/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
 * Copyright (C) 2014 The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.analysis;

import java.util.ArrayList;
import java.util.List;

import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentI;

/**
 * grab bag of useful alignment manipulation operations
 * Expect these to be refactored elsewhere at some point.
 * @author jimp
 *
 */
public class AlignmentUtils
{

  /**
   * given an existing alignment, create a new alignment including all, or up to flankSize additional symbols from each sequence's dataset sequence
   * @param core
   * @param flankSize
   * @return AlignmentI
   */
  public static AlignmentI expandContext(AlignmentI core, int flankSize)
  {
    List<SequenceI> sq = new ArrayList<SequenceI>();
    int maxoffset = 0;
    for (SequenceI s:core.getSequences())
    {
      SequenceI newSeq = s.deriveSequence();
      if (newSeq.getStart()>maxoffset && newSeq.getDatasetSequence().getStart()<s.getStart())
      {
        maxoffset = newSeq.getStart();
      }
      sq.add(newSeq);
    }
    if (flankSize>-1) {
      maxoffset = flankSize;
    }
    // now add offset to create a new expanded alignment
    for (SequenceI s:sq)
    {
      SequenceI ds = s;
      while (ds.getDatasetSequence()!=null) {
        ds=ds.getDatasetSequence();
      }
      int s_end = s.findPosition(s.getStart()+s.getLength());
      // find available flanking residues for sequence
      int ustream_ds=s.getStart()-ds.getStart(),dstream_ds=ds.getEnd()-s_end;
      
      // build new flanked sequence
      
      // compute gap padding to start of flanking sequence
      int offset=maxoffset - ustream_ds;
      
      // padding is gapChar x ( maxoffset - min(ustream_ds, flank)
      if (flankSize>=0) {
        if (flankSize<ustream_ds)
        {
        // take up to flankSize residues
        offset = maxoffset-flankSize;
        ustream_ds = flankSize;
      }
        if (flankSize<dstream_ds)
        {
          dstream_ds=flankSize;
        }
      }
      char[] upstream = new String(ds.getSequence(s.getStart()-1-ustream_ds, s.getStart()-1)).toLowerCase().toCharArray();
      char[] downstream = new String(ds.getSequence(s_end-1,s_end+1+dstream_ds)).toLowerCase().toCharArray();
      char[] coreseq=s.getSequence();
      char[] nseq = new char[offset+upstream.length+downstream.length+coreseq.length]; 
      char c = core.getGapCharacter();
      // TODO could lowercase the flanking regions
      int p=0;
      for (; p<offset;p++)
      {
        nseq[p] = c;
      }
//      s.setSequence(new String(upstream).toLowerCase()+new String(coreseq) + new String(downstream).toLowerCase());
      System.arraycopy(upstream, 0, nseq, p, upstream.length);
      System.arraycopy(coreseq, 0, nseq, p+upstream.length, coreseq.length);
      System.arraycopy(downstream, 0, nseq, p+coreseq.length+upstream.length, downstream.length);
      s.setSequence(new String(nseq));
      s.setStart(s.getStart()-ustream_ds);
      s.setEnd(s_end+downstream.length);
    }
    AlignmentI newAl = new jalview.datamodel.Alignment(sq.toArray(new SequenceI[0]));
    newAl.setDataset(core.getDataset());
    return newAl;
  }
}