X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=8e02a9c3c7cbce6c68e5ada9b25730e11b81d724;hb=d2f3c59deebfd9ea52b0021ab31467c18b9d2c14;hp=00f27aaac335738f261495cec9644fc724b1c073;hpb=8f56279671fd43b29887fcb33efb52795287342c;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 00f27aa..8e02a9c 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -32,6 +32,8 @@ import java.io.*;
 
 import javax.swing.*;
 
+import org.biojava.dasobert.eventmodel.*;
+
 
 /**
  * DOCUMENT ME!
@@ -40,7 +42,7 @@ import javax.swing.*;
  * @version $Revision$
  */
 public class AlignmentPanel extends GAlignmentPanel
-    implements AdjustmentListener, Printable
+    implements AdjustmentListener, Printable, FeatureListener
 {
   public AlignViewport av;
   OverviewPanel overviewPanel;
@@ -92,11 +94,8 @@ public class AlignmentPanel extends GAlignmentPanel
 
     setScrollValues(0, 0);
 
-    annotationPanel.adjustPanelHeight();
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
-                                                 getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.
-                                        getPreferredSize());
+    adjustAnnotationHeight();
+
     setAnnotationVisible(av.getShowAnnotation());
 
     hscroll.addAdjustmentListener(this);
@@ -161,18 +160,15 @@ public class AlignmentPanel extends GAlignmentPanel
             break;
 
           case KeyEvent.VK_DELETE:
-            if(av.cursorMode)
-            {
-              seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
-            }
-            break;
-
           case KeyEvent.VK_BACK_SPACE:
             if(!av.cursorMode)
             {
               alignFrame.cut_actionPerformed(null);
               seqPanel.seqCanvas.repaint();
             }
+            else
+              seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
+
             break;
 
           case KeyEvent.VK_S:
@@ -249,6 +245,22 @@ public class AlignmentPanel extends GAlignmentPanel
     });
   }
 
+  public void comeBackLater(FeatureEvent evt)
+  {}
+
+  public void newFeatures(FeatureEvent evt)
+  {
+    if (evt.getFeatures().length > 0)
+    {
+      seqPanel.seqCanvas.fr.featuresAdded();
+      repaint();
+    }
+    else
+    {
+      System.out.println("No Features found for "+evt.getDasSource().getNickname());
+    }
+  }
+
   /**
    * DOCUMENT ME!
    */
@@ -371,16 +383,21 @@ public class AlignmentPanel extends GAlignmentPanel
       }
       else
       {
-        int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-        if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
-        {
-          vscroll.setValue(start / cwidth);
-          av.startRes = vscroll.getValue() * cwidth;
-        }
+        scrollToWrappedVisible(start);
       }
     }
   }
 
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+    if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -416,6 +433,37 @@ public class AlignmentPanel extends GAlignmentPanel
     repaint();
   }
 
+  public void adjustAnnotationHeight()
+  {
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+          while(alignFrame.getHeight()==0)
+          {
+            Thread.yield();
+          }
+
+        int height = annotationPanel.adjustPanelHeight();
+
+        if (height > alignFrame.getHeight() / 2)
+        {
+          height = alignFrame.getHeight() / 2;
+        }
+
+        annotationScroller.setPreferredSize(
+            new Dimension(annotationScroller.getWidth(),
+                          height));
+
+        annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            annotationSpaceFillerHolder.getWidth(),
+            height));
+
+        annotationPanel.repaint();
+      }
+    });
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -941,7 +989,6 @@ public class AlignmentPanel extends GAlignmentPanel
   {
     int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
     int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
-
     if (idPanel.getWidth() == 0)
     {
       width += calculateIdWidth().getWidth() + 4;
@@ -950,7 +997,15 @@ public class AlignmentPanel extends GAlignmentPanel
     if (av.getWrapAlignment())
     {
       height = getWrappedHeight();
-      width = seqPanel.getWidth() + idPanel.getWidth();
+      if (System.getProperty("java.awt.headless") != null
+          && System.getProperty("java.awt.headless").equals("true"))
+      {
+        width = alignFrame.getWidth() - 22;
+      }
+      else
+
+        width = seqPanel.getWidth() + idPanel.getWidth();
+
     }
     else if (av.getShowAnnotation())
     {
@@ -1123,9 +1178,9 @@ public class AlignmentPanel extends GAlignmentPanel
                       if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
                         text.append(" " + features[f].getDescription());
 
-                      if (features[f].getStatus() != null && features[f].getStatus().length()>0)
+                      if (features[f].getValue("status") != null )
                       {
-                        text.append(" (" + features[f].getStatus() + ")");
+                        text.append(" (" + features[f].getValue("status") + ")");
                       }
                     }
                   }
@@ -1153,9 +1208,19 @@ public class AlignmentPanel extends GAlignmentPanel
 
   int getWrappedHeight()
   {
+    int seqPanelWidth = seqPanel.seqCanvas.getWidth();
+
+    //If headless, seqPanel will have 0 width
+    if (System.getProperty("java.awt.headless") != null
+              && System.getProperty("java.awt.headless").equals("true"))
+    {
+      int idWidth = calculateIdWidth().width + 4;
+      seqPanelWidth = alignFrame.getWidth() - idWidth;
+    }
 
     int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
-        seqPanel.seqCanvas.getWidth());
+        seqPanelWidth
+          );
 
     int hgap = av.charHeight;
     if (av.scaleAboveWrapped)