X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=507d38b169e2962a103944add22483bf790a2671;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=40ad37254b6624d3bb8ecfbebed408711fc420cb;hpb=587e55e539d6268657467be71a904f011b890181;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 40ad372..507d38b 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,299 +1,470 @@
-package jalview.analysis;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-import jalview.io.*;
-
-import java.util.*;
-
-/** Data structure to hold and manipulate a multiple sequence alignment
- */
-public class AlignmentSorter {
-
-  private AlignmentSorter() {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  public static void sortGroups(AlignmentI align) {
-    Vector groups = align.getGroups();
-    int    nGroup = groups.size();
-
-    float[]  arr = new float [nGroup];
-    Object[] s   = new Object[nGroup];
-
-    for (int i=0; i < nGroup; i++) {
-      arr[i] = ((SequenceGroup)groups.elementAt(i)).getSize();
-      s[i]   = groups.elementAt(i);
-    }
-
-    QuickSort.sort(arr,s);
-
-    Vector newg = new Vector(nGroup);
-
-    for (int i=nGroup-1; i >= 0; i--) {
-      newg.addElement(s[i]);
-    }
-
-    //    align.setGroups(newg);
-  }
-
-  /**
-   * Sort by Percentage Identity
-   *
-   * @param align AlignmentI
-   * @param s SequenceI
-   */
-  public static void sortByPID(AlignmentI align, SequenceI s) {
-    int nSeq = align.getHeight();
-
-    float     scores[] = new float[nSeq];
-    SequenceI seqs[]   = new SequenceI[nSeq];
-
-    for (int i = 0; i < nSeq; i++) {
-      scores[i] = Comparison.compare(align.getSequenceAt(i),s);
-      seqs[i]   = align.getSequenceAt(i);
-    }
-
-    QuickSort.sort(scores,0,scores.length-1,seqs);
-
-   setReverseOrder(align,seqs);
-  }
-
-  private static void setReverseOrder(AlignmentI align, SequenceI [] seqs) {
-    int nSeq = seqs.length;
-
-    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
-    for (int i = 0; i < len; i++) {
-      //SequenceI tmp = seqs[i];
-      align.getSequences().setElementAt(seqs[nSeq-i-1],i);
-      align.getSequences().setElementAt(seqs[i],nSeq-i-1);
-    }
-  }
-
-  private static void setOrder(AlignmentI align, Vector tmp) {
-    setOrder(align,vectorSubsetToArray(tmp, align.getSequences()));
-  }
-
-  private static void setOrder(AlignmentI align, SequenceI [] seqs) {
-      // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-
-      Vector algn = align.getSequences();
-
-      for (int i = 0, p = 0; i < seqs.length; i++)
-        algn.setElementAt(seqs[i], p++);
-  }
-  /**    */
-  static boolean sortIdAscending = true;
-  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);
-
-    if(sortIdAscending)
-      setReverseOrder(align,seqs);
-    else
-      setOrder(align, seqs);
-
-    sortIdAscending = !sortIdAscending;
-  }
-  static int lastGroupHash = 0;
-  static boolean sortGroupAscending = true;
-
-  public static void sortByGroup(AlignmentI align) {
-    int    nSeq = align.getHeight();
-    Vector groups = align.getGroups();
-    if (groups.hashCode()!=lastGroupHash) {
-      sortGroupAscending=true;
-      lastGroupHash = groups.hashCode();
-    } else
-      sortGroupAscending = ! sortGroupAscending;
-
-    Vector seqs = new Vector();
-
-    for (int i=0; i < groups.size(); i++) {
-      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-
-      for (int j = 0; j < sg.getSize(); j++) {
-        seqs.addElement(sg.getSequenceAt(j));
-      }
-    }
-
-    // Deletions can happen so this check may fail
-    /*
-     if (seqs.size() != nSeq) {
-      System.err.println("ERROR: tmp.size() != nseq in sortByGroups");
-      if (seqs.size() < nSeq) {
-        addStrays(align,seqs);
-      }
-    }
-*/
-    if(sortGroupAscending)
-      setOrder(align,seqs);
-    else
-      setReverseOrder( align, vectorSubsetToArray(seqs, align.getSequences()));
-
-  }
-
-  private static SequenceI [] vectorToArray(Vector tmp) {
-    SequenceI[] seqs = new SequenceI[tmp.size()];
-
-    for (int i=0; i < tmp.size(); i++) {
-      seqs[i] = (SequenceI)tmp.elementAt(i);
-    }
-    return seqs;
-  }
-
-  private static SequenceI [] vectorSubsetToArray(Vector tmp, Vector mask) {
-    Vector seqs = new Vector();
-    int i,m, p;
-    boolean[] tmask = new boolean[m=mask.size()];
-    for (i=0; i<m; i++)
-      tmask[i] = true;
-    for (i=0; i < tmp.size(); i++) {
-      Object sq;
-      if (mask.contains(sq=tmp.elementAt(i))) {
-        tmask[mask.indexOf(sq)] = false;
-        seqs.addElement(sq);
-        m--;
-      }
-    }
-    for (i=0; i<tmask.length; i++)
-      if (tmask[i])
-        seqs.addElement(mask.elementAt(i));
-    return vectorToArray(seqs);
-  }
-
-  static AlignmentOrder lastOrder = null;
-  static boolean sortOrderAscending = true;
-
-  public static void sortBy(AlignmentI align, AlignmentOrder order) {
-    // Get an ordered vector of sequences which may also be present in align
-    Vector tmp = order.getOrder();
-//    if (tmp.size()<align.getHeight())
-//      addStrays(align, tmp);
-    if (lastOrder==order)
-      sortOrderAscending=!sortOrderAscending;
-    else
-      sortOrderAscending=true;
-
-    if (sortOrderAscending)
-      setOrder(align, tmp);
-    else
-      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
-  }
-  static NJTree lastTree = null;
-  static boolean sortTreeAscending = true;
-
-  public static Vector getOrderByTree(AlignmentI align, NJTree tree) {
-    int nSeq = align.getHeight();
-
-    Vector tmp = new Vector();
-
-    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("ERROR: tmp.size()="+tmp.size()+" != nseq="+nSeq+" in getOrderByTree");
-
-    }
-    return tmp;
-  }
-
-  public static void sortByTree(AlignmentI align, NJTree tree) {
-    Vector tmp = getOrderByTree(align, tree);
-    // tmp should properly permute align with tree.
