From be415b56e8ce1bc00f5004c64793ce5d0cb17be8 Mon Sep 17 00:00:00 2001 From: janengelhardt Date: Fri, 29 Jul 2011 14:38:27 +0200 Subject: [PATCH] JAL-885; Implementation of StructureFrequency.java and according methods in AlignViewport.java; completeConsensus is still missing; Change-Id: I3678fc75af84aa5a8974faed6b76f47c76a74638 --- src/jalview/analysis/AAFrequency.java | 1 + src/jalview/analysis/Conservation.java | 1 - src/jalview/analysis/Rna.java | 5 +- src/jalview/analysis/StructureFrequency.java | 488 ++++++++++++++++++++++++++ src/jalview/datamodel/SequenceFeature.java | 4 +- src/jalview/gui/AlignFrame.java | 1 + src/jalview/gui/AlignViewport.java | 131 ++++++- src/jalview/gui/AnnotationPanel.java | 4 +- src/jalview/gui/Desktop.java | 2 +- 9 files changed, 626 insertions(+), 11 deletions(-) create mode 100644 src/jalview/analysis/StructureFrequency.java diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 31cb7ad..16754a1 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -85,6 +85,7 @@ public class AAFrequency public static final void calculate(SequenceI[] sequences, int start, int end, Hashtable[] result, boolean profile) { + System.out.println("AAFrequence.calculate"); Hashtable residueHash; int maxCount, nongap, i, j, v, jSize = sequences.length; String maxResidue; diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 2ffb4de..04914fc 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -87,7 +87,6 @@ public class Conservation public Conservation(String name, Hashtable propHash, int threshold, Vector sequences, int start, int end) { - this.name = name; this.propHash = propHash; this.threshold = threshold; diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java index 69a228b..f2ef118 100644 --- a/src/jalview/analysis/Rna.java +++ b/src/jalview/analysis/Rna.java @@ -76,8 +76,8 @@ public class Rna { int begin = Integer.parseInt(pairs.elementAt(p).toString()); int end = Integer.parseInt(pairs.elementAt(p + 1).toString()); - - outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin, + + outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin, end, ""); } @@ -159,7 +159,6 @@ public class Rna // Record helix as featuregroup pairs[i].setFeatureGroup(Integer.toString(helix)); - pairs[i].setFeatureGroup(Integer.toString(helix)); lastopen = open; lastclose = close; diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java new file mode 100644 index 0000000..a666bc0 --- /dev/null +++ b/src/jalview/analysis/StructureFrequency.java @@ -0,0 +1,488 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 + * 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 . + */ +package jalview.analysis; + +import java.util.*; + +import jalview.datamodel.*; + +/** + * Takes in a vector or array of sequences and column start and column end and + * 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 $Revision$ + */ +public class StructureFrequency +{ + // No need to store 1000s of strings which are not + // visible to the user. + public static final String MAXCOUNT = "C"; + + public static final String MAXRESIDUE = "R"; + + public static final String PID_GAPS = "G"; + + public static final String PID_NOGAPS = "N"; + + public static final String PROFILE = "P"; + + public static final Hashtable[] calculate(Vector sequences, int start, + int end) + { + return calculate(sequences, start, end, false); + } + + public static final Hashtable[] calculate(Vector sequences, int start, + int end, boolean profile) + { + SequenceI[] seqs = new SequenceI[sequences.size()]; + int width = 0; + for (int i = 0; i < sequences.size(); i++) + { + seqs[i] = (SequenceI) sequences.elementAt(i); + if (seqs[i].getLength() > width) + { + width = seqs[i].getLength(); + } + } + + Hashtable[] reply = new Hashtable[width]; + + if (end >= width) + { + end = width; + } + + calculate(seqs, start, end, reply, profile); + + return reply; + } + + public static final void calculate(SequenceI[] sequences, int start, + int end, Hashtable[] result) + { + calculate(sequences, start, end, result, false); + } + + public static final void calculate(SequenceI[] sequences, int start, + int end, Hashtable[] result, boolean profile) + { + Hashtable residueHash; + int maxCount, nongap, i, j, v, jSize = sequences.length; + String maxResidue; + char c; + float percentage; + + int[] values = new int[255]; + + char[] seq; + + for (i = start; i < end; i++) + { + residueHash = new Hashtable(); + maxCount = 0; + maxResidue = ""; + nongap = 0; + values = new int[255]; + + 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) + { + c = seq[i]; + + if (c == '.' || c == ' ') + { + c = '-'; + } + + if (c == '-') + { + values['-']++; + continue; + } + else if ('a' <= c && c <= 'z') + { + c -= 32; // ('a' - 'A'); + } + + nongap++; + values[c]++; + + } + else + { + values['-']++; + } + } + + for (v = 'A'; v < 'Z'; v++) + { + if (values[v] < 2 || values[v] < maxCount) + { + continue; + } + + if (values[v] > maxCount) + { + maxResidue = String.valueOf((char) v); + } + else if (values[v] == maxCount) + { + maxResidue += String.valueOf((char) v); + } + maxCount = values[v]; + } + + if (maxResidue.length() == 0) + { + maxResidue = "-"; + } + if (profile) + { + residueHash.put(PROFILE, new int[][] + { values, new