X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=75dec63ac63c6930428fba667e573786f5c38a36;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=21d990c8a63e093fa826fb59b7e7c5c0484e8413;hpb=8cc3de5e7d587045f6d8e907ab9c630afb625d99;p=jalview.git diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 21d990c..75dec63 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -24,11 +24,12 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.schemes.ResidueProperties; import java.awt.Color; -import java.util.Enumeration; import java.util.Hashtable; import java.util.List; +import java.util.Map; import java.util.Vector; /** @@ -45,13 +46,14 @@ public class Conservation int end; - Vector seqNums; // vector of int vectors where first is sequence checksum + Vector seqNums; // vector of int vectors where first is sequence + // checksum int maxLength = 0; // used by quality calcs boolean seqNumsChanged = false; // updated after any change via calcSeqNum; - Hashtable[] total; + Map[] total; boolean canonicaliseAa = true; // if true then conservation calculation will @@ -60,22 +62,18 @@ public class Conservation // symbol /** Stores calculated quality values */ - public Vector quality; + private Vector quality; /** Stores maximum and minimum values of quality values */ - public Double[] qualityRange = new Double[2]; + private double[] qualityRange = new double[2]; - String consString = ""; + private Sequence consSequence; - Sequence consSequence; + private int threshold; - Hashtable propHash; + private String name = ""; - int threshold; - - String name = ""; - - int[][] cons2; + private int[][] cons2; private String[] consSymbs; @@ -84,8 +82,6 @@ public class Conservation * * @param name * Name of conservation - * @param propHash - * hash of properties for each symbol * @param threshold * to count the residues in residueHash(). commonly used value is 3 * @param sequences @@ -95,11 +91,10 @@ public class Conservation * @param end * end residue position */ - public Conservation(String name, Hashtable propHash, int threshold, + public Conservation(String name, int threshold, List sequences, int start, int end) { this.name = name; - this.propHash = propHash; this.threshold = threshold; this.start = start; this.end = end; @@ -151,7 +146,7 @@ public class Conservation seqNums.addElement(new int[sq.length() + 1]); } - if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0]) + if (sq.hashCode() != seqNums.elementAt(i)[0]) { int j; int len; @@ -193,12 +188,9 @@ public class Conservation */ public void calculate() { - Hashtable resultHash, ht; int thresh, j, jSize = sequences.length; int[] values; // Replaces residueHash - String type, res = null; char c; - Enumeration enumeration2; total = new Hashtable[maxLength]; @@ -214,8 +206,7 @@ public class Conservation if (canonicaliseAa) { // lookup the base aa code symbol - c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j] - .getCharAt(i)]; + c = (char) ResidueProperties.aaIndex[sequences[j].getCharAt(i)]; if (c > 20) { c = '-'; @@ -223,7 +214,7 @@ public class Conservation else { // recover canonical aa symbol - c = jalview.schemes.ResidueProperties.aa[c].charAt(0); + c = ResidueProperties.aa[c].charAt(0); } } else @@ -249,21 +240,18 @@ public class Conservation thresh = (threshold * (jSize)) / 100; // loop over all the found residues - resultHash = new Hashtable(); + Hashtable resultHash = new Hashtable(); for (char v = '-'; v < 'Z'; v++) { if (values[v] > thresh) { - res = String.valueOf(v); + String res = String.valueOf(v); // Now loop over the properties - enumeration2 = propHash.keys(); - - while (enumeration2.hasMoreElements()) + for (String type : ResidueProperties.propHash.keySet()) { - type = (String) enumeration2.nextElement(); - ht = (Hashtable) propHash.get(type); + Map ht = ResidueProperties.propHash.get(type); // Have we ticked this before? if (!resultHash.containsKey(type)) @@ -277,7 +265,7 @@ public class Conservation