JAL-2759 Moved alignment annotation code out of HiddenColumns

[jalview.git] / src / jalview / datamodel / HiddenColumns.java

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index c666a41..49f82f5 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1058,119 +1058,6 @@ public class HiddenColumns
     }
   }
 
-  /**
-   * delete any columns in alignmentAnnotation that are hidden (including
-   * sequence associated annotation).
-   * 
-   * @param alignmentAnnotation
-   */
-  public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
-  {
-    if (alignmentAnnotation != null
-            && alignmentAnnotation.annotations != null)
-    {
-      makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
-            alignmentAnnotation);
-    }
-  }
-
-  /**
-   * delete any columns in alignmentAnnotation that are hidden (including
-   * sequence associated annotation).
-   * 
-   * @param start
-   *          remove any annotation to the right of this column
-   * @param end
-   *          remove any annotation to the left of this column
-   * @param alignmentAnnotation
-   *          the annotation to operate on
-   */
-  public void makeVisibleAnnotation(int start, int end,
-          AlignmentAnnotation alignmentAnnotation)
-  {
-    try
-    {
-      LOCK.readLock().lock();
-
-      int startFrom = start;
-      int endAt = end;
-
-      if (alignmentAnnotation != null
-              && alignmentAnnotation.annotations != null)
-      {
-        if (!hiddenColumns.isEmpty())
-        {
-          removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
-        }
-        else
-        {
-          alignmentAnnotation.restrict(startFrom, endAt);
-        }
-      }
-    } finally
-    {
-      LOCK.readLock().unlock();
-    }
-  }
-
-  private void removeHiddenAnnotation(int start, int end,
-          AlignmentAnnotation alignmentAnnotation)
-  {
-    // mangle the alignmentAnnotation annotation array
-    ArrayList<Annotation[]> annels = new ArrayList<>();
-    Annotation[] els = null;
-
-    int w = 0;
-    
-    Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
-            hiddenColumns);
-
-    int copylength;
-    int annotationLength;
-    while (blocks.hasNext())
-    {
-      int[] block = blocks.next();
-      annotationLength = block[1] - block[0] + 1;
-    
-      if (blocks.hasNext())
-      {
-        // copy just the visible segment of the annotation row
-        copylength = annotationLength;
-      }
-      else
-      {
-        if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
-        {
-          // copy just the visible segment of the annotation row
-          copylength = annotationLength;
-        }
-        else
-        {
-          // copy to the end of the annotation row
-          copylength = alignmentAnnotation.annotations.length - block[0];
-        }
-      }
-      
-      els = new Annotation[annotationLength];
-      annels.add(els);
-      System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
-              copylength);
-      w += annotationLength;
-    }
-    
-    if (w != 0)
-    {
-      alignmentAnnotation.annotations = new Annotation[w];
-
-      w = 0;
-      for (Annotation[] chnk : annels)
-      {
-        System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
-                chnk.length);
-        w += chnk.length;
-      }
-    }
-  }
 
   /**
    *