X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=93b6f168b46b9c453089b42acd45ffd961d67d82;hb=4389a166735bf1203894abdf3cf7dd57c4856dbc;hp=f5d34a64835791d768e7809a3b709c7fe79877c0;hpb=3d731dad51b259b16c50834ec24550280fb7dd64;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index f5d34a6..93b6f16 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,27 +1,37 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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. - * + * 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 . + * 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.Enumeration; -import java.util.Hashtable; +import java.util.ArrayList; +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! @@ -31,71 +41,71 @@ 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 List bps = null; + /** * RNA secondary structure contact positions */ public SequenceFeature[] _rnasecstr = null; + /** - * position of annotation resulting in invalid WUSS parsing or -1 + * position of annotation resulting in invalid WUSS parsing or -1. -2 means + * there was no RNA structure in this annotation */ - private long invalidrnastruc=-1; + 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 + * map of positions in the associated annotation */ - 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; + private Map sequenceMapping; - /** DOCUMENT ME!! */ + /** + * lower range for quantitative data + */ public float graphMin; - /** DOCUMENT ME!! */ + /** + * Upper range for quantitative data + */ public float graphMax; /** @@ -162,18 +172,6 @@ public class AlignmentAnnotation 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")) @@ -203,6 +201,7 @@ public class AlignmentAnnotation public AlignmentAnnotation(String label, String description, Annotation[] annotations) { + setAnnotationId(); // always editable? editable = true; this.label = label; @@ -213,6 +212,245 @@ public class AlignmentAnnotation } /** + * Copy constructor creates a new independent annotation row with the same + * associated sequenceRef + * + * @param annotation + */ + 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; + 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++) + { + 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. + } + + /** + * copy constructor with edit based on the hidden columns marked in colSel + * + * @param alignmentAnnotation + * @param colSel + */ + public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation, + HiddenColumns hidden) + { + this(alignmentAnnotation); + if (annotations == null) + { + return; + } + hidden.makeVisibleAnnotation(this); + } + + /** + * 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) + { + setAnnotationId(); + // graphs are not editable + editable = graphType == 0; + + this.label = label; + this.description = description; + this.annotations = annotations; + graph = graphType; + graphMin = min; + graphMax = max; + validateRangeAndDisplay(); + } + + /** + * Score only annotation + * + * @param label + * @param description + * @param score + */ + public AlignmentAnnotation(String label, String description, double score) + { + this(label, description, null); + setScore(score); + } + + /** + * Updates the _rnasecstr field Determines the positions that base pair and + * the positions of helices based on secondary structure from a Stockholm file + * + * @param rnaAnnotation + */ + private void _updateRnaSecStr(CharSequence rnaAnnotation) + { + try + { + _rnasecstr = Rna.getHelixMap(rnaAnnotation); + invalidrnastruc = -1; + } catch (WUSSParseException px) + { + // DEBUG System.out.println(px); + invalidrnastruc = px.getProblemPos(); + } + if (invalidrnastruc > -1) + { + return; + } + + 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); + } + + /** * Checks if annotation labels represent secondary structures * */ @@ -237,7 +475,39 @@ public class AlignmentAnnotation else // Check for RNA secondary structure { - if (annotations[i].secondaryStructure == 'S') + // 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; @@ -257,20 +527,25 @@ public class AlignmentAnnotation 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' + 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) { @@ -318,68 +593,95 @@ public class AlignmentAnnotation _updateRnaSecStr(new AnnotCharSequence()); } } - - annotationId = this.hashCode() + ""; } + /** - * flyweight access to positions in the alignment annotation row for RNA processing + * flyweight access to positions in the alignment annotation row for RNA + * processing + * * @author jimp - * + * */ - private class AnnotCharSequence implements CharSequence + private class AnnotCharSequence implements CharSequence { - int offset=0; - int max=0; - - public AnnotCharSequence() { - this(0,annotations.length); + int offset = 0; + + int max = 0; + + public AnnotCharSequence() + { + this(0, annotations.length); } - public AnnotCharSequence(int start, int end) { - offset=start; - max=end; + + AnnotCharSequence(int start, int end) + { + offset = start; + max = end; } + @Override public CharSequence subSequence(int start, int end) { - return new AnnotCharSequence(offset+start, offset+end); + return new AnnotCharSequence(offset + start, offset + end); } - + @Override public int length() { - return max-offset; + 