apply version 2.7 copyright

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 638a1c9..359c500 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -132,6 +132,24 @@ public class AnnotationPanel extends JPanel implements MouseListener,
    */
   public int adjustPanelHeight()
   {
+    int height=calcPanelHeight();
+    this.setPreferredSize(new Dimension(1, height));
+    if (ap != null)
+    {
+      // revalidate only when the alignment panel is fully constructed
+      ap.validate();
+    }
+
+    return height;
+  }
+
+  /**
+   * calculate the height for visible annotation, revalidating bounds where necessary
+   * ABSTRACT GUI METHOD
+   * @return total height of annotation
+   */
+  public int calcPanelHeight()
+  {
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
     int height = 0;
@@ -175,19 +193,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         height += aa[i].height;
       }
     }
-    if (height==0)
+    if (height == 0)
     {
       // set minimum
       height = 20;
     }
-
-    this.setPreferredSize(new Dimension(1, height));
-    if (ap != null)
-    {
-      // revalidate only when the alignment panel is fully constructed
-      ap.validate();
-    }
-
     return height;
   }
 
@@ -200,7 +210,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
   public void actionPerformed(ActionEvent evt)
   {
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    if (aa==null)
+    if (aa == null)
     {
       return;
     }
@@ -919,9 +929,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
               if (v == column)
               {
-                g
-                        .fillRect(x * av.charWidth, y, av.charWidth,
-                                av.charHeight);
+                g.fillRect(x * av.charWidth, y, av.charWidth, av.charHeight);
               }
             }
           }
@@ -1096,9 +1104,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           if (sCol == 0 || row.annotations[sCol - 1] == null
                   || row.annotations[sCol - 1].secondaryStructure != 'H')
           {
-            g
-                    .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8,
-                            90, 180);
+            g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
             x1 += av.charWidth / 2;
           }
 
@@ -1380,7 +1386,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }
       }
       // draw profile if available
-      if (aa.annotations[column].value != 0 && renderProfile)
+      if (renderProfile && aa.annotations[column].value != 0)
       {
         int profl[] = getProfileFor(aa, column);
         int ht = y1, htn = y2 - y1;// aa.graphHeight;
@@ -1416,8 +1422,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                                                       // group(aa.groupRef.cs==null)
                                                       // ? av.textColour2 :
                                                       // cs.findColour(dc));
-            g.drawChars(dc, 0, 1, x * av.charWidth, (int) (ht + lm
-                    .getHeight()));
+            g.drawChars(dc, 0, 1, x * av.charWidth,
+                    (int) (ht + lm.getHeight()));
             // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
           }
         }
@@ -1447,16 +1453,16 @@ public class AnnotationPanel extends JPanel implements MouseListener,
               && aa.groupRef.isShowSequenceLogo())
       {
         return AAFrequency.extractProfile(
-                aa.groupRef.consensusData[column], aa.groupRef
-                        .getIgnoreGapsConsensus());
+                aa.groupRef.consensusData[column],
+                aa.groupRef.getIgnoreGapsConsensus());
       }
       // TODO extend annotation row to enable dynamic and static profile data to
       // be stored
       if (aa.groupRef == null && aa.sequenceRef == null
               && av.isShowSequenceLogo())
       {
-        return AAFrequency.extractProfile(av.hconsensus[column], av
-                .getIgnoreGapsConsensus());
+        return AAFrequency.extractProfile(av.hconsensus[column],
+                av.getIgnoreGapsConsensus());
       }
     }
     return null;