X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=f56a70b511f02a8ecc813ce5f8d3c06bed471c5c;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=9bdaa10bddfd6e6e2f1ea044ea8f7769a60b41b2;hpb=b8b69cf39fa42b15ec245579d199af4aa589cbe1;p=jalview.git diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index 9bdaa10..f56a70b 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -1,24 +1,26 @@ /* - * 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 2.8.1) + * Copyright (C) 2014 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. - * + * * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.analysis; import java.util.*; +import jalview.util.Format; import jalview.datamodel.*; /** @@ -46,12 +48,15 @@ public class StructureFrequency public static final String PAIRPROFILE = "B"; -/** - * Returns the 3' position of a base pair - * @param pairs Secondary structure annotation - * @param indice 5' position of a base pair - * @return 3' position of a base pair - */ + /** + * Returns the 3' position of a base pair + * + * @param pairs + * Secondary structure annotation + * @param indice + * 5' position of a base pair + * @return 3' position of a base pair + */ public static int findPair(SequenceFeature[] pairs, int indice) { for (int i = 0; i < pairs.length; i++) @@ -96,8 +101,14 @@ public class StructureFrequency values = new int[255]; pairs = new int[255][255]; bpEnd = -1; - - s = struc[i]; + if (i < struc.length) + { + s = struc[i]; + } + else + { + s = '-'; + } if (s == '.' || s == ' ') { s = '-'; @@ -112,40 +123,40 @@ public class StructureFrequency } else { - for (j = 0; j < jSize; j++) // foreach row + bpEnd = findPair(rna, i); + if (bpEnd > -1) { - if (sequences[j] == null) - { - System.err - .println("WARNING: Consensus skipping null sequence - possible race condition."); - continue; - } - seq = sequences[j].getSequence(); - - if (seq.length > i) + for (j = 0; j < jSize; j++) // foreach row { - c = seq[i]; - - // standard representation for gaps in sequence and structure - if (c == '.' || c == ' ') - { - c = '-'; - } - - if (c == '-') + if (sequences[j] == null) { - values['-']++; + System.err + .println("WARNING: Consensus skipping null sequence - possible race condition."); continue; } - bpEnd = findPair(rna, i); - cEnd = seq[bpEnd]; - if (checkBpType(c, cEnd)) + c = sequences[j].getCharAt(i); { - values['H']++; // H means it's a helix (structured) - } - pairs[c][cEnd]++; - maxResidue = "H"; + // standard representation for gaps in sequence and structure + if (c == '.' || c == ' ') + { + c = '-'; + } + + if (c == '-') + { + values['-']++; + continue; + } + cEnd = sequences[j].getCharAt(bpEnd); + if (checkBpType(c, cEnd)) + { + values['(']++; // H means it's a helix (structured) + } + pairs[c][cEnd]++; + + maxResidue = "("; + } } } // nonGap++; @@ -160,12 +171,12 @@ public class StructureFrequency residueHash.put(PAIRPROFILE, pairs); } - count = values['H']; + count = values['(']; residueHash.put(MAXCOUNT, new Integer(count)); residueHash.put(MAXRESIDUE, maxResidue); - percentage = ((float) count * 100) / (float) jSize; + percentage = ((float) count * 100) / jSize; residueHash.put(PID_GAPS, new Float(percentage)); // percentage = ((float) count * 100) / (float) nongap; @@ -176,6 +187,27 @@ public class StructureFrequency } if (bpEnd > 0) { + values[')'] = values['(']; + values['('] = 0; + + residueHash = new Hashtable(); + maxResidue = ")"; + + if (profile) + { + residueHash.put(PROFILE, new int[][] + { values, new int[] + { jSize, (jSize - values['-']) } }); + + residueHash.put(PAIRPROFILE, pairs); + } + + residueHash.put(MAXCOUNT, new Integer(count)); + residueHash.put(MAXRESIDUE, maxResidue); + + percentage = ((float) count * 100) / jSize; + residueHash.put(PID_GAPS, new Float(percentage)); + result[bpEnd] = residueHash; } } @@ -267,18 +299,7 @@ public class StructureFrequency public static void completeConsensus(AlignmentAnnotation consensus, Hashtable[] hconsensus, int iStart, int width, boolean ignoreGapsInConsensusCalculation, - boolean includeAllConsSymbols) - { - completeConsensus(consensus, hconsensus, iStart, width, - ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new - // char[] - // { 'A', 'C', 'G', 'T', 'U' }); - } - - public static void completeConsensus(AlignmentAnnotation consensus, - Hashtable[] hconsensus, int iStart, int width, - boolean ignoreGapsInConsensusCalculation, - boolean includeAllConsSymbols, char[] alphabet) + boolean includeAllConsSymbols, long nseq) { float tval, value; if (consensus == null || consensus.annotations == null @@ -288,9 +309,22 @@ public class StructureFrequency // initialised properly return; } + String fmtstr="%3.1f"; + int precision=2; + while (nseq>100) { + precision++; + nseq/=10; + } + if (precision>2) + { + fmtstr = "%"+(2+precision)+"."