X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=4e487ffe8fb83c7f1e55bd0ccd735ab7dc67944d;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=32a4e29e7b57f7a70cfe906035778b54c0d430a9;hpb=3e7ebcfda0bc54b3b91905e21835142bfd1fe8a0;p=jalview.git diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index 32a4e29..4e487ff 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * @@ -14,13 +14,14 @@ * 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.*; /** @@ -59,15 +60,15 @@ public class StructureFrequency */ public static int findPair(SequenceFeature[] pairs, int indice) { - System.out.print("indice"+indice+" "); + for (int i = 0; i < pairs.length; i++) { if (pairs[i].getBegin() == indice) - + { - System.out.println(pairs[i].getEnd()); + return pairs[i].getEnd(); - + } } return -1; @@ -88,19 +89,11 @@ public class StructureFrequency int end, Hashtable[] result, boolean profile, AlignmentAnnotation rnaStruc) { -// System.out.println("longueur="+sequences.length); -// for(int l=0;l<=(sequences.length-1);l++){ -// System.out.println("sequences "+l+":"+sequences[l].getSequenceAsString()); -// } -// System.out.println("start="+start); - System.out.println("end="+end); -// System.out.println("result="+result.length); -// -// System.out.println("profile="+profile); -// System.out.println("rnaStruc="+rnaStruc); + Hashtable residueHash; String maxResidue; char[] struc = rnaStruc.getRNAStruc().toCharArray(); + SequenceFeature[] rna = rnaStruc._rnasecstr; char c, s, cEnd; int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length; @@ -108,7 +101,6 @@ public class StructureFrequency int[][] pairs; float percentage; boolean wooble = true; - for (i = start; i < end; i++) // foreach column { residueHash = new Hashtable(); @@ -116,11 +108,11 @@ public class StructureFrequency values = new int[255]; pairs = new int[255][255]; bpEnd = -1; - //System.out.println("s="+struc[i]); + // System.out.println("s="+struc[i]); if (i < struc.length) { s = struc[i]; - + } else { @@ -140,57 +132,54 @@ public class StructureFrequency } else { - - + bpEnd = findPair(rna, i); - - if (bpEnd>-1) - { - for (j = 0; j < jSize; j++) // foreach row + + 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; - } - c = sequences[j].getCharAt(i); - //System.out.println("c="+c); - + if (sequences[j] == null) + { + System.err + .println("WARNING: Consensus skipping null sequence - possible race condition."); + continue; + } + c = sequences[j].getCharAt(i); + // System.out.println("c="+c); // standard representation for gaps in sequence and structure if (c == '.' || c == ' ') { - System.err - .println("WARNING: Consensus skipping null sequence - possible race condition."); + c = '-'; + } + + if (c == '-') + { + values['-']++; continue; } cEnd = sequences[j].getCharAt(bpEnd); - - - System.out.println("pairs ="+c+","+cEnd); - if (checkBpType(c, cEnd)==true) + + // System.out.println("pairs ="+c+","+cEnd); + if (checkBpType(c, cEnd) == true) { values['(']++; // H means it's a helix (structured) maxResidue = "("; - wooble=true; - System.out.println("It's a pair wc"); - + wooble = true; + // System.out.println("It's a pair wc"); + } - if (checkBpType(c, cEnd)==false) + if (checkBpType(c, cEnd) == false) { - wooble =false; + wooble = false; values['[']++; // H means it's a helix (structured) maxResidue = "["; - System.out.println("It's an pair non canonic"); - System.out.println(sequences[j].getRNA()); - System.out.println(rnaStruc.getRNAStruc().charAt(i)); + } - pairs[c][cEnd]++; - - - } + pairs[c][cEnd]++; + } } // nonGap++; } @@ -203,13 +192,13 @@ public class StructureFrequency residueHash.put(PAIRPROFILE, pairs); } - if (wooble==true) + if (wooble == true) { - count = values['(']; + count = values['(']; } - if (wooble==false) + if (wooble == false) { - count = values['[']; + count = values['[']; } residueHash.put(MAXCOUNT, new Integer(count)); residueHash.put(MAXRESIDUE, maxResidue); @@ -225,18 +214,20 @@ public class StructureFrequency } if (bpEnd > 0) { - values[')'] = values['(']; + values[')'] = values['(']; values[']'] = values['[']; values['('] = 0; values['['] = 0; residueHash = new Hashtable(); - if (wooble==true){ - System.out.println(maxResidue+","+wooble); - maxResidue = ")"; + if (wooble == true) + { + // System.out.println(maxResidue+","+wooble); + maxResidue = ")"; } - if(wooble==false){ - System.out.println(maxResidue+","+wooble); - maxResidue = "]"; + if (wooble == false) + { + // System.out.println(maxResidue+","+wooble); + maxResidue = "]"; } if (profile) { @@ -254,6 +245,7 @@ public class StructureFrequency residueHash.put(PID_GAPS, new Float(percentage)); result[bpEnd] = residueHash; + } } } @@ -344,7 +336,7 @@ 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 @@ -354,6 +346,18 @@ 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++) { Hashtable hci; @@ -430,7 +434,7 @@ public class StructureFrequency 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++; } @@ -440,7 +444,7 @@ public class StructureFrequency } else { - mouseOver += ((int) value + "%"); + mouseOver += (fmt.form(value) + "%"); } consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);