X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=2b5a8f6a89e133d8ca1a4ca5fa26e6ed9109a6d3;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=7e72dcd638cab9e327cbb4c5a01d502c452cc3fb;hpb=0a5ce6145bb76fc7eb8a5cc2670e20453fbedd29;p=jalview.git diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 7e72dcd..2b5a8f6 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -20,12 +20,14 @@ */ package jalview.analysis; +import jalview.analysis.scoremodels.ScoreMatrix; +import jalview.analysis.scoremodels.ScoreModels; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.ResidueCount; +import jalview.datamodel.ResidueCount.SymbolCounts; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; -import jalview.datamodel.ResidueCount.SymbolCounts; import jalview.schemes.ResidueProperties; import jalview.util.Comparison; @@ -33,27 +35,36 @@ import java.awt.Color; import java.util.List; import java.util.Map; import java.util.Map.Entry; +import java.util.SortedMap; import java.util.TreeMap; import java.util.Vector; /** * Calculates conservation values for a given set of sequences - * - * @author $author$ - * @version $Revision$ */ public class Conservation { + /* + * need to have a minimum of 3% of sequences with a residue + * for it to be included in the conservation calculation + */ + private static final int THRESHOLD_PERCENT = 3; + private static final int TOUPPERCASE = 'a' - 'A'; + private static final int GAP_INDEX = -1; + SequenceI[] sequences; int start; int end; - Vector seqNums; // vector of int vectors where first is sequence - // checksum + /* + * a list whose i'th element is an array whose first entry is the checksum + * of the i'th sequence, followed by residues encoded to score matrix index + */ + Vector seqNums; int maxLength = 0; // used by quality calcs @@ -66,17 +77,17 @@ public class Conservation */ Map[] total; - boolean canonicaliseAa = true; // if true then conservation calculation will - - // map all symbols to canonical aa numbering - // rather than consider conservation of that - // symbol + /* + * if true then conservation calculation will map all symbols to canonical aa + * numbering rather than consider conservation of that symbol + */ + boolean canonicaliseAa = true; - /** Stores calculated quality values */ private Vector quality; - /** Stores maximum and minimum values of quality values */ - private double[] qualityRange = new double[2]; + private double qualityMinimum; + + private double qualityMaximum; private Sequence consSequence; @@ -87,17 +98,23 @@ public class Conservation private String name = ""; + /* + * an array, for each column, of counts of symbols (by score matrix index) + */ private int[][] cons2; + /* + * gap counts for each column + */ + private int[] cons2GapCounts; + private String[] consSymbs; /** - * Creates a new Conservation object. + * Constructor using default threshold of 3% * * @param name * Name of conservation - * @param threshold - * to count the residues in residueHash(). commonly used value is 3 * @param sequences * sequences to be used in calculation * @param start @@ -105,6 +122,27 @@ public class Conservation * @param end * end residue position */ + public Conservation(String name, List sequences, int start, + int end) + { + this(name, THRESHOLD_PERCENT, sequences, start, end); + } + + /** + * Constructor + * + * @param name + * Name of conservation + * @param threshold + * percentage of sequences at or below which property conservation is + * ignored + * @param sequences + * sequences to be used in calculation + * @param start + * start column position + * @param end + * end column position + */ public Conservation(String name, int threshold, List sequences, int start, int end) { @@ -139,27 +177,29 @@ public class Conservation } /** - * Translate sequence i into a numerical representation and store it in the - * i'th position of the seqNums array. + * Translate sequence i into score matrix indices and store it in the i'th + * position of the seqNums array. * * @param i + * @param sm */ - private void calcSeqNum(int i) + private void calcSeqNum(int i, ScoreMatrix sm) { - String sq = null; // for dumb jbuilder not-inited exception warning - int[] sqnum = null; - int sSize = sequences.length; if ((i > -1) && (i < sSize)) { - sq = sequences[i].getSequenceAsString(); + String sq = sequences[i].getSequenceAsString(); if (seqNums.size() <= i) { seqNums.addElement(new int[sq.length() + 1]); } + /* + * the first entry in the array is the sequence's hashcode, + * following entries are matrix indices of sequence characters + */ if (sq.hashCode() != seqNums.elementAt(i)[0]) { int j; @@ -172,14 +212,26 @@ public class Conservation maxLength = len; } - sqnum = new int[len + 1]; // better to always make a new array - + int[] sqnum = new int[len + 1]; // better to always make a new array - // sequence can change its length sqnum[0] = sq.hashCode(); for (j = 1; j <= len; j++) { - sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq - .charAt(j - 1)]; + // sqnum[j] = ResidueProperties.aaIndex[sq.charAt(j - 1)]; + char residue = sq.charAt(j - 1); + if (Comparison.isGap(residue)) + { + sqnum[j] = GAP_INDEX; + } + else + { + sqnum[j] = sm.getMatrixIndex(residue); + if (sqnum[j] == -1) + { + sqnum[j] = GAP_INDEX; + } + } } seqNums.setElementAt(sqnum, i); @@ -210,7 +262,9 @@ public class Conservation { ResidueCount values = countResidues(column); - // TODO is threshold a percentage or count value? + /* + * percentage count at or below which we ignore residues + */ int thresh = (threshold * height) / 100; /* @@ -219,7 +273,7 @@ public class Conservation * or not conserved (-1) * Using TreeMap means properties are displayed in alphabetical order */ - Map resultHash = new TreeMap(); + SortedMap resultHash = new TreeMap(); SymbolCounts symbolCounts = values.getSymbolCounts(); char[] symbols = symbolCounts.symbols; int[] counts = symbolCounts.values; @@ -494,7 +548,7 @@ public class Conservation * * @return Conservation sequence */ - public Sequence getConsSequence() + public SequenceI getConsSequence() { return consSequence; } @@ -502,137 +556,133 @@ public class Conservation // From Alignment.java in jalview118 public void findQuality() { - findQuality(0, maxLength - 1); + findQuality(0, maxLength - 1, ScoreModels.getInstance().getBlosum62()); } /** * DOCUMENT ME! + * + * @param sm */ - private void percentIdentity2() + private void percentIdentity(ScoreMatrix sm) { seqNums = new Vector(); - // calcSeqNum(s); int i = 0, iSize = sequences.length; // Do we need to calculate this again? for (i = 0; i < iSize; i++) { - calcSeqNum(i); + calcSeqNum(i, sm); } if ((cons2 == null) || seqNumsChanged) { + // FIXME remove magic number 24 without changing calc + // sm.getSize() returns 25 so doesn't quite do it... cons2 = new int[maxLength][24]; + cons2GapCounts = new int[maxLength]; - // Initialize the array - for (int j = 0; j < 24; j++) - { - for (i = 0; i < maxLength; i++) - { - cons2[i][j] = 0; - } - } - - int[] sqnum; int j = 0; while (j < sequences.length) { - sqnum = seqNums.elementAt(j); + int[] sqnum = seqNums.elementAt(j); for (i = 1; i < sqnum.length; i++) { - cons2[i - 1][sqnum[i]]++; + int index = sqnum[i]; + if (index == GAP_INDEX) + { + cons2GapCounts[i - 1]++; + } + else + { + cons2[i - 1][index]++; + } } + // TODO should this start from sqnum.length? for (i = sqnum.length - 1; i < maxLength; i++) { - cons2[i][23]++; // gap count + cons2GapCounts[i]++; } - j++; } - - // unnecessary ? - - /* - * for (int i=start; i <= end; i++) { int max = -1000; int maxi = -1; int - * maxj = -1; - * - * for (int j=0;j<24;j++) { if (cons2[i][j] > max) { max = cons2[i][j]; - * maxi = i; maxj = j; } } } - */ } } /** - * Calculates the quality of the set of sequences + * Calculates the quality of the set of sequences over the given inclusive + * column range, using the specified substitution score matrix * - * @param startRes - * Start residue - * @param endRes - * End residue + * @param startCol + * @param endCol + * @param scoreMatrix */ - public void findQuality(int startRes, int endRes) + protected void findQuality(int startCol, int endCol, ScoreMatrix scoreMatrix) { quality = new Vector(); - double max = -10000; - int[][] BLOSUM62 = ResidueProperties.getBLOSUM62(); + double max = -Double.MAX_VALUE; + float[][] scores = scoreMatrix.getMatrix(); - // Loop over columns // JBPNote Profiling info - // long ts = System.currentTimeMillis(); - // long te = System.currentTimeMillis(); - percentIdentity2(); + percentIdentity(scoreMatrix); int size = seqNums.size(); int[] lengths = new