X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=dca904710f0096e8df615f5aab3cac62e1f992a5;hb=0751c58086542f9e0466201b624f84d1efd547bb;hp=a5c899a853396767e9d2a652f346a0595200288a;hpb=e82c0bb610425c3829037bec88b6c03509d07e36;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a5c899a..dca9047 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -39,6 +39,7 @@ import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
@@ -223,7 +224,7 @@ f   */
 
     setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
     setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
-    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+    autoCalculateConsensusAndConservation = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
     setPadGaps(Cache.getDefault("PAD_GAPS", true));
     setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
@@ -264,14 +265,13 @@ f   */
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+		alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
 
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
-    if (hconsensus == null && !isDataset)
+		if (hconsensus == null && !isDataset)
     {
-      if (!alignment.isNucleotide())
+			if (!alignment.isNucleotide())
       {
         showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
         showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@ -283,13 +283,19 @@ f   */
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
       normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
               false);
+      // for now, use consensus options for Information till it gets its own
+      setShowHMMSequenceLogo(showSequenceLogo);
+      setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+      setShowInformationHistogram(showConsensusHistogram);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
 
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
-    String colourProperty = alignment.isNucleotide()
+    // initInformation();
+
+		String colourProperty = alignment.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -312,11 +318,11 @@ f   */
 
     if (residueShading != null)
     {
-      residueShading.setConsensus(hconsensus);
+			residueShading.setConsensus(hconsensus);
     }
     setColourAppliesToAllGroups(true);
   }
-
+  
   boolean validCharWidth;
 
   /**
@@ -401,7 +407,7 @@ f   */
     /*
      * replace mappings on our alignment
      */
-    if (alignment != null && align != null)
+		if (alignment != null && align != null)
     {
       alignment.setCodonFrames(align.getCodonFrames());
     }
@@ -454,7 +460,7 @@ f   */
   }
 
   /**
-   * returns the visible column regions of the alignment
+   * Returns an iterator over the visible column regions of the alignment
    * 
    * @param selectedRegionOnly
    *          true to just return the contigs intersecting with the selected
@@ -474,8 +480,9 @@ f   */
     {
       end = alignment.getWidth();
     }
-    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
-            false));
+
+    return (alignment.getHiddenColumns().getVisContigsIterator(start,
+            end, false));
   }
 
   /**
@@ -525,7 +532,7 @@ f   */
   }
 
   public boolean followSelection = true;
-
+  
   /**
    * @return true if view selection should always follow the selections
    *         broadcast by other selection sources
@@ -590,18 +597,20 @@ f   */
     return StructureSelectionManager
             .getStructureSelectionManager(Desktop.getInstance());
   }
-
+  
   @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
   }
 
-  public void setNormaliseSequenceLogo(boolean state)
+  @Override
+public void setNormaliseSequenceLogo(boolean state)
   {
     normaliseSequenceLogo = state;
   }
 
+
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -611,7 +620,7 @@ f   */
   {
     return validCharWidth;
   }
-
+  
   private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
@@ -754,7 +763,8 @@ f   */
     }
 
     ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
-    firePropertyChange("alignment", null, getAlignment().getSequences());
+    notifyAlignment();
+
   }
 
   /**
@@ -1090,6 +1100,9 @@ f   */
     {
       FeatureColourI preferredColour = featureSettings
               .getFeatureColour(type);
+      FeatureMatcherSetI preferredFilters = featureSettings
+              .getFeatureFilters(type);
+
       FeatureColourI origColour = fr.getFeatureStyle(type);
       if (!mergeOnly || (!origRenderOrder.contains(type)
               || origColour == null
@@ -1104,6 +1117,11 @@ f   */
         {
           fr.setColour(type, preferredColour);
         }
+        if (preferredFilters != null
+                && (!mergeOnly || fr.getFeatureFilter(type) != null))
+        {
+          fr.setFeatureFilter(type, preferredFilters);
+        }
         if (featureSettings.isFeatureDisplayed(type))
         {
           displayed.setVisible(type);
@@ -1147,4 +1165,5 @@ f   */
   {
     this.viewName = viewName;
   }
+
 }