int[] + { jSize, nongap } }); + } + residueHash.put(MAXCOUNT, new Integer(maxCount)); + residueHash.put(MAXRESIDUE, maxResidue); + + percentage = ((float) maxCount * 100) / (float) jSize; + residueHash.put(PID_GAPS, new Float(percentage)); + + percentage = ((float) maxCount * 100) / (float) nongap; + residueHash.put(PID_NOGAPS, new Float(percentage)); + result[i] = residueHash; + } + } + + /** + * Method to calculate a 'base pair consensus row', very similar + * to nucleotide consensus but takes into account a given structure + * @param sequences + * @param start + * @param end + * @param result + * @param profile + * @param rnaStruc + */ + public static final void calculate(SequenceI[] sequences, int start, + int end, Hashtable[] result, boolean profile, AlignmentAnnotation rnaStruc){ + //TODO Consider to use AlignmentAnnotation instead of structure string + + Hashtable residueHash; + + char[] seq, struc=rnaStruc.getRNAStruc().toCharArray(); + SequenceFeature[] rna =rnaStruc._rnasecstr; + char c,s,cEnd; + int count,nonGap,i,j,jSize = sequences.length; + int[] values = new int[255]; + float percentage; + + + for (i = start; i < end; i++) //foreach column + { + residueHash = new Hashtable(); + 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]; + s = struc[i]; + nonGap=0; + + //standard representation for gaps in sequence and structure + if (c == '.' || c == ' ') + { + c = '-'; + } + if (s == '.' || s == ' ') + { + s = '-'; + } + + if (c == '-') + { + values['-']++; + continue; + } + if(s == '-'){ + values['-']++; + continue; + } + nonGap++; + cEnd=seq[rna[i].getEnd()]; + if(checkBpType(c,cEnd)){ + values['H']++; //H means it's a helix (structured) + } + } + } + /*UPDATE this for new values + if (profile) + { + residueHash.put(PROFILE, new int[][] + { values, new int[] + { jSize, nongap } }); + } + */ + + count=values['H']; + + 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)); + result[i] = residueHash; + + } + } + + + /** + * 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; + } + + /** + * Compute all or part of the annotation row from the given consensus + * hashtable + * + * @param consensus + * - pre-allocated annotation row + * @param hconsensus + * @param iStart + * @param width + * @param ignoreGapsInConsensusCalculation + * @param includeAllConsSymbols + */ + 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) + { + float tval, value; + if (consensus == null || consensus.annotations == null + || consensus.annotations.length < width) + { + // called with a bad alignment annotation row - wait for it to be + // initialised properly + return; + } + for (int i = iStart; i < width; i++) + { + if (i >= hconsensus.length) + { + // happens if sequences calculated over were shorter than alignment + // width + consensus.annotations[i] = null; + continue; + } + value = 0; + if (ignoreGapsInConsensusCalculation) + { + value = ((Float) hconsensus[i].get(StructureFrequency.PID_NOGAPS)) + .floatValue(); + } + else + { + value = ((Float) hconsensus[i].get(StructureFrequency.PID_GAPS)) + .floatValue(); + } + + 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) + { + mouseOver = ""; + 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[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); + 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++; + + } + } + + } + } + else + { + mouseOver += ((int) value + "%"); + } + consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', + value); + } + } + + /** + * get the sorted profile for the given position of the consensus + * + * @param hconsensus + * @return + */ + public static int[] extractProfile(Hashtable hconsensus, + boolean ignoreGapsInConsensusCalculation) + { + int[] rtnval = new int[64]; + 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]; + rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + : 0]); + } + } + return rtnval; + } + + enum base {A,T,g,C}; + + + 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/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 012f842..184123f 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -40,7 +40,7 @@ public class SequenceFeature public Hashtable otherDetails; public java.util.Vector links; - + // Feature group can be set from a features file // as a group of features between STARTGROUP and ENDGROUP markers public String featureGroup; @@ -95,7 +95,7 @@ public class SequenceFeature } } } - + public SequenceFeature(String type, String desc, String status, int begin, int end, String featureGroup) { diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index f05d873..5beebfd 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -589,6 +589,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } ap.av.updateConservation(ap); ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); } } diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 26fb890..98cae4c 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -139,8 +139,12 @@ public class AlignViewport implements SelectionSource, VamsasSource /** DOCUMENT ME!! */ public Hashtable[] hconsensus; - + + public Hashtable[] hStrucConsensus; + AlignmentAnnotation consensus; + + AlignmentAnnotation strucConsensus; AlignmentAnnotation conservation; @@ -151,6 +155,9 @@ public