X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=d1a3c37b45e1c932a06714eca9e53d45d91d99e6;hb=efa724edf32b5803396087cf7c94521e3d597836;hp=73a9dee824d4fdf98a8215c82e4136ec397d805a;hpb=9f6812a0b52a027056dff1425d20f674d114e55c;p=jalview.git diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 73a9dee..d1a3c37 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -20,9 +20,12 @@ */ package jalview.analysis; -import jalview.analysis.ResidueCount.SymbolCounts; +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.schemes.ResidueProperties; @@ -32,17 +35,21 @@ 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'; SequenceI[] sequences; @@ -60,7 +67,7 @@ public class Conservation /* * a map per column with {property, conservation} where conservation value is - * 1 (property is conserved), 0 (property is negatively conserved) or -1 + * 1 (property is conserved), 0 (absence of property is conserved) or -1 * (property is not conserved i.e. column has residues with and without it) */ Map[] total; @@ -91,12 +98,10 @@ public class Conservation 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 @@ -104,6 +109,27 @@ 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) { @@ -138,27 +164,30 @@ 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 gapIndex = sm.getMatrixIndex(' '); 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; @@ -171,14 +200,18 @@ 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)]; + sqnum[j] = sm.getMatrixIndex(sq.charAt(j - 1)); + if (sqnum[j] == -1) + { + sqnum[j] = gapIndex; + } } seqNums.setElementAt(sqnum, i); @@ -209,16 +242,18 @@ 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; /* * check observed residues in column and record whether each - * physico-chemical property is conserved (+1), negatively conserved (0), + * physico-chemical property is conserved (+1), absence conserved (0), * 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; @@ -442,7 +477,7 @@ public class Conservation if (result == -1) { /* - * not conserved either positively or negatively + * not conserved (present or absent) */ continue; } @@ -458,7 +493,7 @@ public class Conservation if (result == 0 && !positiveOnly) { /* - * negatively conserved property (all residues lack it) + * absense of property is conserved (all residues lack it) */ negatives.append(negatives.length() == 0 ? "" : " "); negatives.append("!").append(type); @@ -493,7 +528,7 @@ public class Conservation * * @return Conservation sequence */ - public Sequence getConsSequence() + public SequenceI getConsSequence() { return consSequence; } @@ -506,37 +541,32 @@ public class Conservation /** * 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); } + int gapIndex = sm.getMatrixIndex(' '); + 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]; - // 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++) { @@ -545,21 +575,10 @@ public class Conservation for (i = sqnum.length - 1; i < maxLength; i++) { - cons2[i][23]++; // gap count + cons2[i][gapIndex]++; // gap count } - 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; } } } - */ } } @@ -575,13 +594,15 @@ public class Conservation { quality = new Vector(); - double max = -10000; - int[][] BLOSUM62 = ResidueProperties.getBLOSUM62(); + double max = -Double.MAX_VALUE; + ScoreMatrix blosum62 = ScoreModels.getInstance().getBlosum62(); + float[][] blosumScores = blosum62.getMatrix(); + int gapIndex = blosum62.getMatrixIndex(' '); // Loop over columns // JBPNote Profiling info // long ts = System.currentTimeMillis(); // long te = System.currentTimeMillis(); - percentIdentity2(); + percentIdentity(blosum62); int size = seqNums.size(); int[] lengths = new int[size]; @@ -594,20 +615,24 @@ public class Conservation lengths[l] = seqNums.elementAt(l).length - 1; } + // todo ? remove '*' (unused?) from score matrix and + // use getSize() here instead of getSize() - 1 ?? + final int symbolCount = blosum62.getSize() - 1; // 24; + for (j = startRes; j <= endRes; j++) { bigtot = 0; // First Xr = depends on column only - x = new double[24]; + x = new double[symbolCount]; - for (ii = 0; ii < 24; ii++) + for (ii = 0; ii < symbolCount; ii++) { x[ii] = 0; - for (i2 = 0; i2 < 24; i2++) + for (i2 = 0; i2 < symbolCount; i2++) { - x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) + 4); + x[ii] += (((double) cons2[j][i2] * blosumScores[ii][i2]) + 4); } x[ii] /= size; @@ -617,18 +642,16 @@ public class Conservation for (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 + xx = new double[symbolCount]; + seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] : gapIndex; + // Sequence, or gap at the end // This is a loop over r - for (i = 0; i < 23; i++) + for (i = 0; i < symbolCount - 1; i++) { sr = 0; - sr = (double) BLOSUM62[i][seqNum] + 4; + sr = (double) blosumScores[i][seqNum] + 4; // Calculate X with another loop over residues // System.out.println("Xi " + i + " " + x[i] + " " + sr); @@ -652,12 +675,13 @@ public class Conservation // Need to normalize by gaps } - double newmax = -10000; + double newmax = -Double.MAX_VALUE; for (j = startRes; j <= endRes; j++) { tmp = quality.elementAt(j).doubleValue(); - tmp = ((max - tmp) * (size - cons2[j][23])) / size; + // tmp = ((max - tmp) * (size - cons2[j][23])) / size; + tmp = ((max - tmp) * (size - cons2[j][gapIndex])) / size; // System.out.println(tmp+ " " + j); quality.setElementAt(new Double(tmp), j); @@ -780,9 +804,6 @@ 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 @@ -798,10 +819,10 @@ 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); @@ -816,7 +837,8 @@ public class Conservation /** * Returns the computed tooltip (annotation description) for a given column. * The tip is empty if the conservation score is zero, otherwise holds the - * positively (and, optionally, negatively) conserved properties. + * conserved properties (and, optionally, properties whose absence is + * conserved). * * @param column * @return