Merge branch 'spike/JAL-1950_hmmer3client' into features/mchmmer_merge_JAL-1950

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 93b6f16..0a569b5 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -332,7 +332,7 @@ public class AlignmentAnnotation
     {
       return;
     }
-    hidden.makeVisibleAnnotation(this);
+    makeVisibleAnnotation(hidden);
   }
 
   /**
@@ -925,6 +925,7 @@ public class AlignmentAnnotation
    * @param seqRef
    * @param startRes
    * @param alreadyMapped
+   *          - annotation are at aligned columns
    */
   public void createSequenceMapping(SequenceI seqRef, int startRes,
           boolean alreadyMapped)
@@ -1473,6 +1474,115 @@ public class AlignmentAnnotation
     return graphMin < graphMax;
   }
 
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param hiddenColumns
+   *          the set of hidden columns
+   */
+  public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
+  {
+    if (annotations != null)
+    {
+      makeVisibleAnnotation(0, annotations.length, hiddenColumns);
+    }
+  }
+
+  /**
+   * 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 hiddenColumns
+   *          the set of hidden columns
+   */
+  public void makeVisibleAnnotation(int start, int end,
+          HiddenColumns hiddenColumns)
+  {
+    if (annotations != null)
+    {
+      if (hiddenColumns.hasHiddenColumns())
+      {
+        removeHiddenAnnotation(start, end, hiddenColumns);
+      }
+      else
+      {
+        restrict(start, end);
+      }
+    }
+  }
+
+  /**
+   * The actual implementation of deleting hidden annotation columns
+   * 
+   * @param start
+   *          remove any annotation to the right of this column
+   * @param end
+   *          remove any annotation to the left of this column
+   * @param hiddenColumns
+   *          the set of hidden columns
+   */
+  private void removeHiddenAnnotation(int start, int end,
+          HiddenColumns hiddenColumns)
+  {
+    // mangle the alignmentAnnotation annotation array
+    ArrayList<Annotation[]> annels = new ArrayList<>();
+    Annotation[] els = null;
+
+    int w = 0;
+
+    Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
+            end + 1, false);
+
+    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] <= annotations.length)
+        {
+          // copy just the visible segment of the annotation row
+          copylength = annotationLength;
+        }
+        else
+        {
+          // copy to the end of the annotation row
+          copylength = annotations.length - block[0];
+        }
+      }
+
+      els = new Annotation[annotationLength];
+      annels.add(els);
+      System.arraycopy(annotations, block[0], els, 0, copylength);
+      w += annotationLength;
+    }
+
+    if (w != 0)
+    {
+      annotations = new Annotation[w];
+
+      w = 0;
+      for (Annotation[] chnk : annels)
+      {
+        System.arraycopy(chnk, 0, annotations, w, chnk.length);
+        w += chnk.length;
+      }
+    }
+  }
+
   public static Iterable<AlignmentAnnotation> findAnnotations(
           Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
           String label)