X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=b60813950ae4c84a22587a8e3c769765fa0a966d;hb=d62b90cb6effb7b380e5f7d590691dd884b024cf;hp=989d62ad2cb4f5d70fce59505828399fa866451e;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 989d62a..b608139 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,17 +20,18 @@ */ package jalview.datamodel; +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; + import jalview.analysis.Rna; import jalview.analysis.SecStrConsensus.SimpleBP; - import jalview.analysis.WUSSParseException; -import java.util.ArrayList; -import java.util.Enumeration; -import java.util.Hashtable; - -import fr.orsay.lri.varna.models.rna.RNA; - /** * DOCUMENT ME! * @@ -39,23 +40,39 @@ import fr.orsay.lri.varna.models.rna.RNA; */ public class AlignmentAnnotation { + /* + * 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; - /** 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 ArrayList bps = null; @@ -66,9 +83,10 @@ public class AlignmentAnnotation 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 @@ -101,11 +119,51 @@ public class AlignmentAnnotation isrna = true; showAllColLabels = true; scaleColLabel = true; + _markRnaHelices(); } // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup()); + } - public java.util.Hashtable sequenceMapping; + 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; @@ -259,6 +317,8 @@ public class AlignmentAnnotation // 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 == '<' @@ -320,9 +380,7 @@ public class AlignmentAnnotation // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure firstChar != ' ' && firstChar != '$' - && firstChar != '�' // JBPNote should explicitly express as - // unicode number to avoid source code - // translation problems + && firstChar != 0xCE && firstChar != '(' && firstChar != '[' && firstChar != '>' @@ -443,13 +501,13 @@ public class AlignmentAnnotation @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); + || annotations[index + offset] == null || (annotations[index + + offset].secondaryStructure < ' ') ? ' ' + : annotations[index + offset].secondaryStructure); } + @Override public String toString() { char[] string = new char[max - offset]; @@ -457,9 +515,8 @@ public class AlignmentAnnotation for (int i = offset; i < mx; i++) { - String dc; - string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter - .trim()).length() < 1) ? '.' : dc.charAt(0); + string[i] = (annotations[i] == null || (annotations[i].secondaryStructure < 32)) ? ' ' + : annotations[i].secondaryStructure; } return new String(string); } @@ -603,7 +660,9 @@ public class AlignmentAnnotation { 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; @@ -622,6 +681,14 @@ public class AlignmentAnnotation 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; @@ -630,9 +697,9 @@ public class AlignmentAnnotation { 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++) { @@ -645,24 +712,27 @@ public class AlignmentAnnotation } } } - ; - 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) @@ -672,10 +742,10 @@ public class AlignmentAnnotation } } } - else - { - this.sequenceMapping = null; - } + } + else + { + this.sequenceMapping = null; } } // TODO: check if we need to do this: JAL-952 @@ -701,13 +771,21 @@ 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) { @@ -721,11 +799,11 @@ 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)); @@ -768,9 +846,10 @@ 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++) { @@ -843,7 +922,7 @@ public class AlignmentAnnotation { return; } - sequenceMapping = new java.util.Hashtable(); + sequenceMapping = new HashMap(); int seqPos; @@ -869,7 +948,9 @@ public class AlignmentAnnotation public void adjustForAlignment() { if (sequenceRef == null) + { return; + } if (annotations == null) { @@ -895,7 +976,7 @@ public class AlignmentAnnotation { position = sequenceRef.findIndex(a) - 1; - temp[position] = (Annotation) sequenceMapping.get(index); + temp[position] = sequenceMapping.get(index); } } @@ -916,8 +997,10 @@ public class AlignmentAnnotation if (annotations[i] == null) { if (i + 1 < iSize) + { System.arraycopy(annotations, i + 1, annotations, i, iSize - i - 1); + } iSize--; } else @@ -948,10 +1031,14 @@ 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. @@ -1051,11 +1138,15 @@ public class AlignmentAnnotation for (int i = 0; i < annotations.length; i++) { if (annotations[i] == null) + { annotations[i] = new Annotation(String.valueOf(gapchar), null, ' ', 0f, null); + } else if (annotations[i].displayCharacter == null || annotations[i].displayCharacter.equals(" ")) + { annotations[i].displayCharacter = String.valueOf(gapchar); + } } } } @@ -1099,6 +1190,11 @@ public class AlignmentAnnotation 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 */ @@ -1113,4 +1209,171 @@ 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, 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.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); + + } }