X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=f56a70b511f02a8ecc813ce5f8d3c06bed471c5c;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=42e8847fb301940d3c88188fc0c7ec9748b0d38b;hpb=3385d3fe7b3acd45dc5aaa3c7d73f7cce5ea7457;p=jalview.git diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index 42e8847..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.*; /** @@ -121,40 +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) + for (j = 0; j < jSize; j++) // foreach row { - System.err - .println("WARNING: Consensus skipping null sequence - possible race condition."); - continue; - } - seq = sequences[j].getSequence(); - - if (seq.length > i) - { - c = seq[i]; - - // standard representation for gaps in sequence and structure - if (c == '.' || c == ' ') + if (sequences[j] == null) { - c = '-'; - } - - if (c == '-') - { - 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 means it's a helix (structured) - } - pairs[c][cEnd]++; - maxResidue = "("; + // 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++; @@ -174,7 +176,7 @@ public class StructureFrequency 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; @@ -203,7 +205,7 @@ public class StructureFrequency 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)); result[bpEnd] = residueHash; @@ -297,7 +299,7 @@ public class StructureFrequency public static void completeConsensus(AlignmentAnnotation consensus, Hashtable[] hconsensus, int iStart, int width, boolean ignoreGapsInConsensusCalculation, - boolean includeAllConsSymbols) + boolean includeAllConsSymbols, long nseq) { float tval, value; if (consensus == null || consensus.annotations == null @@ -307,9 +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 @@ -317,30 +332,31 @@ 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); - int[][] pairs = (int[][]) hconsensus[i] - .get(StructureFrequency.PAIRPROFILE); + int[][] profile = (int[][]) hci.get(StructureFrequency.PROFILE); + int[][] pairs = (int[][]) hci.get(StructureFrequency.PAIRPROFILE); if (pairs != null && includeAllConsSymbols) // Just responsible for the // tooltip @@ -348,7 +364,9 @@ public class StructureFrequency { mouseOver = ""; - /* TODO It's not sure what is the purpose of the alphabet and wheter it is useful for structure? + /* + * 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) @@ -365,7 +383,7 @@ public class StructureFrequency { ca[x] = new int[] { c, d }; - vl[x] = (float) pairs[c][d]; + vl[x] = pairs[c][d]; x++; } } @@ -376,10 +394,10 @@ public class StructureFrequency { if (vl[c] > 0) { - tval = ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]); mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0] - + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%"; + + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval) + "%"; p++; } @@ -389,7 +407,7 @@ public class StructureFrequency } else { - mouseOver += ((int) value + "%"); + mouseOver += (fmt.form(value) + "%"); } consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); @@ -405,7 +423,7 @@ public class StructureFrequency public static int[] extractProfile(Hashtable hconsensus, boolean ignoreGapsInConsensusCalculation) { - 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); @@ -423,21 +441,23 @@ public class StructureFrequency { ca[x] = new int[] { c, d }; - vl[x] = (float) pairs[c][d]; + vl[x] = pairs[c][d]; x++; } } jalview.util.QuickSort.sort(vl, ca); - rtnval[0] = 1; + 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) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]); + rtnval[1] += rtnval[rtnval[0]++]; } }