X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=ea8d4e58ae553a30a08b5120eba51d40ef6bd9cf;hb=1a0f6886ffdb431de180af2089db4910a1dfb564;hp=8274768ef55e563c276380f610eb12e773949e26;hpb=636c4829ba51f11e71e56c1470fb3ad73eeb81c3;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 8274768..ea8d4e5 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,48 +1,39 @@
+/*
+ * 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.analysis;
 
+import java.util.*;
+
 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);
-  }
+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
@@ -50,163 +41,302 @@ public class AlignmentSorter {
    * @param align AlignmentI
    * @param s SequenceI
    */
-  public static void sortByPID(AlignmentI align, SequenceI s) {
+  public static void sortByPID(AlignmentI align, SequenceI s)
+  {
     int nSeq = align.getHeight();
 
-    float     scores[] = new float[nSeq];
-    SequenceI seqs[]   = new SequenceI[nSeq];
+    float[] scores = new float[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
 
-    for (int i = 0; i < nSeq; i++) {
-      scores[i] = Comparison.PID(align.getSequenceAt(i),s);
-      seqs[i]   = align.getSequenceAt(i);
+    for (int i = 0; i < nSeq; i++)
+    {
+      scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
+                                 s.getSequenceAsString());
+      seqs[i] = align.getSequenceAt(i);
     }
 
-    QuickSort.sort(scores,0,scores.length-1,seqs);
+    QuickSort.sort(scores, 0, scores.length - 1, seqs);
 
-   setReverseOrder(align,seqs);
+    setReverseOrder(align, seqs);
   }
 
-  private static void setReverseOrder(AlignmentI align, SequenceI [] 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;
+
+    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++) {
+    // 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);
+      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()));
+  /**
+   * 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()));
   }
 
-  private static void setOrder(AlignmentI align, SequenceI [] seqs) {
-      // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+  /**
+   * Sets the Alignment object with the given sequences
+   *
+   * @param align DOCUMENT ME!
+   * @param seqs sequences as an array
+   */
+  public static void setOrder(AlignmentI align, SequenceI[] seqs)
+  {
+    // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+    Vector algn = align.getSequences();
+    Vector tmp = new Vector();
 
-      Vector algn = align.getSequences();
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if (algn.contains(seqs[i]))
+      {
+        tmp.addElement(seqs[i]);
+      }
+    }
+
+    algn.removeAllElements();
+    //User may have hidden seqs, then clicked undo or redo
+    for (int i = 0; i < tmp.size(); i++)
+    {
+      algn.addElement(tmp.elementAt(i));
+    }
 
-      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) {
+
+  /**
+   * 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];
+    String[] ids = new String[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
 
-    for (int i = 0; i < nSeq; i++) {
-      ids[i]  = align.getSequenceAt(i).getName();
+    for (int i = 0; i < nSeq; i++)
+    {
+      ids[i] = align.getSequenceAt(i).getName();
       seqs[i] = align.getSequenceAt(i);
     }
 
-    QuickSort.sort(ids,seqs);
+    QuickSort.sort(ids, seqs);
 
-    if(sortIdAscending)
-      setReverseOrder(align,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;
+  /**
+   * 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;
+    }
+    else
+    {
+      sortGroupAscending = !sortGroupAscending;
+    }
 
-    Vector seqs = new Vector();
+    //SORTS GROUPS BY SIZE
+    //////////////////////
+    for (int i = 0; i < align.getGroups().size(); i++)
+    {
+      SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
 
-    for (int i=0; i < groups.size(); i++) {
-      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+      for (int j = 0; j < groups.size(); j++)
+      {
+        SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
 
-      for (int j = 0; j < sg.getSize(); j++) {
-        seqs.addElement(sg.getSequenceAt(j));
+        if (sg.getSize() > sg2.getSize())
+        {
+          groups.insertElementAt(sg, j);
+
+          break;
+        }
+      }
+
+      if (!groups.contains(sg))
+      {
+        groups.addElement(sg);
       }
     }
 
-    // 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);
+    //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()));
 
+    if (sortGroupAscending)
+    {
+      setOrder(align, seqs);
+    }
+    else
+    {
+      setReverseOrder(align,
+                      vectorSubsetToArray(seqs, align.getSequences()));
+    }
   }
 
-  private static SequenceI [] vectorToArray(Vector tmp) {
+  /**
+   * 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);
+    for (int i = 0; i < tmp.size(); i++)
+    {
+      seqs[i] = (SequenceI) tmp.elementAt(i);
     }
+
     return seqs;
   }
 
-  private static SequenceI [] vectorSubsetToArray(Vector tmp, Vector mask) {
+  /**
+   * 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,m, p;
-    boolean[] tmask = new boolean[m=mask.size()];
-    for (i=0; i<m; i++)
+    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;
-      if (mask.contains(sq=tmp.elementAt(i))) {
+    }
+
+    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);
-        m--;
       }
     }
-    for (i=0; i<tmask.length; i++)
+
+    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) {
+  /**
+   * 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 (tmp.size()<align.getHeight())
-//      addStrays(align, tmp);
-    if (lastOrder==order)
-      sortOrderAscending=!sortOrderAscending;
+
+    if (lastOrder == order)
+    {
+      sortOrderAscending = !sortOrderAscending;
+    }
     else
-      sortOrderAscending=true;
+    {
+      sortOrderAscending = true;
+    }
 
     if (sortOrderAscending)
+    {
       setOrder(align, tmp);
+    }
     else
-      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+    {
+      setReverseOrder(align,
+                      vectorSubsetToArray(tmp, align.getSequences()));
+    }
   }
-  static NJTree lastTree = null;
-  static boolean sortTreeAscending = true;
 
-  public static Vector getOrderByTree(AlignmentI align, NJTree tree) {
+  /**
+   * 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();
@@ -218,64 +348,122 @@ public class AlignmentSorter {
       // 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");
 
+      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) {
+  /**
+   * 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) {
+    if (lastTree != tree)
+    {
       sortTreeAscending = true;
       lastTree = tree;
-    } else {
+    }
+    else
+    {
       sortTreeAscending = !sortTreeAscending;
     }
-    if(sortTreeAscending)
-      setOrder(align,tmp);
+
+    if (sortTreeAscending)
+    {
+      setOrder(align, tmp);
+    }
     else
-      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+    {
+      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))) {
+  /**
+   * 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");
+
+    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;}
+  /**
+   * 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();
+    SequenceNode left = (SequenceNode) node.left();
+    SequenceNode right = (SequenceNode) node.right();
 
-    if (left == null && right == null) {
-      if (!node.isPlaceholder() && node.element()!=null)
+    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;
+          {
+            tmp.addElement( (SequenceI) node.element());
+          }
+        }
+      }
 
-    } else {
-      _sortByTree(left,tmp, seqset);
-      _sortByTree(right,tmp, seqset);
+      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
   //
@@ -284,16 +472,15 @@ public class AlignmentSorter {
    * recover the order of sequences given by the safe numbering scheme introducd
    * SeqsetUtils.uniquify.
    */
-  public static void recoverOrder(SequenceI[] alignment) {
+  public static void recoverOrder(SequenceI[] alignment)
+  {
     float[] ids = new float[alignment.length];
-    for (int i=0; i<alignment.length; i++)
+
+    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.util.QuickSort.sort(ids, alignment);
   }
-
 }