X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=25bba51748693aa0fe86fd55880e25e7609190cd;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=81ea36f05b9961e98605549dfb36bf70a5c8635a;hpb=555361f1a668c138550f0cc95cbf089377e84561;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 81ea36f..25bba51 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,40 +1,43 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * 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 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. - * - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.datamodel; +import jalview.analysis.Rna; + import java.util.Enumeration; import java.util.Hashtable; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ public class AlignmentAnnotation { - /** If true, this annotations is calculated every edit, - * eg consensus, quality or conservation graphs */ + /** + * If true, this annotations is calculated every edit, eg consensus, quality + * or conservation graphs + */ public boolean autoCalculated = false; public String annotationId; - + public SequenceI sequenceRef; /** DOCUMENT ME!! */ @@ -46,6 +49,35 @@ public class AlignmentAnnotation /** DOCUMENT ME!! */ public Annotation[] annotations; + /** + * RNA secondary structure contact positions + */ + public SequenceFeature[] _rnasecstr = null; + + public String rnaStructure; + + /** + * 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(String RNAannot) + { + _rnasecstr = Rna.GetBasePairs(RNAannot); + Rna.HelixMap(_rnasecstr); + + setRNAStruc(RNAannot); + + if (_rnasecstr != null && _rnasecstr.length > 0) + { + // show all the RNA secondary structure annotation symbols. + showAllColLabels = true; + scaleColLabel = true; + } + // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup()); + } + public java.util.Hashtable sequenceMapping; /** DOCUMENT ME!! */ @@ -54,32 +86,42 @@ public class AlignmentAnnotation /** DOCUMENT ME!! */ public float graphMax; + /** + * Score associated with label and description. + */ + public double score = Double.NaN; + + /** + * flag indicating if annotation has a score. + */ + public boolean hasScore = false; + public GraphLine threshold; // 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; public int graphHeight = 40; - public boolean padGaps = true; + public boolean padGaps = false; public static final int NO_GRAPH = 0; @@ -87,6 +129,37 @@ public class AlignmentAnnotation public static final int LINE_GRAPH = 2; + public boolean belowAlignment = true; + + 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) + * + * @see java.lang.Object#finalize() + */ + protected void finalize() throws Throwable + { + sequenceRef = null; + groupRef = null; + super.finalize(); + } + public static int getGraphValueFromString(String string) { if (string.equalsIgnoreCase("BAR_GRAPH")) @@ -105,13 +178,16 @@ public class AlignmentAnnotation /** * Creates a new AlignmentAnnotation object. - * - * @param label DOCUMENT ME! - * @param description DOCUMENT ME! - * @param annotations DOCUMENT ME! + * + * @param label + * short label shown under sequence labels + * @param description + * text displayed on mouseover + * @param annotations + * set of positional annotation elements */ public AlignmentAnnotation(String label, String description, - Annotation[] annotations) + Annotation[] annotations) { // always editable? editable = true; @@ -119,83 +195,148 @@ public class AlignmentAnnotation this.description = description; this.annotations = annotations; - validateRangeAndDisplay(); + validateRangeAndDisplay(); } + /** + * Checks if annotation labels represent secondary structures + * + */ void areLabelsSecondaryStructure() { boolean nonSSLabel = false; + boolean isrna = false; + StringBuffer rnastring = new StringBuffer(); + + char firstChar = 0; for (int i = 0; i < annotations.length; i++) { if (annotations[i] == null) { - padGaps = false; continue; } - if (annotations[i].secondaryStructure == 'H' || - annotations[i].secondaryStructure == 'E') + if (annotations[i].secondaryStructure == 'H' + || annotations[i].secondaryStructure == 'E') + { + hasIcons |= true; + } + else + // Check for RNA secondary structure { - hasIcons = true; + if (annotations[i].secondaryStructure == 'S') + { + hasIcons |= true; + isrna |= true; + } } - if (annotations[i].displayCharacter!