X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=8b86a8252cc135b922726e4a9c945c30e8efa6ec;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=2cc0e9f25817fed8190b5217d30e61f473d384e5;hpb=89a0b775abfaa90242a171ca8133784a424a3d7b;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 2cc0e9f..8b86a82 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 
@@ -22,6 +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())
@@ -31,6 +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)
   {
@@ -46,7 +74,10 @@ public class AlignmentView
   {
     return sequences;
   }
-
+  /**
+   * @see CigarArray.getDeletedRegions
+   * @return int[] { vis_start, sym_start, length }
+   */
   public int[] getContigs()
   {
     return contigs;
@@ -71,7 +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;
   }
@@ -201,8 +244,8 @@ public class AlignmentView
                 }
                 else
                 {
-                  alignment[s].setSequence(alignment[s].getSequence() +
-                                           mseq[s].getSequence());
+                  alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                           mseq[s].getSequenceAsString());
                   if (mseq[s].getStart() <= mseq[s].getEnd())
                   {
                     alignment[s].setEnd(mseq[s].getEnd());
@@ -233,8 +276,8 @@ public class AlignmentView
                   }
                   else
                   {
-                    alignment[s].setSequence(alignment[s].getSequence() +
-                                             oseq.getSequence());
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                             oseq.getSequenceAsString());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
                       alignment[s].setEnd(oseq.getEnd());
@@ -260,8 +303,8 @@ public class AlignmentView
             }
             else
             {
-              alignment[s].setSequence(alignment[s].getSequence() +
-                                       hseq.getSequence());
+              alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                       hseq.getSequenceAsString());
               if (hseq.getEnd() >= hseq.getStart())
               {
                 alignment[s].setEnd(hseq.getEnd());
@@ -289,8 +332,8 @@ public class AlignmentView
               }
               else
               {
-                alignment[s].setSequence(alignment[s].getSequence() +
-                                         mseq[s].getSequence());
+                alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                         mseq[s].getSequenceAsString());
                 if (mseq[s].getEnd() >= mseq[s].getStart())
                 {
                   alignment[s].setEnd(mseq[s].getEnd());
@@ -323,8 +366,8 @@ public class AlignmentView
                   }
                   else
                   {
-                    alignment[s].setSequence(alignment[s].getSequence() +
-                                             oseq.getSequence());
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                             oseq.getSequenceAsString());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
                       alignment[s].setEnd(oseq.getEnd());
@@ -352,5 +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;
+  }
 }