X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=05688cbb4deb12e9c23a52782983496b340375f5;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=8cfe728c7a4911a3e5b52bcca1d28294ae02d7c7;hpb=c0d807bc27c3724331c553692b1836049811c9fc;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 8cfe728..05688cb 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,52 +1,174 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * 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. - * - * 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 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! - * + * * @author $author$ * @version $Revision$ */ public class AlignmentAnnotation { - /** If true, this annotations is calculated every edit, - * eg consensus, quality or conservation graphs */ + 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; @@ -57,31 +179,32 @@ public class AlignmentAnnotation /** * Score associated with label and description. */ - public double score= Double.NaN; + public double score = Double.NaN; + /** * flag indicating if annotation has a score. */ - public boolean hasScore=false; + public boolean hasScore = false; public GraphLine threshold; // Graphical hints and tips - /** DOCUMENT ME!! */ + /** Can this row be edited by the user ? */ public boolean editable = false; - /** DOCUMENT ME!! */ + /** Indicates if annotation has a graphical symbol track */ public boolean hasIcons; // - /** DOCUMENT ME!! */ + /** Indicates if annotation has a text character label */ public boolean hasText; - /** DOCUMENT ME!! */ + /** is the row visible */ public boolean visible = true; public int graphGroup = -1; - /** DOCUMENT ME!! */ + /** Displayed height of row in pixels */ public int height = 0; public int graph = 0; @@ -98,6 +221,37 @@ public class AlignmentAnnotation public boolean belowAlignment = true; + public SequenceGroup groupRef = null; + + /** + * display every column label, even if there is a row of identical labels + */ + public boolean showAllColLabels = false; + + /** + * scale the column label to fit within the alignment column. + */ + public boolean scaleColLabel = false; + + /** + * centre the column labels relative to the alignment column + */ + public boolean centreColLabels = false; + + private boolean isrna; + + /* + * (non-Javadoc) + * + * @see java.lang.Object#finalize() + */ + @Override + protected void finalize() throws Throwable + { + sequenceRef = null; + groupRef = null; + super.finalize(); + } public static int getGraphValueFromString(String string) { @@ -115,98 +269,310 @@ 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 DOCUMENT ME! - * @param description DOCUMENT ME! - * @param annotations DOCUMENT ME!about:blank -Loading... + * + * @param label + * short label shown under sequence labels + * @param description + * text displayed on mouseover + * @param annotations + * set of positional annotation elements */ public AlignmentAnnotation(String label, String description, - Annotation[] annotations) + Annotation[] annotations) { + setAnnotationId(); // always editable? editable = true; this.label = label; this.description = description; this.annotations = annotations; - validateRangeAndDisplay(); + validateRangeAndDisplay(); } + /** + * Checks if annotation labels represent secondary structures + * + */ void areLabelsSecondaryStructure() { boolean nonSSLabel = false; + isrna = false; + StringBuffer rnastring = new StringBuffer(); + + char firstChar = 0; for (int i = 0; i < annotations.length; i++) { if (annotations[i] == null) { continue; } - if (annotations[i].secondaryStructure == 'H' || - annotations[i].secondaryStructure == 'E') + if (annotations[i].secondaryStructure == 'H' + || annotations[i].secondaryStructure == 'E') + { + hasIcons |= true; + } + else + // Check for RNA secondary structure { - hasIcons = true; + // 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 - && !annotations[i].displayCharacter.equals("H") - && !annotations[i].displayCharacter.equals("E") - && !annotations[i].displayCharacter.equals("-") - && !annotations[i].displayCharacter.equals(".")) + 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 - [annotations[i].displayCharacter.charAt(0)] < 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) - { - hasText = true; - } + if (annotations[i].displayCharacter.length() > 0) + { + hasText = true; } + } if (nonSSLabel) { hasIcons = false; for (int j = 0; j < annotations.length; j++) { - if (annotations[j] != null && annotations[j].secondaryStructure != ' ') + if (annotations[j] != null + && annotations[j].secondaryStructure != ' ') { - annotations[j].displayCharacter - = String.valueOf(annotations[j].secondaryStructure); + annotations[j].displayCharacter = String + .valueOf(annotations[j].secondaryStructure); annotations[j].secondaryStructure = ' '; } } } + else + { + if (isrna) + { + _updateRnaSecStr(new AnnotCharSequence()); + } + } + } + + /** + * 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); + } + }; - annotationId = this.hashCode() + ""; + private long _lastrnaannot = -1; + + public String getRNAStruc() + { + if (isrna) + { + String rnastruc = new AnnotCharSequence().toString(); + if (_lastrnaannot != rnastruc.hashCode()) + { + // ensure rna structure contacts are up to date + _lastrnaannot = rnastruc.hashCode(); + _updateRnaSecStr(rnastruc); + } + return rnastruc; + } + return null; } + /** * Creates a new AlignmentAnnotation object. - * - * @param label DOCUMENT ME! - * @param description DOCUMENT