From 69b6e688c0a87bffc1fc7ae970fa0f8cd2976007 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 20 Feb 2017 16:04:08 +0000 Subject: [PATCH] JAL-2416 replaced dependency on ResidueProperties with loaded score matrix --- src/jalview/analysis/AlignSeq.java | 167 +++++++++---------------------- test/jalview/analysis/AlignSeqTest.java | 38 +++++-- 2 files changed, 81 insertions(+), 124 deletions(-) diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index 86dd3bc..ceca6d6 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -27,7 +27,6 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; -import jalview.schemes.ResidueProperties; import jalview.util.Comparison; import jalview.util.Format; import jalview.util.MapList; @@ -111,25 +110,22 @@ public class AlignSeq int gapExtend = 20; - float[][] lookup = ScoreModels.getInstance().getBlosum62().getMatrix(); + float[][] lookup; - int defInt = 23; + int gapIndex = 23; StringBuffer output = new StringBuffer(); - String type; + String type; // AlignSeq.PEP or AlignSeq.DNA - private int[] charToInt; + private ScoreMatrix scoreModel; /** * Creates a new AlignSeq object. * - * @param s1 - * DOCUMENT ME! - * @param s2 - * DOCUMENT ME! - * @param type - * DOCUMENT ME! + * @param s1 first sequence for alignment + * @param s2 second sequence for alignment + * @param type molecule type, either AlignSeq.PEP or AlignSeq.DNA */ public AlignSeq(SequenceI s1, SequenceI s2, String type) { @@ -324,82 +320,37 @@ public class AlignSeq return; } - // System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory()); seq1 = new int[s1str.length()]; - // System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory()); seq2 = new int[s2str.length()]; - // System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory()); score = new float[s1str.length()][s2str.length()]; - // System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory()); E = new float[s1str.length()][s2str.length()]; - // System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory()); F = new float[s1str.length()][s2str.length()]; traceback = new int[s1str.length()][s2str.length()]; - // System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory()); - seq1 = stringToInt(s1str, type); - - // System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory()); - seq2 = stringToInt(s2str, type); - - // System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory()); - // long tstart = System.currentTimeMillis(); - // calcScoreMatrix(); - // long tend = System.currentTimeMillis(); - // System.out.println("Time take to calculate score matrix = " + - // (tend-tstart) + " ms"); - // printScoreMatrix(score); - // System.out.println(); - // printScoreMatrix(traceback); - // System.out.println(); - // printScoreMatrix(E); - // System.out.println(); - // /printScoreMatrix(F); - // System.out.println(); - // tstart = System.currentTimeMillis(); - // traceAlignment(); - // tend = System.currentTimeMillis(); - // System.out.println("Time take to traceback alignment = " + (tend-tstart) - // + " ms"); - } - - private void setDefaultParams(String type) - { - setType(type); + seq1 = indexEncode(s1str); - if (type.equals(AlignSeq.PEP)) - { - lookup = ScoreModels.getInstance().getDefaultModel(true).getMatrix(); - } - else if (type.equals(AlignSeq.DNA)) - { - lookup = ScoreModels.getInstance().getDefaultModel(false).getMatrix(); - } + seq2 = indexEncode(s2str); } - private void setType(String type2) + private void setDefaultParams(String moleculeType) { - this.type = type2; - if (type.equals(AlignSeq.PEP)) - { - charToInt = ResidueProperties.aaIndex; - defInt = ResidueProperties.maxProteinIndex; - } - else if (type.equals(AlignSeq.DNA)) - { - charToInt = ResidueProperties.nucleotideIndex; - defInt = ResidueProperties.maxNucleotideIndex; - } - else + if (!PEP.equals(moleculeType) && !DNA.equals(moleculeType)) { output.append("Wrong type = dna or pep only"); throw new Error(MessageManager.formatMessage( - "error.unknown_type_dna_or_pep", new String[] { type2 })); + "error.unknown_type_dna_or_pep", + new String[] { moleculeType })); } + + type = moleculeType; + scoreModel = ScoreModels.getInstance().getDefaultModel( + PEP.equals(type)); + lookup = scoreModel.getMatrix(); + gapIndex = scoreModel.getMatrixIndex(' '); } /** @@ -408,7 +359,7 @@ public class AlignSeq public void traceAlignment() { // Find the maximum score along the rhs or bottom row - float max = -9999; + float max = -Float.MAX_VALUE; for (int i = 0; i < seq1.length; i++) { @@ -442,21 +393,17 @@ public class AlignSeq aseq1 = new int[seq1.length + seq2.length]; aseq2 = new