JAL-3680 check whether a sequence selection exists before sliding the sequence under...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4ff1b4f..61a6af6 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -33,6 +33,7 @@ import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.SimilarityParamsI;
@@ -535,7 +536,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
           }
           break;
 
@@ -546,7 +547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
           }
 
           break;
@@ -559,7 +560,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(-1, 0);
+            alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
           }
 
           break;
@@ -571,7 +572,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(1, 0);
+            alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
           }
           break;
 
@@ -1478,9 +1479,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           closeView(alignPanel);
         }
       }
-
       if (closeAllTabs)
       {
+        if (featureSettings != null && featureSettings.isOpen())
+        {
+          featureSettings.close();
+          featureSettings = null;
+        }
         /*
          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
          * be called recursively, with the frame now in 'closed' state
@@ -1735,19 +1740,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   synchronized void slideSequences(boolean right, int size)
   {
     List<SequenceI> sg = new ArrayList<>();
-    if (viewport.cursorMode)
-    {
-      sg.add(viewport.getAlignment()
-              .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
-    }
-    else if (viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() != viewport
-                    .getAlignment().getHeight())
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
+            .getSize() != viewport.getAlignment().getHeight())
     {
       sg = viewport.getSelectionGroup()
               .getSequences(viewport.getHiddenRepSequences());
     }
 
+    if (sg.size() == 0 && viewport.cursorMode)
+    {
+      sg.add(viewport.getAlignment()
+              .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
+    }
+
     if (sg.size() < 1)
     {
       return;
@@ -2092,7 +2097,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2139,7 +2144,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2445,7 +2450,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
-    viewport.setSelectionGroup(null);
+    viewport.setSearchResults(null);
     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
@@ -3104,7 +3109,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    // TODO: do we actually need to update overview for scale above change ?
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3118,6 +3123,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3131,6 +3137,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3184,9 +3191,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void featureSettings_actionPerformed(ActionEvent e)
   {
+    showFeatureSettingsUI();
+  }
+
+  @Override
+  public FeatureSettingsControllerI showFeatureSettingsUI()
+  {
     if (featureSettings != null)
     {
-      featureSettings.close();
+      featureSettings.closeOldSettings();
       featureSettings = null;
     }
     if (!showSeqFeatures.isSelected())
@@ -3196,6 +3209,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showSeqFeatures_actionPerformed(null);
     }
     featureSettings = new FeatureSettings(this);
+    return featureSettings;
   }
 
   /**
@@ -4489,7 +4503,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             int assocfiles = 0;
             if (filesmatched.size() > 0)
             {
-              boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+              boolean autoAssociate = Cache
+                      .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
               if (!autoAssociate)
               {
                 String msg = MessageManager.formatMessage(
@@ -4679,7 +4694,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             if (parseFeaturesFile(file, sourceType))
             {
-              alignPanel.paintAlignment(true, true);
+              SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+              if (splitFrame != null)
+              {
+                splitFrame.repaint();
+              }
+              else
+              {
+                alignPanel.paintAlignment(true, true);
+              }
             }
           }
           else
@@ -4735,6 +4758,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport = alignPanel.av;
       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
+      if (featureSettings != null && featureSettings.isOpen()
+              && featureSettings.fr.getViewport() != viewport)
+      {
+        if (viewport.isShowSequenceFeatures())
+        {
+          // refresh the featureSettings to reflect UI change
+          showFeatureSettingsUI();
+        }
+        else
+        {
+          // close feature settings for this view.
+          featureSettings.close();
+        }
+      }
+
     }
 
     /*
@@ -4932,6 +4970,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               @Override
               public void finished()
               {
+
+                for (FeatureSettingsModelI srcSettings : dbRefFetcher
+                        .getFeatureSettingsModels())
+                {
+
+                  alignPanel.av.mergeFeaturesStyle(srcSettings);
+                }
                 AlignFrame.this.setMenusForViewport();
               }
             });
@@ -5017,6 +5062,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                   @Override
                                   public void finished()
                                   {
+                                    FeatureSettingsModelI srcSettings = dassource[0]
+                                            .getFeatureColourScheme();
+                                    alignPanel.av.mergeFeaturesStyle(
+                                            srcSettings);
                                     AlignFrame.this.setMenusForViewport();
                                   }
                                 });
@@ -5643,6 +5692,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
   }
+
+  private Rectangle lastFeatureSettingsBounds = null;
+  @Override
+  public void setFeatureSettingsGeometry(Rectangle bounds)
+  {
+    lastFeatureSettingsBounds = bounds;
+  }
+
+  @Override
+  public Rectangle getFeatureSettingsGeometry()
+  {
+    return lastFeatureSettingsBounds;
+  }
 }
 
 class PrintThread extends Thread