X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=18ebf0eb64c794816d71bbfe73512ae2f242481c;hb=32a72d077d2371f4566688fbd103103d8505b27f;hp=9e0bae63f95e8d4ed07c042303b78ee351589598;hpb=8ac358f8762f9a632d5dc70aa32df57ca0755244;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9e0bae6..18ebf0e 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -374,6 +374,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     alignPanels.addElement(ap);
 
+    PaintRefresher.Register(ap, ap.av.getSequenceSetId());
+
     int aSize = alignPanels.size();
 
     tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
@@ -466,10 +468,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   void setMenusFromViewport(AlignViewport av)
   {
+    padGapsMenuitem.setSelected(av.padGaps);
     colourTextMenuItem.setSelected(av.showColourText);
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
     conservationMenuItem.setSelected(av.getConservationSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
+    idRightAlign.setSelected(av.idsAlignRight);
     renderGapsMenuItem.setSelected(av.renderGaps);
     wrapMenuItem.setSelected(av.wrapAlignment);
     annotationPanelMenuItem.setState(av.showAnnotation);
@@ -563,7 +567,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       else
       {
         viewport.alignment.deleteAllGroups();
-        viewport.sequenceColours.clear();
+        viewport.sequenceColours=null;
         while (viewport.alignment.getHeight() > 0)
         {
           viewport.alignment.deleteSequence(0);
@@ -583,7 +587,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       }
 
       FileLoader loader = new FileLoader();
-      loader.LoadFile(viewport, fileName, "File", currentFileFormat);
+      String protocol = fileName.startsWith("http:")? "URL":"File";
+      loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
 
     }
   }
@@ -956,10 +961,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     viewport.redoList.push(command);
     command.undoCommand();
 
+
     viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null,null);
   }
 
   /**
@@ -975,7 +980,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
 
     updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null, null);
   }
 
 
@@ -1351,15 +1356,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
 
     Vector seqs = new Vector();
-    int cutLength = sg.getEndRes()-sg.getStartRes()+1;
-    boolean seqsCut = false;
     SequenceI seq;
     for (int i = 0; i < sg.getSize(false); i++)
     {
       seq = sg.getSequenceAt(i);
       seqs.addElement(seq);
-      if(seq.getLength()<=cutLength)
-        seqsCut = true;
     }
 
 
@@ -1458,7 +1459,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.repaint();
-    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   /**
@@ -1483,7 +1484,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   public void invertColSel_actionPerformed(ActionEvent e)
@@ -1732,6 +1733,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
+  public void idRightAlign_actionPerformed(ActionEvent e)
+  {
+    viewport.idsAlignRight = idRightAlign.isSelected();
+    alignPanel.repaint();
+  }
+
+
 
   /**
    * DOCUMENT ME!