From 46c34fb5b641a5ec57b5eec0e7bf964a9e72219f Mon Sep 17 00:00:00 2001 From: janengelhardt Date: Wed, 10 Aug 2011 01:01:22 +0200 Subject: [PATCH] JAL-891; base-pair logos can now be activated for structure conservation row; Change-Id: Ib3450f328f901eaf12ea094c9c914322f8398a88 --- src/jalview/analysis/StructureFrequency.java | 463 ++++++++++++++------------ src/jalview/gui/AnnotationPanel.java | 6 +- 2 files changed, 258 insertions(+), 211 deletions(-) diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index b9c61c2..4d83019 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -44,6 +44,8 @@ public class StructureFrequency public static final String PROFILE = "P"; + public static final String PAIRPROFILE = "B"; + public static final Hashtable[] calculate(Vector sequences, int start, int end) { @@ -102,13 +104,13 @@ public class StructureFrequency maxResidue = ""; nongap = 0; values = new int[255]; - for (j = 0; j < jSize; j++) { - if (sequences[j]==null) + if (sequences[j] == null) { - System.err.println("WARNING: Consensus skipping null sequence - possible race condition."); + System.err + .println("WARNING: Consensus skipping null sequence - possible race condition."); continue; } seq = sequences[j].getSequence(); @@ -180,19 +182,23 @@ public class StructureFrequency result[i] = residueHash; } } - - public static int findPair(SequenceFeature[] pairs,int indice){ - for(int i=0; i i) - { - c = seq[i]; - - //standard representation for gaps in sequence and structure - if (c == '.' || c == ' ') - { - c = '-'; - } - - if (c == '-') - { - values['-']++; - continue; - } - bpEnd=findPair(rna,i); - cEnd=seq[bpEnd]; - if(checkBpType(c,cEnd)){ - values['H']++; //H means it's a helix (structured) - } - maxResidue="H"; - } - } -// nonGap++; - } - //UPDATE this for new values - if (profile) - { - //System.out.println("profile"); - residueHash.put(PROFILE, new int[][] - { values, new int[] - { jSize, values['H'] } }); - } - - - count=values['H']; - - residueHash.put(MAXCOUNT, new Integer(count)); - residueHash.put(MAXRESIDUE, maxResidue); - - percentage = ((float) count * 100) / (float) jSize; - residueHash.put(PID_GAPS, new Float(percentage)); - - //percentage = ((float) count * 100) / (float) nongap; - //residueHash.put(PID_NOGAPS, new Float(percentage)); - if(result[i]==null){ - result[i] = residueHash; - } - if(bpEnd>0){ - result[bpEnd]=residueHash; - } - } + int end, Hashtable[] result, boolean profile, + AlignmentAnnotation rnaStruc) + { + // System.out.println("StructureFrequency.calculateNEW4"); + Hashtable residueHash; + String maxResidue; + char[] seq, struc = rnaStruc.getRNAStruc().toCharArray(); + SequenceFeature[] rna = rnaStruc._rnasecstr; + char c, s, cEnd; + int count, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length; + int[] values; + int[][] pairs; + float percentage; + + for (i = start; i < end; i++) // foreach column + { + residueHash = new Hashtable(); + maxResidue = "-"; + values = new int[255]; + pairs = new int[255][255]; + bpEnd = -1; + + s = struc[i]; + if (s == '.' || s == ' ') + { + s = '-'; + } + + if (s != '(') + { + if (s == '-') + { + values['-']++; + } + } + else + { + for (j = 0; j < jSize; j++) // foreach row + { + if (sequences[j] == null) + { + 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 == ' ') + { + c = '-'; + } + + if (c == '-') + { + values['-']++; + continue; + } + bpEnd = findPair(rna, i); + cEnd = seq[bpEnd]; + if (checkBpType(c, cEnd)) + { + values['H']++; // H means it's a helix (structured) + } + // System.out.println("pair: "+c+","+cEnd); + pairs[c][cEnd]++; + // System.out.println("pairs: "+c+","+cEnd+" - "+pairs[c][cEnd]); + + maxResidue = "H"; + } + } + // nonGap++; + } + // UPDATE this for new values + if (profile) + { + // System.out.println("profile"); + residueHash.put(PROFILE, new int[][] + { values, new int[] + { jSize, (jSize - values['-']) } }); + + residueHash.put(PAIRPROFILE, pairs); + } + + count = values['H']; + + residueHash.put(MAXCOUNT, new Integer(count)); + residueHash.put(MAXRESIDUE, maxResidue); + + percentage = ((float) count * 100) / (float) jSize; + residueHash.put(PID_GAPS, new Float(percentage)); + + // percentage = ((float) count * 100) / (float) nongap; + // residueHash.put(PID_NOGAPS, new Float(percentage)); + if (result[i] == null) + { + result[i] = residueHash; + } + if (bpEnd > 0) + { + result[bpEnd] = residueHash; + } + } } - /** - * Method to check if a base-pair is a canonical or a wobble bp - * @param up 5' base - * @param down 3' base + * Method to check if a base-pair is a canonical or a wobble bp + * + * @param up + * 5' base + * @param down + * 3' base * @return True if it is a canonical/wobble bp */ - public static boolean checkBpType(char up, char down){ - if(up>'Z'){up-=32;} - if(down>'Z'){down-=32;} - - switch (up){ - case 'A': - switch (down){ - case 'T': return true; - case 'U': return true; - } - break; - case 'C': - switch (down){ - case 'G': return true; - } - break; - case 'T': - switch (down){ - case 'A': return true; - case 'G': return true; - } - break; - case 'G': - switch (down){ - case 'C': return true; - case 'T': return true; - case 'U': return true; - } - break; - case 'U': - switch (down){ - case 'A': return