X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=2a065f6cb37fd8adff3d8ad6cccec467af3463a8;hb=6d94bfcf539e558b09a08102b228e65e670f77d8;hp=c216471835ecaec274cb40a6cb2bdb948c6e2122;hpb=7652d1d5889b737d52dbd15f3919d8b0dbdbc48b;p=jalview.git diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index c216471..2a065f6 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -1,23 +1,23 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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. + * + * 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 . */ package jalview.analysis; +import java.awt.Color; import java.util.*; import jalview.datamodel.*; @@ -45,9 +45,10 @@ public class Conservation Hashtable[] total; boolean canonicaliseAa = true; // if true then conservation calculation will - // map all symbols to canonical aa numbering - // rather than consider conservation of that - // symbol + + // map all symbols to canonical aa numbering + // rather than consider conservation of that + // symbol /** Stores calculated quality values */ public Vector quality; @@ -71,18 +72,17 @@ public class Conservation * Creates a new Conservation object. * * @param name - * Name of conservation + * Name of conservation * @param propHash - * hash of properties for each symbol + * hash of properties for each symbol * @param threshold - * to count the residues in residueHash(). commonly used value - * is 3 + * to count the residues in residueHash(). commonly used value is 3 * @param sequences - * sequences to be used in calculation + * sequences to be used in calculation * @param start - * start residue position + * start residue position * @param end - * end residue position + * end residue position */ public Conservation(String name, Hashtable propHash, int threshold, Vector sequences, int start, int end) @@ -95,12 +95,12 @@ public class Conservation this.end = end; maxLength = end - start + 1; // default width includes bounds of - // calculation + // calculation int s, sSize = sequences.size(); SequenceI[] sarray = new SequenceI[sSize]; this.sequences = sarray; - + try { for (s = 0; s < sSize; s++) { sarray[s] = (SequenceI) sequences.elementAt(s); @@ -109,11 +109,17 @@ public class Conservation maxLength = sarray[s].getLength(); } } + } catch (ArrayIndexOutOfBoundsException ex) + { + // bail - another thread has modified the sequence array, so the current calculation is probably invalid. + this.sequences=new SequenceI[0]; + maxLength=0; + } } /** - * Translate sequence i into a numerical - * representation and store it in the i'th position of the seqNums array. + * Translate sequence i into a numerical representation and store it in the + * i'th position of the seqNums array. * * @param i */ @@ -146,7 +152,7 @@ public class Conservation } sqnum = new int[len + 1]; // better to always make a new array - - // sequence can change its length + // sequence can change its length sqnum[0] = sq.hashCode(); for (j = 1; j <= len; j++) @@ -271,12 +277,15 @@ public class Conservation } } - total[i - start] = resultHash; + if (total.length>0) { + total[i - start] = resultHash; + } } } /***************************************************************************** - * count conservation for the j'th column of the alignment + * count conservation for the j'th column of the alignment + * * @return { gap count, conserved residue count} */ public int[] countConsNGaps(int j) @@ -329,10 +338,10 @@ public class Conservation * Calculates the conservation sequence * * @param consflag - * if true, poitiveve conservation; false calculates negative - * conservation + * if true, poitiveve conservation; false calculates negative + * conservation * @param percentageGaps - * commonly used value is 25 + * commonly used value is 25 */ public void verdict(boolean consflag, float percentageGaps) { @@ -477,8 +486,7 @@ public class Conservation * maxj = -1; * * for (int j=0;j<24;j++) { if (cons2[i][j] > max) { max = cons2[i][j]; - * maxi = i; maxj = j; } - * } } + * maxi = i; maxj = j; } } } */ } } @@ -487,9 +495,9 @@ public class Conservation * Calculates the quality of the set of sequences * * @param start - * Start residue + * Start residue * @param end - * End residue + * End residue */ public void findQuality(int start, int end) { @@ -590,4 +598,101 @@ public class Conservation qualityRange[0] = new Double(0); qualityRange[1] = new Double(newmax); } + + /** + * 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. + * + * @param conservation + * conservation annotation row + * @param quality2 + * (optional - may be null) + * @param istart + * first column for conservation + * @param alWidth + * extent of conservation + */ + public void completeAnnotations(AlignmentAnnotation conservation, + AlignmentAnnotation quality2, int istart, int alWidth) + { + char[] sequence = getConsSequence().getSequence(); + float minR; + float minG; + float minB; + float maxR; + float maxG; + float maxB; + minR = 0.3f; + minG = 0.0f; + minB = 0f; + maxR = 1.0f - minR; + maxG = 0.9f - minG; + maxB = 0f - minB; // scalable range for colouring both Conservation and + // Quality + + float min = 0f; + float max = 11f; + float qmin = 0f; + float qmax = 0f; + + char c; + + if (conservation.annotations != null + && conservation.annotations.length < alWidth) + { + conservation.annotations = new Annotation[alWidth]; + } + + if (quality2 != null) + { + quality2.graphMax = qualityRange[1].floatValue(); + if (quality2.annotations != null + && quality2.annotations.length < alWidth) + { + quality2.annotations = new Annotation[alWidth]; + } + qmin = qualityRange[0].floatValue(); + qmax = qualityRange[1].floatValue(); + } + + for (int i = 0; i < alWidth; i++) + { + float value = 0; + + c = sequence[i]; + + if (Character.isDigit(c)) + { + value = (int) (c - '0'); + } + else if (c == '*') + { + value = 11; + } + else if (c == '+') + { + value = 10; + } + + float vprop = value - min; + vprop /= max; + conservation.annotations[i] = new Annotation(String.valueOf(c), + String.valueOf(value), ' ', 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; + vprop /= qmax; + quality2.annotations[i] = new Annotation(" ", + String.valueOf(value), ' ', value, new Color(minR + + (maxR * vprop), minG + (maxG * vprop), minB + + (maxB * vprop))); + } + } + } }