X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=f8782e79a47d80705dbd9fc2b891b5497bbb5ecd;hb=bfb4b56a77352694f4bc445ec31851bbdcdce140;hp=04689cdead5eecd4d6fdfaf276abe465f227cf3b;hpb=80f46a9ba6bea3531ff6e59cf68f9f870e5af4da;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 04689cd..f8782e7 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,331 +1,1366 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 2.8.2) + * 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.SecStrConsensus.SimpleBP; +import jalview.analysis.WUSSParseException; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.Iterator; +import java.util.Map; +import java.util.Map.Entry; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ public class AlignmentAnnotation { - public SequenceI sequenceRef; + /* + * Identifers for different types of profile data + */ + public static final int SEQUENCE_PROFILE = 0; + + public static final int STRUCTURE_PROFILE = 1; + + public static final int CDNA_PROFILE = 2; + + /** + * If true, this annotations is calculated every edit, eg consensus, quality + * or conservation graphs + */ + public boolean autoCalculated = false; + + /** + * unique ID for this annotation, used to match up the same annotation row + * shown in multiple views and alignments + */ + public String annotationId; + + /** + * the sequence this annotation is associated with (or null) + */ + public SequenceI sequenceRef; + + /** label shown in dropdown menus and in the annotation label area */ + public String label; + + /** longer description text shown as a tooltip */ + public String description; + + /** Array of annotations placed in the current coordinate system */ + public Annotation[] annotations; + + public ArrayList bps = null; + + /** + * RNA secondary structure contact positions + */ + public SequenceFeature[] _rnasecstr = null; + + /** + * position of annotation resulting in invalid WUSS parsing or -1. -2 means + * there was no RNA structure in this annotation + */ + private long invalidrnastruc = -2; + + /** + * 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); + bps = Rna.GetModeleBP(RNAannot); + invalidrnastruc = -1; + } catch (WUSSParseException px) + { + // DEBUG System.out.println(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; + _markRnaHelices(); + } + // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup()); + + } + + private void _markRnaHelices() + { + int mxval = 0; + // Figure out number of helices + // Length of rnasecstr is the number of pairs of positions that base pair + // with each other in the secondary structure + for (int x = 0; x < _rnasecstr.length; x++) + { + + /* + * System.out.println(this.annotation._rnasecstr[x] + " Begin" + + * this.annotation._rnasecstr[x].getBegin()); + */ + // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup()); + int val = 0; + try + { + val = Integer.valueOf(_rnasecstr[x].getFeatureGroup()); + if (mxval < val) + { + mxval = val; + } + } catch (NumberFormatException q) + { + } + ; + + annotations[_rnasecstr[x].getBegin()].value = val; + annotations[_rnasecstr[x].getEnd()].value = val; + + // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val; + // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val; + } + setScore(mxval); + } + /** + * map of positions in the associated annotation + */ + private Map sequenceMapping; + + /** DOCUMENT ME!! */ + public float graphMin; + + /** 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 + + /** Can this row be edited by the user ? */ + public boolean editable = false; + + /** Indicates if annotation has a graphical symbol track */ + public boolean hasIcons; // + + /** Indicates if annotation has a text character label */ + public boolean hasText; + + /** is the row visible */ + public boolean visible = true; - /** DOCUMENT ME!! */ - public String label; + public int graphGroup = -1; - /** DOCUMENT ME!! */ - public String description; + /** Displayed height of row in pixels */ + public int height = 0; - /** DOCUMENT ME!! */ - public Annotation[] annotations; + public int graph = 0; - public java.util.Hashtable sequenceMapping; + public int graphHeight = 40; - /** DOCUMENT ME!! */ - public float graphMin; + public boolean padGaps = false; - /** DOCUMENT ME!! */ - public float graphMax; + public static final int NO_GRAPH = 0; - public GraphLine threshold; + public static final int BAR_GRAPH = 1; - // Graphical hints and tips + public static final int LINE_GRAPH = 2; - /** DOCUMENT ME!! */ - public boolean editable = false; + public boolean belowAlignment = true; - /** DOCUMENT ME!! */ - public boolean hasIcons; // + public SequenceGroup groupRef = null; - /** DOCUMENT ME!! */ - public boolean hasText; + /** + * display every column label, even if there is a row of identical labels + */ + public boolean showAllColLabels = false; - /** DOCUMENT ME!! */ - public