int[size]; - double tot, bigtot, sr, tmp; - double[] x, xx; - int l, j, i, ii, i2, k, seqNum; - for (l = 0; l < size; l++) + for (int l = 0; l < size; l++) { lengths[l] = seqNums.elementAt(l).length - 1; } - for (j = startRes; j <= endRes; j++) + final int symbolCount = scoreMatrix.getSize(); + + for (int j = startCol; j <= endCol; j++) { - bigtot = 0; + double bigtot = 0; // First Xr = depends on column only - x = new double[24]; + double[] x = new double[symbolCount]; - for (ii = 0; ii < 24; ii++) + for (int ii = 0; ii < symbolCount; ii++) { x[ii] = 0; - for (i2 = 0; i2 < 24; i2++) + /* + * todo JAL-728 currently assuming last symbol in matrix is * for gap + * (which we ignore as counted separately); true for BLOSUM62 but may + * not be once alternative matrices are supported + */ + for (int i2 = 0; i2 < symbolCount - 1; i2++) { - x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) + 4); + x[ii] += (((double) cons2[j][i2] * scores[ii][i2]) + 4D); } + x[ii] += 4D + cons2GapCounts[j] * scoreMatrix.getMinimumScore(); x[ii] /= size; } // Now calculate D for each position and sum - for (k = 0; k < size; k++) + for (int k = 0; k < size; k++) { - tot = 0; - xx = new double[24]; - seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] : 23; // Sequence, - // or gap - // at the - // end - - // This is a loop over r - for (i = 0; i < 23; i++) - { - sr = 0; + double tot = 0; + double[] xx = new double[symbolCount]; + // sequence character index, or implied gap if sequence too short + int seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] + : GAP_INDEX; - sr = (double) BLOSUM62[i][seqNum] + 4; + for (int i = 0; i < symbolCount - 1; i++) + { + double sr = 4D; + if (seqNum == GAP_INDEX) + { + sr += scoreMatrix.getMinimumScore(); + } + else + { + sr += scores[i][seqNum]; + } - // Calculate X with another loop over residues - // System.out.println("Xi " + i + " " + x[i] + " " + sr); xx[i] = x[i] - sr; tot += (xx[i] * xx[i]); @@ -641,24 +691,18 @@ public class Conservation bigtot += Math.sqrt(tot); } - // This is the quality for one column - if (max < bigtot) - { - max = bigtot; - } + max = Math.max(max, bigtot); - // bigtot = bigtot * (size-cons2[j][23])/size; quality.addElement(new Double(bigtot)); - - // Need to normalize by gaps } - double newmax = -10000; + double newmax = -Double.MAX_VALUE; - for (j = startRes; j <= endRes; j++) + for (int j = startCol; j <= endCol; j++) { - tmp = quality.elementAt(j).doubleValue(); - tmp = ((max - tmp) * (size - cons2[j][23])) / size; + double tmp = quality.elementAt(j).doubleValue(); + // tmp = ((max - tmp) * (size - cons2[j][23])) / size; + tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size; // System.out.println(tmp+ " " + j); quality.setElementAt(new Double(tmp), j); @@ -669,9 +713,8 @@ public class Conservation } } - // System.out.println("Quality " + s); - qualityRange[0] = 0D; - qualityRange[1] = newmax; + qualityMinimum = 0D; + qualityMaximum = newmax; } /** @@ -721,14 +764,14 @@ public class Conservation if (quality2 != null) { - quality2.graphMax = (float) qualityRange[1]; + quality2.graphMax = (float) qualityMaximum; if (quality2.annotations != null && quality2.annotations.length < alWidth) { quality2.annotations = new Annotation[alWidth]; } - qmin = (float) qualityRange[0]; - qmax = (float) qualityRange[1]; + qmin = (float) qualityMinimum; + qmax = (float) qualityMaximum; } for (int i = istart; i < alWidth; i++) @@ -781,9 +824,6 @@ public class Conservation * * @param name * - name of conservation - * @param threshold - * - minimum number of conserved residues needed to indicate - * conservation (typically 3) * @param seqs * @param start * first column in calculation window @@ -799,10 +839,10 @@ public class Conservation * @return Conservation object ready for use in visualization */ public static Conservation calculateConservation(String name, - int threshold, List seqs, int start, int end, - boolean positiveOnly, int maxPercentGaps, boolean calcQuality) + List seqs, int start, int end, boolean positiveOnly, + int maxPercentGaps, boolean calcQuality) { - Conservation cons = new Conservation(name, threshold, seqs, start, end); + Conservation cons = new Conservation(name, seqs, start, end); cons.calculate(); cons.verdict(positiveOnly, maxPercentGaps);