int[seq1.length + seq2.length]; + StringBuilder sb1 = new StringBuilder(aseq1.length); + StringBuilder sb2 = new StringBuilder(aseq2.length); + count = (seq1.length + seq2.length) - 1; - while ((i > 0) && (j > 0)) + while (i > 0 && j > 0) { - if ((aseq1[count] != defInt) && (i >= 0)) - { - aseq1[count] = seq1[i]; - astr1 = s1str.charAt(i) + astr1; - } - - if ((aseq2[count] != defInt) && (j > 0)) - { - aseq2[count] = seq2[j]; - astr2 = s2str.charAt(j) + astr2; - } + aseq1[count] = seq1[i]; + sb1.append(s1str.charAt(i)); + aseq2[count] = seq2[j]; + sb2.append(s2str.charAt(j)); trace = findTrace(i, j); @@ -468,14 +415,14 @@ public class AlignSeq else if (trace == 1) { j--; - aseq1[count] = defInt; - astr1 = "-" + astr1.substring(1); + aseq1[count] = gapIndex; + sb1.replace(sb1.length() - 1, sb1.length(), "-"); } else if (trace == -1) { i--; - aseq2[count] = defInt; - astr2 = "-" + astr2.substring(1); + aseq2[count] = gapIndex; + sb2.replace(sb2.length() - 1, sb2.length(), "-"); } count--; @@ -484,17 +431,24 @@ public class AlignSeq seq1start = i + 1; seq2start = j + 1; - if (aseq1[count] != defInt) + if (aseq1[count] != gapIndex) { aseq1[count] = seq1[i]; - astr1 = s1str.charAt(i) + astr1; + sb1.append(s1str.charAt(i)); } - if (aseq2[count] != defInt) + if (aseq2[count] != gapIndex) { aseq2[count] = seq2[j]; - astr2 = s2str.charAt(j) + astr2; + sb2.append(s2str.charAt(j)); } + + /* + * we built the character strings backwards, so now + * reverse them to convert to sequence strings + */ + astr1 = sb1.reverse().toString(); + astr2 = sb2.reverse().toString(); } /** @@ -804,45 +758,24 @@ public class AlignSeq } /** - * DOCUMENT ME! + * Converts the character string to an array of integers which are the + * corresponding indices to the characters in the score matrix * * @param s - * DOCUMENT ME! - * @param type - * DOCUMENT ME! * - * @return DOCUMENT ME! + * @return */ - int[] stringToInt(String s, String type) + int[] indexEncode(String s) { - int[] seq1 = new int[s.length()]; + int[] encoded = new int[s.length()]; for (int i = 0; i < s.length(); i++) { - // String ss = s.substring(i, i + 1).toUpperCase(); char c = s.charAt(i); - if ('a' <= c && c <= 'z') - { - // TO UPPERCASE !!! - c -= ('a' - 'A'); - } - - try - { - seq1[i] = charToInt[c]; // set accordingly from setType - if (seq1[i] < 0 || seq1[i] > defInt) // set from setType: 23 for - // peptides, or 4 for NA. - { - seq1[i] = defInt; - } - - } catch (Exception e) - { - seq1[i] = defInt; - } + encoded[i] = scoreModel.getMatrixIndex(c); } - return seq1; + return encoded; } /** diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java index 4cb5329..c12f544 100644 --- a/test/jalview/analysis/AlignSeqTest.java +++ b/test/jalview/analysis/AlignSeqTest.java @@ -20,9 +20,11 @@ */ package jalview.analysis; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNull; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertNull; +import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; +import jalview.datamodel.Sequence; import jalview.gui.JvOptionPane; import org.testng.annotations.BeforeClass; @@ -45,10 +47,32 @@ public class AlignSeqTest assertNull(AlignSeq.extractGaps(null, "ACG")); assertNull(AlignSeq.extractGaps("-. ", null)); - assertEquals(" AC-G.T", AlignSeq.extractGaps("", " AC-G.T")); - assertEquals("AC-G.T", AlignSeq.extractGaps(" ", " AC-G.T")); - assertEquals("ACG.T", AlignSeq.extractGaps(" -", " AC-G.T")); - assertEquals("ACGT", AlignSeq.extractGaps(" -.", " AC-G.T .")); - assertEquals(" ACG.T", AlignSeq.extractGaps("-", " AC-G.T")); + assertEquals(AlignSeq.extractGaps("", " AC-G.T"), " AC-G.T"); + assertEquals(AlignSeq.extractGaps(" ", " AC-G.T"), "AC-G.T"); + assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T"); + assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT"); + assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T"); + } + + @Test(groups = { "Functional" }) + public void testIndexEncode_nucleotide() + { + AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), new Sequence( + "s2", "ACGT"), AlignSeq.DNA); + int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, + 7, 7, 8, 8, 9, 9, 10, -1, 11, -1 }; + String s = "aAcCgGtTuUiIxXrRyYnN .-?"; + assertArrayEquals(expected, as.indexEncode(s)); + } + + @Test(groups = { "Functional" }) + public void testIndexEncode_peptide() + { + AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence( + "s2", "RQW"), AlignSeq.PEP); + int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, 23, 24, + -1, -1, -1 }; + String s = "aArRnNzZxX *.-?"; + assertArrayEquals(expected, as.indexEncode(s)); } } -- 1.7.10.2