/*
- * 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
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();
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);
}
/**
* 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)
{
int len = 0;
- if ( (nSeq % 2) == 0)
+ if ((nSeq % 2) == 0)
{
len = nSeq / 2;
}
// 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);
}
/**
* 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)
{
/**
* 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)
{
}
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));
/**
* 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)
{
}
/**
- * 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)
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);
}
}
- //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
- ///////////////////////////////////////////////
+ // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+ // /////////////////////////////////////////////
Vector seqs = new Vector();
for (int i = 0; i < groups.size(); i++)
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)
/**
* 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)
/**
* 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)
{
}
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)
{
// 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);
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");
}
}
/**
* 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)
{
}
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)
{
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)
{
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))
{
{
if (!tmp.contains(node.element()))
{
- tmp.addElement( (SequenceI) node.element());
+ tmp.addElement((SequenceI) node.element());
}
}
}
}
// Ordering Objects
- // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
+ // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
+ // appropriate order
//
/**
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];
}
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);
}
}
git://source.jalview.org / jalview.git / blobdiff