From c3de0b9d18ff5f445536fd5fc818768e28676367 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 20 Feb 2017 10:35:32 +0000 Subject: [PATCH] JAL-2416 remove unused pep, dna alphabets, unused methods, code format tidy --- src/jalview/analysis/AlignSeq.java | 114 +++--------------------------------- 1 file changed, 9 insertions(+), 105 deletions(-) diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index ed4e3bc..86dd3bc 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -20,7 +20,6 @@ */ package jalview.analysis; -import jalview.analysis.scoremodels.PairwiseSeqScoreModel; import jalview.analysis.scoremodels.ScoreMatrix; import jalview.analysis.scoremodels.ScoreModels; import jalview.datamodel.AlignmentAnnotation; @@ -55,12 +54,6 @@ public class AlignSeq private static final String NEWLINE = System.lineSeparator(); - static String[] dna = { "A", "C", "G", "T", "-" }; - - // "C", "T", "A", "G", "-"}; - static String[] pep = { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", - "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" }; - float[][] score; float[][] E; @@ -120,10 +113,6 @@ public class AlignSeq float[][] lookup = ScoreModels.getInstance().getBlosum62().getMatrix(); - // ResidueProperties.getBLOSUM62(); - - String[] intToStr = pep; - int defInt = 23; StringBuffer output = new StringBuffer(); @@ -144,7 +133,7 @@ public class AlignSeq */ public AlignSeq(SequenceI s1, SequenceI s2, String type) { - SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), + seqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type); } @@ -161,7 +150,7 @@ public class AlignSeq public AlignSeq(SequenceI s1, String string1, SequenceI s2, String string2, String type) { - SeqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type); + seqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type); } /** @@ -265,26 +254,6 @@ public class AlignSeq } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceI getS1() - { - return s1; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceI getS2() - { - return s2; - } - - /** * * @return aligned instance of Seq 1 */ @@ -326,36 +295,13 @@ public class AlignSeq * @param type * DNA or PEPTIDE */ - public void SeqInit(SequenceI s1, String string1, SequenceI s2, + public void seqInit(SequenceI s1, String string1, SequenceI s2, String string2, String type) { this.s1 = s1; this.s2 = s2; setDefaultParams(type); - SeqInit(string1, string2); - } - - /** - * Construct score matrix for sequences with custom substitution matrix - * - * @param s1 - * - sequence 1 - * @param string1 - * - string to use for s1 - * @param s2 - * - sequence 2 - * @param string2 - * - string to use for s2 - * @param scoreMatrix - * - substitution matrix to use for alignment - */ - public void SeqInit(SequenceI s1, String string1, SequenceI s2, - String string2, ScoreMatrix scoreMatrix) - { - this.s1 = s1; - this.s2 = s2; - setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP); - lookup = scoreMatrix.getMatrix(); + seqInit(string1, string2); } /** @@ -365,7 +311,7 @@ public class AlignSeq * @param string1 * @param string2 */ - private void SeqInit(String string1, String string2) + private void seqInit(String string1, String string2) { s1str = extractGaps(jalview.util.Comparison.GapChars, string1); s2str = extractGaps(jalview.util.Comparison.GapChars, string2); @@ -440,13 +386,11 @@ public class AlignSeq this.type = type2; if (type.equals(AlignSeq.PEP)) { - intToStr = pep; charToInt = ResidueProperties.aaIndex; defInt = ResidueProperties.maxProteinIndex; } else if (type.equals(AlignSeq.DNA)) { - intToStr = dna; charToInt = ResidueProperties.nucleotideIndex; defInt = ResidueProperties.maxNucleotideIndex; } @@ -603,7 +547,7 @@ public class AlignSeq .append(String.valueOf(s2str.length())).append(")") .append(NEWLINE).append(NEWLINE); - PairwiseSeqScoreModel pam250 = ScoreModels.getInstance().getPam250(); + ScoreMatrix pam250 = ScoreModels.getInstance().getPam250(); for (int j = 0; j < nochunks; j++) { @@ -686,46 +630,6 @@ public class AlignSeq /** * DOCUMENT ME! * - * @param mat - * DOCUMENT ME! - */ - public void printScoreMatrix(int[][] mat) - { - int n = seq1.length; - int m = seq2.length; - - for (int i = 0; i < n; i++) - { - // Print the top sequence - if (i == 0) - { - Format.print(System.out, "%8s", s2str.substring(0, 1)); - - for (int jj = 1; jj < m; jj++) - { - Format.print(System.out, "%5s", s2str.substring(jj, jj + 1)); - } - - System.out.println(); - } - - for (int j = 0; j < m; j++) - { - if (j == 0) - { - Format.print(System.out, "%3s", s1str.substring(i, i + 1)); - } - - Format.print(System.out, "%3d ", mat[i][j] / 10); - } - - System.out.println(); - } - } - - /** - * DOCUMENT ME! - * * @param i * DOCUMENT ME! * @param j @@ -860,7 +764,7 @@ public class AlignSeq * * @return DOCUMENT ME! */ - public float max(float f1, float f2, float f3) + private static float max(float f1, float f2, float f3) { float max = f1; @@ -887,7 +791,7 @@ public class AlignSeq * * @return DOCUMENT ME! */ - public float max(float f1, float f2) + private static float max(float f1, float f2) { float max = f1; @@ -909,7 +813,7 @@ public class AlignSeq * * @return DOCUMENT ME! */ - public int[] stringToInt(String s, String type) + int[] stringToInt(String s, String type) { int[] seq1 = new int[s.length()]; -- 1.7.10.2