X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=dfd120b6363c8ec86e8df74c4249b1e21ec927d8;hb=96356075a122b745936738f478a8ee33ac7e0f0a;hp=a70e382d3594deac5fb9fc5d0c6390ab720bbb9e;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a70e382..dfd120b 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -52,6 +52,7 @@ 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;
@@ -79,7 +80,7 @@ import java.util.Map;
 public abstract class AlignmentViewport implements AlignViewportI,
         CommandListener, VamsasSource
 {
-  protected ViewportRanges ranges;
+  final protected ViewportRanges ranges;
 
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -91,9 +92,21 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   FeaturesDisplayedI featuresDisplayed = null;
 
-  protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> historyList = new ArrayDeque<>();
 
-  protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> redoList = new ArrayDeque<>();
+  
+
+  /**
+   * alignment displayed in the viewport. Please use get/setter
+   */
+  protected AlignmentI alignment;
+
+  public AlignmentViewport(AlignmentI al)
+  {
+    setAlignment(al);
+    ranges = new ViewportRanges(al);
+  }
 
   /**
    * @param name
@@ -555,10 +568,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setSeqNameItalics(default1);
   }
 
-  /**
-   * alignment displayed in the viewport. Please use get/setter
-   */
-  protected AlignmentI alignment;
+
 
   @Override
   public AlignmentI getAlignment()
@@ -600,7 +610,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean ignoreGapsInConsensusCalculation = false;
 
-  protected ResidueShaderI residueShading;
+  protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
+  protected ResidueShaderI residueShading = new ResidueShader();
 
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
@@ -687,6 +699,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected AlignmentAnnotation[] groupConservation;
 
+  protected AlignmentAnnotation hmmConsensus;
+
   /**
    * results of alignment consensus analysis for visible portion of view
    */
@@ -824,7 +838,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
+    if (consensus == null || !autoCalculateConsensus)
     {
       return;
     }
@@ -1104,7 +1118,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setHiddenColumns(HiddenColumns hidden)
   {
     this.alignment.setHiddenColumns(hidden);
-    // this.colSel = colsel;
   }
 
   @Override
@@ -1222,6 +1235,21 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   }
 
+  public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
+  {
+    ignoreBelowBackGroundFrequencyCalculation = b;
+    if (ap != null)
+    {
+      // updateConsensus(ap);
+      if (residueShading != null)
+      {
+        residueShading.setThreshold(residueShading.getThreshold(),
+                ignoreBelowBackGroundFrequencyCalculation);
+      }
+    }
+
+  }
+
   private long sgrouphash = -1, colselhash = -1;
 
   /**
@@ -1276,6 +1304,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ignoreGapsInConsensusCalculation;
   }
 
+  public boolean isIgnoreBelowBackground()
+  {
+    return ignoreBelowBackGroundFrequencyCalculation;
+  }
+
   // property change stuff
   // JBPNote Prolly only need this in the applet version.
   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
@@ -1287,7 +1320,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showConsensus = true;
 
-  private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+  protected boolean showOccupancy = true;
+
+  private Map<SequenceI, Color> sequenceColours = new HashMap<>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -1356,7 +1391,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (start == end)
     {
-      colSel.hideSelectedColumns(start, alignment);
+      colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
     }
     else
     {
@@ -1517,7 +1552,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+      hiddenRepSequences = new Hashtable<>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1725,7 +1760,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public List<int[]> getVisibleRegionBoundaries(int min, int max)
   {
-    ArrayList<int[]> regions = new ArrayList<int[]>();
+    ArrayList<int[]> regions = new ArrayList<>();
     int start = min;
     int end = max;
 
@@ -1768,7 +1803,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
           boolean selectedOnly)
   {
-    ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
     AlignmentAnnotation[] aa;
     if ((aa = alignment.getAlignmentAnnotation()) != null)
     {
@@ -1899,14 +1934,12 @@ 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);
-      gapcounts = new AlignmentAnnotation("Occupancy",
-              "Number of aligned positions",
-              new Annotation[1], 0f, alignment.getHeight(),
-              AlignmentAnnotation.BAR_GRAPH);
-      initGapCounts(gapcounts);
+
+      initGapCounts();
 
       initComplementConsensus();
     }
@@ -1940,7 +1973,9 @@ 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;
@@ -1963,15 +1998,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   // these should be extracted from the view model - style and settings for
   // derived annotation
-  private void initGapCounts(AlignmentAnnotation counts)
+  private void initGapCounts()
   {
-    counts.hasText = false;
-    counts.autoCalculated = true;
-    counts.graph = AlignmentAnnotation.BAR_GRAPH;
-
-    if (showConsensus)
+    if (showOccupancy)
     {
-      alignment.addAnnotation(counts);
+      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);
     }
   }
 
@@ -1982,8 +2022,8 @@ 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;
@@ -1999,7 +2039,7 @@ 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;
@@ -2012,7 +2052,8 @@ 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;
@@ -2117,7 +2158,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     // intersect alignment annotation with alignment groups
 
     AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
-    List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> oldrfs = new ArrayList<>();
     if (aan != null)
     {
       for (int an = 0; an < aan.length; an++)
@@ -2659,6 +2700,18 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setScaleProteinAsCdna(b);
   }
 
+  @Override
+  public boolean isProteinFontAsCdna()
+  {
+    return viewStyle.isProteinFontAsCdna();
+  }
+
+  @Override
+  public void setProteinFontAsCdna(boolean b)
+  {
+    viewStyle.setProteinFontAsCdna(b);
+  }
+
   /**
    * @return true if view should scroll to show the highlighted region of a
    *         sequence
@@ -2818,8 +2871,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionIsDefinedGroup = gps.contains(selectionGroup);
       }
     }
-    return selectionGroup.getContext() == alignment
-            || selectionIsDefinedGroup;
+    return selectionGroup.isDefined() || selectionIsDefinedGroup;
   }
 
   /**
@@ -2844,4 +2896,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return searchResults;
   }
+  
+
 }