X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=baec9867718a9fb65be12bbaa260eb616ab0de78;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=062f6bab49f33ac6635aba28d6a03dcb4f205048;hpb=9793a4e49836be392513c2a51e9fc71a0b0eb417;p=jalview.git diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java index 062f6ba..baec986 100755 --- a/src/jalview/datamodel/BinarySequence.java +++ b/src/jalview/datamodel/BinarySequence.java @@ -1,19 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.datamodel; @@ -42,7 +45,8 @@ public class BinarySequence extends Sequence double[] dbinary; - boolean isNa=false; + boolean isNa = false; + /** * Creates a new BinarySequence object. * @@ -52,16 +56,18 @@ public class BinarySequence extends Sequence public BinarySequence(String s, boolean isNa) { super("", s, 0, s.length()); - this.isNa=isNa; + this.isNa = isNa; } /** - * clear the dbinary matrix + * clear the dbinary matrix + * * @return nores - dimension of sequence symbol encoding for this sequence */ private int initMatrixGetNoRes() { - int nores=(isNa) ? ResidueProperties.maxNucleotideIndex : ResidueProperties.maxProteinIndex; + int nores = (isNa) ? ResidueProperties.maxNucleotideIndex + : ResidueProperties.maxProteinIndex; // Set all matrix to 0 dbinary = new double[getSequence().length * nores]; @@ -71,32 +77,35 @@ public class BinarySequence extends Sequence } return nores; } + private int[] getSymbolmatrix() { - return (isNa) ? ResidueProperties.nucleotideIndex : ResidueProperties.aaIndex; + return (isNa) ? ResidueProperties.nucleotideIndex + : ResidueProperties.aaIndex; } + /** * DOCUMENT ME! */ public void encode() { - int nores=initMatrixGetNoRes(); - final int[] sindex=getSymbolmatrix(); + int nores = initMatrixGetNoRes(); + final int[] sindex = getSymbolmatrix(); for (int i = 0; i < getSequence().length; i++) { - int aanum = nores-1; + int aanum = nores - 1; try { aanum = sindex[getCharAt(i)]; } catch (NullPointerException e) { - aanum = nores-1; + aanum = nores - 1; } if (aanum >= nores) { - aanum = nores-1; + aanum = nores - 1; } dbinary[(i * nores) + aanum] = 1.0; @@ -108,9 +117,10 @@ public class BinarySequence extends Sequence * * @param matrix */ - public void matrixEncode(final ScoreMatrix matrix) throws InvalidSequenceTypeException + public void matrixEncode(final ScoreMatrix matrix) + throws InvalidSequenceTypeException { - if (isNa!=matrix.isDNA()) + if (isNa != matrix.isDNA()) { throw new InvalidSequenceTypeException("matrix " + matrix.getClass().getCanonicalName() @@ -131,21 +141,21 @@ public class BinarySequence extends Sequence // for (int i = 0; i < dbinary.length; i++) { // dbinary[i] = 0.0; // } - for (int i = 0,iSize=getSequence().length; i=nores) + if (aanum >= nores) { - aanum = nores-1; + aanum = nores - 1; } // Do the blosum^H^H^H^H^H score matrix summation thing