JAL-1136 give pre-existing custom settings a special name when job parameter settings...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 304cfb7..9818e6b 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -737,7 +737,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     updateEditMenuBar();
   }
-
+  // methods for implementing IProgressIndicator
+  // need to refactor to a reusable stub class
   Hashtable progressBars, progressBarHandlers;
 
   /*
@@ -829,6 +830,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *
    * @return true if any progress bars are still active
    */
+  @Override
   public boolean operationInProgress()
   {
     if (progressBars != null && progressBars.size() > 0)
@@ -878,7 +880,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         for (int i = 0; i < frames.length; i++)
         {
           if (frames[i] instanceof AlignFrame && frames[i] != this
-                  && ((AlignFrame) frames[i]).fileName.equals(fileName))
+                  && ((AlignFrame) frames[i]).fileName!=null && ((AlignFrame) frames[i]).fileName.equals(fileName))
           {
             try
             {
@@ -1779,6 +1781,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       int alwidth = 0;
+      ArrayList<Integer> newGraphGroups=new ArrayList<Integer>();
+      int fgroup=-1;
 
       if (newAlignment)
       {
@@ -1846,6 +1850,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           newDs.clear(); // tidy up
         }
+        if (alignment.getAlignmentAnnotation()!=null)
+        {
+          for (AlignmentAnnotation alan:alignment.getAlignmentAnnotation())
+          {
+            if (alan.graphGroup>fgroup)
+            {
+              fgroup=alan.graphGroup;
+            }
+          }
+        }
         if (pastedal.getAlignmentAnnotation() != null)
         {
           // Add any annotation attached to alignment.
@@ -1856,6 +1870,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
             {
               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+              if (newann.graphGroup>-1)
+              {
+                if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+                {
+                  for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+              }
+
               newann.padAnnotation(alwidth);
               alignment.addAnnotation(newann);
             }
@@ -1875,11 +1902,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (sequences[i].getAnnotation() != null)
         {
+          AlignmentAnnotation newann;
           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
           {
             annotationAdded = true;
-            sequences[i].getAnnotation()[a].adjustForAlignment();
-            sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+            newann=sequences[i].getAnnotation()[a];
+            newann.adjustForAlignment();
+            newann.padAnnotation(alwidth);
+            if (newann.graphGroup>-1)
+            {
+              if (newann.graphGroup>-1)
+              {
+                if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+                {
+                  for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+              }
+            }
             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
             // was
             // duplicated
@@ -1919,6 +1963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   newann.padAnnotation(avwidth);
                   alview[avnum].addAnnotation(newann); // annotation was
                   // duplicated earlier
+                  // TODO JAL-1145 graphGroups are not updated for sequence annotation added to several views. This may cause strangeness
                   alview[avnum].setAnnotationIndex(newann, a);
                 }
               }
@@ -1928,6 +1973,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         viewport.firePropertyChange("alignment", null,
                 alignment.getSequences());
+        if (alignPanels!=null ) {for (AlignmentPanel ap:((Vector<AlignmentPanel>)alignPanels))
+        {
+          ap.validateAnnotationDimensions(false);
+        }} else { alignPanel.validateAnnotationDimensions(false);}
 
       }
       else
@@ -4112,7 +4161,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   "Secondary Structure Prediction");
           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
           final JMenu analymenu = new JMenu("Analysis");
-          final JMenu dismenu = new JMenu("Disorder");
+          final JMenu dismenu = new JMenu("Protein Disorder");
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@ -4240,6 +4289,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               } catch (Exception e)
               {
+                Cache.log.debug("Exception during web service menu building process.",e);
               }
               ;
             }