JAL-4152 Remove redundant casts from getInstance usages.

[jalview.git] / src / jalview / analysis / AlignmentSorter.java

/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.bin.ApplicationSingletonProvider;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
import jalview.util.QuickSort;

import java.util.ArrayList;
import java.util.BitSet;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;

/**
 * Routines for manipulating the order of a multiple sequence alignment TODO:
 * this class retains some global states concerning sort-order which should be
 * made attributes for the caller's alignment visualization. TODO: refactor to
 * allow a subset of selected sequences to be sorted within the context of a
 * whole alignment. Sort method template is: SequenceI[] tobesorted, [ input
 * data mapping to each tobesorted element to use ], Alignment context of
 * tobesorted that are to be re-ordered, boolean sortinplace, [special data - ie
 * seuqence to be sorted w.r.t.]) sortinplace implies that the sorted vector
 * resulting from applying the operation to tobesorted should be mapped back to
 * the original positions in alignment. Otherwise, normal behaviour is to re
 * order alignment so that tobesorted is sorted and grouped together starting
 * from the first tobesorted position in the alignment. e.g. (a,tb2,b,tb1,c,tb3
 * becomes a,tb1,tb2,tb3,b,c)
 */
public class AlignmentSorter implements ApplicationSingletonI
{

  private AlignmentSorter()
  {
    // private singleton
  }

  public static AlignmentSorter getInstance()
  {
    return ApplicationSingletonProvider.getInstance(AlignmentSorter.class);
  }

  /**
   * types of feature ordering: Sort by score : average score - or total score -
   * over all features in region Sort by feature label text: (or if null -
   * feature type text) - numerical or alphabetical Sort by feature density:
   * based on counts - ignoring individual text or scores for each feature
   */
  public static final String FEATURE_SCORE = "average_score";

  public static final String FEATURE_LABEL = "text";

  public static final String FEATURE_DENSITY = "density";

  /*
   * todo: refactor searches to follow a basic pattern: (search property, last
   * search state, current sort direction)
   */
  boolean sortIdAscending = true;

  int lastGroupHash = 0;

  boolean sortGroupAscending = true;

  AlignmentOrder lastOrder = null;

  boolean sortOrderAscending = true;

  TreeModel lastTree = null;

  boolean sortTreeAscending = true;

  /**
   * last Annotation Label used for sort by Annotation score
   */
  private String lastSortByAnnotation;

  /**
   * string hash of last arguments to sortByFeature (sort order toggles if this
   * is unchanged between sorts)
   */
  private String sortByFeatureCriteria;

  private boolean sortByFeatureAscending = true;

  private boolean sortLengthAscending;

  private static boolean sortEValueAscending;

  private static boolean sortBitScoreAscending;

  /**
   * Sorts sequences in the alignment by Percentage Identity with the given
   * reference sequence, sorting the highest identity to the top
   * 
   * @param align
   *          AlignmentI
   * @param s
   *          SequenceI
   * @param end
   */
  public static void sortByPID(AlignmentI align, SequenceI s)
  {
    int nSeq = align.getHeight();

    float[] scores = new float[nSeq];
    SequenceI[] seqs = new SequenceI[nSeq];
    String refSeq = s.getSequenceAsString();

    SimilarityParams pidParams = new SimilarityParams(true, true, true,
            true);
    for (int i = 0; i < nSeq; i++)
    {
      scores[i] = (float) PIDModel.computePID(
              align.getSequenceAt(i).getSequenceAsString(), refSeq,
              pidParams);
      seqs[i] = align.getSequenceAt(i);
    }

    QuickSort.sort(scores, seqs);
    setReverseOrder(align, seqs);
  }

  /**
   * Sorts by ID. Numbers are sorted before letters.
   * 
   * @param align
   *          The alignment object to sort
   */
  public static void sortByID(AlignmentI align)
  {
    int nSeq = align.getHeight();

    String[] ids = new String[nSeq];
    SequenceI[] seqs = new SequenceI[nSeq];

    for (int i = 0; i < nSeq; i++)
    {
      ids[i] = align.getSequenceAt(i).getName();
      seqs[i] = align.getSequenceAt(i);
    }