=null) + // System.out.println("displaychar " + annotations[i].displayCharacter); + + if (annotations[i].displayCharacter == null + || annotations[i].displayCharacter.length() == 0) { - if (annotations[i].displayCharacter.length() == 1 - && !annotations[i].displayCharacter.equals("H") - && !annotations[i].displayCharacter.equals("E") - && !annotations[i].displayCharacter.equals("-") - && !annotations[i].displayCharacter.equals(".")) + rnastring.append('.'); + continue; + } + if (annotations[i].displayCharacter.length() == 1) + { + firstChar = annotations[i].displayCharacter.charAt(0); + // check to see if it looks like a sequence or is secondary structure + // labelling. + 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 != 'S' + && firstChar != '-' + && firstChar < jalview.schemes.ResidueProperties.aaIndex.length) { - if (jalview.schemes.ResidueProperties.aaIndex - [annotations[i].displayCharacter.charAt(0)] < 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) - { - hasText = true; - } - else - padGaps = false; + if (annotations[i].displayCharacter.length() > 0) + { + hasText = true; } } - if (nonSSLabel) { hasIcons = false; for (int j = 0; j < annotations.length; j++) { - if (annotations[j] != null && annotations[j].secondaryStructure != ' ') + if (annotations[j] != null + && annotations[j].secondaryStructure != ' ') { - annotations[j].displayCharacter - = String.valueOf(annotations[j].secondaryStructure); + annotations[j].displayCharacter = String + .valueOf(annotations[j].secondaryStructure); annotations[j].secondaryStructure = ' '; } } } + else + { + if (isrna) + { + _updateRnaSecStr(rnastring.toString()); + } + } annotationId = this.hashCode() + ""; } - /** + + public void setRNAStruc(String string) { + rnaStructure=string; +} + + public String getRNAStruc(){ + return rnaStructure; + } + +/** * Creates a new AlignmentAnnotation object. - * - * @param label DOCUMENT ME! - * @param description DOCUMENT ME! - * @param annotations DOCUMENT ME! - * @param min DOCUMENT ME! - * @param max DOCUMENT ME! - * @param winLength DOCUMENT ME! + * + * @param label + * DOCUMENT ME! + * @param description + * DOCUMENT ME! + * @param annotations + * DOCUMENT ME! + * @param min + * DOCUMENT ME! + * @param max + * DOCUMENT ME! + * @param winLength + * DOCUMENT ME! */ public AlignmentAnnotation(String label, String description, - Annotation[] annotations, float min, float max, - int graphType) + Annotation[] annotations, float min, float max, int graphType) { // graphs are not editable - editable = graphType==0; + editable = graphType == 0; this.label = label; this.description = description; @@ -205,14 +346,20 @@ public class AlignmentAnnotation graphMax = max; validateRangeAndDisplay(); } + /** - * checks graphMin and graphMax, - * secondary structure symbols, - * sets graphType appropriately, - * sets null labels to the empty string - * if appropriate. + * 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) + { + visible = false; // try to prevent renderer from displaying. + return; // this is a non-annotation row annotation - ie a sequence score. + } + int graphType = graph; float min = graphMin; float max = graphMax; @@ -228,7 +375,8 @@ public class AlignmentAnnotation continue; } - if (drawValues && annotations[i].displayCharacter!=null && annotations[i].displayCharacter.length() > 1) + if (drawValues && annotations[i].displayCharacter != null + && annotations[i].displayCharacter.length() > 1) { drawValues = false; } @@ -243,6 +391,18 @@ public class AlignmentAnnotation min = annotations[i].value; } } + // 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; + } + } } graphMin = min; @@ -263,8 +423,9 @@ public class AlignmentAnnotation } /** - * Copy constructor - * creates a new independent annotation row with the same associated sequenceRef + * Copy constructor creates a new independent annotation row with the same + * associated sequenceRef + * * @param annotation */ public AlignmentAnnotation(AlignmentAnnotation annotation) @@ -277,6 +438,7 @@ public class AlignmentAnnotation this.graph = annotation.graph; this.graphHeight = annotation.graphHeight; this.graphGroup = annotation.graphGroup; + this.groupRef = annotation.groupRef; this.editable = annotation.editable; this.autoCalculated = annotation.autoCalculated; this.hasIcons = annotation.hasIcons; @@ -284,39 +446,52 @@ public class AlignmentAnnotation this.height = annotation.height; this.label = annotation.label; this.padGaps = annotation.padGaps; - if (threshold!