boolean visible = true; + /** + * scale the column label to fit within the alignment column. + */ + public boolean scaleColLabel = false; - public int graphGroup = -1; + /** + * centre the column labels relative to the alignment column + */ + public boolean centreColLabels = false; - /** DOCUMENT ME!! */ - public int height = 0; + private boolean isrna; - public int graph = 0; + /* + * (non-Javadoc) + * + * @see java.lang.Object#finalize() + */ + protected void finalize() throws Throwable + { + sequenceRef = null; + groupRef = null; + super.finalize(); + } - public int graphHeight = 40; + public static int getGraphValueFromString(String string) + { + if (string.equalsIgnoreCase("BAR_GRAPH")) + { + return BAR_GRAPH; + } + else if (string.equalsIgnoreCase("LINE_GRAPH")) + { + return LINE_GRAPH; + } + else + { + return NO_GRAPH; + } + } - public static final int NO_GRAPH = 0; + // JBPNote: what does this do ? + public void ConcenStru(CharSequence RNAannot) throws WUSSParseException + { + bps = Rna.GetModeleBP(RNAannot); + } - public static final int BAR_GRAPH = 1; + /** + * Creates a new AlignmentAnnotation object. + * + * @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) + { + // always editable? + editable = true; + this.label = label; + this.description = description; + this.annotations = annotations; - public static final int LINE_GRAPH = 2; + validateRangeAndDisplay(); + } - public static int getGraphValueFromString(String string) + /** + * 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(string.equalsIgnoreCase("BAR_GRAPH")) - return BAR_GRAPH; - else if(string.equalsIgnoreCase("LINE_GRAPH")) - return LINE_GRAPH; + if (annotations[i] == null) + { + continue; + } + if (annotations[i].secondaryStructure == 'H' + || annotations[i].secondaryStructure == 'E') + { + hasIcons |= true; + } else - return NO_GRAPH; - } - - /** - * Creates a new AlignmentAnnotation object. - * - * @param label DOCUMENT ME! - * @param description DOCUMENT ME! - * @param annotations DOCUMENT ME! - */ - public AlignmentAnnotation(String label, String description, - Annotation[] annotations) - { - // always editable? - editable = true; - this.label = label; - this.description = description; - this.annotations = annotations; - - for (int i = 0; i < annotations.length; i++) + // Check for RNA secondary structure + { + // System.out.println(annotations[i].secondaryStructure); + // TODO: 2.8.2 should this ss symbol validation check be a function in + // RNA/ResidueProperties ? + if (annotations[i].secondaryStructure == '(' + || annotations[i].secondaryStructure == '[' + || annotations[i].secondaryStructure == '<' + || annotations[i].secondaryStructure == '{' + || annotations[i].secondaryStructure == 'A' + || annotations[i].secondaryStructure == 'B' + || annotations[i].secondaryStructure == 'C' + || annotations[i].secondaryStructure == 'D' + || annotations[i].secondaryStructure == 'E' + || annotations[i].secondaryStructure == 'F' + || annotations[i].secondaryStructure == 'G' + || annotations[i].secondaryStructure == 'H' + || annotations[i].secondaryStructure == 'I' + || annotations[i].secondaryStructure == 'J' + || annotations[i].secondaryStructure == 'K' + || annotations[i].secondaryStructure == 'L' + || annotations[i].secondaryStructure == 'M' + || annotations[i].secondaryStructure == 'N' + || annotations[i].secondaryStructure == 'O' + || annotations[i].secondaryStructure == 'P' + || annotations[i].secondaryStructure == 'Q' + || annotations[i].secondaryStructure == 'R' + || annotations[i].secondaryStructure == 'S' + || annotations[i].secondaryStructure == 'T' + || annotations[i].secondaryStructure == 'U' + || annotations[i].secondaryStructure == 'V' + || annotations[i].secondaryStructure == 'W' + || annotations[i].secondaryStructure == 'X' + || annotations[i].secondaryStructure == 'Y' + || annotations[i].secondaryStructure == 'Z') { - if ((annotations[i] != null) && - ((annotations[i].secondaryStructure == 'H') || - (annotations[i].secondaryStructure == 'E'))) - { - hasIcons = true; - } + hasIcons |= true; + isrna |= true; + } + } - if ((annotations[i] != null) && - (annotations[i].displayCharacter.length() > 0)) - { - hasText = true; - } + // System.out.println("displaychar " + annotations[i].displayCharacter); + + if (annotations[i].displayCharacter == null + || annotations[i].displayCharacter.length() == 0) + { + 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 != '$' + && firstChar != 0xCE + && firstChar != '(' + && firstChar != '[' + && firstChar != '>' + && firstChar != '{' + && firstChar != 'A' + && firstChar != 'B' + && firstChar != 'C' + && firstChar != 'D' + && firstChar != 'E' + && firstChar != 'F' + && firstChar != 'G' + && firstChar != 'H' + && firstChar != 'I' + && firstChar != 'J' + && firstChar != 'K' + && firstChar != 'L' + && firstChar != 'M' + && firstChar != 