class AlignViewport implements SelectionSource, VamsasSource AlignmentAnnotation[] groupConservation; boolean autoCalculateConsensus = true; + + boolean autoCalculateStrucConsensus = true; + /** DOCUMENT ME!! */ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! @@ -458,14 +465,20 @@ public class AlignViewport implements SelectionSource, VamsasSource ConservationThread conservationThread; ConsensusThread consensusThread; + + StrucConsensusThread strucConsensusThread; boolean consUpdateNeeded = false; static boolean UPDATING_CONSENSUS = false; + + static boolean UPDATING_STRUC_CONSENSUS = false; static boolean UPDATING_CONSERVATION = false; boolean updatingConsensus = false; + + boolean updatingStrucConsensus = false; boolean updatingConservation = false; @@ -559,7 +572,6 @@ public class AlignViewport implements SelectionSource, VamsasSource AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment.getWidth(), hconsensus, true); updateAnnotation(true); - if (globalColourScheme != null) { globalColourScheme.setConsensus(hconsensus); @@ -604,6 +616,116 @@ public class AlignViewport implements SelectionSource, VamsasSource } } } + + //--------START Structure Conservation + public void updateStrucConsensus(final AlignmentPanel ap) + { + // see note in mantis : issue number 8585 + if (strucConsensus == null || !autoCalculateStrucConsensus) + { + return; + } + strucConsensusThread = new StrucConsensusThread(ap); + strucConsensusThread.start(); + } + + class StrucConsensusThread extends Thread + { + AlignmentPanel ap; + + public StrucConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } + + public void run() + { + updatingStrucConsensus = true; + while (UPDATING_STRUC_CONSENSUS) + { + try + { + if (ap != null) + { + ap.paintAlignment(false); + } + + Thread.sleep(200); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + UPDATING_STRUC_CONSENSUS = true; + + try + { + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null + // pointer + // possibility + // here. + if (aWidth <= 0) + { + updatingStrucConsensus = false; + UPDATING_STRUC_CONSENSUS = false; + return; + } + + strucConsensus.annotations = null; + strucConsensus.annotations = new Annotation[aWidth]; + + hStrucConsensus = new Hashtable[aWidth]; + AlignmentAnnotation rna = ap.av.getAlignment().getAlignmentAnnotation()[0]; + StructureFrequency.calculate(alignment.getSequencesArray(), 0, + alignment.getWidth(), hStrucConsensus, true, rna); + //TODO AlignmentAnnotation rnaStruc!!! + updateAnnotation(true); + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hStrucConsensus); + } + + } catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(consensus); + + strucConsensus = null; + hStrucConsensus = null; + new OOMWarning("calculating structure consensus", error); + } + UPDATING_STRUC_CONSENSUS = false; + updatingStrucConsensus = false; + + if (ap != null) + { + ap.paintAlignment(true); + } + } + + /** + * update the consensus annotation from the sequence profile data using + * current visualization settings. + */ + public void updateAnnotation() + { + updateAnnotation(false); + } + + protected void updateAnnotation(boolean immediate) + { + // TODO: make calls thread-safe, so if another thread calls this method, + // it will either return or wait until one calculation is finished. + if (immediate + || (!updatingConsensus && consensus != null && hconsensus != null)) + { + StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus, 0, + hStrucConsensus.length, ignoreGapsInConsensusCalculation, + showSequenceLogo); + } + } + } + //--------END Structure Conservation /** * get the consensus sequence as displayed under the PID consensus annotation @@ -1732,6 +1854,11 @@ public class AlignViewport implements SelectionSource, VamsasSource { updateConsensus(ap); } + + if(autoCalculateStrucConsensus) + { + updateStrucConsensus(ap); + } // Reset endRes of groups if beyond alignment width int alWidth = alignment.getWidth(); diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 32f9514..6418c76 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -671,11 +671,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, AlignmentAnnotation anot = aa[activeRow]; if(anot.description.equals("secondary structure")){ - System.out.println(anot.description+" "+anot.getRNAStruc()); + //System.out.println(anot.description+" "+anot.getRNAStruc()); } } } - + //TODO mouseClicked-content and drawCursor are quite experimental! public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, int y1) { int pady = av.charHeight / 5; diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 45aed9c..9797694 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -951,7 +951,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } // TODO: update this text for each release or centrally store it for lite // and application - message.append("\nAuthors: Jim Procter, Jan Engelhardt2, Lauren Lui, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton." + message.append("\nAuthors: Jim Procter, Jan Engelhardt, Lauren Lui, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton." + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n" + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n" + "\nIf you use Jalview, please cite:" -- 1.7.10.2