JAL-2480 JAL-2505 guard against duplicating links

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 5f84a5d..fa3a8a7 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,6 +20,17 @@
  */
 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.List;
+import java.util.Map;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
@@ -51,23 +62,13 @@ import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
 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.List;
-import java.util.Map;
-
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -674,6 +675,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected AlignmentAnnotation complementConsensus;
 
+  protected AlignmentAnnotation gapcounts;
+
   protected AlignmentAnnotation strucConsensus;
 
   protected AlignmentAnnotation conservation;
@@ -776,6 +779,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
+  public AlignmentAnnotation getAlignmentGapAnnotation()
+  {
+    return gapcounts;
+  }
+
+  @Override
   public AlignmentAnnotation getComplementConsensusAnnotation()
   {
     return complementConsensus;
@@ -1276,6 +1285,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showConsensus = true;
 
+  protected boolean showOccupancy = true;
+
   private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
@@ -1882,19 +1893,21 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         initRNAStructure();
       }
-      consensus = new AlignmentAnnotation("Consensus", "PID",
+      consensus = new AlignmentAnnotation("Consensus",
+              MessageManager.getString("label.consensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
+      initGapCounts();
 
       initComplementConsensus();
     }
   }
 
   /**
-   * If this is a protein alignment and there are mappings to cDNA, add the cDNA
-   * consensus annotation.
+   * If this is a protein alignment and there are mappings to cDNA, adds the
+   * cDNA consensus annotation and returns true, else returns false.
    */
-  public void initComplementConsensus()
+  public boolean initComplementConsensus()
   {
     if (!alignment.isNucleotide())
     {
@@ -1918,12 +1931,16 @@ public abstract class AlignmentViewport implements AlignViewportI,
         if (doConsensus)
         {
           complementConsensus = new AlignmentAnnotation("cDNA Consensus",
-                  "PID for cDNA", new Annotation[1], 0f, 100f,
+                  MessageManager
+                          .getString("label.complement_consensus_descr"),
+                  new Annotation[1], 0f, 100f,
                   AlignmentAnnotation.BAR_GRAPH);
           initConsensus(complementConsensus);
+          return true;
         }
       }
     }
+    return false;
   }
 
   private void initConsensus(AlignmentAnnotation aa)
@@ -1937,6 +1954,25 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
+  // these should be extracted from the view model - style and settings for
+  // derived annotation
+  private void initGapCounts()
+  {
+    if (showOccupancy)
+    {
+      gapcounts = new AlignmentAnnotation("Occupancy",
+              MessageManager.getString("label.occupancy_descr"),
+              new Annotation[1], 0f,
+              alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+      gapcounts.hasText = true;
+      gapcounts.autoCalculated = true;
+      gapcounts.scaleColLabel = true;
+      gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+      alignment.addAnnotation(gapcounts);
+    }
+  }
+
   private void initConservation()
   {
     if (showConservation)
@@ -1944,8 +1980,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       if (conservation == null)
       {
         conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than "
-                        + getConsPercGaps() + "% gaps", new Annotation[1],
+                MessageManager.formatMessage("label.conservation_descr",
+                        getConsPercGaps()), new Annotation[1],
                 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
@@ -1961,7 +1997,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       if (quality == null)
       {
         quality = new AlignmentAnnotation("Quality",
-                "Alignment Quality based on Blosum62 scores",
+                MessageManager.getString("label.quality_descr"),
                 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         quality.hasText = true;
         quality.autoCalculated = true;
@@ -1974,7 +2010,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (alignment.hasRNAStructure() && strucConsensus == null)
     {
-      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+      strucConsensus = new AlignmentAnnotation("StrucConsensus",
+              MessageManager.getString("label.strucconsensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       strucConsensus.hasText = true;
       strucConsensus.autoCalculated = true;
@@ -2760,7 +2797,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean selectionIsDefinedGroup = false;
 
-
   @Override
   public boolean isSelectionDefinedGroup()
   {