X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=e6684705b23d43bc0c912d534563120b562924b0;hb=0bdaa0deb6ee514912d2ed730e19f618bc44cb69;hp=3524942adc8aa68465f2510e23dca06470275d79;hpb=4eefb40838faa0a3c03be3480ff74ba2ac67a5c1;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 3524942..e668470 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,5 +1,25 @@
+/*
+ * 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;
 
+
+
 /**
  * <p>Title: </p>
  *
@@ -20,6 +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())
@@ -29,6 +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)
   {
@@ -44,11 +74,19 @@ public class AlignmentView
   {
     return sequences;
   }
-
+  /**
+   * @see CigarArray.getDeletedRegions
+   * @return int[] { vis_start, sym_start, length }
+   */
   public int[] getContigs()
   {
     return contigs;
   }
+  /**
+   * get the full alignment and a columnselection object marking the hidden regions
+   * @param gapCharacter char
+   * @return Object[] { SequenceI[], ColumnSelection}
+   */
   public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
     ColumnSelection colsel = new ColumnSelection();
 
@@ -64,12 +102,24 @@ 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;
   }
   /**
-   * 
+   *
    * @return visible number of columns in alignment view
    */
   public int getWidth() {
@@ -79,5 +129,324 @@ public class AlignmentView
   protected void setWidth(int width) {
     this.width = width;
   }
-  
+  /**
+   * get the contiguous subalignments in an alignment view.
+   * @param gapCharacter char
+   * @return SequenceI[][]
+   */
+  public SequenceI[][] getVisibleContigs(char gapCharacter) {
+    SequenceI[][] smsa;
+    int njobs = 1;
+    if (sequences==null || width<=0)
+      return null;
+    if (contigs != null && contigs.length > 0)
+    {
+      int start = 0;
+      njobs = 0;
+      int fwidth = width;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          njobs++;
+        }
+        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        njobs++;
+      }
+      smsa = new SequenceI[njobs][];
+      start = 0;
+      int j = 0;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if (contigs[contig + 1] - start > 0)
+        {
+          SequenceI mseq[] = new SequenceI[sequences.length];
+          for (int s = 0; s < mseq.length; s++)
+          {
+            mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+                contigs[contig + 1]);
+          }
+          smsa[j] = mseq;
+          j++;
+        }
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        SequenceI mseq[] = new SequenceI[sequences.length];
+        for (int s = 0; s < mseq.length; s++)
+        {
+          mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+              fwidth + 1);
+        }
+        smsa[j] = mseq;
+        j++;
+      }
+    }
+    else
+    {
+      smsa = new SequenceI[1][];
+      smsa[0] = new SequenceI[sequences.length];
+      for (int s = 0; s < sequences.length; s++)
+      {
+        smsa[0][s] = sequences[s].getSeq(gapCharacter);
+      }
+    }
+    return smsa;
+  }
+  /**
+   * return full msa and hidden regions with visible blocks replaced with new sub alignments
+   * @param nvismsa SequenceI[][]
+   * @param orders AlignmentOrder[] corresponding to each SequenceI[] block.
+   * @return Object[]
+   */
+  public Object[] getUpdatedView(SequenceI[][] nvismsa, AlignmentOrder[] orders, char gapCharacter) {
+    if (sequences == null || width <= 0)
+    {
+      throw new Error("empty view cannot be updated.");
+    }
+    if (nvismsa == null)
+      throw new Error(
+          "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+    if (contigs != null && contigs.length > 0)
+    {
+      SequenceI[] alignment = new SequenceI[sequences.length];
+      ColumnSelection columnselection = new ColumnSelection();
+      if (contigs != null && contigs.length > 0)
+      {
+        int start = 0;
+        int nwidth = 0;
+        int owidth = width;
+        int j = 0;
+        for (int contig = 0; contig < contigs.length; contig += 3)
+        {
+          owidth += contigs[contig + 2]; // recover final column width
+          if (contigs[contig + 1] - start > 0)
+          {
+            int swidth = 0; // subalignment width
+            if (nvismsa[j] != null)
+            {
+              SequenceI mseq[] = nvismsa[j];
+              AlignmentOrder order=(orders==null) ? null : orders[j];
+              j++;
+              if (mseq.length!=sequences.length)
+                throw new Error("Mismatch between number of sequences in block "+j+" ("+mseq.length+") and the original view ("+sequences.length+")");
+              swidth = mseq[0].getLength(); // JBPNote: could ensure padded here.
