/*
- * 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 (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
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.
+/**
+ * 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;
/**
- * Sort by Percentage Identity
- *
- * @param align AlignmentI
- * @param s SequenceI
+ * compact representation of last arguments to SortByFeatureScore
*/
- public static void sortByPID(AlignmentI align, SequenceI s)
+ 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)
{
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)
{
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.
- * <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+1.0);
}
}
}
-
+
jalview.util.QuickSort.sort(scores, seqs);
- if (lastSortByScore!=scoreLabel)
+ if (lastSortByScore != scoreLabel)
{
lastSortByScore = scoreLabel;
setOrder(alignment, seqs);
- } else {
+ }
+ 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<labs.length;q++)
+ {
+ if (labs[q]!=null && lab.equalsIgnoreCase(labs[q]))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+ public static void sortByFeature(String[] featureLabels, String[] groupLabels, int start, int stop,
+ AlignmentI alignment, String method)
+ {
+ if (method!=FEATURE_SCORE && method!=FEATURE_LABEL && method!=FEATURE_DENSITY)
+ {
+ throw new Error("Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
+ }
+ boolean ignoreScore=method!=FEATURE_SCORE;
+ StringBuffer scoreLabel = new StringBuffer();
+ scoreLabel.append(start+stop+method);
+ // This doesn't work yet - we'd like to have a canonical ordering that can be preserved from call to call
+ for (int i=0;featureLabels!=null && i<featureLabels.length; i++)
+ {
+ scoreLabel.append(featureLabels[i]==null ? "null" : featureLabels[i]);
+ }
+ for (int i=0;groupLabels!=null && i<groupLabels.length; i++)
+ {
+ scoreLabel.append(groupLabels[i]==null ? "null" : groupLabels[i]);
+ }
+ 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];
+ int[] seqScores = new int[seqs.length];
+ Object[] feats = new Object[seqs.length];
+ double min = 0, max = 0;
+ for (int i = 0; i < seqs.length; i++)
+ {
+ SequenceFeature[] sf = seqs[i].getSequenceFeatures();
+ if (sf==null && seqs[i].getDatasetSequence()!=null)
+ {
+ sf = seqs[i].getDatasetSequence().getSequenceFeatures();
+ }
+ if (sf==null)
+ {
+ sf = new SequenceFeature[0];
+ } else {
+ SequenceFeature[] tmp = new SequenceFeature[sf.length];
+ for (int s=0; s<tmp.length;s++)
+ {
+ tmp[s] = sf[s];
+ }
+ sf = tmp;
+ }
+ int sstart = (start==-1) ? start : seqs[i].findPosition(start);
+ int sstop = (stop==-1) ? stop : seqs[i].findPosition(stop);
+ seqScores[i]=0;
+ scores[i]=0.0;
+ int n=sf.length;
+ for (int f=0;f<sf.length;f++)
+ {
+ // filter for selection criteria
+ if (
+ // ignore features outwith alignment start-stop positions.
+ (sf[f].end < sstart || sf[f].begin > 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<sf.length;f++)
+ {
+ if (sf[f]!=null)
+ {
+ ((SequenceFeature[]) feats[i])[n++] = sf[f];
+ }
+ }
+ if (method==FEATURE_LABEL)
+ {
+ // order the labels by alphabet
+ String[] labs = new String[fs.length];
+ for (int l=0;l<labs.length; l++)
+ {
+ labs[l] = (fs[l].getDescription()!=null ? fs[l].getDescription() : fs[l].getType());
+ }
+ jalview.util.QuickSort.sort(labs, ((Object[]) feats[i]));
+ }
+ }
+ if (hasScore[i])
+ {
+ // compute average score
+ scores[i]/=seqScores[i];
+ // update the score bounds.
+ if (hasScores == 1)
+ {
+ max = min = scores[i];
+ }
+ else
+ {
+ if (max < scores[i])
+ {
+ max = scores[i];
+ }
+ if (min > 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<seqs.length; i++)
+ {
+ double nf;
+ scores[i] = (0.05+fr*i)+(nf=((feats[i]==null) ? 0.0 :1.0*((SequenceFeature[]) feats[i]).length));
+ System.err.println("Sorting on Density: seq "+seqs[i].getName()+ " Feats: "+nf+" Score : "+scores[i]);
+ }
+ jalview.util.QuickSort.sort(scores, seqs);
+ }
+ else {
+ if (method==FEATURE_LABEL)
+ {
+ throw new Error("Not yet implemented.");
+ }
+ }
+ if (lastSortByFeatureScore ==null || scoreLabel.equals(lastSortByFeatureScore))
+ {
+ setOrder(alignment, seqs);
+ }
+ else
+ {
setReverseOrder(alignment, seqs);
}
+ lastSortByFeatureScore = scoreLabel.toString();
}
+
}
git://source.jalview.org / jalview.git / blobdiff