    QuickSort.sort(ids, seqs);
    AlignmentSorter as = getInstance();
    as.sortIdAscending = !as.sortIdAscending;
    set(align, seqs, as.sortIdAscending);
  }

  /**
   * Sorts by sequence length
   * 
   * @param align
   *          The alignment object to sort
   */
  public static void sortByLength(AlignmentI align)
  {
    int nSeq = align.getHeight();

    float[] length = new float[nSeq];
    SequenceI[] seqs = new SequenceI[nSeq];

    for (int i = 0; i < nSeq; i++)
    {
      seqs[i] = align.getSequenceAt(i);
      length[i] = (seqs[i].getEnd() - seqs[i].getStart());
    }

    QuickSort.sort(length, seqs);
    AlignmentSorter as = getInstance();
    as.sortLengthAscending = !as.sortLengthAscending;
    set(align, seqs, as.sortLengthAscending);
  }

  /**
   * Sorts by sequence evalue. Currently moves all sequences without an evalue to
   * the top of the alignment.
   * 
   * @param align
   *                The alignment object to sort
   */
  public static void sortByEValue(AlignmentI align)
  {
    int nSeq = align.getHeight();

    double[] evalue = new double[nSeq];
    SequenceI[] seqs = new SequenceI[nSeq];

    for (int i = 0; i < nSeq; i++)
    {
      seqs[i] = align.getSequenceAt(i);
      AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores");
      if (ann != null)
      {
        evalue[i] = ann[0].getEValue();
      }
      else
      {
        evalue[i] = -1;
      }
    }

    QuickSort.sort(evalue, seqs);

    if (sortEValueAscending)
    {
      setReverseOrder(align, seqs);
    }
    else
    {
      setOrder(align, seqs);
    }

    sortEValueAscending = !sortEValueAscending;
  }

  /**
   * Sorts by sequence bit score. Currently moves all sequences without a bit
   * score to the top of the alignment
   * 
   * @param align
   *                The alignment object to sort
   */
  public static void sortByBitScore(AlignmentI align)
  {
    int nSeq = align.getHeight();

    double[] score = new double[nSeq];
    SequenceI[] seqs = new SequenceI[nSeq];

    for (int i = 0; i < nSeq; i++)
    {
      seqs[i] = align.getSequenceAt(i);
      AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores");
      if (ann != null)
      {
        score[i] = ann[0].getEValue();
      }
      else
      {
        score[i] = -1;
      }
    }

    QuickSort.sort(score, seqs);

    if (sortBitScoreAscending)
    {
      setReverseOrder(align, seqs);
    }
    else
    {
      setOrder(align, seqs);
    }

    sortBitScoreAscending = !sortBitScoreAscending;
  }

  /**
   * Sorts the alignment by size of group. <br>
   * Maintains the order of sequences in each group by order in given alignment
   * object.
   * 
   * @param align
   *          sorts the given alignment object by group
   */
  public static void sortByGroup(AlignmentI align)
  {
    // MAINTAINS ORIGNAL SEQUENCE ORDER,
    // ORDERS BY GROUP SIZE
    List<SequenceGroup> groups = new ArrayList<>();

    AlignmentSorter as = getInstance();

    if (groups.hashCode() != as.lastGroupHash)
    {
      as.sortGroupAscending = true;
      as.lastGroupHash = groups.hashCode();
    }
    else
    {
      as.sortGroupAscending = !as.sortGroupAscending;
    }

    // SORTS GROUPS BY SIZE
    // ////////////////////
    for (SequenceGroup sg : align.getGroups())
    {
      for (int j = 0; j < groups.size(); j++)
      {
        SequenceGroup sg2 = groups.get(j);

        if (sg.getSize() > sg2.getSize())
        {
          groups.add(j, sg);

          break;
        }
      }

      if (!groups.contains(sg))
      {
        groups.add(sg);
      }
    }

    // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
    // /////////////////////////////////////////////
    List<SequenceI> tmp = new ArrayList<>();

    for (int i = 0; i < groups.size(); i++)
    {
      SequenceGroup sg = groups.get(i);
      SequenceI[] orderedseqs = sg.getSequencesInOrder(align);

      for (int j = 0; j < orderedseqs.length; j++)
      {
        tmp.add(orderedseqs[j]);
      }
    }
    set(align, tmp, as.sortGroupAscending);
  }