+              for (int s = 0; s < mseq.length; s++)
+              {
+                if (alignment[s] == null)
+                {
+                  alignment[s] = mseq[s];
+                }
+                else
+                {
+                  alignment[s].setSequence(alignment[s].getSequence() +
+                                           mseq[s].getSequence());
+                  if (mseq[s].getStart() <= mseq[s].getEnd())
+                  {
+                    alignment[s].setEnd(mseq[s].getEnd());
+                  }
+                  if (order!=null) {
+                    order.updateSequence(mseq[s], alignment[s]);
+                  }
+                }
+              }
+            }
+            else
+            {
+              // recover original alignment block or place gaps
+              if (true)
+              {
+                // recover input data
+                for (int s = 0; s < sequences.length; s++)
+                {
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+                      contigs[contig + 1]);
+                  if (swidth < oseq.getLength())
+                  {
+                    swidth = oseq.getLength();
+                  }
+                  if (alignment[s] == null)
+                  {
+                    alignment[s] = oseq;
+                  }
+                  else
+                  {
+                    alignment[s].setSequence(alignment[s].getSequence() +
+                                             oseq.getSequence());
+                    if (oseq.getEnd() >= oseq.getStart())
+                    {
+                      alignment[s].setEnd(oseq.getEnd());
+                    }
+                  }
+                }
+
+              }
+              j++;
+            }
+            nwidth += swidth;
+          }
+          // advance to begining of visible region
+          start = contigs[contig + 1] + contigs[contig + 2];
+          // add hidden segment to right of next region
+          for (int s = 0; s < sequences.length; s++)
+          {
+            SequenceI hseq = sequences[s].getSeq(gapCharacter).getSubSequence(contigs[contig +
+                1], start);
+            if (alignment[s] == null)
+            {
+              alignment[s] = hseq;
+            }
+            else
+            {
+              alignment[s].setSequence(alignment[s].getSequence() +
+                                       hseq.getSequence());
+              if (hseq.getEnd() >= hseq.getStart())
+              {
+                alignment[s].setEnd(hseq.getEnd());
+              }
+            }
+          }
+          // mark hidden segment as hidden in the new alignment
+          columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
+          nwidth += contigs[contig + 2];
+        }
+        // Do final segment - if it exists
+        if (j < nvismsa.length)
+        {
+          int swidth = 0;
+          if (nvismsa[j] != null)
+          {
+            SequenceI mseq[] = nvismsa[j];
+            AlignmentOrder order = (orders!=null) ? orders[j] : null;
+            swidth = mseq[0].getLength();
+            for (int s = 0; s < mseq.length; s++)
+            {
+              if (alignment[s] == null)
+              {
+                alignment[s] = mseq[s];
+              }
+              else
+              {
+                alignment[s].setSequence(alignment[s].getSequence() +
+                                         mseq[s].getSequence());
+                if (mseq[s].getEnd() >= mseq[s].getStart())
+                {
+                  alignment[s].setEnd(mseq[s].getEnd());
+                }
+                if (order!=null) {
+                  order.updateSequence(mseq[s], alignment[s]);
+                }
+              }
+            }
+          }
+          else
+          {
+            if (start < owidth)
+            {
+              // recover input data or place gaps
+              if (true)
+              {
+                // recover input data
+                for (int s = 0; s < sequences.length; s++)
+                {
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+                      owidth + 1);
+                  if (swidth < oseq.getLength())
+                  {
+                    swidth = oseq.getLength();
+                  }
+                  if (alignment[s] == null)
+                  {
+                    alignment[s] = oseq;
+                  }
+                  else
+                  {
+                    alignment[s].setSequence(alignment[s].getSequence() +
+                                             oseq.getSequence());
+                    if (oseq.getEnd() >= oseq.getStart())
+                    {
+                      alignment[s].setEnd(oseq.getEnd());
+                    }
+                  }
+                }
+                nwidth += swidth;
+              }
+              else
+              {
+                // place gaps.
+                throw new Error("Padding not yet implemented.");
+              }
+            }
+          }
+        }
+      }
+      return new Object[] { alignment, columnselection};
+    } else {
+      if (nvismsa.length!=1)
+        throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="+nvismsa.length);
+      if (nvismsa[0]!=null)
+        return new Object[] { nvismsa[0], new ColumnSelection()};
+      else
+        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;
+  }
 }