/*
* Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
* Copyright (C) 2009 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.*;
/**
* 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;
/**
* last Annotation Label used by sortByScore
*/
private static String lastSortByScore;
/**
* compact representation of last arguments to SortByFeatureScore
*/
private static String lastSortByFeatureScore;
private static boolean sortLengthAscending;
/**
* Sort by Percentage Identity w.r.t. s
*
* @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)
{
sortByPID(align,s,tosort,0,-1);
}
/**
* 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 start start column (0 for beginning
* @param end
*/
public static void sortByPID(AlignmentI align, SequenceI s,
SequenceI[] tosort,int start, int end)
{
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)
.getSequenceAsString(), s.getSequenceAsString());
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
*/
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();
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));
}
}
/**
* 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 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] = (float) (seqs[i].getEnd()-seqs[i].getStart());
}
QuickSort.sort(length, seqs);
if (sortLengthAscending)
{
setReverseOrder(align, seqs);
}
else
{
setOrder(align, seqs);
}
sortLengthAscending = !sortLengthAscending;
}
/**
* Sorts the alignment by size of group.
* 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() > sg2.getSize())
{
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);
}
/**
* 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);
if (lastSortByScore != scoreLabel)
{
lastSortByScore = scoreLabel;
setOrder(alignment, seqs);
}
else
{
setReverseOrder(alignment, seqs);
}
}
/**
* 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 String FEATURE_SCORE="average_score";
public static String FEATURE_LABEL="text";
public static String FEATURE_DENSITY="density";
/**
* sort the alignment using the features on each sequence found between start and stop with the given featureLabel (and optional group qualifier)
* @param featureLabel (may not be null)
* @param groupLabel (may be null)
* @param start (-1 to include non-positional features)
* @param stop (-1 to only sort on non-positional features)
* @param alignment - aligned sequences containing features
* @param method - one of the string constants FEATURE_SCORE, FEATURE_LABEL, FEATURE_DENSITY
*/
public static void sortByFeature(String featureLabel, String groupLabel, int start, int stop,
AlignmentI alignment, String method)
{
sortByFeature(featureLabel==null ? null : new String[] {featureLabel},
groupLabel==null ? null : new String[] {groupLabel}, start, stop, alignment, method);
}
private static boolean containsIgnoreCase(final String lab, final String[] labs)
{
if (labs==null)
{
return true;
}
if (lab==null)
{
return false;
}
for (int q=0;q sstop)
||
// or ignore based on selection criteria
(featureLabels != null && !AlignmentSorter.containsIgnoreCase(sf[f].type, featureLabels))
|| (groupLabels != null
// problem here: we cannot eliminate null feature group features
&& (sf[f].getFeatureGroup() != null
&& !AlignmentSorter.containsIgnoreCase(sf[f].getFeatureGroup(), groupLabels))))
{
// forget about this feature
sf[f] = null;
n--;
} else {
// or, also take a look at the scores if necessary.
if (!ignoreScore && sf[f].getScore()!=Float.NaN)
{
if (seqScores[i]==0)
{
hasScores++;
}
seqScores[i]++;
hasScore[i] = true;
scores[i] += sf[f].getScore(); // take the first instance of this
// score.
}
}
}
SequenceFeature[] fs;
feats[i] = fs = new SequenceFeature[n];
if (n>0)
{
n=0;
for (int f=0;f scores[i])
{
min = scores[i];
}
}
}
}
if (method==FEATURE_SCORE)
{
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 + 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]);
}
}
}
jalview.util.QuickSort.sort(scores, seqs);
}
else
if (method==FEATURE_DENSITY)
{
// break ties between equivalent numbers for adjacent sequences by adding 1/Nseq*i on the original order
double fr = 0.9/(1.0*seqs.length);
for (int i=0;i