-    if(lastTree!=tree) {
-      sortTreeAscending = true;
-      lastTree = tree;
-    } else {
-      sortTreeAscending = !sortTreeAscending;
-    }
-    if(sortTreeAscending)
-      setOrder(align,tmp);
-    else
-      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
-  }
-
-  private static void addStrays(AlignmentI align, Vector seqs) {
-    int    nSeq = align.getHeight();
-    for (int i=0;i<nSeq;i++) {
-      if (!seqs.contains(align.getSequenceAt(i))) {
-        seqs.addElement(align.getSequenceAt(i));
-      }
-    }
-    if (nSeq != seqs.size()) {
-      System.err.println("ERROR: Size still not right even after addStrays");
-    }
-  }
-
-  public static Vector _sortByTree(SequenceNode node, Vector tmp, Vector 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()))
-              tmp.addElement((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] = (new Float(alignment[i].getName().substring(8))).floatValue();
-    jalview.util.QuickSort.sort(ids, alignment);
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-  }
-
-}
+/*
+* 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.analysis;
+
+import jalview.datamodel.*;
+
+import jalview.util.*;
+
+import java.util.*;
+
+
+/** Data structure to hold and manipulate a multiple sequence alignment
+ */
+public class AlignmentSorter
+{
+    static boolean sortIdAscending = true;
+    static int lastGroupHash = 0;
+    static boolean sortGroupAscending = true;
+    static AlignmentOrder lastOrder = null;
+    static boolean sortOrderAscending = true;
+    static NJTree lastTree = null;
+    static boolean sortTreeAscending = true;
+
+    /**
+     * Sort by Percentage Identity
+     *
+     * @param align AlignmentI
+     * @param s SequenceI
+     */
+    public static void sortByPID(AlignmentI align, SequenceI s)
+    {
+        int nSeq = align.getHeight();
+
+        float[] scores = new float[nSeq];
+        SequenceI[] seqs = new SequenceI[nSeq];
+
+        for (int i = 0; i < nSeq; i++)
+        {
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),
+                                       s.getSequence());
+            seqs[i] = align.getSequenceAt(i);
+        }
+
+        QuickSort.sort(scores, 0, scores.length - 1, seqs);
+
+        setReverseOrder(align, seqs);
+    }
+
+    /**
+     * Reverse the order of the sort
+     *
+     * @param align DOCUMENT ME!
+     * @param seqs DOCUMENT ME!
+     */
+    private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
+    {
+        int nSeq = seqs.length;
+
+        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
+        for (int i = 0; i < len; i++)
+        {
+            //SequenceI tmp = seqs[i];
+            align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
+            align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
+        }
+    }
+
+    /**
+     * Sets the Alignment object with the given sequences
+     *
+     * @param align Alignment object to be updated
+     * @param tmp sequences as a vector
+     */
+    private static void setOrder(AlignmentI align, Vector tmp)
+    {
+        setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+    }
+
+    /**
+     * Sets the Alignment object with the given sequences
+     *
+     * @param align DOCUMENT ME!
