Main tool that builds the clusters (multiple alignments) - so far; to be heavily refactored; most methods should find their proper homes in other classes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@74 348d0f76-0448-11de-a6fe-93d51630548a
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package org.broadinstitute.sting.indels;
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public class PileBuilder {
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private StrictlyUpperTriangularMatrix distances ;
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private Matrix<PairwiseAlignment> alignments ;
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private static class SelectedPair {
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private int i_;
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private int j_;
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private double d_;
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private SelectedPair(int i, int j, double d) {
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set(i,j,d);
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}
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private SelectedPair() {
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set(-1,-1,1e100);
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}
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private double d() { return d_; }
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private int i() { return i_; }
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private int j() { return j_; }
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private void set(int i, int j, double d) {
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i_ = i;
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j_ = j;
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d_ = d;
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}
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/** Returns true if any of the two indices kept by this pair is equal to i.
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*
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* @param i
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* @return
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*/
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private boolean contains(int i) {
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return ( ( i_ == i ) || ( j_ == i ) );
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}
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}
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public PileBuilder() {}
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public void initPairwiseAlignments( IndexedSequence [] seqs ) {
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distances = new StrictlyUpperTriangularMatrix( seqs.length );
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alignments = new Matrix<PairwiseAlignment>( seqs.length );
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for( int i = 0; i < seqs.length ; i++ ) {
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for ( int j = i+1 ; j < seqs.length ; j++ ) {
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PairwiseAlignment a = new PairwiseAlignment(seqs[i],seqs[j],i,j); // compute pairwise alignment
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alignments.set(i, j, a); // save it
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distances.set(i,j,a.distance());
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}
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}
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}
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/** Finds the best pairwise alignment across all available ones. The object must be initialized first,
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* so that the alignments are pre-computed.
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* @return id's of the two sequences and the distance between them in a compound object.
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*/
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public SelectedPair findBest() {
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SelectedPair p = new SelectedPair(-1,-1,1e100);
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for( int i = 0; i < distances.size() ; i++ ) {
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for ( int j = i+1 ; j < distances.size() ; j++ ) {
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double d = distances.get(i,j);
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if ( d < p.d() ) p.set(i,j,d);
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}
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}
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return p;
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}
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/** Finds the worst pairwise alignment across all available ones. The object must be initialized first,
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* so that the alignments are pre-computed.
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* @return id's of the two sequences and the distance between them in a compound object.
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*/
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public SelectedPair findWorst() {
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SelectedPair p = new SelectedPair(-1,-1,-1.0);
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for( int i = 0; i < distances.size() ; i++ ) {
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for ( int j = i+1 ; j < distances.size() ; j++ ) {
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double d = distances.get(i,j);
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if ( d > p.d() ) p.set(i,j,d);
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}
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}
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return p;
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}
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/** Finds the best pairwise alignment across all available ones, subject to the constraint that neither
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* of the two sequences found can be listed (by its id) in the supplied SelectedPair object. If the best pair is passed
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* as an argument, this method will find the next best pair.
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*
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* @param pexclude neither of the two sequences in the returned pair can have its id listed in pexclude pair.
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* @return Best pairwise alignment excluding alignments between pairs involving at least one sequence from pexclude
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*/
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public SelectedPair findBest(SelectedPair pexclude) {
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SelectedPair p = new SelectedPair(-1,-1,1e100);
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for( int i = 0; i < distances.size() ; i++ ) {
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if ( pexclude.contains(i) ) continue;
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for ( int j = i+1 ; j < distances.size() ; j++ ) {
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if ( pexclude.contains(j)) continue;
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double d = distances.get(i,j);
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if ( d < p.d() ) p.set(i,j,d);
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}
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}
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return p;
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}
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/** Finds the closest sequence to the specified pile among all sequences, which are not yet in that pile. Being
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* the 'closest' is defined in terms of minimum distance.
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*
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* @param a alignment pile to find the closest sequence for
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* @return a compound SelectedPair object that contains the index of the closest sequence found (is guaranteed to
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* be not in the pile), the index of the sequence in the pile it is closest to, and the actual distance between the two.
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*/
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public SelectedPair findClosest(MultipleAlignment a) {
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SelectedPair p = new SelectedPair(-1,-1,1e100);
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for ( Integer id : a ) {
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for (int i = 0; i < id; i++) {
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if (a.contains(i)) continue; // a already contains both sequences (i,id)
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double d = distances.get(i, id);
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if (d < p.d() ) p.set(i,id,d);
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}
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for (int j = id + 1; j < distances.size() ; j++) {
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if (a.contains(j)) continue; // a already contains both sequences (id, j)
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double d = distances.get(id, j);
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if (d < p.d()) p.set(id,j,d);
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}
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}
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return p;
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}
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/** Finds, among all sequences, the one farthest from the specified pile. Being
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* the 'farthest' is defined as having the largest lower bound of the distances to all sequences in the pile.