resultHash.put(type, ht.get("-")); } } - else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false) + else if (!resultHash.get(type).equals(ht.get(res))) { resultHash.put(type, new Integer(-1)); } @@ -364,7 +352,7 @@ public class Conservation * Calculates the conservation sequence * * @param consflag - * if true, poitiveve conservation; false calculates negative + * if true, positive conservation; false calculates negative * conservation * @param percentageGaps * commonly used value is 25 @@ -372,13 +360,6 @@ public class Conservation public void verdict(boolean consflag, float percentageGaps) { StringBuffer consString = new StringBuffer(); - String type; - Integer result; - int[] gapcons; - int totGaps, count; - float pgaps; - Hashtable resultHash; - Enumeration enumeration; // NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY // EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE @@ -390,26 +371,23 @@ public class Conservation consSymbs = new String[end - start + 1]; for (int i = start; i <= end; i++) { - gapcons = countConsNGaps(i); - totGaps = gapcons[1]; - pgaps = ((float) totGaps * 100) / sequences.length; + int[] gapcons = countConsNGaps(i); + int totGaps = gapcons[1]; + float pgaps = ((float) totGaps * 100) / sequences.length; consSymbs[i - start] = new String(); if (percentageGaps > pgaps) { - resultHash = total[i - start]; + Map resultHash = total[i - start]; // Now find the verdict - count = 0; - enumeration = resultHash.keys(); - - while (enumeration.hasMoreElements()) + int count = 0; + for (String type : resultHash.keySet()) { - type = (String) enumeration.nextElement(); - result = (Integer) resultHash.get(type); + int result = resultHash.get(type).intValue(); // Do we want to count +ve conservation or +ve and -ve cons.? if (consflag) { - if (result.intValue() == 1) + if (result == 1) { consSymbs[i - start] = type + " " + consSymbs[i - start]; count++; @@ -417,19 +395,16 @@ public class Conservation } else { - if (result.intValue() != -1) + if (result != -1) { + if (result == 0) { - if (result.intValue() == 0) - { - consSymbs[i - start] = consSymbs[i - start] + " !" + type; - } - else - { - consSymbs[i - start] = type + " " + consSymbs[i - start]; - } + consSymbs[i - start] = consSymbs[i - start] + " !" + type; + } + else + { + consSymbs[i - start] = type + " " + consSymbs[i - start]; } - count++; } } @@ -474,7 +449,7 @@ public class Conservation */ private void percentIdentity2() { - seqNums = new Vector(); + seqNums = new Vector(); // calcSeqNum(s); int i = 0, iSize = sequences.length; // Do we need to calculate this again? @@ -501,7 +476,7 @@ public class Conservation while (j < sequences.length) { - sqnum = (int[]) seqNums.elementAt(j); + sqnum = seqNums.elementAt(j); for (i = 1; i < sqnum.length; i++) { @@ -531,17 +506,17 @@ public class Conservation /** * Calculates the quality of the set of sequences * - * @param start + * @param startRes * Start residue - * @param end + * @param endRes * End residue */ - public void findQuality(int start, int end) + public void findQuality(int startRes, int endRes) { - quality = new Vector(); + quality = new Vector(); double max = -10000; - int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62(); + int[][] BLOSUM62 = ResidueProperties.getBLOSUM62(); // Loop over columns // JBPNote Profiling info // long ts = System.currentTimeMillis(); @@ -556,10 +531,10 @@ public class Conservation for (l = 0; l < size; l++) { - lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1; + lengths[l] = seqNums.elementAt(l).length - 1; } - for (j = start; j <= end; j++) + for (j = startRes; j <= endRes; j++) { bigtot = 0; @@ -583,8 +558,10 @@ public class Conservation { tot = 0; xx = new double[24]; - seqNum = (j < lengths[k]) ? ((int[]) seqNums.elementAt(k))[j + 1] - : 23; // Sequence, or gap at the end + 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++) @@ -617,9 +594,9 @@ public class Conservation double newmax = -10000; - for (j = start; j <= end; j++) + for (j = startRes; j <= endRes; j++) { - tmp = ((Double) quality.elementAt(j)).doubleValue(); + tmp = quality.elementAt(j).doubleValue(); tmp = ((max - tmp) * (size - cons2[j][23])) / size; // System.out.println(tmp+ " " + j); @@ -632,12 +609,12 @@ public class Conservation } // System.out.println("Quality " + s); - qualityRange[0] = new Double(0); - qualityRange[1] = new Double(newmax); + qualityRange[0] = 0D; + qualityRange[1] = newmax; } /** - * complete the given consensus and quuality annotation rows. Note: currently + * Complete the given consensus and quuality annotation rows. Note: currently * this method will enlarge the given annotation row if it is too small, * otherwise will leave its length unchanged. * @@ -675,7 +652,7 @@ public class Conservation char c; - if (conservation.annotations != null + if (conservation != null && conservation.annotations != null && conservation.annotations.length < alWidth) { conservation.annotations = new Annotation[alWidth]; @@ -683,14 +660,14 @@ public class Conservation if (quality2 != null) { - quality2.graphMax = qualityRange[1].floatValue(); + quality2.graphMax = (float) qualityRange[1]; if (quality2.annotations != null && quality2.annotations.length < alWidth) { quality2.annotations = new Annotation[alWidth]; } - qmin = qualityRange[0].floatValue(); - qmax = qualityRange[1].floatValue(); + qmin = (float) qualityRange[0]; + qmax = (float) qualityRange[1]; } for (int i = istart; i < alWidth; i++) @@ -712,20 +689,23 @@ public class Conservation value = 10; } - float vprop = value - min; - vprop /= max; - int consp = i - start; - String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp] - : ""; - conservation.annotations[i] = new Annotation(String.valueOf(c), - conssym, ' ', value, new Color(minR + (maxR * vprop), minG - + (maxG * vprop), minB + (maxB * vprop))); + if (conservation != null) + { + float vprop = value - min; + vprop /= max; + int consp = i - start; + String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp] + : ""; + conservation.annotations[i] = new Annotation(String.valueOf(c), + conssym, ' ', value, new Color(minR + (maxR * vprop), minG + + (maxG * vprop), minB + (maxB * vprop))); + } // Quality calc if (quality2 != null) { - value = ((Double) quality.elementAt(i)).floatValue(); - vprop = value - qmin; + value = quality.elementAt(i).floatValue(); + float vprop = value - qmin; vprop /= qmax; quality2.annotations[i] = new Annotation(" ", String.valueOf(value), ' ', value, new Color(minR @@ -740,9 +720,6 @@ public class Conservation * * @param name * - name of conservation - * @param consHash - * - hash table of properties for each amino acid (normally - * ResidueProperties.propHash) * @param threshold * - minimum number of conserved residues needed to indicate * conservation (typically 3) @@ -760,29 +737,12 @@ public class Conservation * @return Conservation object ready for use in visualization */ public static Conservation calculateConservation(String name, - Hashtable consHash, int threshold, List seqs, - int start, int end, boolean posOrNeg, int consPercGaps, - boolean calcQuality) - { - Conservation cons = new Conservation(name, consHash, threshold, seqs, - start, end); - return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality); - } - - /** - * @param b - * positive (true) or negative (false) conservation - * @param consPercGaps - * percentage of gaps tolerated in column - * @param calcQuality - * flag indicating if alignment quality should be calculated - * @return Conservation object ready for use in visualization - */ - public static Conservation calculateConservation(Conservation cons, - boolean b, int consPercGaps, boolean calcQuality) + int threshold, List seqs, int start, int end, + boolean posOrNeg, int consPercGaps, boolean calcQuality) { + Conservation cons = new Conservation(name, threshold, seqs, start, end); cons.calculate(); - cons.verdict(b, consPercGaps); + cons.verdict(posOrNeg, consPercGaps); if (calcQuality) {