'N' + && firstChar != 'O' + && firstChar != 'P' + && firstChar != 'Q' + && firstChar != 'R' + && firstChar != 'S' + && firstChar != 'T' + && firstChar != 'U' + && firstChar != 'V' + && firstChar != 'W' + && firstChar != 'X' + && firstChar != 'Y' + && firstChar != 'Z' + && firstChar != '-' + && firstChar < jalview.schemes.ResidueProperties.aaIndex.length) + { + 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; + } } - /** - * 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! - */ - public AlignmentAnnotation(String label, String description, - Annotation[] annotations, float min, float max, int graphType) - { - // graphs are not editable - this.label = label; - this.description = description; - this.annotations = annotations; - graph = graphType; - - boolean drawValues = true; - - if (min == max) + if (nonSSLabel) + { + hasIcons = false; + for (int j = 0; j < annotations.length; j++) + { + if (annotations[j] != null + && annotations[j].secondaryStructure != ' ') { - min = 999999999; - for (int i = 0; i < annotations.length; i++) - { - if (annotations[i] == null) - { - continue; - } - - if(drawValues && annotations[i].displayCharacter.length() > 1 ) - { - drawValues = false; - } - - if (annotations[i].value > max) - { - max = annotations[i].value; - } - - if (annotations[i].value < min) - { - min = annotations[i].value; - } - } + 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) + { + return ((index + offset < 0) || (index + offset) >= max + || annotations[index + offset] == null || (annotations[index + + offset].secondaryStructure < ' ') ? ' ' + : annotations[index + offset].secondaryStructure); + } + + @Override + public String toString() + { + char[] string = new char[max - offset]; + int mx = annotations.length; + + for (int i = offset; i < mx; i++) + { + string[i] = (annotations[i] == null || (annotations[i].secondaryStructure < 32)) ? ' ' + : annotations[i].secondaryStructure; + } + 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! + */ + public AlignmentAnnotation(String label, String description, + 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(); + } + + /** + * 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; + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] == null) + { + continue; } - graphMin = min; - graphMax = max; + if (drawValues && annotations[i].displayCharacter != null + && annotations[i].displayCharacter.length() > 1) + { + drawValues = false; + } - for (int i = 0; i < annotations.length; i++) + if (annotations[i].value > max) { - if (!hasIcons - && annotations[i] != null - && ((annotations[i].secondaryStructure == 'H') || - (annotations[i].secondaryStructure == 'E'))) - { - hasIcons = true; - } + max = annotations[i].value; + } - if (!hasText - && annotations[i]!=null - && annotations[i].displayCharacter.length() > 0) + if (annotations[i].value < min) + { + 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; + } + } + } + + graphMin = min; + graphMax = max; + + areLabelsSecondaryStructure(); + + if (!drawValues && graphType != NO_GRAPH) + { + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] != null) + { + annotations[i].displayCharacter = "X"; + } + } + } + } + + /** + * 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 (annotation.properties!=null) + { + properties = new HashMap(); + for (Map.Entry val:annotation.properties.entrySet()) + { + properties.put(val.getKey(), val.getValue()); + } + } + if (this.hasScore = annotation.hasScore) + { + this.score = annotation.score; + } + if (annotation.threshold != null) + { + threshold = new GraphLine(annotation.threshold); + } + Annotation[] ann = annotation.annotations; + if (annotation.annotations != null) + { + 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 HashMap(); + Iterator pos = annotation.sequenceMapping.keySet() + .iterator(); + while (pos.hasNext()) + { + // could optimise this! + p = pos.next(); + Annotation a = annotation.sequenceMapping.get(p); + if (a == null) + { + continue; + } + if (ann != null) + { + for (int i = 0; i < ann.length; i++) { - hasText = true; + 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. + } - if(!drawValues && graphType!=NO_GRAPH) + /** + * 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) + { + Map newmapping = new HashMap(); + Iterator e = sequenceMapping.keySet().iterator(); + while (e.hasNext()) { - for (int i = 0; i < annotations.length; i++) + Integer pos = e.next(); + if (pos.intValue() >= spos && pos.intValue() <= epos) { - if (annotations[i] != null) - annotations[i].displayCharacter = ""; + newmapping.put(pos, sequenceMapping.get(pos)); } } + sequenceMapping.clear(); + sequenceMapping = newmapping; + } } + annotations = temp; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String toString() + /** + * 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) { - StringBuffer buffer = new StringBuffer(); + 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; - for (int i = 0; i < annotations.length; i++) - { - if (annotations[i] != null) - { - if (graph!