formatting

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

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 492683d..59cdb11 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -27,8 +27,9 @@ import jalview.datamodel.*;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
 
-public class AnnotationPanel extends Panel implements AwtRenderPanelI, AdjustmentListener,
-        ActionListener, MouseListener, MouseMotionListener
+public class AnnotationPanel extends Panel implements AwtRenderPanelI,
+        AdjustmentListener, ActionListener, MouseListener,
+        MouseMotionListener
 {
   AlignViewport av;
 
@@ -110,7 +111,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -133,7 +134,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     }
 
     String label = "";
-    if (av.getColumnSelection() != null && av.getColumnSelection().size() > 0
+    if (av.getColumnSelection() != null
+            && av.getColumnSelection().size() > 0
             && anot[av.getColumnSelection().getMin()] != null)
       label = anot[av.getColumnSelection().getMin()].displayCharacter;
 
@@ -326,7 +328,9 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
         item = new MenuItem(STEM);
         item.addActionListener(this);
         pop.add(item);
-      } else {
+      }
+      else
+      {
         item = new MenuItem(HELIX);
         item.addActionListener(this);
         pop.add(item);
@@ -390,7 +394,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
         av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
       }
       graphStretchY = evt.getY();
-      calcPanelHeight();
+      av.calcPanelHeight();
       needValidating = true;
       ap.paintAlignment(true);
     }
@@ -464,7 +468,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
 
   public int adjustPanelHeight(boolean repaint)
   {
-    int height = calcPanelHeight();
+    int height = av.calcPanelHeight();
     this.setSize(new Dimension(getSize().width, height));
     if (repaint)
     {
@@ -472,59 +476,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     }
     return height;
   }
+
   /**
-   * calculate the height for visible annotation, revalidating bounds where necessary
-   * ABSTRACT GUI METHOD
+   * 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.getAlignment().getAlignmentAnnotation();
-    int height = 0;
-
-    if (aa != null)
-    {
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (!aa[i].visible)
-        {
-          continue;
-        }
-
-        aa[i].height = 0;
-
-        if (aa[i].hasText)
-        {
-          aa[i].height += av.charHeight;
-        }
-
-        if (aa[i].hasIcons)
-        {
-          aa[i].height += 16;
-        }
-
-        if (aa[i].graph > 0)
-        {
-          aa[i].height += aa[i].graphHeight;
-        }
-
-        if (aa[i].height == 0)
-        {
-          aa[i].height = 20;
-        }
-
-        height += aa[i].height;
-      }
-    }
-    if (height == 0)
-    {
-      height = 20;
-    }
-
-    return height;
-
-  }
 
   public void addEditableColumn(int i)
   {
@@ -568,11 +526,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     Dimension d = getSize();
     imgWidth = d.width;
     // (av.endRes - av.startRes + 1) * av.charWidth;
-    if (imgWidth<1 || d.height<1)
+    if (imgWidth < 1 || d.height < 1)
     {
       return;
     }
-    if (image == null || imgWidth != image.getWidth(this) || d.height != image.getHeight(this))
+    if (image == null || imgWidth != image.getWidth(this)
+            || d.height != image.getHeight(this))
     {
       image = createImage(imgWidth, d.height);
       gg = image.getGraphics();
@@ -597,7 +556,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
 
   public void fastPaint(int horizontal)
   {
-    if (horizontal == 0 || av.getAlignment().getAlignmentAnnotation() == null
+    if (horizontal == 0
+            || av.getAlignment().getAlignmentAnnotation() == null
             || av.getAlignment().getAlignmentAnnotation().length < 1)
     {
       repaint();
@@ -630,7 +590,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param g
    *          DOCUMENT ME!
    * @param startRes