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); + 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 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) + if (_linecolour == null && annotations[i].colour != null) { - annotations[i].displayCharacter = ""; + _linecolour = annotations[i].colour; } } - } - } - - /** - * 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++) + // ensure zero is origin for min/max ranges on only one side of zero + if (min > 0) { - annotations[i] = new Annotation(ann[i]); + min = 0; } - ; - if (annotation.sequenceRef != null) + else { - 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 + if (max < 0) { - this.sequenceMapping = null; + max = 0; } } } - // TODO: check if we need to do this: JAL-952 - //if (this.isrna=annotation.isrna) + + graphMin = min; + graphMax = max; + + areLabelsSecondaryStructure(); + + if (!drawValues && graphType != NO_GRAPH) { - // _rnasecstr=new SequenceFeature[annotation._rnasecstr]; + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] != null) + { + annotations[i].displayCharacter = ""; + } + } } - validateRangeAndDisplay(); // construct hashcodes, etc. } /** @@ -594,18 +784,26 @@ 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) { - System.arraycopy(annotations, startRes, temp, 0, endRes - startRes - + 1); + System.arraycopy(annotations, startRes, temp, 0, + endRes - startRes + 1); } if (sequenceRef != null) { @@ -614,11 +812,11 @@ 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)); @@ -661,9 +859,14 @@ public class AlignmentAnnotation * * @return DOCUMENT ME! */ + @Override public String toString() { - StringBuffer buffer = new StringBuffer(); + if (annotations == null) + { + return ""; + } + StringBuilder buffer = new StringBuilder(256); for (int i = 0; i < annotations.length; i++) { @@ -736,7 +939,7 @@ public class AlignmentAnnotation { return; } - sequenceMapping = new java.util.Hashtable(); + sequenceMapping = new HashMap<>(); int seqPos; @@ -759,10 +962,18 @@ 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) { @@ -780,18 +991,20 @@ 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; } @@ -809,8 +1022,10 @@ public class AlignmentAnnotation if (annotations[i] == null) { if (i + 1 < iSize) - System.arraycopy(annotations, i + 1, annotations, i, iSize - i - - 1); + { + System.arraycopy(annotations, i + 1, annotations, i, + iSize - i - 1); + } iSize--; } else @@ -826,11 +1041,11 @@ 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 @@ -841,10 +1056,17 @@ public class AlignmentAnnotation { if (sequenceRef != null) { + boolean rIsDs = sequenceRef.getDatasetSequence() == null, + tIsDs = sequenceI.getDatasetSequence() == null; if (sequenceRef != sequenceI - && !sequenceRef.equals(sequenceI) - && sequenceRef.getDatasetSequence() != sequenceI - .getDatasetSequence()) + && (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. @@ -905,36 +1127,6 @@ public class AlignmentAnnotation 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; @@ -944,11 +1136,15 @@ 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); + } } } } @@ -964,11 +1160,12 @@ public class AlignmentAnnotation { if (seqname && this.sequenceRef != null) { - int i=description.toLowerCase().indexOf(""); - if (i>-1) + 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.substring(i + 6); } return sequenceRef.getName() + " : " + description; } @@ -977,8 +1174,9 @@ public class AlignmentAnnotation public boolean isValidStruc() { - return invalidrnastruc==-1; + return invalidrnastruc == -1; } + public long getInvalidStrucPos() { return invalidrnastruc; @@ -987,7 +1185,19 @@ public class AlignmentAnnotation /** * machine readable ID string indicating what generated this annotation */ - protected String calcId=""; + private 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; @@ -997,5 +1207,334 @@ public class AlignmentAnnotation { 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++; + } + + /** + * + * @return true for rows that have a range of values in their annotation set + */ + public boolean isQuantitative() + { + return graphMin < graphMax; + } + + public static Iterable findAnnotations( + Iterable list, SequenceI seq, String calcId, + String label) + { + List aa = new ArrayList<>(); + for (AlignmentAnnotation ann : list) + { + if ((calcId == null || (ann.getCalcId() != null + && ann.getCalcId().equals(calcId))) + && (seq == null || (ann.sequenceRef != null + && ann.sequenceRef == seq)) + && (label == null + || (ann.label != null && ann.label.equals(label)))) + { + aa.add(ann); + } + } + return aa; + } + + /** + * Answer true if any annotation matches the calcId passed in (if not null). + * + * @param list + * annotation to search + * @param calcId + * @return + */ + public static boolean hasAnnotation(List list, + String calcId) + { + + if (calcId != null && !"".equals(calcId)) + { + for (AlignmentAnnotation a : list) + { + if (a.getCalcId() == calcId) + { + return true; + } + } + } + return false; + } + + public static Iterable findAnnotation( + List list, String calcId) + { + List aa = new ArrayList<>(); + if (calcId == null) + { + return aa; + } + for (AlignmentAnnotation a : list) + { + + if (a.getCalcId() == calcId || (a.getCalcId() != null + && calcId != null && a.getCalcId().equals(calcId))) + { + aa.add(a); + } + } + return aa; + } }