  /**
   * Sorts by a given AlignmentOrder object
   * 
   * @param align
   *          Alignment to order
   * @param order
   *          specified order for alignment
   */
  public static void sortBy(AlignmentI align, AlignmentOrder order)
  {
    // Get an ordered vector of sequences which may also be present in align
    List<SequenceI> tmp = order.getOrder();

    AlignmentSorter as = getInstance();

    if (as.lastOrder == order)
    {
      as.sortOrderAscending = !as.sortOrderAscending;
    }
    else
    {
      as.sortOrderAscending = true;
    }
    set(align, tmp, as.sortOrderAscending);
  }

  /**
   * DOCUMENT ME!
   * 
   * @param align
   *          alignment to order
   * @param tree
   *          tree which has
   * 
   * @return DOCUMENT ME!
   */
  private static List<SequenceI> getOrderByTree(AlignmentI align,
          TreeModel tree)
  {
    int nSeq = align.getHeight();

    List<SequenceI> tmp = new ArrayList<>();

    tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());

    if (tmp.size() != nSeq)
    {
      // TODO: JBPNote - decide if this is always an error
      // (eg. not when a tree is associated to another alignment which has more
      // sequences)
      if (tmp.size() != nSeq)
      {
        addStrays(align, tmp);
      }

      if (tmp.size() != nSeq)
      {
        System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
                + nSeq
                + " in getOrderByTree - tree contains sequences not in alignment");
      }
    }

    return tmp;
  }

  /**
   * Sorts the alignment by a given tree
   * 
   * @param align
   *          alignment to order
   * @param tree
   *          tree which has
   */
  public static void sortByTree(AlignmentI align, TreeModel tree)
  {
    List<SequenceI> tmp = getOrderByTree(align, tree);

    AlignmentSorter as = getInstance();

    // tmp should properly permute align with tree.
    if (as.lastTree != tree)
    {
      as.sortTreeAscending = true;
      as.lastTree = tree;
    }
    else
    {
      as.sortTreeAscending = !as.sortTreeAscending;
    }
    set(align, tmp, as.sortTreeAscending);
  }

  /**
   * DOCUMENT ME!
   * 
   * @param align
   *          DOCUMENT ME!
   * @param tmp
   *          DOCUMENT ME!
   */
  private static void addStrays(AlignmentI align, List<SequenceI> tmp)
  {
    int nSeq = align.getHeight();

    for (int i = 0; i < nSeq; i++)
    {
      if (!tmp.contains(align.getSequenceAt(i)))
      {
        tmp.add(align.getSequenceAt(i));
      }
    }

    if (nSeq != tmp.size())
    {
      System.err
              .println("ERROR: Size still not right even after addStrays");
    }
  }

  /**
   * DOCUMENT ME!
   * 
   * @param node
   *          DOCUMENT ME!
   * @param tmp
   *          DOCUMENT ME!
   * @param seqset
   *          DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  private static List<SequenceI> _sortByTree(SequenceNode node,
          List<SequenceI> tmp, List<SequenceI> seqset)
  {
    if (node == null)
    {
      return tmp;
    }

    SequenceNode left = (SequenceNode) node.left();
    SequenceNode right = (SequenceNode) node.right();

    if ((left == null) && (right == null))
    {
      if (!node.isPlaceholder() && (node.element() != null))
      {
        if (node.element() instanceof SequenceI)
        {
          if (!tmp.contains(node.element())) // && (seqset==null ||
                                             // seqset.size()==0 ||
                                             // seqset.contains(tmp)))
          {
            tmp.add((SequenceI) node.element());
          }
        }
      }

      return tmp;
    }
    else
    {
      _sortByTree(left, tmp, seqset);
      _sortByTree(right, tmp, seqset);
    }

    return tmp;
  }

  // Ordering Objects
  // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
  // appropriate order
  //

