Merge branch 'Jalview-JS/develop' into merge_js_develop

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 4311d14..4aec9d2 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -87,6 +87,9 @@ import java.util.Map;
 public abstract class AlignmentViewport
         implements AlignViewportI, CommandListener, VamsasSource
 {
+  public static final String PROPERTY_ALIGNMENT = "alignment";
+  public static final String PROPERTY_SEQUENCE = "sequence";
+
   protected ViewportRanges ranges;
 
   protected ViewStyleI viewStyle = new ViewStyle();
@@ -630,10 +633,31 @@ public abstract class AlignmentViewport
 
   protected ColumnSelection colSel = new ColumnSelection();
 
-  public boolean autoCalculateConsensus = true;
+  protected boolean autoCalculateConsensusAndConservation = true;
+
+  public boolean getAutoCalculateConsensusAndConservation()
+  { // BH 2019.07.24
+    return autoCalculateConsensusAndConservation;
+  }
+
+  public void setAutoCalculateConsensusAndConservation(boolean b)
+  {
+    autoCalculateConsensusAndConservation = b;
+  }
 
   protected boolean autoCalculateStrucConsensus = true;
 
+  public boolean getAutoCalculateStrucConsensus()
+  { // BH 2019.07.24
+    return autoCalculateStrucConsensus;
+  }
+
+  public void setAutoCalculateStrucConsensus(boolean b)
+  {
+    autoCalculateStrucConsensus = b;
+  }
+
+
   protected boolean ignoreGapsInConsensusCalculation = false;
 
   protected ResidueShaderI residueShading = new ResidueShader();
@@ -861,7 +885,7 @@ public abstract class AlignmentViewport
     // see note in mantis : issue number 8585
     if (alignment.isNucleotide()
             || (conservation == null && quality == null)
-            || !autoCalculateConsensus)
+            || !autoCalculateConsensusAndConservation)
     {
       return;
     }
@@ -879,7 +903,7 @@ public abstract class AlignmentViewport
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (consensus == null || !autoCalculateConsensus)
+    if (consensus == null || !autoCalculateConsensusAndConservation)
     {
       return;
     }
@@ -1389,21 +1413,22 @@ public abstract class AlignmentViewport
    * checks current colsel against record of last hash value, and optionally
    * updates record.
    * 
-   * @param b
+   * @param updateHash
    *          update the record of last hash value
    * @return true if colsel changed since last call (when b is true)
    */
-  public boolean isColSelChanged(boolean b)
+  public boolean isColSelChanged(boolean updateHash)
   {
     int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
     if (hc != -1 && hc != colselhash)
     {
-      if (b)
+      if (updateHash)
       {
         colselhash = hc;
       }
       return true;
     }
+    notifySequence();
     return false;
   }
 
@@ -1476,22 +1501,6 @@ public abstract class AlignmentViewport
     }
   }
 
-  /**
-   * Property change listener for changes in alignment
-   * 
-   * @param prop
-   *          DOCUMENT ME!
-   * @param oldvalue
-   *          DOCUMENT ME!
-   * @param newvalue
-   *          DOCUMENT ME!
-   */
-  public void firePropertyChange(String prop, Object oldvalue,
-          Object newvalue)
-  {
-    changeSupport.firePropertyChange(prop, oldvalue, newvalue);
-  }
-
   // common hide/show column stuff
 
   public void hideSelectedColumns()
@@ -1556,13 +1565,14 @@ public abstract class AlignmentViewport
 
       ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
 
-      firePropertyChange("alignment", null, alignment.getSequences());
       // used to set hasHiddenRows/hiddenRepSequences here, after the property
       // changed event
+      notifySequence();
       sendSelection();
     }
   }
 
+
   public void showSequence(int index)
   {
     int startSeq = ranges.getStartSeq();
@@ -1585,8 +1595,7 @@ public abstract class AlignmentViewport
       }
 
       ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
-
-      firePropertyChange("alignment", null, alignment.getSequences());
+      notifyAlignment();
       sendSelection();
     }
   }
@@ -1620,7 +1629,7 @@ public abstract class AlignmentViewport
         setSequenceAnnotationsVisible(seq[i], false);
       }
       ranges.setStartSeq(startSeq);
-      firePropertyChange("alignment", null, alignment.getSequences());
+      notifyAlignment();
     }
   }
 
@@ -1985,11 +1994,11 @@ public abstract class AlignmentViewport
     {
       alignment.padGaps();
     }
-    if (autoCalculateConsensus)
+    if (autoCalculateConsensusAndConservation)
     {
       updateConsensus(ap);
     }
-    if (hconsensus != null && autoCalculateConsensus)
+    if (hconsensus != null && autoCalculateConsensusAndConservation)
     {
       updateConservation(ap);
     }
@@ -3244,7 +3253,6 @@ public abstract class AlignmentViewport
       codingComplement.setUpdateStructures(needToUpdateStructureViews);
     }
   }
-
   /**
    * Filters out sequences with an eValue higher than the specified value. The
    * filtered sequences are hidden or deleted. Sequences with no eValues are also
@@ -3285,5 +3293,21 @@ public abstract class AlignmentViewport
         hideSequence(new SequenceI[] { seq });
       }
     }
+  }  
+
+  /**
+   * Notify TreePanel and AlignmentPanel of some sort of alignment change.
+   */
+  public void notifyAlignment()
+  {
+    changeSupport.firePropertyChange(PROPERTY_ALIGNMENT, null, alignment.getSequences());
+  }
+  
+  /**
+   * Notify AlignmentPanel of a sequence column selection or visibility changes.
+   */
+  public void notifySequence()
+  {
+    changeSupport.firePropertyChange(PROPERTY_SEQUENCE, null, null);
   }
 }