X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=fe2cfc7c7dfb70d5861f72c2dbc52831a3e3c743;hb=5c212e384ee48b37d899cc88fc3d12c5028cc3b4;hp=a3493f7d69363c7b7a274b84f3a44aaeb419e584;hpb=198a4921d78d176afc0cb709bdbcb4627afd1e8b;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index a3493f7..fe2cfc7 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -23,34 +23,51 @@ import java.util.*;
 import jalview.datamodel.*;
 import jalview.util.*;
 
-/** 
- * 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)
+/**
+ * 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
 {
   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;
+
   private static String lastSortByScore;
 
   /**
    * Sort by Percentage Identity w.r.t. s
-   *
-   * @param align AlignmentI
-   * @param s SequenceI
-   * @param tosort sequences from align that are to be sorted.
+   * 
+   * @param align
+   *                AlignmentI
+   * @param s
+   *                SequenceI
+   * @param tosort
+   *                sequences from align that are to be sorted.
    */
-  public static void sortByPID(AlignmentI align, SequenceI s, SequenceI[] tosort)
+  public static void sortByPID(AlignmentI align, SequenceI s,
+          SequenceI[] tosort)
   {
     int nSeq = align.getHeight();
 
@@ -59,8 +76,8 @@ public class AlignmentSorter
 
     for (int i = 0; i < nSeq; i++)
     {
-      scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
-                                 s.getSequenceAsString());
+      scores[i] = Comparison.PID(align.getSequenceAt(i)
+              .getSequenceAsString(), s.getSequenceAsString());
       seqs[i] = align.getSequenceAt(i);
     }
 
@@ -71,9 +88,11 @@ public class AlignmentSorter
 
   /**
    * Reverse the order of the sort
-   *
-   * @param align DOCUMENT ME!
-   * @param seqs DOCUMENT ME!
+   * 
+   * @param align
+   *                DOCUMENT ME!
+   * @param seqs
+   *                DOCUMENT ME!
    */
   private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
   {
@@ -81,7 +100,7 @@ public class AlignmentSorter
 
     int len = 0;
 
-    if ( (nSeq % 2) == 0)
+    if ((nSeq % 2) == 0)
     {
       len = nSeq / 2;
     }
@@ -93,7 +112,7 @@ public class AlignmentSorter
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
     for (int i = 0; i < len; i++)
     {
-      //SequenceI tmp = seqs[i];
+      // SequenceI tmp = seqs[i];
       align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
       align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
     }
@@ -101,9 +120,11 @@ public class AlignmentSorter
 
   /**
    * Sets the Alignment object with the given sequences
-   *
-   * @param align Alignment object to be updated
-   * @param tmp sequences as a vector
+   * 
+   * @param align
+   *                Alignment object to be updated
+   * @param tmp
+   *                sequences as a vector
    */
   private static void setOrder(AlignmentI align, Vector tmp)
   {
@@ -112,9 +133,11 @@ public class AlignmentSorter
 
   /**
    * Sets the Alignment object with the given sequences
-   *
-   * @param align DOCUMENT ME!
-   * @param seqs sequences as an array
+   * 
+   * @param align
+   *                DOCUMENT ME!
+   * @param seqs
+   *                sequences as an array
    */
   public static void setOrder(AlignmentI align, SequenceI[] seqs)
   {
@@ -131,7 +154,7 @@ public class AlignmentSorter
     }
 
     algn.removeAllElements();
-    //User may have hidden seqs, then clicked undo or redo
+    // User may have hidden seqs, then clicked undo or redo
     for (int i = 0; i < tmp.size(); i++)
     {
       algn.addElement(tmp.elementAt(i));
@@ -141,8 +164,9 @@ public class AlignmentSorter
 
   /**
    * Sorts by ID. Numbers are sorted before letters.
-   *
-   * @param align The alignment object to sort
+   * 
+   * @param align
+   *                The alignment object to sort
    */
   public static void sortByID(AlignmentI align)
   {
@@ -172,16 +196,17 @@ public class AlignmentSorter
   }
 
   /**
-   * 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
+   * 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
+    // MAINTAINS ORIGNAL SEQUENCE ORDER,
+    // ORDERS BY GROUP SIZE
     Vector groups = new Vector();
 
     if (groups.hashCode() != lastGroupHash)
@@ -194,8 +219,8 @@ public class AlignmentSorter
       sortGroupAscending = !sortGroupAscending;
     }
 
-    //SORTS GROUPS BY SIZE
-    //////////////////////
+    // SORTS GROUPS BY SIZE
+    // ////////////////////
     for (int i = 0; i < align.getGroups().size(); i++)
     {
       SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
@@ -218,8 +243,8 @@ public class AlignmentSorter
       }
     }
 
-    //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
-    ///////////////////////////////////////////////
+    // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+    // /////////////////////////////////////////////
     Vector seqs = new Vector();
 
     for (int i = 0; i < groups.size(); i++)
@@ -240,16 +265,16 @@ public class AlignmentSorter
     else
     {
       setReverseOrder(align,
-                      vectorSubsetToArray(seqs, align.getSequences()));
+              vectorSubsetToArray(seqs, align.getSequences()));
     }
   }
 
   /**
-   * Converts Vector to array.
-   * java 1.18 does not have Vector.toArray()
-   *
-   * @param tmp Vector of SequenceI objects
-   *
+   * 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)
@@ -266,10 +291,12 @@ public class AlignmentSorter
 