true; - case 'G': return true; - } - break; - } - return false; + public static boolean checkBpType(char up, char down) + { + if (up > 'Z') + { + up -= 32; + } + if (down > 'Z') + { + down -= 32; + } + + switch (up) + { + case 'A': + switch (down) + { + case 'T': + return true; + case 'U': + return true; + } + break; + case 'C': + switch (down) + { + case 'G': + return true; + } + break; + case 'T': + switch (down) + { + case 'A': + return true; + case 'G': + return true; + } + break; + case 'G': + switch (down) + { + case 'C': + return true; + case 'T': + return true; + case 'U': + return true; + } + break; + case 'U': + switch (down) + { + case 'A': + return true; + case 'G': + return true; + } + break; + } + return false; } - + /** * Compute all or part of the annotation row from the given consensus * hashtable @@ -360,7 +406,7 @@ public class StructureFrequency { completeConsensus(consensus, hconsensus, iStart, width, ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new - // char[] + // char[] // { 'A', 'C', 'G', 'T', 'U' }); } @@ -369,7 +415,8 @@ public class StructureFrequency boolean ignoreGapsInConsensusCalculation, boolean includeAllConsSymbols, char[] alphabet) { - System.out.println("StructureFrequency.completeConsensus "+includeAllConsSymbols); + System.out.println("StructureFrequency.completeConsensus " + + includeAllConsSymbols); float tval, value; if (consensus == null || consensus.annotations == null || consensus.annotations.length < width) @@ -398,18 +445,22 @@ public class StructureFrequency value = ((Float) hconsensus[i].get(StructureFrequency.PID_GAPS)) .floatValue(); } - - String maxRes = hconsensus[i].get(StructureFrequency.MAXRESIDUE).toString(); - String mouseOver = hconsensus[i].get(StructureFrequency.MAXRESIDUE) + " "; + + String maxRes = hconsensus[i].get(StructureFrequency.MAXRESIDUE) + .toString(); + String mouseOver = hconsensus[i].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 tooltip + int[][] profile = (int[][]) hconsensus[i] + .get(StructureFrequency.PROFILE); + if (profile != null && includeAllConsSymbols) // Just responsible for the + // tooltip { - //System.out.println("StructureFrequency.includeAllConsSymbols"); + // System.out.println("StructureFrequency.includeAllConsSymbols"); mouseOver = ""; if (alphabet != null) { @@ -425,7 +476,7 @@ public class StructureFrequency } else { - //System.out.println("StructureFrequency.NOTincludeAllConsSymbols"); + // System.out.println("StructureFrequency.NOTincludeAllConsSymbols"); Object[] ca = new Object[profile[0].length]; float[] vl = new float[profile[0].length]; for (int c = 0; c < ca.length; c++) @@ -469,59 +520,55 @@ public class StructureFrequency * @return */ public static int[] extractProfile(Hashtable hconsensus, - boolean ignoreGapsInConsensusCalculation, - int column) + boolean ignoreGapsInConsensusCalculation, int column) { - //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[22]; - int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE); - if (profile == null) - return null; - - Object[] ca = new Object[profile[0].length]; - float[] vl = new float[profile[0].length]; - for (int c = 0; c < ca.length; c++) - { - ca[c] = new char[] - { (char) c }; - vl[c] = (float) profile[0][c]; - } - ; - jalview.util.QuickSort.sort(vl, ca); - rtnval[0] = 1; - 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]; - //System.out.println("rtnval-"+c+": "+((char[]) ca[c])[0]); - rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 - : 0]); - } - } - for(int i=0; i 0) + { + rtnval[rtnval[0]++] = j; + rtnval[rtnval[0]++] = k; + rtnval[rtnval[0]++] = (int) ((float) pairs[j][k] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + : 0]); + } + } + } + + return rtnval; } - public static void main(String args[]){ - //Short test to see if checkBpType works - ArrayList test = new ArrayList(); - test.add("A"); - test.add("c"); - test.add("g"); - test.add("T"); - test.add("U"); - for (String i : test) { - for (String j : test) { - System.out.println(i+"-"+j+": "+StructureFrequency.checkBpType(i.charAt(0),j.charAt(0))); - } - } + public static void main(String args[]) + { + // Short test to see if checkBpType works + ArrayList test = new ArrayList(); + test.add("A"); + test.add("c"); + test.add("g"); + test.add("T"); + test.add("U"); + for (String i : test) + { + for (String j : test) + { + System.out.println(i + "-" + j + ": " + + StructureFrequency.checkBpType(i.charAt(0), j.charAt(0))); + } + } } } diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 1acc0ca..ca9b95f 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1572,12 +1572,12 @@ public class AnnotationPanel extends JPanel implements MouseListener, char[] dc; /** - * profl.length == 11 indicates that the profile of a secondary + * profl.length == 51 indicates that the profile of a secondary * structure conservation row was accesed. * Therefore dc gets length 2, to have space for a basepair instead of * just a single nucleotide */ - if (profl.length == 22) + if (profl.length == 51) { dc = new char[2]; } @@ -1593,7 +1593,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (aa.label.startsWith("StrucConsensus")) { - dc[1] = 'A'; + dc[1] = (char) profl[c++]; } wdth = av.charWidth; -- 1.7.10.2