X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=8f5b63d1428ca0a5d695c60a2f583dcfa33bdd29;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=c675a759bb71fe620a4fd7e5c2bf4f939b9f9e22;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index c675a75..8f5b63d 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,33 +1,41 @@ /* - * 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 2.8.0b1) + * 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; + /** * 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; @@ -43,6 +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!! */ @@ -51,37 +102,82 @@ 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 = false; + public static final int NO_GRAPH = 0; public static final int BAR_GRAPH = 1; 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; + + private boolean isrna; + + /* + * (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")) @@ -100,13 +196,16 @@ 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; @@ -114,37 +213,86 @@ public class AlignmentAnnotation this.description = description; this.annotations = annotations; - areLabelsSecondaryStructure(); + 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++) { if (annotations[i] == null) { continue; } - - if (annotations[i].secondaryStructure == 'H' || - annotations[i].secondaryStructure == 'E') + 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.length() == 1 - && !annotations[i].displayCharacter.equals("H") - && !annotations[i].displayCharacter.equals("E") - && !annotations[i].displayCharacter.equals("-") - && !annotations[i].displayCharacter.equals(".")) + if (annotations[i].displayCharacter == null + || annotations[i].displayCharacter.length() == 0) + { + rnastring.append('.'); + continue; + } + if (annotations[i].displayCharacter.length() == 1) { - if (jalview.schemes.ResidueProperties.aaIndex - [annotations[i].displayCharacter.charAt(0)] < 23) + 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) { - nonSSLabel = true; + 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) { @@ -157,42 +305,155 @@ public class AlignmentAnnotation 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(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! - * @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; + this.label = label; this.description = description; this.annotations = annotations; graph = graphType; + graphMin = min; + graphMax = max; + validateRangeAndDisplay(); + } - boolean drawValues = true; + /** + * checks graphMin and graphMax, secondary structure symbols, sets graphType + * appropriately, sets null labels to the empty string if appropriate. + */ + 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; + boolean drawValues = true; + _linecolour = null; if (min == max) { min = 999999999; @@ -203,7 +464,8 @@ public class AlignmentAnnotation continue; } - if (drawValues && annotations[i].displayCharacter.length() > 1) + if (drawValues && annotations[i].displayCharacter != null + && annotations[i].displayCharacter.length() > 1) { drawValues = false; } @@ -217,6 +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; + } } } @@ -238,8 +516,178 @@ public class AlignmentAnnotation } /** + * Copy constructor creates a new independent annotation row with the same + * associated sequenceRef + * + * @param annotation + */ + public AlignmentAnnotation(AlignmentAnnotation annotation) + { + this.label = new String(annotation.label); + if (annotation.description != null) + this.description = new String(annotation.description); + this.graphMin = annotation.graphMin; + this.graphMax = annotation.graphMax; + 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; + this.hasText = annotation.hasText; + this.height = annotation.height; + 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 (annotation.threshold != null) + { + threshold = new GraphLine(annotation.threshold); + } + if (annotation.annotations != null) + { + Annotation[] ann = annotation.annotations; + this.annotations = new Annotation[ann.length]; + for (int i = 0; i < ann.length; i++) + { + if (ann[i] != null) + { + annotations[i] = new Annotation(ann[i]); + if (_linecolour != null) + { + _linecolour = annotations[i].colour; + } + } + } + ; + if (annotation.sequenceRef != null) + { + this.sequenceRef = annotation.sequenceRef; + if (annotation.sequenceMapping != null) + { + Integer p = null; + sequenceMapping = new Hashtable(); + Enumeration pos = annotation.sequenceMapping.keys(); + while (pos.hasMoreElements()) + { + // could optimise this! + p = (Integer) pos.nextElement(); + Annotation a = (Annotation) annotation.sequenceMapping.get(p); + if (a == null) + { + continue; + } + for (int i = 0; i < ann.length; i++) + { + if (ann[i] == a) + { + sequenceMapping.put(p, annotations[i]); + } + } + } + } + else + { + this.sequenceMapping = null; + } + } + } + // TODO: check if we need to do this: JAL-952 + // if (this.isrna=annotation.isrna) + { + // _rnasecstr=new SequenceFeature[annotation._rnasecstr]; + } + validateRangeAndDisplay(); // construct hashcodes, etc. + } + + /** + * clip the annotation to the columns given by startRes and endRes (inclusive) + * and prune any existing sequenceMapping to just those columns. + * + * @param startRes + * @param endRes + */ + public void restrict(int startRes, int endRes) + { + if (annotations == null) + { + // non-positional + return; + } + if (startRes < 0) + startRes = 0; + if (startRes >= 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) + { + // Clip the mapping, if it exists. + int spos = sequenceRef.findPosition(startRes); + int epos = sequenceRef.findPosition(endRes); + 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) + { + newmapping.put(pos, sequenceMapping.get(pos)); + } + } + sequenceMapping.clear(); + sequenceMapping = newmapping; + } + } + annotations = temp; + } + + /** + * set the annotation row to be at least length Annotations + * + * @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) + { + return true; // annotation row is correct - null == not visible and + // undefined length + } + if (annotations.length < length) + { + Annotation[] na = new Annotation[length]; + System.arraycopy(annotations, 0, na, 0, annotations.length); + annotations = na; + return true; + } + return annotations.length > length; + + } + + /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String toString() @@ -266,8 +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"); @@ -296,24 +744,29 @@ 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++) @@ -337,11 +790,19 @@ public class AlignmentAnnotation public void adjustForAlignment() { + if (sequenceRef == null) + return; + + if (annotations == null) + { + return; + } + int a = 0, aSize = sequenceRef.getLength(); if (aSize == 0) { - //Its been deleted + // Its been deleted return; } @@ -362,4 +823,217 @@ public class AlignmentAnnotation annotations = temp; } + + /** + * remove any null entries in annotation row and return the number of non-null + * annotation elements. + * + * @return + */ + public int compactAnnotationArray() + { + int i = 0, iSize = annotations.length; + while (i < iSize) + { + if (annotations[i] == null) + { + if (i + 1 < iSize) + System.arraycopy(annotations, i + 1, annotations, i, iSize - i + - 1); + iSize--; + } + else + { + i++; + } + } + Annotation[] ann = annotations; + annotations = new Annotation[i]; + System.arraycopy(ann, 0, annotations, 0, i); + ann = null; + return iSize; + } + + /** + * Associate this annotion with the aligned residues of a particular sequence. + * sequenceMapping will be updated in the following way: null sequenceI - + * existing mapping will be discarded but annotations left in mapped + * positions. valid sequenceI not equal to current sequenceRef: mapping is + * discarded and rebuilt assuming 1:1 correspondence TODO: overload with + * parameter to specify correspondence between current and new sequenceRef + * + * @param sequenceI + */ + public void setSequenceRef(SequenceI sequenceI) + { + if (sequenceI != null) + { + if (sequenceRef != null) + { + if (sequenceRef != sequenceI + && !sequenceRef.equals(sequenceI) + && sequenceRef.getDatasetSequence() != sequenceI + .getDatasetSequence()) + { + // if sequenceRef isn't intersecting with sequenceI + // throw away old mapping and reconstruct. + sequenceRef = null; + if (sequenceMapping != null) + { + sequenceMapping = null; + // compactAnnotationArray(); + } + createSequenceMapping(sequenceI, 1, true); + adjustForAlignment(); + } + else + { + // Mapping carried over + sequenceRef = sequenceI; + } + } + else + { + // No mapping exists + createSequenceMapping(sequenceI, 1, true); + adjustForAlignment(); + } + } + else + { + // throw away the mapping without compacting. + sequenceMapping = null; + sequenceRef = null; + } + } + + /** + * @return the score + */ + public double getScore() + { + return score; + } + + /** + * @param score + * the score to set + */ + public void setScore(double score) + { + hasScore = true; + this.score = score; + } + + /** + * + * @return true if annotation has an associated score + */ + public boolean hasScore() + { + return hasScore || !Double.isNaN(score); + } + + /** + * Score only annotation + * + * @param label + * @param description + * @param score + */ + public AlignmentAnnotation(String label, String description, double score) + { + this(label, description, null); + setScore(score); + } + + /** + * copy constructor with edit based on the hidden columns marked in colSel + * + * @param alignmentAnnotation + * @param colSel + */ + public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation, + ColumnSelection colSel) + { + this(alignmentAnnotation); + if (annotations == null) + { + return; + } + colSel.makeVisibleAnnotation(this); + } + + public void setPadGaps(boolean padgaps, char gapchar) + { + this.padGaps = padgaps; + if (padgaps) + { + hasText = true; + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] == null) + annotations[i] = new Annotation(String.valueOf(gapchar), null, + ' ', 0f); + else if (annotations[i].displayCharacter == null + || annotations[i].displayCharacter.equals(" ")) + annotations[i].displayCharacter = String.valueOf(gapchar); + } + } + } + + /** + * format description string for display + * + * @param seqname + * @return Get the annotation description string optionally prefixed by + * associated sequence name (if any) + */ + public String getDescription(boolean seqname) + { + 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; + } + }