X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=05688cbb4deb12e9c23a52782983496b340375f5;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=4f7fd9340cc4b211fb9a8d500d7e8e16246593cf;hpb=1e184475a6f6ba43584580b55351331a8b57b350;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 4f7fd93..05688cb 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,25 +1,36 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.datamodel; -import java.util.Enumeration; -import java.util.Hashtable; +import jalview.analysis.Rna; +import jalview.analysis.SecStrConsensus.SimpleBP; +import jalview.analysis.WUSSParseException; + +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; /** * DOCUMENT ME! @@ -29,26 +40,135 @@ import java.util.Hashtable; */ public class AlignmentAnnotation { + private static final String ANNOTATION_ID_PREFIX = "ann"; + + /* + * 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; + + private static long counter = 0; + /** * 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; - /** DOCUMENT ME!! */ + /** label shown in dropdown menus and in the annotation label area */ public String label; - /** DOCUMENT ME!! */ + /** longer description text shown as a tooltip */ public String description; - /** DOCUMENT ME!! */ + /** Array of annotations placed in the current coordinate system */ public Annotation[] annotations; - public java.util.Hashtable sequenceMapping; + public List 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 + { + bps = Rna.getModeleBP(RNAannot); + _rnasecstr = Rna.getBasePairs(bps); + 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; @@ -70,21 +190,21 @@ 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 +221,34 @@ 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; - - /* (non-Javadoc) + /** + * 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() */ + @Override protected void finalize() throws Throwable { + sequenceRef = null; groupRef = null; super.finalize(); } @@ -129,19 +269,26 @@ public class AlignmentAnnotation } } + // JBPNote: what does this do ? + public void ConcenStru(CharSequence RNAannot) throws WUSSParseException + { + bps = Rna.getModeleBP(RNAannot); + } + /** * 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) { + setAnnotationId(); // always editable? editable = true; this.label = label; @@ -151,9 +298,16 @@ 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 +318,56 @@ public class AlignmentAnnotation if (annotations[i].secondaryStructure == 'H' || annotations[i].secondaryStructure == 'E') { - hasIcons = true; + hasIcons |= true; + } + else + // 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') + { + 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) { + rnastring.append('.'); continue; } if (annotations[i].displayCharacter.length() == 1) @@ -176,25 +375,67 @@ 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 != '$' + && firstChar != 0xCE + && firstChar != '(' + && firstChar != '[' + && firstChar != '>' + && firstChar != '{' + && firstChar != 'A' + && firstChar != 'B' + && firstChar != 'C' + && firstChar != 'D' && firstChar != 'E' - && firstChar != '-' + && 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) + 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) { @@ -217,29 +458,119 @@ public class AlignmentAnnotation } } + else + { + if (isrna) + { + _updateRnaSecStr(new AnnotCharSequence()); + } + } + } + + /** + * 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); + } + + 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].displayCharacter == null + || annotations[index + offset].displayCharacter + .length() == 0 ? annotations[index + offset].secondaryStructure + : annotations[index + offset].displayCharacter + .charAt(0)); + } + + @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].displayCharacter == null + || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure + : annotations[i].displayCharacter.charAt(0)); + } + return new String(string); + } + }; + + private long _lastrnaannot = -1; - annotationId = this.hashCode() + ""; + 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) { + setAnnotationId(); // graphs are not editable editable = graphType == 0; @@ -256,12 +587,13 @@ 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) { visible = false; // try to prevent renderer from displaying. + invalidrnastruc = -1; return; // this is a non-annotation row annotation - ie a sequence score. } @@ -269,7 +601,7 @@ public class AlignmentAnnotation float min = graphMin; float max = graphMax; boolean drawValues = true; - + _linecolour = null; if (min == max) { min = 999999999; @@ -295,6 +627,22 @@ 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; + } } } @@ -323,9 +671,12 @@ public class AlignmentAnnotation */ public AlignmentAnnotation(AlignmentAnnotation annotation) { + setAnnotationId(); 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; @@ -340,40 +691,62 @@ 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 (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 (threshold != null) + if (annotation.threshold != null) { threshold = new GraphLine(annotation.threshold); } + Annotation[] ann = annotation.annotations; if (annotation.annotations != null) { - Annotation[] ann = annotation.annotations; 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) + } + if (annotation.sequenceRef != null) + { + this.sequenceRef = annotation.sequenceRef; + if (annotation.sequenceMapping != null) { - this.sequenceRef = annotation.sequenceRef; - if (annotation.sequenceMapping != null) + Integer p = null; + sequenceMapping = new HashMap(); + Iterator pos = annotation.sequenceMapping.keySet() + .iterator(); + while (pos.hasNext()) { - Integer p = null; - sequenceMapping = new Hashtable(); - Enumeration pos = annotation.sequenceMapping.keys(); - while (pos.hasMoreElements()) + // could optimise this! + p = pos.next(); + Annotation a = annotation.sequenceMapping.get(p); + if (a == null) + { + continue; + } + if (ann != null) { - // 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) @@ -383,12 +756,17 @@ public class AlignmentAnnotation } } } - else - { - this.sequenceMapping = null; - } + } + 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. } @@ -407,13 +785,21 @@ public class AlignmentAnnotation 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) { @@ -427,11 +813,11 @@ public class AlignmentAnnotation