Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 75cb45b..7e0b6b4 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;
@@ -55,24 +72,13 @@ import jalview.util.Comparison;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.IdColumns;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
 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 +106,11 @@ 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 +675,7 @@ 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,
@@ -925,7 +935,7 @@ public abstract class AlignmentViewport
     }
     if (calculator.workingInvolvedWith(alignmentAnnotation))
     {
-      // System.err.println("grey out ("+alignmentAnnotation.label+")");
+      // jalview.bin.Console.errPrintln("grey out ("+alignmentAnnotation.label+")");
       return true;
     }
     return false;
@@ -1198,7 +1208,7 @@ public abstract class AlignmentViewport
   {
     if (sequenceSetID != null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Warning - overwriting a sequenceSetId for a viewport!");
     }
     sequenceSetID = new String(newid);
@@ -1821,9 +1831,8 @@ 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
         {
@@ -2092,7 +2101,7 @@ public abstract class AlignmentViewport
       {
         if (aa == null)
         {
-          System.err.println("Null annotation row: ignoring.");
+          jalview.bin.Console.errPrintln("Null annotation row: ignoring.");
           continue;
         }
         if (!aa.visible)
@@ -2124,7 +2133,7 @@ public abstract class AlignmentViewport
 
         if (aa.graph > 0)
         {
-          aa.height += aa.graphHeight;
+          aa.height += aa.graphHeight+20;
         }
 
         if (aa.height == 0)
@@ -2285,7 +2294,7 @@ public abstract class AlignmentViewport
   {
     if (this == av)
     {
-      System.err.println("Ignoring recursive setCodingComplement request");
+      jalview.bin.Console.errPrintln("Ignoring recursive setCodingComplement request");
     }
     else
     {
@@ -2616,6 +2625,8 @@ public abstract class AlignmentViewport
     {
       this.historyList.push(command);
       broadcastCommand(command, false);
+      setSavedUpToDate(false);
+      Jalview2XML.setStateSavedUpToDate(false);
     }
   }
 
@@ -2933,6 +2944,19 @@ 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.
@@ -2987,7 +3011,8 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
+  public AlignmentExportData getAlignExportData(
+          AlignExportSettingsI options)
   {
     AlignmentI alignmentToExport = null;
     String[] omitHidden = null;
@@ -3015,7 +3040,7 @@ 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 +3122,46 @@ public abstract class AlignmentViewport
     return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
             false));
   }
+
+  /**
+   * ordered list of annotation values displayed per sequence in ID panel
+   */
+  private IdColumns id_columns = null;
+
+  /**
+   * available and currently visible columns for this view
+   */
+  @Override
+  public IdColumns getIdColumns()
+  {
+    if (alignment == null)
+    {
+      return null;
+    }
+    if (id_columns == null)
+    {
+      id_columns = new IdColumns(alignment);
+    }
+    return id_columns;
+  }
+
+  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;
+  }
 }