Sequence is char []

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 7340d3b..58b379b 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -40,6 +40,7 @@ public class AlignmentView
     private SeqCigar[] sequences = null;
   private int[] contigs = null;
   private int width=0;
+  private int firstCol=0;
   public AlignmentView(CigarArray seqcigararray)
   {
     if (!seqcigararray.isSeqCigarArray())
@@ -49,6 +50,15 @@ public class AlignmentView
     sequences = seqcigararray.getSeqCigarArray();
     width = seqcigararray.getWidth(); // visible width
   }
+  /**
+   * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment
+   * @param sdata
+   * @param firstcol
+   */
+  public AlignmentView(CigarArray sdata, int firstcol) {
+    this(sdata);
+    firstCol=firstcol;
+  }
 
   public void setSequences(SeqCigar[] sequences)
   {
@@ -64,7 +74,10 @@ public class AlignmentView
   {
     return sequences;
   }
-
+  /**
+   * @see CigarArray.getDeletedRegions
+   * @return int[] { vis_start, sym_start, length }
+   */
   public int[] getContigs()
   {
     return contigs;
@@ -89,7 +102,19 @@ public class AlignmentView
   {
     String[] seqs=new String[sequences.length];
     for (int n=0; n<sequences.length; n++) {
-      seqs[n] = sequences[n].getSequenceString(c);
+      String fullseq = sequences[n].getSequenceString(c);
+      if (contigs != null)
+      {
+        seqs[n] = "";
+        int p = 0;
+        for (int h = 0; h < contigs.length; h += 3)
+        {
+          seqs[n] += fullseq.substring(p, contigs[h + 1]);
+          p = contigs[h + 1] + contigs[h + 2];
+        }
+        seqs[n] += fullseq.substring(p);
+      } else
+        seqs[n] = fullseq;
     }
     return seqs;
   }
@@ -219,7 +244,7 @@ public class AlignmentView
                 }
                 else
                 {
-                  alignment[s].setSequence(alignment[s].getSequence() +
+                  alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                            mseq[s].getSequence());
                   if (mseq[s].getStart() <= mseq[s].getEnd())
                   {
@@ -251,7 +276,7 @@ public class AlignmentView
                   }
                   else
                   {
-                    alignment[s].setSequence(alignment[s].getSequence() +
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                              oseq.getSequence());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
@@ -278,7 +303,7 @@ public class AlignmentView
             }
             else
             {
-              alignment[s].setSequence(alignment[s].getSequence() +
+              alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                        hseq.getSequence());
               if (hseq.getEnd() >= hseq.getStart())
               {
@@ -307,7 +332,7 @@ public class AlignmentView
               }
               else
               {
-                alignment[s].setSequence(alignment[s].getSequence() +
+                alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                          mseq[s].getSequence());
                 if (mseq[s].getEnd() >= mseq[s].getStart())
                 {
@@ -341,7 +366,7 @@ public class AlignmentView
                   }
                   else
                   {
-                    alignment[s].setSequence(alignment[s].getSequence() +
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                              oseq.getSequence());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
@@ -370,5 +395,58 @@ public class AlignmentView
         return getAlignmentAndColumnSelection(gapCharacter);
     }
   }
-
+  /**
+   * returns simple array of start end positions of visible range on alignment.
+   * vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment.
+   * @return int[] { start_i, end_i } for 1<i<n visible regions.
+   */
+  public int[] getVisibleContigs() {
+    if (contigs != null && contigs.length > 0)
+    {
+      int start = 0;
+      int nvis = 0;
+      int fwidth = width;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          nvis++;
+        }
+        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        nvis++;
+      }
+      int viscontigs[] = new int[nvis*2];
+      nvis=0;
+      start=0;
+      for (int contig=0; contig<contigs.length; contig+=3) {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          viscontigs[nvis] = start;
+          viscontigs[nvis+1]=contigs[contig+1]-1; // end is inclusive
+          nvis+=2;
+        }
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start<fwidth) {
+        viscontigs[nvis] = start;
+        viscontigs[nvis+1]=fwidth; // end is inclusive
+        nvis+=2;
+      }
+      return viscontigs;
+    } else {
+      return new int[] { 0, width};
+    }
+  }
+  /**
+   *
+   * @return position of first visible column of AlignmentView within its parent's alignment reference frame
+   */
+  public int getAlignmentOrigin() {
+    // TODO Auto-generated method stub
+    return firstCol;
+  }
 }