X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=8f5b63d1428ca0a5d695c60a2f583dcfa33bdd29;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=236e8ee0cb95d0d05742333eacd04f108d5f71dc;hpb=63cbb86a2d771d2d99d2f38a7b6cf639bf5c19c8;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 236e8ee..8f5b63d 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,22 +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 2.8.0b1) + * 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.datamodel; +import jalview.analysis.Rna; +import jalview.analysis.WUSSParseException; + import java.util.Enumeration; import java.util.Hashtable; @@ -47,6 +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!! */ @@ -117,6 +164,8 @@ public class AlignmentAnnotation */ public boolean centreColLabels = false; + private boolean isrna; + /* * (non-Javadoc) * @@ -167,9 +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++) { @@ -182,9 +238,22 @@ public class AlignmentAnnotation { 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) @@ -205,6 +274,7 @@ public class AlignmentAnnotation firstChar != ' ' && firstChar != 'H' && firstChar != 'E' + && firstChar != 'S' && firstChar != '-' && firstChar < jalview.schemes.ResidueProperties.aaIndex.length) { @@ -219,6 +289,10 @@ public class AlignmentAnnotation } } } + else + { + rnastring.append(annotations[i].displayCharacter.charAt(1)); + } if (annotations[i].displayCharacter.length() > 0) { @@ -241,11 +315,97 @@ 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 @@ -280,7 +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) @@ -293,7 +453,7 @@ public class AlignmentAnnotation float min = graphMin; float max = graphMax; boolean drawValues = true; - + _linecolour = null; if (min == max) { min = 999999999; @@ -319,6 +479,10 @@ 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) @@ -376,6 +540,10 @@ 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; @@ -390,7 +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) @@ -425,6 +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. } @@ -813,8 +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; + } + }