JAL-2629 revising hmmer annotation updating (wip)

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 0c85925..7ce6837 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * 
  * This file is part of Jalview.
  * 
@@ -25,14 +25,11 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
@@ -59,6 +56,12 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  java.awt.Frame nullFrame;
+
+  protected FeatureSettings featureSettings = null;
+
+  private float heightScale = 1, widthScale = 1;
+
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     super(al);
@@ -200,7 +203,8 @@ public class AlignViewport extends AlignmentViewport
       if (colour != null)
       {
         residueShading = new ResidueShader(
-                ColourSchemeProperty.getColourScheme(alignment, colour));
+                ColourSchemeProperty.getColourScheme(getAlignment(),
+                        colour));
         if (residueShading != null)
         {
           residueShading.setConsensus(hconsensus);
@@ -214,15 +218,8 @@ public class AlignViewport extends AlignmentViewport
       }
     }
     initAutoAnnotation();
-
   }
 
-  java.awt.Frame nullFrame;
-
-  protected FeatureSettings featureSettings = null;
-
-  private float heightScale = 1, widthScale = 1;
-
   /**
    * {@inheritDoc}
    */
@@ -417,6 +414,4 @@ public class AlignViewport extends AlignmentViewport
     return normaliseHMMSequenceLogo;
   }
 
-
-
 }

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index d1e7b83..676f318 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -278,6 +278,7 @@ public class SequenceGroup implements AnnotatedCollectionI
         seqs[ipos].setDescription(seq.getDescription());
         seqs[ipos].setDBRefs(seq.getDBRefs());
         seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+        seqs[ipos].setIsHMMConsensusSequence(seq.isHMMConsensusSequence());
         if (seq.getDatasetSequence() != null)
         {
           seqs[ipos].setDatasetSequence(seq.getDatasetSequence());

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b490a4b..ef95161 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -94,6 +94,12 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  boolean validCharWidth;
+
+  public boolean followSelection = true;
+
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
+
   /**
    * Creates a new AlignViewport object.
    * 
@@ -256,14 +262,14 @@ public class AlignViewport extends AlignmentViewport
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+    AlignmentI al = getAlignment();
+    al.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 (!alignment.isNucleotide())
+      if (!al.isNucleotide())
       {
         showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
         showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@ -281,10 +287,9 @@ public class AlignViewport extends AlignmentViewport
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
-    initInformation();
+    // initInformation();
 
-
-    String colourProperty = alignment.isNucleotide()
+    String colourProperty = al.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -295,7 +300,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(alignment, schemeName);
+            .getColourScheme(al, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -311,8 +316,6 @@ public class AlignViewport extends AlignmentViewport
     }
   }
 
-  boolean validCharWidth;
-
   /**
    * {@inheritDoc}
    */
@@ -395,9 +398,9 @@ public class AlignViewport extends AlignmentViewport
     /*
      * replace mappings on our alignment
      */
-    if (alignment != null && align != null)
+    if (getAlignment() != null && align != null)
     {
-      alignment.setCodonFrames(align.getCodonFrames());
+      getAlignment().setCodonFrames(align.getCodonFrames());
     }
   }
 
@@ -466,9 +469,10 @@ public class AlignViewport extends AlignmentViewport
     }
     else
     {
-      end = alignment.getWidth();
+      end = getAlignment().getWidth();
     }
-    viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
+    viscontigs = getAlignment().getHiddenColumns().getVisibleContigs(start,
+            end);
     return viscontigs;
   }
 
@@ -518,8 +522,6 @@ public class AlignViewport extends AlignmentViewport
     return false;
   }
 
-  public boolean followSelection = true;
-
   /**
    * @return true if view selection should always follow the selections
    *         broadcast by other selection sources
@@ -597,7 +599,7 @@ public class AlignViewport extends AlignmentViewport
     for (PDBEntry pdb : pdbEntries)
     {
       List<SequenceI> choosenSeqs = new ArrayList<>();
-      for (SequenceI sq : alignment.getSequences())
+      for (SequenceI sq : getAlignment().getSequences())
       {
         Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
                 .getAllPDBEntries();
@@ -664,8 +666,6 @@ public class AlignViewport extends AlignmentViewport
     return validCharWidth;
   }
 
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
-
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
     return calcIdParams.get(calcId);

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 46ebe01..ecca699 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -99,11 +99,73 @@ public abstract class AlignmentViewport
 
   protected Deque<CommandI> redoList = new ArrayDeque<>();
 