+     * @param seqs sequences as an array
+     */
+    private static void setOrder(AlignmentI align, SequenceI[] seqs)
+    {
+        // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+        Vector algn = align.getSequences();
+
+        for (int i = 0; i < seqs.length; i++)
+        {
+            algn.setElementAt(seqs[i], i);
+        }
+    }
+
+    /**
+     * 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);
+
+        if (sortIdAscending)
+        {
+            setReverseOrder(align, seqs);
+        }
+        else
+        {
+            setOrder(align, seqs);
+        }
+
+        sortIdAscending = !sortIdAscending;
+    }
+
+    /**
+     * 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
+        Vector groups = new Vector();
+
+        if (groups.hashCode() != lastGroupHash)
+        {
+            sortGroupAscending = true;
+            lastGroupHash = groups.hashCode();
+        }
+        else
+        {
+            sortGroupAscending = !sortGroupAscending;
+        }
+
+        //SORTS GROUPS BY SIZE
+        //////////////////////
+        for (int i = 0; i < align.getGroups().size(); i++)
+        {
+            SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
+
+            for (int j = 0; j < groups.size(); j++)
+            {
+                SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
+
+                if (sg.getSize(false) > sg2.getSize(false))
+                {
+                    groups.insertElementAt(sg, j);
+
+                    break;
+                }
+            }
+
+            if (!groups.contains(sg))
+            {
+                groups.addElement(sg);
+            }
+        }
+
+        //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+        ///////////////////////////////////////////////
+        Vector seqs = new Vector();
+
+        for (int i = 0; i < groups.size(); i++)
+        {
+            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+            SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
+
+            for (int j = 0; j < orderedseqs.length; j++)
+            {
+                seqs.addElement(orderedseqs[j]);
+            }
+        }
+
+        if (sortGroupAscending)
+        {
+            setOrder(align, seqs);
+        }
+        else
+        {
+            setReverseOrder(align,
+                vectorSubsetToArray(seqs, align.getSequences()));
+        }
+    }
+
+    /**
+     * Converts Vector to array.
+     * java 1.18 does not have Vector.toArray()
+     *
+     * @param tmp Vector of SequenceI objects
+     *
+     * @return array of Sequence[]
+     */
+    private static SequenceI[] vectorToArray(Vector tmp)
+    {
+        SequenceI[] seqs = new SequenceI[tmp.size()];
+
+        for (int i = 0; i < tmp.size(); i++)
+        {
+            seqs[i] = (SequenceI) tmp.elementAt(i);
+        }
+
+        return seqs;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tmp DOCUMENT ME!
+     * @param mask DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+    {
+        Vector seqs = new Vector();
+        int i;
+        boolean[] tmask = new boolean[mask.size()];
+
+        for (i = 0; i < mask.size(); i++)
+            tmask[i] = true;
+
+        for (i = 0; i < tmp.size(); i++)
+        {
+            Object sq = tmp.elementAt(i);
+
+            if (mask.contains(sq) && tmask[mask.indexOf(sq)])
+            {
+                tmask[mask.indexOf(sq)] = false;
+                seqs.addElement(sq);
+            }
+        }
+
+        for (i = 0; i < tmask.length; i++)
+            if (tmask[i])
+            {
+                seqs.addElement(mask.elementAt(i));
+            }
+
+        return vectorToArray(seqs);
+    }
+
+    /**
+     * 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
+        Vector tmp = order.getOrder();
+
+        if (lastOrder == order)
+        {
+            sortOrderAscending = !sortOrderAscending;
+        }
+        else
+        {
+            sortOrderAscending = true;
+        }
+
+        if (sortOrderAscending)
+        {
+            setOrder(align, tmp);
+        }
+        else
+        {
+            setReverseOrder(align,
+                vectorSubsetToArray(tmp, align.getSequences()));
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param align alignment to order
+     * @param tree tree which has
+     *
+     * @return DOCUMENT ME!
+     */
+    private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+    {
+        int nSeq = align.getHeight();
+
+        Vector tmp = new Vector();
+
+        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("ERROR: tmp.size()=" + tmp.size() +
+                    " != nseq=" + nSeq + " in getOrderByTree");
+            }
+        }
+
+        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, NJTree tree)
+    {
+        Vector tmp = getOrderByTree(align, tree);
+
+        // tmp should properly permute align with tree.
+        if (lastTree != tree)
+        {
+            sortTreeAscending = true;
+            lastTree = tree;
+        }
+        else
+        {
+            sortTreeAscending = !sortTreeAscending;
+        }
+
+        if (sortTreeAscending)
+        {
+            setOrder(align, tmp);
+        }
+        else
+        {
+            setReverseOrder(align,
+                vectorSubsetToArray(tmp, align.getSequences()));
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param align DOCUMENT ME!
+     * @param seqs DOCUMENT ME!
+     */
+    private static void addStrays(AlignmentI align, Vector seqs)
+    {
+        int nSeq = align.getHeight();
+
+        for (int i = 0; i < nSeq; i++)
+        {
+            if (!seqs.contains(align.getSequenceAt(i)))
+            {
+                seqs.addElement(align.getSequenceAt(i));
+            }
+        }
+
+        if (nSeq != seqs.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 Vector _sortByTree(SequenceNode node, Vector tmp,
+        Vector 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()))
+                    {
+                        tmp.addElement((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] = (new Float(alignment[i].getName().substring(8))).floatValue();
+
+        jalview.util.QuickSort.sort(ids, alignment);
+    }
+}