JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 4941b11..98f44c6 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -83,7 +84,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
 
     sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
-
     alabels = new AnnotationLabels(this);
 
     setAnnotationVisible(av.showAnnotation);
@@ -137,7 +137,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
         }
       }
     });
-
   }
 
   public SequenceRenderer getSequenceRenderer()
@@ -434,6 +433,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       annotationSpaceFillerHolder.setVisible(b);
       annotationPanelHolder.setVisible(b);
+    } else {
+      annotationSpaceFillerHolder.setVisible(false);
+      annotationPanelHolder.setVisible(false);
     }
     validate();
     repaint();
@@ -479,12 +481,27 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     int mheight = height;
     Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
     int seqandannot = d.height - scalePanelHolder.getSize().height;
-    // sets initial preferred height
-    if ((height + 40) > seqandannot / 2)
+
+    if (adjustPanelHeight)
     {
-      height = seqandannot / 2;
+      // NOTE: this logic is different in the application. Need a better algorithm to define behaviour
+      // sets initial preferred height
+      // try and set height according to alignment
+      float sscaling = (float) ((av.getCharHeight() * av.getAlignment().getHeight())/(1.0*mheight));
+      if (sscaling > 0.5)
+      {
+        // if the alignment is too big then
+        // default is 0.5 split
+        height = seqandannot / 2;
+      }
+      else
+      {
+        // otherwise just set the panel so that one row of sequence is visible 
+        height = -av.getCharHeight() * 1
+                + (int) (seqandannot * (1 - sscaling));
+      }
     }
-    if (!adjustPanelHeight)
+    else
     {
       // maintain same window layout whilst updating sliders
       height = annotationPanelHolder.getSize().height;
@@ -498,7 +515,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     alabels.setSize(new Dimension(e.width, height));
     annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
     annotationPanelHolder.setSize(new Dimension(d.width, height));
-    seqPanelHolder.setSize(d.width, seqandannot - height);
+    // seqPanelHolder.setSize(d.width, seqandannot - height);
     seqPanel.seqCanvas
             .setSize(d.width, seqPanel.seqCanvas.getSize().height);
     int s = apvscroll.getValue();
@@ -507,8 +524,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       s = 0;
     }
     apvscroll.setValues(s, height, 0, mheight);
-    annotationPanel.setScrollOffset(apvscroll.getValue());
-    alabels.setScrollOffset(apvscroll.getValue());
+    annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+    alabels.setScrollOffset(apvscroll.getValue(), false);
   }
 
   public void setWrapAlignment(boolean wrap)
@@ -530,12 +547,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       annotationPanelHolder.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
     }
-
+    
     idSpaceFillerPanel1.setVisible(!wrap);
 
     fontChanged(); // This is so that the scalePanel is resized correctly
 
     validate();
+    sequenceHolderPanel.revalidate();
     repaint();
 
   }
@@ -672,8 +690,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if (evt == null || evt.getSource() == apvscroll)
     {
-      annotationPanel.setScrollOffset(apvscroll.getValue());
-      alabels.setScrollOffset(apvscroll.getValue());
+      annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+      alabels.setScrollOffset(apvscroll.getValue(), false);
       // annotationPanel.image=null;
       // alabels.image=null;
       // alabels.repaint();
@@ -803,12 +821,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-    alabels.repaint();
-
     seqPanel.seqCanvas.repaint();
-    scalePanel.repaint();
-    annotationPanel.repaint();
     idPanel.idCanvas.repaint();
+    if (!av.wrapAlignment) 
+    {
+      if (av.showAnnotation)
+      {
+        alabels.repaint();
+        annotationPanel.repaint();
+      }
+      scalePanel.repaint();
+    }
+    
   }
 
   protected Panel sequenceHolderPanel = new Panel();