X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=7e77b0fb8985a61fa965fd097df14beab3e5a0fd;hb=9793a4e49836be392513c2a51e9fc71a0b0eb417;hp=4bff6ef10941d5d30b1103bedadee91872e04c81;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 4bff6ef..7e77b0f 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -1,18 +1,18 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * + * 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 + * * 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 + * 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 + * + * 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; @@ -26,7 +26,7 @@ import jalview.datamodel.*; * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied. * This class is used extensively in calculating alignment colourschemes that * depend on the amount of conservation in each alignment column. - * + * * @author $author$ * @version $Revision$ */ @@ -44,20 +44,21 @@ public class AAFrequency public static final String PROFILE = "P"; - public static final Hashtable[] calculate(Vector sequences, int start, + public static final Hashtable[] calculate(List list, int start, int end) { - return calculate(sequences, start, end, false); + return calculate(list, start, end, false); } - public static final Hashtable[] calculate(Vector sequences, int start, + public static final Hashtable[] calculate(List sequences, int start, int end, boolean profile) { SequenceI[] seqs = new SequenceI[sequences.size()]; int width = 0; + synchronized (sequences) { for (int i = 0; i < sequences.size(); i++) { - seqs[i] = (SequenceI) sequences.elementAt(i); + seqs[i] = sequences.get(i); if (seqs[i].getLength() > width) { width = seqs[i].getLength(); @@ -72,9 +73,9 @@ public class AAFrequency } calculate(seqs, start, end, reply, profile); - return reply; } + } public static final void calculate(SequenceI[] sequences, int start, int end, Hashtable[] result) @@ -105,6 +106,11 @@ public class AAFrequency for (j = 0; j < jSize; j++) { + if (sequences[j]==null) + { + System.err.println("WARNING: Consensus skipping null sequence - possible race condition."); + continue; + } seq = sequences[j].getSequence(); if (seq.length > i) { @@ -166,10 +172,10 @@ public class AAFrequency residueHash.put(MAXCOUNT, new Integer(maxCount)); residueHash.put(MAXRESIDUE, maxResidue); - percentage = ((float) maxCount * 100) / (float) jSize; + percentage = ((float) maxCount * 100) / jSize; residueHash.put(PID_GAPS, new Float(percentage)); - percentage = ((float) maxCount * 100) / (float) nongap; + percentage = ((float) maxCount * 100) / nongap; residueHash.put(PID_NOGAPS, new Float(percentage)); result[i] = residueHash; } @@ -178,7 +184,7 @@ public class AAFrequency /** * Compute all or part of the annotation row from the given consensus * hashtable - * + * * @param consensus * - pre-allocated annotation row * @param hconsensus @@ -213,33 +219,40 @@ public class AAFrequency } for (int i = iStart; i < width; i++) { - if (i >= hconsensus.length) + Hashtable hci; + if (i >= hconsensus.length || ((hci=hconsensus[i])==null)) { // happens if sequences calculated over were shorter than alignment // width consensus.annotations[i] = null; continue; } + value = 0; + Float fv; if (ignoreGapsInConsensusCalculation) { - value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)) - .floatValue(); + fv = (Float) hci.get(AAFrequency.PID_NOGAPS); } else { - value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) - .floatValue(); + fv = (Float) hci.get(AAFrequency.PID_GAPS); } - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; + if (fv==null) + { + consensus.annotations[i] = null; + // data has changed below us .. give up and + continue; + } + value = fv.floatValue(); + String maxRes = hci.get(AAFrequency.MAXRESIDUE).toString(); + String mouseOver = hci.get(AAFrequency.MAXRESIDUE) + " "; if (maxRes.length() > 1) { mouseOver = "[" + maxRes + "] "; maxRes = "+"; } - int[][] profile = (int[][]) hconsensus[i].get(AAFrequency.PROFILE); + int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE); if (profile != null && includeAllConsSymbols) { mouseOver = ""; @@ -247,9 +260,9 @@ public class AAFrequency { for (int c = 0; c < alphabet.length; c++) { - tval = ((float) profile[0][alphabet[c]]) + tval = profile[0][alphabet[c]] * 100f - / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " " + ((int) tval) + "%"; @@ -263,7 +276,7 @@ public class AAFrequency { ca[c] = new char[] { (char) c }; - vl[c] = (float) profile[0][c]; + vl[c] = profile[0][c]; } ; jalview.util.QuickSort.sort(vl, ca); @@ -271,9 +284,9 @@ public class AAFrequency { if (((char[]) ca[c])[0] != '-') { - tval = ((float) profile[0][((char[]) ca[c])[0]]) + tval = profile[0][((char[]) ca[c])[0]] * 100f - / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0] + " " + ((int) tval) + "%"; @@ -295,7 +308,7 @@ public class AAFrequency /** * get the sorted profile for the given position of the consensus - * + * * @param hconsensus * @return */ @@ -312,18 +325,20 @@ public class AAFrequency { ca[c] = new char[] { (char) c }; - vl[c] = (float) profile[0][c]; + vl[c] = profile[0][c]; } ; jalview.util.QuickSort.sort(vl, ca); - rtnval[0] = 1; + rtnval[0] = 2; + rtnval[1]=0; for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--) { if (((char[]) ca[c])[0] != '-') { rtnval[rtnval[0]++] = ((char[]) ca[c])[0]; - rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]); + rtnval[1]+=rtnval[rtnval[0]++]; } } return rtnval;