X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=79e0ba22d55f18ae04e17152b5729beacc5fee1c;hb=f980095ff022f62822f1522c221957e49a7bbfc7;hp=727bc76c76f9053d65f40b40b8859b339d1746a6;hpb=108d9a136d1794445f2169c04d80b7662085390d;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 727bc76..79e0ba2 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) 2007 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;
 
 /**
@@ -14,18 +32,34 @@ package jalview.datamodel;
  */
 public class AlignmentView
 {
-    /**
-     * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
-     */
-    private SeqCigar[] sequences = null;
+  /**
+   * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
+   */
+  private SeqCigar[] sequences = null;
   private int[] contigs = null;
+  private int width = 0;
+  private int firstCol = 0;
   public AlignmentView(CigarArray seqcigararray)
   {
     if (!seqcigararray.isSeqCigarArray())
+    {
       throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences.");
+    }
     //contigs = seqcigararray.applyDeletions();
     contigs = seqcigararray.getDeletedRegions();
     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)
@@ -43,15 +77,30 @@ public class AlignmentView
     return sequences;
   }
 
+  /**
+   * @see CigarArray.getDeletedRegions
+   * @return int[] { vis_start, sym_start, length }
+   */
   public int[] getContigs()
   {
     return contigs;
   }
-  public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
+
+  /**
+   * 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();
 
-    return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, contigs), colsel};
+    return new Object[]
+        {
+        SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
+                                          contigs), colsel};
   }
+
   /**
    * getSequenceStrings
    *
@@ -60,10 +109,402 @@ public class AlignmentView
    */
   public String[] getSequenceStrings(char c)
   {
-    String[] seqs=new String[sequences.length];
-    for (int n=0; n<sequences.length; n++) {
-      seqs[n] = sequences[n].getSequenceString(c);
+    String[] seqs = new String[sequences.length];
+    for (int n = 0; n < sequences.length; n++)
+    {
+      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()
+  {
+    return width;
+  }
+
+  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].getSequenceAsString() +
+                                           mseq[s].getSequenceAsString());
+                  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].getSequenceAsString() +
+                                             oseq.getSequenceAsString());
+                    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].getSequenceAsString() +
+                                       hseq.getSequenceAsString());
+              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].getSequenceAsString() +
+                                         mseq[s].getSequenceAsString());
+                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].getSequenceAsString() +
+                                             oseq.getSequenceAsString());
+                    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;
+  }
 }