+  protected String sequenceSetID;
+
+  /*
+   * probably unused indicator that view is of a dataset rather than an
+   * alignment
+   */
+  protected boolean isDataset = false;
+
+  private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+
+  protected ColumnSelection colSel = new ColumnSelection();
+
+  public boolean autoCalculateConsensus = true;
+
+  public boolean autoCalculateInformation = true;
+
+  protected boolean autoCalculateStrucConsensus = true;
+
+  protected boolean ignoreGapsInConsensusCalculation = false;
+
+  protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
+  protected boolean infoLetterHeight = false;
+
+  protected ResidueShaderI residueShading = new ResidueShader();
+
+  protected AlignmentAnnotation consensus;
+
+  protected AlignmentAnnotation complementConsensus;
+
+  protected AlignmentAnnotation occupancy;
+
+  protected AlignmentAnnotation strucConsensus;
+
+  protected AlignmentAnnotation conservation;
+
+  protected AlignmentAnnotation quality;
+
+  protected List<AlignmentAnnotation> information = new ArrayList<>();
+
+  /**
+   * alignment displayed in the viewport
+   */
+  private AlignmentI alignment;
+
+  /**
+   * results of alignment consensus analysis for visible portion of view
+   */
+  protected ProfilesI hconsensus = null;
+
+  /**
+   * results of information annotation analysis for the visible portion of view
+   */
+  protected List<ProfilesI> hinformation = new ArrayList<>();
+
+  /**
+   * results of cDNA complement consensus visible portion of view
+   */
+  protected Hashtable[] hcomplementConsensus = null;
 
   /**
-   * alignment displayed in the viewport. Please use get/setter
+   * results of secondary structure base pair consensus for visible portion of
+   * view
    */
-  protected AlignmentI alignment;
+  protected Hashtable[] hStrucConsensus = null;
+
+  protected Conservation hconservation = null;
 
   public AlignmentViewport(AlignmentI al)
   {
@@ -584,14 +646,6 @@ public abstract class AlignmentViewport
     return alignment.getGapCharacter();
   }
 
-  protected String sequenceSetID;
-
-  /**
-   * probably unused indicator that view is of a dataset rather than an
-   * alignment
-   */
-  protected boolean isDataset = false;
-
   public void setDataset(boolean b)
   {
     isDataset = b;
@@ -602,24 +656,6 @@ public abstract class AlignmentViewport
     return isDataset;
   }
 
-  private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
-
-  protected ColumnSelection colSel = new ColumnSelection();
-
-  public boolean autoCalculateConsensus = true;
-
-  public boolean autoCalculateInformation = true;
-
-  protected boolean autoCalculateStrucConsensus = true;
-
-  protected boolean ignoreGapsInConsensusCalculation = false;
-
-  protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
-
-  protected boolean infoLetterHeight = false;
-
-  protected ResidueShaderI residueShading = new ResidueShader();
-
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
@@ -692,50 +728,6 @@ public abstract class AlignmentViewport
   {
     return residueShading;
   }
-
-  protected AlignmentAnnotation consensus;
-
-  protected AlignmentAnnotation complementConsensus;
-
-  protected AlignmentAnnotation gapcounts;
-
-  protected AlignmentAnnotation strucConsensus;
-
-  protected AlignmentAnnotation conservation;
-
-  protected AlignmentAnnotation quality;
-
-  protected AlignmentAnnotation[] groupConsensus;
-
-  protected AlignmentAnnotation[] groupConservation;
-
-  protected List<AlignmentAnnotation> groupInformation = new ArrayList<>();
-
-  protected List<AlignmentAnnotation> information = new ArrayList<>();
-
-  /**
-   * results of alignment consensus analysis for visible portion of view
-   */
-  protected ProfilesI hconsensus = null;
-
-  /**
-   * results of information annotation analysis for the visible portion of view
-   */
-  protected List<ProfilesI> hinformation = new ArrayList<>();
-
-  /**
-   * results of cDNA complement consensus visible portion of view
-   */
-  protected Hashtable[] hcomplementConsensus = null;
-
-  /**
-   * results of secondary structure base pair consensus for visible portion of
-   * view
-   */
-  protected Hashtable[] hStrucConsensus = null;
-
-  protected Conservation hconservation = null;
-
   @Override
   public void setConservation(Conservation cons)
   {
@@ -846,7 +838,7 @@ public abstract class AlignmentViewport
   @Override
   public AlignmentAnnotation getAlignmentGapAnnotation()
   {
-    return gapcounts;
+    return occupancy;
   }
 
   @Override
@@ -1012,12 +1004,10 @@ public abstract class AlignmentViewport
     strucConsensus = null;
     conservation = null;
     quality = null;
-    groupConsensus = null;
-    groupConservation = null;
     hconsensus = null;
     hconservation = null;
     hcomplementConsensus = null;
-    gapcounts = null;
+    occupancy = null;
     calculator = null;
     residueShading = null; // may hold a reference to Consensus
     changeSupport = null;
@@ -2099,7 +2089,7 @@ public abstract class AlignmentViewport
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
 
-      initGapCounts();
+      initOccupancy();
 
       initComplementConsensus();
     }
@@ -2182,20 +2172,20 @@ public abstract class AlignmentViewport
 
   // these should be extracted from the view model - style and settings for
   // derived annotation
-  private void initGapCounts()
+  private void initOccupancy()
   {
     if (showOccupancy)
     {
-      gapcounts = new AlignmentAnnotation("Occupancy",
+      occupancy = 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;
+      occupancy.hasText = true;
+      occupancy.autoCalculated = true;
+      occupancy.scaleColLabel = true;
+      occupancy.graph = AlignmentAnnotation.BAR_GRAPH;
 
-      alignment.addAnnotation(gapcounts);
+      alignment.addAnnotation(occupancy);
     }
   }