X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5529f2c59b4bde5ea61213a9ac395616de27d531;hb=acfc0d246c770a0a1e9cea7cb7fc40cf11f03ca7;hp=45a0c856f812c828ed6bb9f34be7738e5e8e09ae;hpb=98897348951ee59ce6c6ff7e0e2789a5f115030f;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 45a0c85..5529f2c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -610,7 +610,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showTranslation.setVisible(nucleotide);
     conservationMenuItem.setEnabled(!nucleotide);
     modifyConservation.setEnabled(!nucleotide);
-
+    showGroupConservation.setEnabled(!nucleotide);
     // Remember AlignFrame always starts as protein
     if (!nucleotide)
     {
@@ -655,6 +655,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showUnconservedMenuItem.setSelected(av.showUnconserved);
     showGroupConsensus.setSelected(av.showGroupConsensus);
     showGroupConservation.setSelected(av.showGroupConservation);
+    showConsensusHistogram.setSelected(av.showConsensusHistogram);
+    showConsensusProfile.setSelected(av.showConsensusProfile);
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
@@ -685,20 +687,21 @@ 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 +718,7 @@ 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 +1252,7 @@ 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 +1299,7 @@ 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 +1327,7 @@ 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 +2497,12 @@ 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 +3597,8 @@ 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;
   }
@@ -3767,9 +3778,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   .getServiceClient(sh);
           impl.attachWSMenuEntry(seqsrchmenu, this);
         }
-        // finally, add the whole shebang onto the webservices menu
         wsmenu.add(seqsrchmenu);
       }
+      // finally, add the whole shebang onto the webservices menu
       resetWebServiceMenu();
       for (int i = 0, j = wsmenu.size(); i < j; i++)
       {
@@ -3792,6 +3803,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     webService.removeAll();
     build_fetchdbmenu(webService);
+    build_urlServiceMenu(webService);
+  }
+
+  /**
+   * construct any groupURL type service menu entries.
+   * @param webService
+   */
+  private void build_urlServiceMenu(JMenu webService)
+  {
+    jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(webService, this);
   }
 
   /*
@@ -4471,7 +4492,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showGroupConsensus_actionPerformed(ActionEvent e)
   {
     viewport.setShowGroupConsensus(showGroupConsensus.getState());
-    alignPanel.updateAnnotation();
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
 
   }
 
@@ -4485,7 +4506,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showGroupConservation_actionPerformed(ActionEvent e)
   {
     viewport.setShowGroupConservation(showGroupConservation.getState());
-    alignPanel.updateAnnotation();
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt.event.ActionEvent)
+   */
+  protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt.event.ActionEvent)
+   */
+  protected void showConsensusProfile_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowConsensusProfile(showConsensusProfile.getState());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
+  protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+  {
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
 
   /*