  /**
   * recover the order of sequences given by the safe numbering scheme introducd
   * SeqsetUtils.uniquify.
   */
  public static void recoverOrder(SequenceI[] alignment)
  {
    float[] ids = new float[alignment.length];

    for (int i = 0; i < alignment.length; i++)
    {
      ids[i] = (Float.valueOf(alignment[i].getName().substring(8)))
              .floatValue();
    }

    jalview.util.QuickSort.sort(ids, alignment);
  }

  /**
   * Sort sequence in order of increasing score attribute for annotation with a
   * particular scoreLabel. Or reverse if same label was used previously
   * 
   * @param scoreLabel
   *          exact label for sequence associated AlignmentAnnotation scores to
   *          use for sorting.
   * @param alignment
   *          sequences to be sorted
   */
  public static void sortByAnnotationScore(String scoreLabel,
          AlignmentI alignment)
  {
    SequenceI[] seqs = alignment.getSequencesArray();
    boolean[] hasScore = new boolean[seqs.length]; // per sequence score
    // presence
    int hasScores = 0; // number of scores present on set
    double[] scores = new double[seqs.length];
    double min = 0, max = 0;
    for (int i = 0; i < seqs.length; i++)
    {
      AlignmentAnnotation[] scoreAnn = seqs[i].getAnnotation(scoreLabel);
      if (scoreAnn != null)
      {
        hasScores++;
        hasScore[i] = true;
        scores[i] = scoreAnn[0].getScore(); // take the first instance of this
        // score.
        if (hasScores == 1)
        {
          max = min = scores[i];
        }
        else
        {
          if (max < scores[i])
          {
            max = scores[i];
          }
          if (min > scores[i])
          {
            min = scores[i];
          }
        }
      }
      else
      {
        hasScore[i] = false;
      }
    }
    if (hasScores == 0)
    {
      return; // do nothing - no scores present to sort by.
    }
    if (hasScores < seqs.length)
    {
      for (int i = 0; i < seqs.length; i++)
      {
        if (!hasScore[i])
        {
          scores[i] = (max + i + 1.0);
        }
      }
    }

    jalview.util.QuickSort.sort(scores, seqs);

    AlignmentSorter as = getInstance();

    if (as.lastSortByAnnotation != scoreLabel)
    {
      as.lastSortByAnnotation = scoreLabel;
      setOrder(alignment, seqs);
    }
    else
    {
      setReverseOrder(alignment, seqs);
    }
  }

  /**
   * Sort sequences by feature score or density, optionally restricted by
   * feature types, feature groups, or alignment start/end positions.
   * <p>
   * If the sort is repeated for the same combination of types and groups, sort
   * order is reversed.
   * 
   * @param featureTypes
   *          a list of feature types to include (or null for all)
   * @param groups
   *          a list of feature groups to include (or null for all)
   * @param startCol
   *          start column position to include (base zero)
   * @param endCol
   *          end column position to include (base zero)
   * @param alignment
   *          the alignment to be sorted
   * @param method
   *          either "average_score" or "density" ("text" not yet implemented)
   */
  public static void sortByFeature(List<String> featureTypes,
          List<String> groups, final int startCol, final int endCol,
          AlignmentI alignment, String method)
  {
    if (method != FEATURE_SCORE && method != FEATURE_LABEL
            && method != FEATURE_DENSITY)
    {
      String msg = String.format(
              "Implementation Error - sortByFeature method must be either '%s' or '%s'",
              FEATURE_SCORE, FEATURE_DENSITY);
      System.err.println(msg);
      return;
    }

    flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol,
            endCol);

    SequenceI[] seqs = alignment.getSequencesArray();

    boolean[] hasScore = new boolean[seqs.length]; // per sequence score
    // presence
    int hasScores = 0; // number of scores present on set
    double[] scores = new double[seqs.length];
    int[] seqScores = new int[seqs.length];
    Object[][] feats = new Object[seqs.length][];
    double min = 0d;
    double max = 0d;

    for (int i = 0; i < seqs.length; i++)
    {
      /*
       * get sequence residues overlapping column region
       * and features for residue positions and specified types
       */
      String[] types = featureTypes == null ? null
              : featureTypes.toArray(new String[featureTypes.size()]);
      List<SequenceFeature> sfs = seqs[i].findFeatures(startCol + 1,
              endCol + 1, types);

      seqScores[i] = 0;
      scores[i] = 0.0;

      Iterator<SequenceFeature> it = sfs.listIterator();
      while (it.hasNext())
      {
        SequenceFeature sf = it.next();