int epos = sequenceRef.findPosition(endRes); if (sequenceMapping != null) { - Hashtable newmapping = new Hashtable(); - Enumeration e = sequenceMapping.keys(); - while (e.hasMoreElements()) + Map newmapping = new HashMap(); + Iterator e = sequenceMapping.keySet().iterator(); + while (e.hasNext()) { - Integer pos = (Integer) e.nextElement(); + Integer pos = e.next(); if (pos.intValue() >= spos && pos.intValue() <= epos) { newmapping.put(pos, sequenceMapping.get(pos)); @@ -448,7 +834,7 @@ 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 +842,7 @@ public class AlignmentAnnotation if (annotations == null) { return true; // annotation row is correct - null == not visible and - // undefined length + // undefined length } if (annotations.length < length) { @@ -474,9 +860,10 @@ public class AlignmentAnnotation * * @return DOCUMENT ME! */ + @Override public String toString() { - StringBuffer buffer = new StringBuffer(); + StringBuilder buffer = new StringBuilder(256); for (int i = 0; i < annotations.length; i++) { @@ -498,8 +885,8 @@ 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"); @@ -549,7 +936,7 @@ public class AlignmentAnnotation { return; } - sequenceMapping = new java.util.Hashtable(); + sequenceMapping = new HashMap(); int seqPos; @@ -572,10 +959,18 @@ public class AlignmentAnnotation } + /** + * When positional annotation and a sequence reference is present, clears and + * resizes the annotations array to the current alignment width, and adds + * annotation according to aligned positions of the sequenceRef given by + * sequenceMapping. + */ public void adjustForAlignment() { if (sequenceRef == null) + { return; + } if (annotations == null) { @@ -593,18 +988,20 @@ public class AlignmentAnnotation int position; Annotation[] temp = new Annotation[aSize]; Integer index; - - for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) + if (sequenceMapping != null) { - index = new Integer(a); - if (sequenceMapping.containsKey(index)) + for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) { - position = sequenceRef.findIndex(a) - 1; + index = new Integer(a); + Annotation annot = sequenceMapping.get(index); + if (annot != null) + { + position = sequenceRef.findIndex(a) - 1; - temp[position] = (Annotation) sequenceMapping.get(index); + temp[position] = annot; + } } } - annotations = temp; } @@ -622,8 +1019,10 @@ public class AlignmentAnnotation if (annotations[i] == null) { if (i + 1 < iSize) + { System.arraycopy(annotations, i + 1, annotations, i, iSize - i - 1); + } iSize--; } else @@ -639,11 +1038,11 @@ public class AlignmentAnnotation } /** - * 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 + * Associate this annotation 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 @@ -654,10 +1053,15 @@ public class AlignmentAnnotation { if (sequenceRef != null) { + boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI + .getDatasetSequence() == null; if (sequenceRef != sequenceI - && !sequenceRef.equals(sequenceI) - && sequenceRef.getDatasetSequence() != 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. @@ -701,7 +1105,7 @@ public class AlignmentAnnotation /** * @param score - * the score to set + * the score to set */ public void setScore(double score) { @@ -757,11 +1161,15 @@ public class AlignmentAnnotation for (int i = 0; i < annotations.length; i++) { if (annotations[i] == null) + { annotations[i] = new Annotation(String.valueOf(gapchar), null, - ' ', 0f); + ' ', 0f, null); + } else if (annotations[i].displayCharacter == null || annotations[i].displayCharacter.equals(" ")) + { annotations[i].displayCharacter = String.valueOf(gapchar); + } } } } @@ -777,8 +1185,305 @@ 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 = ""; + + /** + * 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 + } + } + } + + /** + * 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, HashMap mapping, + int from, int to, int idxoffset) + { + if (mapping != null) + { + Map old = sequenceMapping; + Map remap = new HashMap(); + int index = -1; + for (int mp[] : mapping.values()) + { + 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.emptyList(); + } + return properties.keySet(); + } + + /** + * Returns the Annotation for the given sequence position (base 1) if any, + * else null + * + * @param position + * @return + */ + public Annotation getAnnotationForPosition(int position) + { + return sequenceMapping == null ? null : sequenceMapping.get(position); + + } + + /** + * Set the id to "ann" followed by a counter that increments so as to be + * unique for the lifetime of the JVM + */ + protected final void setAnnotationId() + { + this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId()); + } + + /** + * Returns the match for the last unmatched opening RNA helix pair symbol + * preceding the given column, or '(' if nothing found to match. + * + * @param column + * @return + */ + public String getDefaultRnaHelixSymbol(int column) + { + String result = "("; + if (annotations == null) + { + return result; + } + + /* + * for each preceding column, if it contains an open bracket, + * count whether it is still unmatched at column, if so return its pair + * (likely faster than the fancy alternative using stacks) + */ + for (int col = column - 1; col >= 0; col--) + { + Annotation annotation = annotations[col]; + if (annotation == null) + { + continue; + } + String displayed = annotation.displayCharacter; + if (displayed == null || displayed.length() != 1) + { + continue; + } + char symbol = displayed.charAt(0); + if (!Rna.isOpeningParenthesis(symbol)) + { + continue; + } + + /* + * found an opening bracket symbol + * count (closing-opening) symbols of this type that follow it, + * up to and excluding the target column; if the count is less + * than 1, the opening bracket is unmatched, so return its match + */ + String closer = String.valueOf(Rna + .getMatchingClosingParenthesis(symbol)); + String opener = String.valueOf(symbol); + int count = 0; + for (int j = col + 1; j < column; j++) + { + if (annotations[j] != null) + { + String s = annotations[j].displayCharacter; + if (closer.equals(s)) + { + count++; + } + else if (opener.equals(s)) + { + count--; + } + } + } + if (count < 1) + { + return closer; + } + } + return result; + } + + protected static synchronized long nextId() + { + return counter++; + } }