JAL-1551 spotless

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 08af2ec..a8c93cf 100644 (file)
--- 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 +50,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.ProfilesI;
@@ -45,6 +60,8 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.QuitHandler;
+import jalview.project.Jalview2XML;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
@@ -61,18 +78,6 @@ 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 +105,11 @@ 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;
@@ -2614,6 +2624,8 @@ public abstract class AlignmentViewport
     {
       this.historyList.push(command);
       broadcastCommand(command, false);
+      setSavedUpToDate(false);
+      Jalview2XML.setStateSavedUpToDate(false);
     }
   }
 
@@ -2931,6 +2943,19 @@ public abstract class AlignmentViewport
     return searchResults;
   }
 
+  @Override
+  public ContactListI getContactList(AlignmentAnnotation _aa, int column)
+  {
+    return alignment.getContactListFor(_aa, column);
+  }
+
+  @Override
+  public ContactMatrixI getContactMatrix(
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    return alignment.getContactMatrixFor(alignmentAnnotation);
+  }
+
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.
@@ -3096,4 +3121,24 @@ public abstract class AlignmentViewport
     return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
             false));
   }
+
+  public void setSavedUpToDate(boolean s)
+  {
+    setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES);
+  }
+
+  public void setSavedUpToDate(boolean s, QuitHandler.Message m)
+  {
+    Console.debug(
+            "Setting " + this.getViewId() + " setSavedUpToDate to " + s);
+    savedUpToDate = s;
+    QuitHandler.setMessage(m);
+  }
+
+  public boolean savedUpToDate()
+  {
+    Console.debug("Returning " + this.getViewId() + " savedUpToDate value: "
+            + savedUpToDate);
+    return savedUpToDate;
+  }
 }