=0) - { - buffer.append(annotations[i].value); - } - else if (hasIcons) - { - buffer.append(annotations[i].secondaryStructure); - } - else - { - buffer.append(annotations[i].displayCharacter); - } - } + } - buffer.append(", "); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public String toString() + { + StringBuilder buffer = new StringBuilder(256); + + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] != null) + { + if (graph != 0) + { + buffer.append(annotations[i].value); + } + else if (hasIcons) + { + buffer.append(annotations[i].secondaryStructure); } + else + { + buffer.append(annotations[i].displayCharacter); + } + } + + buffer.append(", "); + } + // TODO: remove disgusting hack for 'special' treatment of consensus line. + if (label.indexOf("Consensus") == 0) + { + buffer.append("\n"); - if (label.equals("Consensus")) + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] != null) { - buffer.append("\n"); + buffer.append(annotations[i].description); + } - for (int i = 0; i < annotations.length; i++) - { - if (annotations[i] != null) - { - buffer.append(annotations[i].description); - } + buffer.append(", "); + } + } - buffer.append(", "); - } + return buffer.toString(); + } + + public void setThreshold(GraphLine line) + { + threshold = line; + } + + public GraphLine getThreshold() + { + return threshold; + } + + /** + * 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) + { + + if (seqRef == null) + { + return; + } + sequenceRef = seqRef; + if (annotations == null) + { + return; + } + sequenceMapping = new HashMap(); + + int seqPos; + + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] != null) + { + if (alreadyMapped) + { + seqPos = seqRef.findPosition(i); + } + else + { + seqPos = i + startRes; } - return buffer.toString(); + sequenceMapping.put(new Integer(seqPos), annotations[i]); } + } - public void setThreshold(GraphLine line) + } + + public void adjustForAlignment() + { + if (sequenceRef == null) + { + return; + } + + if (annotations == null) + { + return; + } + + int a = 0, aSize = sequenceRef.getLength(); + + if (aSize == 0) + { + // Its been deleted + return; + } + + int position; + Annotation[] temp = new Annotation[aSize]; + Integer index; + + for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) + { + index = new Integer(a); + if (sequenceMapping.containsKey(index)) { - threshold = line; + position = sequenceRef.findIndex(a) - 1; + + temp[position] = sequenceMapping.get(index); } + } + + annotations = temp; + } - public GraphLine getThreshold() + /** + * 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 { - return threshold; + i++; } + } + Annotation[] ann = annotations; + annotations = new Annotation[i]; + System.arraycopy(ann, 0, annotations, 0, i); + ann = null; + return iSize; + } - /** - * Attach the annotation to seqRef, starting from startRes position. - * @param seqRef - * @param startRes - */ - public void createSequenceMapping(SequenceI seqRef, int startRes) + /** + * 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) + { + boolean rIsDs=sequenceRef.getDatasetSequence()==null,tIsDs=sequenceI.getDatasetSequence()==null; + if (sequenceRef != sequenceI + && (rIsDs && !tIsDs && sequenceRef != sequenceI + .getDatasetSequence()) + && (!rIsDs && tIsDs && sequenceRef.getDatasetSequence() != sequenceI) + && (!rIsDs && !tIsDs && sequenceRef.getDatasetSequence() != sequenceI + .getDatasetSequence()) + && !sequenceRef.equals(sequenceI)) + { + // 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 { - if(seqRef == null) - return; + // No mapping exists + createSequenceMapping(sequenceI, 1, true); + adjustForAlignment(); + } + } + else + { + // throw away the mapping without compacting. + sequenceMapping = null; + sequenceRef = null; + } + } - sequenceMapping = new java.util.Hashtable(); + /** + * @return the score + */ + public double getScore() + { + return score; + } - sequenceRef = seqRef; + /** + * @param score + * the score to set + */ + public void setScore(double score) + { + hasScore = true; + this.score = score; + } - if(startRes < sequenceRef.getStart()) - startRes = sequenceRef.getStart(); + /** + * + * @return true if annotation has an associated score + */ + public boolean hasScore() + { + return hasScore || !Double.isNaN(score); + } - int seqPos; + /** + * Score only annotation + * + * @param label + * @param description + * @param score + */ + public AlignmentAnnotation(String label, String description, double score) + { + this(label, description, null); + setScore(score); + } - int fileOffset = 0; - if(startRes > sequenceRef.getStart()) + /** + * 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) { - fileOffset = startRes - sequenceRef.getStart(); + annotations[i] = new Annotation(String.valueOf(gapchar), null, + ' ', 0f, null); } - - for(int i = 0; i < annotations.length; i++) + else if (annotations[i].displayCharacter == null + || annotations[i].displayCharacter.equals(" ")) { - seqPos = sequenceRef.findPosition(i + fileOffset); - if(seqPos"); + if (i > -1) { - int a=0, aSize = sequenceRef.getLength(); + // move the html tag to before the sequence reference. + return "" + sequenceRef.getName() + " : " + + description.substring(i + 6); + } + return sequenceRef.getName() + " : " + description; + } + return description; + } - if(aSize == 0) - { - //Its been deleted - return; - } + public boolean isValidStruc() + { + return invalidrnastruc == -1; + } - int position; - Annotation[] temp = new Annotation[aSize]; - Integer index; + public long getInvalidStrucPos() + { + return invalidrnastruc; + } - for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) - { - index = new Integer(a); - if(sequenceMapping.containsKey(index)) - { - position = sequenceRef.findIndex(a)-1; + /** + * machine readable ID string indicating what generated this annotation + */ + protected String calcId = ""; - temp[position] = (Annotation)sequenceMapping.get(index); - } + /** + * properties associated with the calcId + */ + protected Map properties = new HashMap(); + + /** + * 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; + } + + public boolean isRNA() + { + return isrna; + } + + /** + * transfer annotation to the given sequence using the given mapping from the + * current positions or an existing sequence mapping + * + * @param sq + * @param sp2sq + * map involving sq as To or From + */ + public void liftOver(SequenceI sq, Mapping sp2sq) + { + if (sp2sq.getMappedWidth() != sp2sq.getWidth()) + { + // TODO: employ getWord/MappedWord to transfer annotation between cDNA and Protein reference frames + throw new Error("liftOver currently not implemented for transfer of annotation between different types of seqeunce"); + } + boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq + .getTo() == sq.getDatasetSequence()) : false; + + // TODO build a better annotation element map and get rid of annotations[] + Map mapForsq = new HashMap(); + if (sequenceMapping != null) + { + if (sp2sq != null) + { + for (Entry ie : sequenceMapping.entrySet()) + { + Integer mpos = Integer.valueOf(mapIsTo ? sp2sq + .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie + .getKey())); + if (mpos >= sq.getStart() && mpos <= sq.getEnd()) + { + mapForsq.put(mpos, ie.getValue()); } + } + sequenceMapping = mapForsq; + sequenceRef = sq; + adjustForAlignment(); + } + else + { + // trim positions + } + } + } - annotations = temp; + /** + * like liftOver but more general. + * + * Takes an array of int pairs that will be used to update the internal + * sequenceMapping and so shuffle the annotated positions + * + * @param newref + * - new sequence reference for the annotation row - if null, + * sequenceRef is left unchanged + * @param mapping + * array of ints containing corresponding positions + * @param from + * - column for current coordinate system (-1 for index+1) + * @param to + * - column for destination coordinate system (-1 for index+1) + * @param idxoffset + * - offset added to index when referencing either coordinate system + * @note no checks are made as to whether from and/or to are sensible + * @note caller should add the remapped annotation to newref if they have not + * already + */ + public void remap(SequenceI newref, int[][] mapping, int from, int to, + int idxoffset) + { + if (mapping != null) + { + Map old = sequenceMapping; + Map remap = new HashMap(); + int index = -1; + for (int mp[] : mapping) + { + if (index++ < 0) + { + continue; + } + Annotation ann = null; + if (from == -1) + { + ann = sequenceMapping.get(Integer.valueOf(idxoffset + index)); + } + else + { + if (mp != null && mp.length > from) + { + ann = sequenceMapping.get(Integer.valueOf(mp[from])); + } + } + if (ann != null) + { + if (to == -1) + { + remap.put(Integer.valueOf(idxoffset + index), ann); + } + else + { + if (to > -1 && to < mp.length) + { + remap.put(Integer.valueOf(mp[to]), ann); + } + } + } } -} + sequenceMapping = remap; + old.clear(); + if (newref != null) + { + sequenceRef = newref; + } + adjustForAlignment(); + } + } + public String getProperty(String property) + { + if (properties == null) + { + return null; + } + return properties.get(property); + } + public void setProperty(String property, String value) + { + if (properties==null) + { + properties = new HashMap(); + } + properties.put(property, value); + } + + public boolean hasProperties() + { + return properties != null && properties.size() > 0; + } + + public Collection getProperties() + { + if (properties == null) + { + return Collections.EMPTY_LIST; + } + return properties.keySet(); + } +}