JAL-2133 refactored duplicated code to AlignmentViewport

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index b70e92b..eab4aa5 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1078,6 +1078,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       updateHiddenColumns();
     }
+    isColSelChanged(true);
   }
 
   /**
@@ -1206,8 +1207,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isColSelChanged(boolean b)
   {
-    int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel
-            .hashCode();
+    int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
     if (hc != -1 && hc != colselhash)
     {
       if (b)
@@ -1308,7 +1308,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     colSel.hideSelectedColumns();
     setSelectionGroup(null);
-
+    isColSelChanged(true);
   }
 
   public void hideColumns(int start, int end)
@@ -1321,17 +1321,19 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       colSel.hideColumns(start, end);
     }
+    isColSelChanged(true);
   }
 
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
-
+    isColSelChanged(true);
   }
 
   public void showAllHiddenColumns()
   {
     colSel.revealAllHiddenColumns();
+    isColSelChanged(true);
   }
 
   // common hide/show seq stuff
@@ -1411,6 +1413,39 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
+   * Hides the specified sequence, or the sequences it represents
+   * 
+   * @param sequence
+   *          the sequence to hide, or keep as representative
+   * @param representGroup
+   *          if true, hide the current selection group except for the
+   *          representative sequence
+   */
+  public void hideSequences(SequenceI sequence, boolean representGroup)
+  {
+    if (selectionGroup == null || selectionGroup.getSize() < 1)
+    {
+      hideSequence(new SequenceI[] { sequence });
+      return;
+    }
+
+    if (representGroup)
+    {
+      hideRepSequences(sequence, selectionGroup);
+      setSelectionGroup(null);
+      return;
+    }
+
+    int gsize = selectionGroup.getSize();
+    SequenceI[] hseqs = selectionGroup.getSequences().toArray(
+            new SequenceI[gsize]);
+
+    hideSequence(hseqs);
+    setSelectionGroup(null);
+    sendSelection();
+  }
+
+  /**
    * Set visibility for any annotations for the given sequence.
    * 
    * @param sequenceI
@@ -1418,11 +1453,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
   protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
           boolean visible)
   {
-    for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    if (anns != null)
     {
-      if (ann.sequenceRef == sequenceI)
+      for (AlignmentAnnotation ann : anns)
       {
-        ann.visible = visible;
+        if (ann.sequenceRef == sequenceI)
+        {
+          ann.visible = visible;
+        }
       }
     }
   }
@@ -1463,13 +1502,42 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   }
 
+  /**
+   * 
+   * @return null or the current reference sequence
+   */
+  public SequenceI getReferenceSeq()
+  {
+    return alignment.getSeqrep();
+  }
+
+  /**
+   * @param seq
+   * @return true iff seq is the reference for the alignment
+   */
+  public boolean isReferenceSeq(SequenceI seq)
+  {
+    return alignment.getSeqrep() == seq;
+  }
+
+  /**
+   * 
+   * @param seq
+   * @return true if there are sequences represented by this sequence that are
+   *         currently hidden
+   */
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return alignment.getSeqrep() == seq
-            || (hiddenRepSequences != null && hiddenRepSequences
+    return (hiddenRepSequences != null && hiddenRepSequences
                     .containsKey(seq));
   }
 
+  /**
+   * 
+   * @param seq
+   * @return null or a sequence group containing the sequences that seq
+   *         represents
+   */
   public SequenceGroup getRepresentedSequences(SequenceI seq)
   {
     return (SequenceGroup) (hiddenRepSequences == null ? null
@@ -1557,6 +1625,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
+    return getViewAsString(selectedRegionOnly, true);
+  }
+
+  @Override
+  public String[] getViewAsString(boolean selectedRegionOnly,
+          boolean exportHiddenSeqs)
+  {
     String[] selection = null;
     SequenceI[] seqs = null;
     int i, iSize;
@@ -1570,13 +1645,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     else
     {
-      if (hasHiddenRows())
+      if (hasHiddenRows() && exportHiddenSeqs)
       {
-        iSize = alignment.getHiddenSequences().getFullAlignment()
-                .getHeight();
-        seqs = alignment.getHiddenSequences().getFullAlignment()
-                .getSequencesArray();
-        end = alignment.getHiddenSequences().getFullAlignment().getWidth();
+        AlignmentI fullAlignment = alignment.getHiddenSequences()
+                .getFullAlignment();
+        iSize = fullAlignment.getHeight();
+        seqs = fullAlignment.getSequencesArray();
+        end = fullAlignment.getWidth();
       }
       else
       {
@@ -2688,4 +2763,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
       }
     }
   }
+
+
 }