   /**
    * DOCUMENT ME!
-   *
-   * @param tmp DOCUMENT ME!
-   * @param mask DOCUMENT ME!
-   *
+   * 
+   * @param tmp
+   *                DOCUMENT ME!
+   * @param mask
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
@@ -307,9 +334,11 @@ public class AlignmentSorter
 
   /**
    * Sorts by a given AlignmentOrder object
-   *
-   * @param align Alignment to order
-   * @param order specified order for alignment
+   * 
+   * @param align
+   *                Alignment to order
+   * @param order
+   *                specified order for alignment
    */
   public static void sortBy(AlignmentI align, AlignmentOrder order)
   {
@@ -331,17 +360,18 @@ public class AlignmentSorter
     }
     else
     {
-      setReverseOrder(align,
-                      vectorSubsetToArray(tmp, align.getSequences()));
+      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param align alignment to order
-   * @param tree tree which has
-   *
+   * 
+   * @param align
+   *                alignment to order
+   * @param tree
+   *                tree which has
+   * 
    * @return DOCUMENT ME!
    */
   private static Vector getOrderByTree(AlignmentI align, NJTree tree)
@@ -356,7 +386,7 @@ 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)
+      // sequences)
       if (tmp.size() < nSeq)
       {
         addStrays(align, tmp);
@@ -364,8 +394,8 @@ public class AlignmentSorter
 
       if (tmp.size() != nSeq)
       {
-        System.err.println("ERROR: tmp.size()=" + tmp.size() +
-                           " != nseq=" + nSeq + " in getOrderByTree");
+        System.err.println("ERROR: tmp.size()=" + tmp.size() + " != nseq="
+                + nSeq + " in getOrderByTree");
       }
     }
 
@@ -374,9 +404,11 @@ public class AlignmentSorter
 
   /**
    * Sorts the alignment by a given tree
-   *
-   * @param align alignment to order
-   * @param tree tree which has
+   * 
+   * @param align
+   *                alignment to order
+   * @param tree
+   *                tree which has
    */
   public static void sortByTree(AlignmentI align, NJTree tree)
   {
@@ -399,16 +431,17 @@ public class AlignmentSorter
     }
     else
     {
-      setReverseOrder(align,
-                      vectorSubsetToArray(tmp, align.getSequences()));
+      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param align DOCUMENT ME!
-   * @param seqs DOCUMENT ME!
+   * 
+   * @param align
+   *                DOCUMENT ME!
+   * @param seqs
+   *                DOCUMENT ME!
    */
   private static void addStrays(AlignmentI align, Vector seqs)
   {
@@ -424,22 +457,25 @@ public class AlignmentSorter
 
     if (nSeq != seqs.size())
     {
-      System.err.println(
-          "ERROR: Size still not right even after addStrays");
+      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!
-   *
+   * 
+   * @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)
+          Vector seqset)
   {
     if (node == null)
     {
@@ -449,7 +485,7 @@ public class AlignmentSorter
     SequenceNode left = (SequenceNode) node.left();
     SequenceNode right = (SequenceNode) node.right();
 
-    if ( (left == null) && (right == null))
+    if ((left == null) && (right == null))
     {
       if (!node.isPlaceholder() && (node.element() != null))
       {
@@ -457,7 +493,7 @@ public class AlignmentSorter
         {
           if (!tmp.contains(node.element()))
           {
-            tmp.addElement( (SequenceI) node.element());
+            tmp.addElement((SequenceI) node.element());
           }
         }
       }
@@ -474,7 +510,8 @@ public class AlignmentSorter
   }
 
   // Ordering Objects
-  // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
+  // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
+  // appropriate order
   //
 
   /**
@@ -487,42 +524,52 @@ public class AlignmentSorter
 
     for (int i = 0; i < alignment.length; i++)
     {
-      ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
+      ids[i] = (new Float(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
+   * 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)
+  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
+    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;
+    double min = 0, max = 0;
     for (int i = 0; i < seqs.length; i++)
     {
       AlignmentAnnotation[] scoreAnn = seqs[i].getAnnotation(scoreLabel);
-      if (scoreAnn!=null)
+      if (scoreAnn != null)
       {
         hasScores++;
         hasScore[i] = true;
-        scores[i] = scoreAnn[0].getScore(); // take the first instance of this score.
-        if (hasScores==1)
+        scores[i] = scoreAnn[0].getScore(); // take the first instance of this
+                                            // score.
+        if (hasScores == 1)
         {
           max = min = scores[i];
-        } else
+        }
+        else
         {
-          if (max<scores[i])
+          if (max < scores[i])
           {
             max = scores[i];
           }
-          if (min>scores[i])
+          if (min > scores[i])
           {
             min = scores[i];
           }
@@ -533,27 +580,29 @@ public class AlignmentSorter
         hasScore[i] = false;
       }
     }
-    if (hasScores==0)
+    if (hasScores == 0)
     {
       return; // do nothing - no scores present to sort by.
     }
-    if (hasScores<seqs.length)
+    if (hasScores < seqs.length)
     {
-      for (int i=0; i<seqs.length;i++)
+      for (int i = 0; i < seqs.length; i++)
       {
         if (!hasScore[i])
         {
-          scores[i] = (max+i);
+          scores[i] = (max + i);
         }
       }
     }
-    
+
     jalview.util.QuickSort.sort(scores, seqs);
-    if (lastSortByScore!=scoreLabel)
+    if (lastSortByScore != scoreLabel)
     {
       lastSortByScore = scoreLabel;
       setOrder(alignment, seqs);
-    } else {
+    }
+    else
+    {
       setReverseOrder(alignment, seqs);
     }
   }