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*
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* @param a alignment pile to find the closest sequence for
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* @return index of the farthest sequence
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*/
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public int findFarthest(MultipleAlignment a) {
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double dmaxmin = 0;
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int i_out = -1;
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for ( int i = 0 ; i < distances.size() ; i++ ) {
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if ( a.contains(i) ) continue;
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double d_min = 1e100; // smallest distance from sequence i to the pile
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for ( Integer id : a ) {
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double d = ( i < id ? distances.get(i, id) : distances.get(id,i) );
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if (d < d_min ) d_min = d;
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}
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// d_min is the smallest distance from sequence i to pile a
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if ( d_min > dmaxmin ) {
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// sequence i is so far the farthest...
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dmaxmin = d_min;
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i_out = i;
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}
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}
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return i_out;
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}
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public double distance(MultipleAlignment a1, MultipleAlignment a2) {
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double d = 1e100;
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for ( Integer id1 : a1 ) {
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for ( Integer id2 : a2 ) {
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if ( id1 < id2 && distances.get(id1,id2) < d ) d = distances.get(id1,id2);
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if ( id1 > id2 && distances.get(id2,id1) < d ) d = distances.get(id2,id1);
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}
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}
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return d;
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}
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/** Computes the distances from each sequence in the pile to its closest
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* neighbor (within the same pile), and returns the greatest among these distances.
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* In other words, no sequence in the pile is farther than diameter() from its closest neighbor.
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* @param a alignment pile to compute diameter for
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* @return the greatest distance from a sequence to its closest neighbor within the pile
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*/
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public double diameter(MultipleAlignment a) {
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double dmaxmin = 0.0;
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for ( Integer id1 : a ) {
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double d = 1e100;
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for ( Integer id2 : a ) {
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if ( id2 <= id1 ) continue;
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if ( distances.get(id1,id2) < d ) d = distances.get(id1,id2);
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}
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// d = distance from id1 to its closest neighbor within the pile
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if ( d < 1e99 ) System.out.printf("%8.4g",d);
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if ( d < 1e99 && d > dmaxmin ) dmaxmin = d;
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}
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// dmaxmin = the largest distance from a sequence in this pile to its closest neighbor
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System.out.println();
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return dmaxmin;
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}
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public static void main(String argv[]) {
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int K=8;
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// IndexedSequence [] seqs = testSet1(K); // initialize test set data
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// IndexedSequence [] seqs = testSet2(K); // initialize test set data
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IndexedSequence [] seqs = testSet3(K); // initialize test set data
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PileBuilder pb = new PileBuilder();
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// two piles we are going to grow until all sequences are assigned to one of them.
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// we intend to keep the piles disjoint, e.g. no sequence should be placed in both
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MultipleAlignment pile1 = new MultipleAlignment();
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MultipleAlignment pile2 = new MultipleAlignment();
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pb.initPairwiseAlignments(seqs);
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// all the pairwise alignments are computed and disjoint best and next-best pairs are found
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System.out.println( pb.distances.format("%8.4g "));
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/*
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SelectedPair pworst = pb.findWorst();
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pile1.add(seqs[pworst.i()].getSequence(), pworst.i());
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pile2.add(seqs[pworst.j()].getSequence(), pworst.j());
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*/
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// initialize piles with best and next-best pairs
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SelectedPair p_best = pb.findBest();
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SelectedPair p_nextbest = pb.findBest(p_best);
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pile1.add( pb.alignments.get(p_best.i(), p_best.j()),p_best.i(),p_best.j());
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pile2.add( pb.alignments.get(p_nextbest.i(), p_nextbest.j()),p_nextbest.i(),p_nextbest.j());
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/*
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System.out.println("Best pair ("+p_best.i() + "," + p_best.j()+", d="+p_best.d()+"):");
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System.out.println(pile1.toString());
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System.out.println("Next best pair ("+p_nextbest.i() + "," + p_nextbest.j()+", d="+p_nextbest.d()+ "):");
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System.out.println(pile2.toString());
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*/
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SelectedPair p1 = null;
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SelectedPair p2 = null;
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// grow piles hierarchical clustering-style
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while ( pile1.size() + pile2.size() < seqs.length ) {
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// find candidate sequences closest to each of the two piles
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p1 = pb.findClosest(pile1);
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p2 = pb.findClosest(pile2);
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int id1_cand = pile1.selectExternal(p1.i(), p1.j()); // id of the sequence closest to the pile 1
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int id2_cand = pile2.selectExternal(p2.i(), p2.j()); // id of the sequence closest to the pile 2
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if ( pile2.contains(id1_cand) && pile1.contains(id2_cand)) {
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// pile1 and pile 2 are mutually the closest, so we need to merge them.