        /*
         * accept all features with null or empty group, otherwise
         * check group is one of the currently visible groups
         */
        String featureGroup = sf.getFeatureGroup();
        if (groups != null && featureGroup != null
                && !"".equals(featureGroup)
                && !groups.contains(featureGroup))
        {
          it.remove();
        }
        else
        {
          float score = sf.getScore();
          if (FEATURE_SCORE.equals(method) && !Float.isNaN(score))
          {
            if (seqScores[i] == 0)
            {
              hasScores++;
            }
            seqScores[i]++;
            hasScore[i] = true;
            scores[i] += score;
            // take the first instance of this score // ??
          }
        }
      }

      feats[i] = sfs.toArray(new SequenceFeature[sfs.size()]);
      if (!sfs.isEmpty())
      {
        if (method == FEATURE_LABEL)
        {
          // order the labels by alphabet (not yet implemented)
          String[] labs = new String[sfs.size()];
          for (int l = 0; l < sfs.size(); l++)
          {
            SequenceFeature sf = sfs.get(l);
            String description = sf.getDescription();
            labs[l] = (description != null ? description : sf.getType());
          }
          QuickSort.sort(labs, feats[i]);
        }
      }
      if (hasScore[i])
      {
        // compute average score
        scores[i] /= seqScores[i];
        // update the score bounds.
        if (hasScores == 1)
        {
          min = scores[i];
          max = min;
        }
        else
        {
          max = Math.max(max, scores[i]);
          min = Math.min(min, scores[i]);
        }
      }
    }

    boolean doSort = false;

    if (FEATURE_SCORE.equals(method))
    {
      if (hasScores == 0)
      {
        return; // do nothing - no scores present to sort by.
      }
      // pad score matrix
      if (hasScores < seqs.length)
      {
        for (int i = 0; i < seqs.length; i++)
        {
          if (!hasScore[i])
          {
            scores[i] = (max + 1 + i);
          }
          else
          {
            // int nf = (feats[i] == null) ? 0
            // : ((SequenceFeature[]) feats[i]).length;
            // // System.err.println("Sorting on Score: seq " +
            // seqs[i].getName()
            // + " Feats: " + nf + " Score : " + scores[i]);
          }
        }
      }
      doSort = true;
    }
    else if (FEATURE_DENSITY.equals(method))
    {
      for (int i = 0; i < seqs.length; i++)
      {
        int featureCount = feats[i] == null ? 0
                : ((SequenceFeature[]) feats[i]).length;
        scores[i] = featureCount;
        // System.err.println("Sorting on Density: seq "+seqs[i].getName()+
        // " Feats: "+featureCount+" Score : "+scores[i]);
      }
      doSort = true;
    }
    if (doSort)
    {
      QuickSort.sortByDouble(scores, seqs,
              getInstance().sortByFeatureAscending);
    }
    setOrder(alignment, seqs);
  }

  /**
   * Builds a string hash of criteria for sorting, and if unchanged from last
   * time, reverse the sort order
   * 
   * @param method
   * @param featureTypes
   * @param groups
   * @param startCol
   * @param endCol
   */
  protected static void flipFeatureSortIfUnchanged(String method,
          List<String> featureTypes, List<String> groups,
          final int startCol, final int endCol)
  {
    StringBuilder sb = new StringBuilder(64);
    sb.append(startCol).append(method).append(endCol);
    if (featureTypes != null)
    {
      Collections.sort(featureTypes);
      sb.append(featureTypes.toString());
    }
    if (groups != null)
    {
      Collections.sort(groups);
      sb.append(groups.toString());
    }
    String scoreCriteria = sb.toString();

    /*
     * if resorting on the same criteria, toggle sort order
     */
    AlignmentSorter as = getInstance();
    if (as.sortByFeatureCriteria == null
            || !scoreCriteria.equals(as.sortByFeatureCriteria))
    {
      as.sortByFeatureAscending = true;
    }
    else
    {
      as.sortByFeatureAscending = !as.sortByFeatureAscending;
    }
    as.sortByFeatureCriteria = scoreCriteria;
  }

