multiple web service jobs from visible blocks of an alignment.

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 727bc76..3524942 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -19,6 +19,7 @@ public class AlignmentView
      */
     private SeqCigar[] sequences = null;
   private int[] contigs = null;
+  private int width=0;
   public AlignmentView(CigarArray seqcigararray)
   {
     if (!seqcigararray.isSeqCigarArray())
@@ -26,6 +27,7 @@ public class AlignmentView
     //contigs = seqcigararray.applyDeletions();
     contigs = seqcigararray.getDeletedRegions();
     sequences = seqcigararray.getSeqCigarArray();
+    width = seqcigararray.getWidth(); // visible width
   }
 
   public void setSequences(SeqCigar[] sequences)
@@ -66,4 +68,16 @@ public class AlignmentView
     }
     return seqs;
   }
+  /**
+   * 
+   * @return visible number of columns in alignment view
+   */
+  public int getWidth() {
+    return width;
+  }
+
+  protected void setWidth(int width) {
+    this.width = width;
+  }
+  
 }