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// if piles are mutually the closest, then p1 and p2 are the same pair (id1, id2),
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// so we just merge on one of the (redundant) instances:
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pile1.add(pile2, pb.alignments.get( p1.i(), p1.j()),p1.i(), p1.j());
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pile2.clear(); // need to reset pile 2 to something else
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int z = pb.findFarthest(pile1); // get sequence farthest from merged pile 1
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pile2.add(seqs[z].getSequence(), z); // and reinitialize pile 2 with that sequence
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} else {
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if ( p1.d() < p2.d() ) {
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if ( pile2.contains(id1_cand) ) {
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pile1.add(pile2, pb.alignments.get( p1.i(), p1.j()),p1.i(), p1.j());
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pile2.clear(); // need to reset pile 2 to something else
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int z = pb.findFarthest(pile1); // get sequence farthest from merged pile 1
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pile2.add(seqs[z].getSequence(), z); // and reinitialize pile 2 with that sequence
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} else pile1.add( pb.alignments.get(p1.i(), p1.j()) );
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} else {
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if ( pile1.contains(id2_cand) ) {
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pile2.add(pile1, pb.alignments.get( p2.i(), p2.j()),p2.i(), p2.j());
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pile1.clear(); // need to reset pile 2 to something else
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int z = pb.findFarthest(pile2); // get sequence farthest from merged pile 1
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pile1.add(seqs[z].getSequence(), z); // and reinitialize pile 2 with that sequence
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} else pile2.add( pb.alignments.get(p2.i(), p2.j()) );
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}
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}
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System.out.println("PILE 1: \n"+pile1.toString());
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System.out.println("PILE 2: \n"+pile2.toString());
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} // end WHILE
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System.out.println("Distance between final piles: "+pb.distance(pile1, pile2));
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System.out.println("Diameter of PILE1: "+ pb.diameter(pile1));
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System.out.println("Diameter of PILE2: "+ pb.diameter(pile2));
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/*
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* System.out.println("Closest distance to the pile: " + best_d
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+ "(adding: " + best_i + "," + best_j + "):");
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System.out.println(pile.toString());
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}
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*/
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}
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public static IndexedSequence[] testSet1(int K) {
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IndexedSequence [] seqs = new IndexedSequence[9];
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seqs[0] = new IndexedSequence("CAAAAAAAGCAAAACTCTGAAGAAAGAGAGAGAGAGGGAGAGAGGGAGAGAGAAAGGGAGAGACGATGAGAGACAG",K);
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seqs[1] = new IndexedSequence("GCAAAACTCTGAAGAAAGAGAGAGAGAGGGAGAGAGGGAGAGAGAAAGGAAGAGACGAT",K);
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seqs[2] = new IndexedSequence("AACTCTGAAGAAAGAGAGAGAGAGGGAGAGAGGGAGAGAGAAAGGAAGAGACGATGAGA",K);
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seqs[3] = new IndexedSequence("GAGAGGGAGAGAGAAAGGAAGAGACGATGAGAGACAGAGAAGGAGAGAGAAAGTACAAAAGAACGAATGAACGAAC",K);
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seqs[4] = new IndexedSequence("ACGATGAGAGACAGAGAAGGAGAGAGAAAGTACAAAAGAACGAATGAACGAACAAACTAGAAATCGAGCAGGAAAA",K);
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seqs[5] = new IndexedSequence("GAGAGACAGAGAAGGAGAGAGAAAGTACAAAAGAACGAATGAACGAACAAACTAGAAATCGAGCAGGAACCTTGGA",K);
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seqs[6] = new IndexedSequence("TGAGACAGAGAAGGAGAGAGAAAGTACAAAAGAACGAATGAACGAACAAACTAGAAATC",K);
