X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=f36a5c4584eab1b045896d11d853e412cbc103ea;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=0fcf43dc0ca1ff782c1482d516ac8c055c67bd08;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 0fcf43d..f36a5c4 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,33 +1,36 @@
/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
-
-import fr.orsay.lri.varna.models.rna.RNA;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Map.Entry;
/**
* DOCUMENT ME!
@@ -37,37 +40,57 @@ import fr.orsay.lri.varna.models.rna.RNA;
*/
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 ArrayList bps=null;
+ public ArrayList 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
@@ -77,15 +100,15 @@ public class AlignmentAnnotation
*/
private void _updateRnaSecStr(CharSequence RNAannot)
{
- try {
- _rnasecstr = Rna.GetBasePairs(RNAannot);
- bps = Rna.GetModeleBP(RNAannot);
- invalidrnastruc=-1;
- }
- catch (WUSSParseException px)
+ try
+ {
+ _rnasecstr = Rna.GetBasePairs(RNAannot);
+ bps = Rna.GetModeleBP(RNAannot);
+ invalidrnastruc = -1;
+ } catch (WUSSParseException px)
{
// DEBUG System.out.println(px);
- invalidrnastruc=px.getProblemPos();
+ invalidrnastruc = px.getProblemPos();
}
if (invalidrnastruc > -1)
{
@@ -100,11 +123,52 @@ public class AlignmentAnnotation
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);
}
- public java.util.Hashtable sequenceMapping;
+ /**
+ * map of positions in the associated annotation
+ */
+ private Map sequenceMapping;
/** DOCUMENT ME!! */
public float graphMin;
@@ -203,11 +267,13 @@ public class AlignmentAnnotation
return NO_GRAPH;
}
}
- // JBPNote: what does this do ?
+
+ // JBPNote: what does this do ?
public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
{
- bps = Rna.GetModeleBP(RNAannot);
+ bps = Rna.GetModeleBP(RNAannot);
}
+
/**
* Creates a new AlignmentAnnotation object.
*
@@ -221,6 +287,7 @@ public class AlignmentAnnotation
public AlignmentAnnotation(String label, String description,
Annotation[] annotations)
{
+ setAnnotationId();
// always editable?
editable = true;
this.label = label;
@@ -255,37 +322,39 @@ public class AlignmentAnnotation
else
// Check for RNA secondary structure
{
- //System.out.println(annotations[i].secondaryStructure);
+ // 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')
+ || 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;
@@ -317,7 +386,7 @@ 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 != '>'
@@ -395,8 +464,6 @@ public class AlignmentAnnotation
_updateRnaSecStr(new AnnotCharSequence());
}
}
-
- annotationId = this.hashCode() + "";
}
/**
@@ -438,13 +505,17 @@ 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].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];
@@ -452,9 +523,10 @@ 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].displayCharacter == null
+ || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure
+ : annotations[i].displayCharacter.charAt(0));
}
return new String(string);
}
@@ -497,6 +569,7 @@ public class AlignmentAnnotation
public AlignmentAnnotation(String label, String description,
Annotation[] annotations, float min, float max, int graphType)
{
+ setAnnotationId();
// graphs are not editable
editable = graphType == 0;
@@ -582,7 +655,7 @@ public class AlignmentAnnotation
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "X";
+ annotations[i].displayCharacter = "";
}
}
}
@@ -596,9 +669,12 @@ 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;
@@ -617,6 +693,14 @@ 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;
@@ -625,9 +709,9 @@ 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++)
{
@@ -640,24 +724,27 @@ 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)
@@ -667,10 +754,10 @@ public class AlignmentAnnotation
}
}
}
- else
- {
- this.sequenceMapping = null;
- }
+ }
+ else
+ {
+ this.sequenceMapping = null;
}
}
// TODO: check if we need to do this: JAL-952
@@ -696,13 +783,21 @@ 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)
{
@@ -716,11 +811,11 @@ 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));
@@ -763,9 +858,10 @@ 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++)
{
@@ -838,7 +934,7 @@ public class AlignmentAnnotation
{
return;
}
- sequenceMapping = new java.util.Hashtable();
+ sequenceMapping = new HashMap();
int seqPos;
@@ -861,10 +957,18 @@ 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)
{
@@ -882,18 +986,20 @@ 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;
}
@@ -911,8 +1017,10 @@ public class AlignmentAnnotation
if (annotations[i] == null)
{
if (i + 1 < iSize)
+ {
System.arraycopy(annotations, i + 1, annotations, i, iSize - i
- 1);
+ }
iSize--;
}
else
@@ -928,11 +1036,11 @@ 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
@@ -943,10 +1051,15 @@ 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.
@@ -1046,11 +1159,15 @@ 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);
+ ' ', 0f, null);
+ }
else if (annotations[i].displayCharacter == null
|| annotations[i].displayCharacter.equals(" "))
+ {
annotations[i].displayCharacter = String.valueOf(gapchar);
+ }
}
}
}
@@ -1094,6 +1211,11 @@ 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
*/
@@ -1108,4 +1230,187 @@ 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);
+
+ }
+
+ /**
+ * 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());
+ }
+
+ protected static synchronized long nextId()
+ {
+ return counter++;
+ }
}