X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=6024cf995bf2cbdefeeee3cfe493178ad99e4514;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=91b55189137115eaa13fdfa1f3af6e3da302357b;hpb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 91b5518..6024cf9 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;
@@ -79,9 +80,9 @@ public class AlignViewport extends AlignmentViewport
 
   boolean antiAlias = false;
 
-  private Rectangle explodedGeometry;
+  private Rectangle explodedGeometry = null;
 
-  private String viewName;
+  private String viewName = null;
 
   /*
    * Flag set true on the view that should 'gather' multiple views of the same
@@ -208,7 +209,7 @@ public class AlignViewport extends AlignmentViewport
    */
   private void applyViewProperties()
   {
-    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+    antiAlias = Cache.getDefault("ANTI_ALIAS", true);
 
     viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
     setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
@@ -256,14 +257,13 @@ public class AlignViewport extends AlignmentViewport
 
     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);
@@ -275,13 +275,19 @@ public class AlignViewport extends AlignmentViewport
       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);
@@ -304,11 +310,11 @@ public class AlignViewport extends AlignmentViewport
 
     if (residueShading != null)
     {
-      residueShading.setConsensus(hconsensus);
+			residueShading.setConsensus(hconsensus);
     }
     setColourAppliesToAllGroups(true);
   }
-
+  
   boolean validCharWidth;
 
   /**
@@ -393,7 +399,7 @@ public class AlignViewport extends AlignmentViewport
     /*
      * replace mappings on our alignment
      */
-    if (alignment != null && align != null)
+		if (alignment != null && align != null)
     {
       alignment.setCodonFrames(align.getCodonFrames());
     }
@@ -446,7 +452,7 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * 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
@@ -466,8 +472,9 @@ public class AlignViewport extends AlignmentViewport
     {
       end = alignment.getWidth();
     }
-    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
-            false));
+
+    return (alignment.getHiddenColumns().getVisContigsIterator(start,
+            end, false));
   }
 
   /**
@@ -517,7 +524,7 @@ public class AlignViewport extends AlignmentViewport
   }
 
   public boolean followSelection = true;
-
+  
   /**
    * @return true if view selection should always follow the selections
    *         broadcast by other selection sources
@@ -582,18 +589,20 @@ public class AlignViewport extends AlignmentViewport
     return StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
   }
-
+  
   @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
@@ -603,7 +612,7 @@ public class AlignViewport extends AlignmentViewport
   {
     return validCharWidth;
   }
-
+  
   private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
@@ -921,10 +930,9 @@ public class AlignViewport extends AlignmentViewport
     if (ap != null)
     {
       // modify GUI elements to reflect geometry change
-      Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
-              .getPreferredSize();
+      Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
       idw.width = i;
-      getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+      ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
     }
   }
 
@@ -1075,6 +1083,9 @@ public class AlignViewport extends AlignmentViewport
     {
       FeatureColourI preferredColour = featureSettings
               .getFeatureColour(type);
+      FeatureMatcherSetI preferredFilters = featureSettings
+              .getFeatureFilters(type);
+
       FeatureColourI origColour = fr.getFeatureStyle(type);
       if (!mergeOnly || (!origRenderOrder.contains(type)
               || origColour == null
@@ -1089,6 +1100,11 @@ public class AlignViewport extends AlignmentViewport
         {
           fr.setColour(type, preferredColour);
         }
+        if (preferredFilters != null
+                && (!mergeOnly || fr.getFeatureFilter(type) != null))
+        {
+          fr.setFeatureFilter(type, preferredFilters);
+        }
         if (featureSettings.isFeatureDisplayed(type))
         {
           displayed.setVisible(type);