From b5c03446e1c939f40b560fa672e1dc503d7f2ff8 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 20 Sep 2016 10:46:22 +0100 Subject: [PATCH] JAL-1306 calculate Quality also when Conservation not enabled --- src/jalview/analysis/Conservation.java | 146 ++++++++++++-------------- src/jalview/viewmodel/AlignmentViewport.java | 3 +- test/jalview/gui/AlignViewportTest.java | 35 +++++- 3 files changed, 100 insertions(+), 84 deletions(-) diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 21d990c..01a14c9 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; + Hashtable[] total; boolean canonicaliseAa = true; // if true then conservation calculation will @@ -60,16 +62,14 @@ public class Conservation // symbol /** Stores calculated quality values */ - public Vector quality; + public Vector quality; /** Stores maximum and minimum values of quality values */ - public Double[] qualityRange = new Double[2]; - - String consString = ""; + private double[] qualityRange = new double[2]; Sequence consSequence; - Hashtable propHash; + Map> propHash; int threshold; @@ -151,7 +151,7 @@ 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 +193,9 @@ 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 +211,7 @@ 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 +219,7 @@ 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 +245,19 @@ 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 : propHash.keySet()) { - type = (String) enumeration2.nextElement(); - ht = (Hashtable) propHash.get(type); + Hashtable ht = (Hashtable) propHash + .get(type); // Have we ticked this before? if (!resultHash.containsKey(type)) @@ -277,7 +271,7 @@ 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 +358,7 @@ 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 +366,6 @@ 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 +377,23 @@ 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]; + Hashtable 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 +401,16 @@ 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 +455,7 @@ 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 +482,7 @@ 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 +512,17 @@ 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 +537,10 @@ 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; @@ -583,7 +564,7 @@ public class Conservation { tot = 0; xx = new double[24]; - seqNum = (j < lengths[k]) ? ((int[]) seqNums.elementAt(k))[j + 1] + seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] : 23; // Sequence, or gap at the end // This is a loop over r @@ -617,9 +598,9 @@ 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 +613,12 @@ 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 +656,7 @@ 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 +664,14 @@ 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 +693,23 @@ 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 diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 47227d5..a746e1f 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -807,7 +807,8 @@ public abstract class AlignmentViewport implements AlignViewportI, public void updateConservation(final AlignmentViewPanel ap) { // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null + if (alignment.isNucleotide() + || (conservation == null && quality == null) || !autoCalculateConsensus) { return; diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index eff3fdc..bbad963 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -26,9 +26,13 @@ import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; +import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.Sequence; @@ -55,8 +59,7 @@ public class AlignViewportTest @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - jalview.bin.Jalview.main(new String[] { "-props", - "test/jalview/testProps.jvprops" }); + Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" }); } @BeforeMethod(alwaysRun = true) @@ -297,4 +300,32 @@ public class AlignViewportTest assertTrue(ssmMappings.contains(acf2)); assertFalse(ssmMappings.contains(acf3)); } + + /** + * Test for JAL-1306 - conservation thread should run even when only Quality + * (and not Conservation) is enabled in Preferences + */ + @Test(groups = { "Functional" }) + public void testUpdateConservation_qualityOnly() + { + Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("SHOW_QUALITY", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Boolean.FALSE.toString()); + Cache.applicationProperties.setProperty("SHOW_IDENTITY", + Boolean.FALSE.toString()); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", FormatAdapter.FILE); + AlignmentAnnotation[] anns = af.viewport.getAlignment().getAlignmentAnnotation(); + assertNotNull("No annotations found", anns); + assertEquals("More than one annotation found", 1, anns.length); + assertTrue("Annotation is not Quality", + anns[0].description.startsWith("Alignment Quality")); + Annotation[] annotations = anns[0].annotations; + assertNotNull("Quality annotations are null", annotations); + assertNotNull("Quality in column 1 is null", annotations[0]); + assertTrue("No quality value in column 1", annotations[0].value > 10f); + } } -- 1.7.10.2