X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=8f5b63d1428ca0a5d695c60a2f583dcfa33bdd29;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=4f7fd9340cc4b211fb9a8d500d7e8e16246593cf;hpb=1e184475a6f6ba43584580b55351331a8b57b350;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 4f7fd93..8f5b63d 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,23 +1,26 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.datamodel; +import jalview.analysis.Rna; +import jalview.analysis.WUSSParseException; + import java.util.Enumeration; import java.util.Hashtable; @@ -48,6 +51,49 @@ public class AlignmentAnnotation /** DOCUMENT ME!! */ public Annotation[] annotations; + /** + * RNA secondary structure contact positions + */ + public SequenceFeature[] _rnasecstr = null; + + /** + * position of annotation resulting in invalid WUSS parsing or -1 + */ + private long invalidrnastruc = -1; + + /** + * Updates the _rnasecstr field Determines the positions that base pair and + * the positions of helices based on secondary structure from a Stockholm file + * + * @param RNAannot + */ + private void _updateRnaSecStr(CharSequence RNAannot) + { + try + { + _rnasecstr = Rna.GetBasePairs(RNAannot); + invalidrnastruc = -1; + } catch (WUSSParseException px) + { + invalidrnastruc = px.getProblemPos(); + } + if (invalidrnastruc > -1) + { + return; + } + Rna.HelixMap(_rnasecstr); + // setRNAStruc(RNAannot); + + if (_rnasecstr != null && _rnasecstr.length > 0) + { + // show all the RNA secondary structure annotation symbols. + isrna = true; + showAllColLabels = true; + scaleColLabel = true; + } + // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup()); + } + public java.util.Hashtable sequenceMapping; /** DOCUMENT ME!! */ @@ -70,21 +116,21 @@ public class AlignmentAnnotation // Graphical hints and tips - /** DOCUMENT ME!! */ + /** Can this row be edited by the user ? */ public boolean editable = false; - /** DOCUMENT ME!! */ + /** Indicates if annotation has a graphical symbol track */ public boolean hasIcons; // - /** DOCUMENT ME!! */ + /** Indicates if annotation has a text character label */ public boolean hasText; - /** DOCUMENT ME!! */ + /** is the row visible */ public boolean visible = true; public int graphGroup = -1; - /** DOCUMENT ME!! */ + /** Displayed height of row in pixels */ public int height = 0; public int graph = 0; @@ -101,14 +147,33 @@ public class AlignmentAnnotation public boolean belowAlignment = true; - public SequenceGroup groupRef =null ; + public SequenceGroup groupRef = null; + + /** + * display every column label, even if there is a row of identical labels + */ + public boolean showAllColLabels = false; + + /** + * scale the column label to fit within the alignment column. + */ + public boolean scaleColLabel = false; + + /** + * centre the column labels relative to the alignment column + */ + public boolean centreColLabels = false; - - /* (non-Javadoc) + private boolean isrna; + + /* + * (non-Javadoc) + * * @see java.lang.Object#finalize() */ protected void finalize() throws Throwable { + sequenceRef = null; groupRef = null; super.finalize(); } @@ -133,11 +198,11 @@ public class AlignmentAnnotation * Creates a new AlignmentAnnotation object. * * @param label - * short label shown under sequence labels + * short label shown under sequence labels * @param description - * text displayed on mouseover + * text displayed on mouseover * @param annotations - * set of positional annotation elements + * set of positional annotation elements */ public AlignmentAnnotation(String label, String description, Annotation[] annotations) @@ -151,9 +216,16 @@ public class AlignmentAnnotation validateRangeAndDisplay(); } + /** + * Checks if annotation labels represent secondary structures + * + */ void areLabelsSecondaryStructure() { boolean nonSSLabel = false; + isrna = false; + StringBuffer rnastring = new StringBuffer(); + char firstChar = 0; for (int i = 0; i < annotations.length; i++) { @@ -164,11 +236,24 @@ public class AlignmentAnnotation if (annotations[i].secondaryStructure == 'H' || annotations[i].secondaryStructure == 'E') { - hasIcons = true; + hasIcons |= true; } + else + // Check for RNA secondary structure + { + if (annotations[i].secondaryStructure == 'S') + { + hasIcons |= true; + isrna |= true; + } + } + + // System.out.println("displaychar " + annotations[i].displayCharacter); - if (annotations[i].displayCharacter == null) + if (annotations[i].displayCharacter == null + || annotations[i].displayCharacter.length() == 0) { + rnastring.append('.'); continue; } if (annotations[i].displayCharacter.length() == 1) @@ -176,25 +261,38 @@ public class AlignmentAnnotation firstChar = annotations[i].displayCharacter.charAt(0); // check to see if it looks like a sequence or is secondary structure // labelling. - if ( - // Uncomment to only catch case where displayCharacter==secondary - // Structure - // to correctly redisplay SS annotation imported from Stockholm, - // exported to JalviewXML and read back in again. - // && - // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure - firstChar != 'H' + if (annotations[i].secondaryStructure != ' ' + && !hasIcons + && + // Uncomment to only catch case where + // displayCharacter==secondary + // Structure + // to correctly redisplay SS annotation imported from Stockholm, + // exported to JalviewXML and read back in again. + // && + // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure + firstChar != ' ' + && firstChar != 'H' && firstChar != 'E' - && firstChar != '-' + && firstChar != 'S' && firstChar != '-' && firstChar < jalview.schemes.ResidueProperties.aaIndex.length) { - if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) + if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO: + // parameterise + // to + // gap + // symbol + // number { nonSSLabel = true; } } } + else + { + rnastring.append(annotations[i].displayCharacter.charAt(1)); + } if (annotations[i].displayCharacter.length() > 0) { @@ -217,25 +315,111 @@ public class AlignmentAnnotation } } + else + { + if (isrna) + { + _updateRnaSecStr(new AnnotCharSequence()); + } + } annotationId = this.hashCode() + ""; } /** + * flyweight access to positions in the alignment annotation row for RNA + * processing + * + * @author jimp + * + */ + private class AnnotCharSequence implements CharSequence + { + int offset = 0; + + int max = 0; + + public AnnotCharSequence() + { + this(0, annotations.length); + } + + public AnnotCharSequence(int start, int end) + { + offset = start; + max = end; + } + + @Override + public CharSequence subSequence(int start, int end) + { + return new AnnotCharSequence(offset + start, offset + end); + } + + @Override + public int length() + { + return max - offset; + } + + @Override + public char charAt(int index) + { + String dc; + return ((index + offset < 0) || (index + offset) >= max + || annotations[index + offset] == null || (dc = annotations[index + + offset].displayCharacter.trim()).length() < 1) ? '.' : dc + .charAt(0); + } + + public String toString() + { + char[] string = new char[max - offset]; + int mx = annotations.length; + + for (int i = offset; i < mx; i++) + { + String dc; + string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter + .trim()).length() < 1) ? '.' : dc.charAt(0); + } + return new String(string); + } + }; + + private long _lastrnaannot = -1; + + public String getRNAStruc() + { + if (isrna) + { + String rnastruc = new AnnotCharSequence().toString(); + if (_lastrnaannot != rnastruc.hashCode()) + { + // ensure rna structure contacts are up to date + _lastrnaannot = rnastruc.hashCode(); + _updateRnaSecStr(rnastruc); + } + return rnastruc; + } + return null; + } + + /** * Creates a new AlignmentAnnotation object. * * @param label - * DOCUMENT ME! + * DOCUMENT ME! * @param description - * DOCUMENT ME! + * DOCUMENT ME! * @param annotations - * DOCUMENT ME! + * DOCUMENT ME! * @param min - * DOCUMENT ME! + * DOCUMENT ME! * @param max - * DOCUMENT ME! + * DOCUMENT ME! * @param winLength - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignmentAnnotation(String