=null) { + this.visible = annotation.visible; + if (this.hasScore = annotation.hasScore) + { + this.score = annotation.score; + } + if (annotation.threshold != null) + { threshold = new GraphLine(annotation.threshold); } - if (annotation.annotations!=null) { + if (annotation.annotations != null) + { Annotation[] ann = annotation.annotations; this.annotations = new Annotation[ann.length]; - for (int i=0; i= annotations.length) + startRes = annotations.length - 1; + if (endRes >= annotations.length) + endRes = annotations.length - 1; + if (annotations == null) + return; + Annotation[] temp = new Annotation[endRes - startRes + 1]; + if (startRes < annotations.length) + { + System.arraycopy(annotations, startRes, temp, 0, endRes - startRes + + 1); } - if (sequenceRef!=null) { + if (sequenceRef != null) + { // Clip the mapping, if it exists. int spos = sequenceRef.findPosition(startRes); int epos = sequenceRef.findPosition(endRes); - if (sequenceMapping!=null) + if (sequenceMapping != null) { Hashtable newmapping = new Hashtable(); Enumeration e = sequenceMapping.keys(); while (e.hasMoreElements()) { Integer pos = (Integer) e.nextElement(); - if (pos.intValue()>=spos && pos.intValue()<=epos) + if (pos.intValue() >= spos && pos.intValue() <= epos) { newmapping.put(pos, sequenceMapping.get(pos)); } @@ -357,33 +548,37 @@ public class AlignmentAnnotation sequenceMapping = newmapping; } } - annotations=temp; + annotations = temp; } + /** * set the annotation row to be at least length Annotations - * @param length minimum number of columns required in the annotation row + * + * @param length + * minimum number of columns required in the annotation row * @return false if the annotation row is greater than length */ - public boolean padAnnotation(int length) { - if (annotations==null) + public boolean padAnnotation(int length) + { + if (annotations == null) { - annotations = new Annotation[length]; - return true; + return true; // annotation row is correct - null == not visible and + // undefined length } - if (annotations.lengthlength; - + return annotations.length > length; + } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String toString() @@ -410,8 +605,8 @@ 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"); @@ -440,24 +635,29 @@ public class AlignmentAnnotation } /** - * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions. + * Attach the annotation to seqRef, starting from startRes position. If + * alreadyMapped is true then the indices of the annotation[] array are + * sequence positions rather than alignment column positions. + * * @param seqRef * @param startRes * @param alreadyMapped */ - public void createSequenceMapping(SequenceI seqRef, - int startRes, - boolean alreadyMapped) + public void createSequenceMapping(SequenceI seqRef, int startRes, + boolean alreadyMapped) { if (seqRef == null) { return; } - + sequenceRef = seqRef; + if (annotations == null) + { + return; + } sequenceMapping = new java.util.Hashtable(); - sequenceRef = seqRef; int seqPos; for (int i = 0; i < annotations.length; i++) @@ -481,14 +681,19 @@ public class AlignmentAnnotation public void adjustForAlignment() { - if (sequenceRef==null) + if (sequenceRef == null) return; + if (annotations == null) + { + return; + } + int a = 0, aSize = sequenceRef.getLength(); if (aSize == 0) { - //Its been deleted + // Its been deleted return; } @@ -509,31 +714,45 @@ public class AlignmentAnnotation annotations = temp; } + /** - * remove any null entries in annotation row and return the - * number of non-null annotation elements. + * remove any null entries in annotation row and return the number of non-null + * annotation elements. + * * @return */ - private int compactAnnotationArray() { - int j=0; - for (int i=0;i