+precision+"f"; + } + Format fmt = new Format(fmtstr); + 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 @@ -298,76 +332,82 @@ public class StructureFrequency continue; } value = 0; + Float fv; if (ignoreGapsInConsensusCalculation) { - value = ((Float) hconsensus[i].get(StructureFrequency.PID_NOGAPS)) - .floatValue(); + fv = (Float) hci.get(StructureFrequency.PID_NOGAPS); } else { - value = ((Float) hconsensus[i].get(StructureFrequency.PID_GAPS)) - .floatValue(); + fv = (Float) hci.get(StructureFrequency.PID_GAPS); } - - String maxRes = hconsensus[i].get(StructureFrequency.MAXRESIDUE) - .toString(); - String mouseOver = hconsensus[i].get(StructureFrequency.MAXRESIDUE) - + " "; + if (fv == null) + { + consensus.annotations[i] = null; + // data has changed below us .. give up and + continue; + } + value = fv.floatValue(); + String maxRes = hci.get(StructureFrequency.MAXRESIDUE).toString(); + String mouseOver = hci.get(StructureFrequency.MAXRESIDUE) + " "; if (maxRes.length() > 1) { mouseOver = "[" + maxRes + "] "; maxRes = "+"; } - int[][] profile = (int[][]) hconsensus[i] - .get(StructureFrequency.PROFILE); - if (profile != null && includeAllConsSymbols) // Just responsible for the + int[][] profile = (int[][]) hci.get(StructureFrequency.PROFILE); + int[][] pairs = (int[][]) hci.get(StructureFrequency.PAIRPROFILE); + + if (pairs != null && includeAllConsSymbols) // Just responsible for the // tooltip + // TODO Update tooltips for Structure row { mouseOver = ""; - if (alphabet != null) + + /* + * TODO It's not sure what is the purpose of the alphabet and wheter it + * is useful for structure? + * + * if (alphabet != null) { for (int c = 0; c < alphabet.length; c++) { + * tval = ((float) profile[0][alphabet[c]]) 100f / (float) + * profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; mouseOver += + * ((c == 0) ? "" : "; ") + alphabet[c] + " " + ((int) tval) + "%"; } } + * else { + */ + Object[] ca = new Object[625]; + float[] vl = new float[625]; + int x = 0; + for (int c = 65; c < 90; c++) { - for (int c = 0; c < alphabet.length; c++) + for (int d = 65; d < 90; d++) { - tval = ((float) profile[0][alphabet[c]]) - * 100f - / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 - : 0]; - mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " " - + ((int) tval) + "%"; + ca[x] = new int[] + { c, d }; + vl[x] = pairs[c][d]; + x++; } } - else + jalview.util.QuickSort.sort(vl, ca); + int p = 0; + + for (int c = 624; c > 0; c--) { - Object[] ca = new Object[profile[0].length]; - float[] vl = new float[profile[0].length]; - for (int c = 0; c < ca.length; c++) + if (vl[c] > 0) { - ca[c] = new char[] - { (char) c }; - vl[c] = (float) profile[0][c]; - } - ; - jalview.util.QuickSort.sort(vl, ca); - for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--) - { - if (((char[]) ca[c])[0] != '-') - { - tval = ((float) profile[0][((char[]) ca[c])[0]]) - * 100f - / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 - : 0]; - mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0] - + " " + ((int) tval) + "%"; - p++; + tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1 + : 0]); + mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0] + + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval) + "%"; + p++; - } } - } + + // } } else { - mouseOver += ((int) value + "%"); + mouseOver += (fmt.form(value) + "%"); } consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); @@ -381,33 +421,43 @@ public class StructureFrequency * @return profile of the given column */ public static int[] extractProfile(Hashtable hconsensus, - boolean ignoreGapsInConsensusCalculation, int column) + boolean ignoreGapsInConsensusCalculation) { - // TODO is there a more elegant way to acces the column number? - /* - * calculate the frequence of the 16 bp variations for this column 'somehow' - * transfer this via getProfile and let it correctly draw - */ - int[] rtnval = new int[51]; // 2*(5*5)+1 + int[] rtnval = new int[74]; // 2*(5*5)+2 int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE); int[][] pairs = (int[][]) hconsensus .get(StructureFrequency.PAIRPROFILE); if (profile == null) return null; - - rtnval[0] = 1; - for (int j = 65; j <= 90; j++) + + // TODO fix the object length, also do it in completeConsensus + Object[] ca = new Object[625]; + float[] vl = new float[625]; + int x = 0; + for (int c = 65; c < 90; c++) { - for (int k = 65; k <= 90; k++) + for (int d = 65; d < 90; d++) { - if (pairs[j][k] > 0) - { - rtnval[rtnval[0]++] = j; - rtnval[rtnval[0]++] = k; - rtnval[rtnval[0]++] = (int) ((float) pairs[j][k] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 - : 0]); - } + ca[x] = new int[] + { c, d }; + vl[x] = pairs[c][d]; + x++; + } + } + jalview.util.QuickSort.sort(vl, ca); + + rtnval[0] = 2; + rtnval[1] = 0; + for (int c = 624; c > 0; c--) + { + if (vl[c] > 0) + { + rtnval[rtnval[0]++] = ((int[]) ca[c])[0]; + rtnval[rtnval[0]++] = ((int[]) ca[c])[1]; + rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1 + : 0]); + rtnval[1] += rtnval[rtnval[0]++]; } }