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seqs[7] = new IndexedSequence("AGACAGAGAAGGAGAGAGAAAGTACAAAAGAACGAATGAACGAACAAACTAGAAATCGAGCAGGAACCTTGGAGGA",K);
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seqs[8] = new IndexedSequence("AGACAGAGAAGGAGAGAGAAAGTACAAAAGAACGAATGAACGAACAAACTAGAAATCGAGCAGGAACCTTGGAGGA",K);
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return seqs;
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}
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public static IndexedSequence[] testSet2(int K) {
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IndexedSequence [] seqs = new IndexedSequence[11];
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seqs[0] = new IndexedSequence("TGCAATGAGATGAGATCGTGCCTCTGCACTCCAGCCTGGGCGACAGAGTGAGAGACCCTGTCTCAAAAACACAAAA",K);
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seqs[1] = new IndexedSequence("AATGAGATGAGATCGTGCCTCTGCACTCCAGCCTGGGCGACAGAGTGAGAGACCCTGTCTCAAAAACACAAAAACA",K);
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seqs[2] = new IndexedSequence("CCTCTGCACTCCAGCCTGGGCGACAGAGTGAGAGACCCTGTCTCAAAAACACAAAAACAACAACAACAAAAAAACA",K);
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seqs[3] = new IndexedSequence("CAGAGTGAGAGACCCTGTCTCAAAAACACAAAAACAACAACAACAAAAAAACACCAATCTGAGCAAATACTGCCCT",K);
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seqs[4] = new IndexedSequence("CAGAGTGAGAGACCCTGTCTCAAAAACACAAAAACAACAACAACAAAAAAACACCAATCTGAGCAAATACTGCCCT",K);
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seqs[5] = new IndexedSequence("GAGACCCTGTCTCAAAAACACAAAAACAACAACAACAAAAAAACACCAATCTGAGCAAATACTGCCCTAAACCGAG",K);
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seqs[6] = new IndexedSequence("CCCTGTCTCAAAAACACAAAAACAACAACAACAAAAAAACACCAATCTGAGCAAATACTGCCCTAAACCGAGTGTT",K);
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seqs[7] = new IndexedSequence("CCAAAAACAACAACAACAAAAAAACACCAATCTGAGCAAATACTGCCCTAAACCGAGTG",K);
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seqs[8] = new IndexedSequence("CAAAAACAACAACAACAAAAAAACACCAATCTGAGCAAATACTGCCCTAAACCGAGTGTTGTTATCTCTGGGGAGT",K);
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seqs[9] = new IndexedSequence("AACAACAACAACAAAAAAACACCAATCTGAGCAAATACTGCCCTAAACCGAGTGTTGTTATCTCTGGGTAGTTTGG",K);
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seqs[10] = new IndexedSequence("ACAACAACAACAAAAAAACACCAATCTGAGCAAATACTGCCCTAAACCGAGTGTTGTTATCTCTGGGTAGCTTGGA",K);
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return seqs;
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}
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public static IndexedSequence[] testSet3(int K) {
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IndexedSequence [] seqs = new IndexedSequence[11];
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seqs[0] = new IndexedSequence("TGGAAATTTATTTCTCAGAGTACTGGAAGCTGGGAATCCAAGATCAAAATGCCAGCAGATTCTAAGTCTGGTGAGG",K);
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seqs[1] = new IndexedSequence("TGGAAATTTATTTCTCAAAGTACTGGAAGCTGGGAATCCAAGATCAAAATGCCAGCAGATTCTAAGTCTGGTGAGG",K);
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seqs[2] = new IndexedSequence("GGAAATTTATTTCTCAGAGTACTGGAAGCTGGGAATCCAAGATCAAAATGCCAGCAGATTCTAAGTCTGGTGAGGG",K);
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seqs[3] = new IndexedSequence("GGAAATTTATTTCACAGAGTAATGGAAGCTGGGAATCCAAGATCAAAATGCCAGCAGCTTCTAAGTCTGCTGAGGG",K);
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seqs[4] = new IndexedSequence("ATTTCTCAGAGTACTGGAAGCTGGGAATCCAAGATCGAAATGCCAGCAGATTCTAAGTC",K);
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seqs[5] = new IndexedSequence("ATTTCTCAGAGTACTGGAAGCTGGGACTCCAAGATCAAAATGCCAGCAGATTCTAAGTCTGGTGAGGGTAGGGTGC",K);
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seqs[6] = new IndexedSequence("GTACTGGAAGCTGGGAATCCAAGATCAAAATGCCAGCAGATTCTAAGTCTGGTGAGGGTAGGGTGCACTCTCTGCT",K);
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seqs[7] = new IndexedSequence("AATCCAAGATCAAAATGCCAGCAGATTCTAAGTCTGGTGAGGGTAGGGTGCACTCTCTGCTTCATAAATGGGTCTC",K);
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seqs[8] = new IndexedSequence("CAAGATCAAAATGCCAGCAGATTCTAAGTCTGGTGAGGGTAGGGCGCACTCTCTGCTTCATAAATGGGTCTCTTGC",K);
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seqs[9] = new IndexedSequence("ATCAAAATGCCAGCAGATTCTAAGTCTGGTGAGGGTAGGGTGCACTCTCTGCTTCATAAATGGGTCTCTTGCCGCA",K);
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seqs[10] = new IndexedSequence("GTCTGGTGAGGGTAGGGTGCACTCTCTGCTTCATAAATGGGTCTCTTGCCGCAAAAAAATCTGTTTGCTCCTCCAG",K);
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return seqs;
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}
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}
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