ME! - * @param annotations DOCUMENT ME! - * @param min DOCUMENT ME! - * @param max DOCUMENT ME! - * @param winLength DOCUMENT ME! + * + * @param label + * DOCUMENT ME! + * @param description + * DOCUMENT ME! + * @param annotations + * DOCUMENT ME! + * @param min + * DOCUMENT ME! + * @param max + * DOCUMENT ME! + * @param winLength + * DOCUMENT ME! */ public AlignmentAnnotation(String label, String description, - Annotation[] annotations, float min, float max, - int graphType) + Annotation[] annotations, float min, float max, int graphType) { + setAnnotationId(); // graphs are not editable - editable = graphType==0; + editable = graphType == 0; this.label = label; this.description = description; @@ -216,18 +582,18 @@ Loading... graphMax = max; validateRangeAndDisplay(); } + /** - * checks graphMin and graphMax, - * secondary structure symbols, - * sets graphType appropriately, - * sets null labels to the empty string - * if appropriate. + * 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) + if (annotations == null) { - visible=false; // try to prevent renderer from displaying. + visible = false; // try to prevent renderer from displaying. + invalidrnastruc = -1; return; // this is a non-annotation row annotation - ie a sequence score. } @@ -235,7 +601,7 @@ Loading... float min = graphMin; float max = graphMax; boolean drawValues = true; - + _linecolour = null; if (min == max) { min = 999999999; @@ -246,9 +612,8 @@ Loading... continue; } - if (drawValues - && annotations[i].displayCharacter!=null - && annotations[i].displayCharacter.length() > 1) + if (drawValues && annotations[i].displayCharacter != null + && annotations[i].displayCharacter.length() > 1) { drawValues = false; } @@ -262,6 +627,22 @@ Loading... { 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; + } } } @@ -283,20 +664,25 @@ Loading... } /** - * Copy constructor - * creates a new independent annotation row with the same associated sequenceRef + * 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; @@ -305,46 +691,81 @@ Loading... 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); } - if (annotation.annotations!=null) { - Annotation[] ann = annotation.annotations; + Annotation[] ann = annotation.annotations; + if (annotation.annotations != null) + { this.annotations = new Annotation[ann.length]; - for (int i=0; i(); + 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) + if (ann[i] == a) { sequenceMapping.put(p, annotations[i]); } } } - } 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. } @@ -352,41 +773,52 @@ Loading... /** * 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) + 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) + 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 newmapping = new HashMap(); + Iterator e = sequenceMapping.keySet().iterator(); + while (e.hasNext()) { - Integer pos = (Integer) e.nextElement(); - if (pos.intValue()>=spos && pos.intValue()<=epos) + Integer pos = e.next(); + if (pos.intValue() >= spos && pos.intValue() <= epos) { newmapping.put(pos, sequenceMapping.get(pos)); } @@ -395,37 +827,43 @@ Loading... sequenceMapping = newmapping; } } - annotations=temp; + annotations = temp; } + /** * set the annotation row to be at least length Annotations - * @param length minimum number of columns required in the annotation row + * + * @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) + public boolean padAnnotation(int length) + { + if (annotations == null) { - return true; // annotation row is correct - null == not visible and undefined length + return true; // annotation row is correct - null == not visible and + // undefined length } - if (annotations.lengthlength; + return annotations.length > length; } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public String toString() { - StringBuffer buffer = new StringBuffer(); + StringBuilder buffer = new StringBuilder(256); for (int i = 0; i < annotations.length; i++) { @@ -447,8 +885,8 @@ Loading... buffer.append(", "); } - - if (label.equals("Consensus")) + // TODO: remove disgusting hack for 'special' treatment of consensus line. + if (label.indexOf("Consensus") == 0) { buffer.append("\n"); @@ -477,26 +915,28 @@ Loading... } /** - * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions. + * Attach the annotation to seqRef, starting from startRes position. If + * alreadyMapped is true then the indices of the annotation[] array are + * sequence positions rather than alignment column positions. + * * @param seqRef * @param startRes * @param alreadyMapped */ - public void createSequenceMapping(SequenceI seqRef, - int startRes, - boolean alreadyMapped) + public void createSequenceMapping(SequenceI seqRef, int startRes, + boolean alreadyMapped) { if (seqRef == null) { return; } - sequenceRef=seqRef; - if (annotations==null) + sequenceRef = seqRef; + if (annotations == null) { return; } - sequenceMapping = new java.util.Hashtable(); + sequenceMapping = new HashMap(); int seqPos; @@ -519,12 +959,20 @@ Loading... } + /** + * 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) + if (sequenceRef == null) + { return; + } - if (annotations==null) + if (annotations == null) { return; } @@ -533,41 +981,52 @@ Loading... if (aSize == 0) { - //Its been deleted + // Its been deleted return; } 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; } + /** - * remove any null entries in annotation row and return the - * number of non-null annotation elements. + * 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