  /**
   * Set the alignment's sequences list to contain the sequences from a
   * temporary list, first adding all the elements from the tmp list, then adding all sequences in the alignment that
   * are not in the list. Option to do the final sort either in order or in reverse order.
   * 
   * @param align The alignment being sorted
   * @param tmp
   *          the temporary sequence list
   * @param ascending
   *          false for reversed order; only sequences already in
   *          the alignment will be used (which is actually already guaranteed
   *          by vectorSubsetToArray)
   */
  private static void set(AlignmentI align, List<SequenceI> tmp,
          boolean ascending)
  {
    set(align, vectorSubsetToArray(align.getSequences(), tmp), ascending);
  }

  /**
   * Set the alignment's sequences list to contain these sequences, either in
   * this order or its reverse.
   * 
   * @param align
   * @param seqs
   *          the new sequence array
   * @param ascending
   *          false for reversed order; if ascending, only sequences already in
   *          the alignment will be used; if descending, then a direct 1:1
   *          replacement is made
   */
  private static void set(AlignmentI align, SequenceI[] seqs,
          boolean ascending)
  {
    if (ascending)
    {
      setOrder(align, seqs);
    }
    else
    {
      setReverseOrder(align, seqs);
    }

  }

  /**
   * Replace the alignment's sequences with values in an array, clearing the
   * alignment's sequence list and filtering for sequences that are actually in
   * the alignment already.
   * 
   * @param align
   *          the Alignment
   * @param seqs
   *          the array of replacement values, of any length
   */
  public static void setOrder(AlignmentI align, SequenceI[] seqs)
  {
    // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
    List<SequenceI> seqList = align.getSequences();
    synchronized (seqList)
    {
      List<SequenceI> tmp = new ArrayList<>();

      for (int i = 0; i < seqs.length; i++)
      {
        if (seqList.contains(seqs[i]))
        {
          tmp.add(seqs[i]);
        }
      }

      seqList.clear();
      // User may have hidden seqs, then clicked undo or redo
      for (int i = 0; i < tmp.size(); i++)
      {
        seqList.add(tmp.get(i));
      }
    }
  }

  /**
   * Replace the alignment's sequences or a subset of those sequences with
   * values in an array in reverse order. All sequences are replaced; no check
   * is made that these sequences are in the alignment already.
   * 
   * @param align
   *          the Alignment
   * @param seqs
   *          the array of replacement values, length must be less than or equal
   *          to Alignment.sequences.size()
   */
  private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
  {
    int nSeq = seqs.length;

    int len = (nSeq + (nSeq % 2)) / 2;
    // int len = 0;
    //
    // if ((nSeq % 2) == 0)
    // {
    // len = nSeq / 2;
    // }
    // else
    // {
    // len = (nSeq + 1) / 2;
    // }

    // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
    List<SequenceI> seqList = align.getSequences();
    synchronized (seqList)
    {
      for (int i = 0; i < len; i++)
      {
        // SequenceI tmp = seqs[i];
        seqList.set(i, seqs[nSeq - i - 1]);
        seqList.set(nSeq - i - 1, seqs[i]);
      }
    }
  }

  /**
   * Create and array of reordered sequences in order first from tmp that are
   * present in seqList already, then, after that, any remaining sequences in
   * seqList not in tmp. Any sequences in tmp that are not in seqList already
   * are discarded.
   * 
   * @param seqList
   *          thread safe collection of sequences originally in the alignment
   * @param tmp
   *          thread safe collection of sequences or subsequences possibly in
   *          seqList
   * 
   * @return intersect(tmp,seqList)+intersect(complement(tmp),seqList)
   */
  private static SequenceI[] vectorSubsetToArray(List<SequenceI> seqList,
          List<SequenceI> tmp)
  {
    ArrayList<SequenceI> seqs = new ArrayList<>();
    int n = seqList.size();
    BitSet bs = new BitSet(n);
    bs.set(0, n);
    for (int i = 0, nt = tmp.size(); i < nt; i++)
    {
      SequenceI sq = tmp.get(i);
      int idx = seqList.indexOf(sq);
      if (idx >= 0 && bs.get(idx))
      {
        seqs.add(sq);
        bs.clear(idx);
      }
    }

    for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
    {
      seqs.add(seqList.get(i));
    }

    return seqs.toArray(new SequenceI[seqs.size()]);
  }

}