FeatureColourI removed

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 45a0c85..dcb4b21 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -685,20 +685,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     JPanel progressPanel;
+    Long lId=new Long(id);
     GridLayout layout = (GridLayout) statusPanel.getLayout();
-    if (progressBars.get(new Long(id)) != null)
+    if (progressBars.get(lId) != null)
     {
       progressPanel = (JPanel) progressBars.get(new Long(id));
       statusPanel.remove(progressPanel);
-      progressBars.remove(progressPanel);
+      progressBars.remove(lId);
       progressPanel = null;
       if (message != null)
       {
         statusBar.setText(message);
       }
-      if (progressBarHandlers.contains(new Long(id)))
+      if (progressBarHandlers.contains(lId))
       {
-        progressBarHandlers.remove(new Long(id));
+        progressBarHandlers.remove(lId);
       }
       layout.setRows(layout.getRows() - 1);
     }
@@ -715,7 +716,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       layout.setRows(layout.getRows() + 1);
       statusPanel.add(progressPanel);
 
-      progressBars.put(new Long(id), progressPanel);
+      progressBars.put(lId, progressPanel);
     }
     // update GUI
     setMenusForViewport();
@@ -1249,7 +1250,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.historyList.push(command);
       viewport.redoList.clear();
       updateEditMenuBar();
-      viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      viewport.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
     }
   }
 
@@ -1296,7 +1297,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (originalSource != null)
     {
-      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
       originalSource.firePropertyChange("alignment", null,
               originalSource.alignment.getSequences());
     }
@@ -1324,7 +1325,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (originalSource != null)
     {
-      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
       originalSource.firePropertyChange("alignment", null,
               originalSource.alignment.getSequences());
     }
@@ -2494,6 +2495,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       featureSettings.close();
       featureSettings = null;
     }
+    if (!showSeqFeatures.isSelected())
+    {
+      // make sure features are actually displayed
+      showSeqFeatures.setSelected(true);
+      showSeqFeatures_actionPerformed(null);
+    }
     featureSettings = new FeatureSettings(this);
   }
 
@@ -3588,6 +3595,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       seqs.setSequences(new SeqCigar[]
       { seqs.getSequences()[0] });
+      // TODO: if seqs.getSequences().length>1 then should really have warned user!
+
     }
     return seqs;
   }