (c < forCurrentX.getContactHeight())
+          c = to;
+          while (c < forCurrentX.getContactHeight())
+          {
+            cval = forCurrentX.getContactAt(c);
+            if (// cr.getMin() <= cval &&
+            cval <= thresh)
             {
-              cval = forCurrentX.getContactAt(c);
-              if (// cr.getMin() <= cval &&
-              cval <= thresh)
-              {
-                int[] cols = forCurrentX.getMappedPositionsFor(c, c);
-                if (cols != null)
-                {
-                  av.getColumnSelection().addRangeOfElements(cols, true);
-                }
-              }
-              else
+              int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+              if (cols != null)
               {
-                break;
+                av.getColumnSelection().addRangeOfElements(cols, true);
               }
-              c++;
-
             }
+            else
+            {
+              break;
+            }
+            c++;
+
           }
+        }
       }
     }
     ap.paintAlignment(false, false);
@@ -767,6 +768,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     av.sendSelection();
     return true;
   }
+
   /**
    * Construct and display a context menu at the right-click position
    * 
@@ -1031,7 +1033,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
     if (rowIndex[0] != toRowIndex[0])
     {
-      jalview.bin.Console.trace("Drag went to another row. needs to be clipped");
+      jalview.bin.Console
+              .trace("Drag went to another row. needs to be clipped");
     }
 
     // rectangular selection on matrix style annotation
@@ -1073,16 +1076,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         for (int pair = 0; pair < mappedPos.length; pair += 2)
         {
           for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
-//          {
-//            if (cma.sequenceRef != null)
-//            {
-//              int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
-//              av.getColumnSelection().addElement(col);
-//            }
-//            else
-            {
-              av.getColumnSelection().addElement(c);
-            }
+          // {
+          // if (cma.sequenceRef != null)
+          // {
+          // int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+          // av.getColumnSelection().addElement(col);
+          // }
+          // else
+          {
+            av.getColumnSelection().addElement(c);
+          }
         }
       }
       // and again for most recent corner of drag
@@ -1094,16 +1097,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         for (int pair = 0; pair < mappedPos.length; pair += 2)
         {
           jalview.bin.Console.trace("Marking " + fr + " to " + to
-                  + " mapping to sequence positions " + mappedPos[pair] + " to "
-                  + mappedPos[pair+1]);
+                  + " mapping to sequence positions " + mappedPos[pair]
+                  + " to " + mappedPos[pair + 1]);
           for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
           {
-//            if (cma.sequenceRef != null)
-//            {
-//              int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
-//              av.getColumnSelection().addElement(col);
-//            }
-//            else
+            // if (cma.sequenceRef != null)
+            // {
+            // int col =
+            // cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+            // av.getColumnSelection().addElement(col);
+            // }
+            // else
             {
               av.getColumnSelection().addElement(c);
             }
@@ -1280,7 +1284,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
         tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
                 + " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
-        
+
         int col = ann.sequenceRef.findPosition(column);
         int[][] highlightPos;
         int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd);