X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=a648b348efa986e239a00f56afdf26a39d267168;hb=17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35;hp=75cb45b718e84224215197065fcc87b84c990d79;hpb=6b13a606027284408286d1cd2833470d1f9b9bfe;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 75cb45b..a648b34 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,6 +20,18 @@
  */
 package jalview.viewmodel;
 
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
@@ -29,6 +41,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeaturesDisplayedI;
 import jalview.api.ViewStyleI;
+import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
@@ -37,6 +50,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.ProfilesI;
@@ -45,6 +59,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.project.Jalview2XML;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
@@ -61,18 +76,6 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -100,6 +103,11 @@ public abstract class AlignmentViewport
   protected Deque<CommandI> redoList = new ArrayDeque<>();
 
   /**
+   * used to determine if quit should be confirmed
+   */
+  private boolean savedUpToDate = false;
+
+  /**
    * alignment displayed in the viewport. Please use get/setter
    */
   protected AlignmentI alignment;
@@ -664,8 +672,7 @@ public abstract class AlignmentViewport
          * retain any colour thresholds per group while
          * changing choice of colour scheme (JAL-2386)
          */
-        sg.setColourScheme(
-                cs == null ? null : cs.getInstance(this, sg));
+        sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg));
         if (cs != null)
         {
           sg.getGroupColourScheme().alignmentChanged(sg,
@@ -1821,9 +1828,8 @@ public abstract class AlignmentViewport
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
         if (selectedOnly && selectionGroup != null)
         {
-          clone.makeVisibleAnnotation(
-                  selectionGroup.getStartRes(), selectionGroup.getEndRes(),
-                  alignment.getHiddenColumns());
+          clone.makeVisibleAnnotation(selectionGroup.getStartRes(),
+                  selectionGroup.getEndRes(), alignment.getHiddenColumns());
         }
         else
         {
@@ -2616,6 +2622,8 @@ public abstract class AlignmentViewport
     {
       this.historyList.push(command);
       broadcastCommand(command, false);
+      setSavedUpToDate(false);
+      Jalview2XML.setStateSavedUpToDate(false);
     }
   }
 
@@ -2933,6 +2941,12 @@ public abstract class AlignmentViewport
     return searchResults;
   }
 
+  @Override
+  public ContactListI getContactList(AlignmentAnnotation _aa, int column)
+  {
+    return alignment.getContactListFor(_aa, column);
+  }
+
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.
@@ -2987,7 +3001,8 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
+  public AlignmentExportData getAlignExportData(
+          AlignExportSettingsI options)
   {
     AlignmentI alignmentToExport = null;
     String[] omitHidden = null;
@@ -3015,7 +3030,7 @@ public abstract class AlignmentViewport
             omitHidden, alignmentStartEnd);
     return ed;
   }
-  
+
   /**
    * flag set to indicate if structure views might be out of sync with sequences
    * in the alignment
@@ -3097,4 +3112,18 @@ public abstract class AlignmentViewport
     return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
             false));
   }
+
+  public void setSavedUpToDate(boolean s)
+  {
+    Console.debug(
+            "Setting " + this.getViewId() + " setSavedUpToDate to " + s);
+    savedUpToDate = s;
+  }
+
+  public boolean savedUpToDate()
+  {
+    Console.debug("Returning " + this.getViewId() + " savedUpToDate value: "
+            + savedUpToDate);
+    return savedUpToDate;
+  }
 }