label, String description, Annotation[] annotations, float min, float max, int graphType) @@ -256,7 +440,7 @@ public class AlignmentAnnotation * checks graphMin and graphMax, secondary structure symbols, sets graphType * appropriately, sets null labels to the empty string if appropriate. */ - private void validateRangeAndDisplay() + public void validateRangeAndDisplay() { if (annotations == null) @@ -269,7 +453,7 @@ public class AlignmentAnnotation float min = graphMin; float max = graphMax; boolean drawValues = true; - + _linecolour = null; if (min == max) { min = 999999999; @@ -295,6 +479,22 @@ public class AlignmentAnnotation { min = annotations[i].value; } + if (_linecolour == null && annotations[i].colour != null) + { + _linecolour = annotations[i].colour; + } + } + // ensure zero is origin for min/max ranges on only one side of zero + if (min > 0) + { + min = 0; + } + else + { + if (max < 0) + { + max = 0; + } } } @@ -340,11 +540,15 @@ public class AlignmentAnnotation this.label = annotation.label; this.padGaps = annotation.padGaps; this.visible = annotation.visible; + this.centreColLabels = annotation.centreColLabels; + this.scaleColLabel = annotation.scaleColLabel; + this.showAllColLabels = annotation.showAllColLabels; + this.calcId = annotation.calcId; if (this.hasScore = annotation.hasScore) { this.score = annotation.score; } - if (threshold != null) + if (annotation.threshold != null) { threshold = new GraphLine(annotation.threshold); } @@ -354,7 +558,14 @@ public class AlignmentAnnotation this.annotations = new Annotation[ann.length]; for (int i = 0; i < ann.length; i++) { - annotations[i] = new Annotation(ann[i]); + if (ann[i] != null) + { + annotations[i] = new Annotation(ann[i]); + if (_linecolour != null) + { + _linecolour = annotations[i].colour; + } + } } ; if (annotation.sequenceRef != null) @@ -389,6 +600,11 @@ public class AlignmentAnnotation } } } + // TODO: check if we need to do this: JAL-952 + // if (this.isrna=annotation.isrna) + { + // _rnasecstr=new SequenceFeature[annotation._rnasecstr]; + } validateRangeAndDisplay(); // construct hashcodes, etc. } @@ -448,7 +664,7 @@ public class AlignmentAnnotation * set the annotation row to be at least length Annotations * * @param length - * minimum number of columns required in the annotation row + * minimum number of columns required in the annotation row * @return false if the annotation row is greater than length */ public boolean padAnnotation(int length) @@ -456,7 +672,7 @@ public class AlignmentAnnotation if (annotations == null) { return true; // annotation row is correct - null == not visible and - // undefined length + // undefined length } if (annotations.length < length) { @@ -498,8 +714,8 @@ public class AlignmentAnnotation buffer.append(", "); } - - if (label.equals("Consensus")) + // TODO: remove disgusting hack for 'special' treatment of consensus line. + if (label.indexOf("Consensus") == 0) { buffer.append("\n"); @@ -701,7 +917,7 @@ public class AlignmentAnnotation /** * @param score - * the score to set + * the score to set */ public void setScore(double score) { @@ -777,8 +993,47 @@ public class AlignmentAnnotation { if (seqname && this.sequenceRef != null) { + int i = description.toLowerCase().indexOf(""); + if (i > -1) + { + // move the html tag to before the sequence reference. + return "" + sequenceRef.getName() + " : " + + description.substring(i + 6); + } return sequenceRef.getName() + " : " + description; } return description; } + + public boolean isValidStruc() + { + return invalidrnastruc == -1; + } + + public long getInvalidStrucPos() + { + return invalidrnastruc; + } + + /** + * machine readable ID string indicating what generated this annotation + */ + protected String calcId = ""; + + /** + * base colour for line graphs. If null, will be set automatically by + * searching the alignment annotation + */ + public java.awt.Color _linecolour; + + public String getCalcId() + { + return calcId; + } + + public void setCalcId(String calcId) + { + this.calcId = calcId; + } + }