X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=9550e836ed809b93c5e2fdbfcc4468f912c3ebef;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=8115af4677f66f179eb8ce8879085c45cb902686;hpb=a923c0fa51ce22d052ac06f54b006c57385cc8e0;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8115af4..9550e83 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,32 +1,37 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.Collection;
+import java.util.Collections;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
-
-import fr.orsay.lri.varna.models.rna.RNA;
+import java.util.Map;
+import java.util.Map.Entry;
/**
* DOCUMENT ME!
@@ -42,31 +47,38 @@ public class AlignmentAnnotation
*/
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
@@ -76,15 +88,15 @@ 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)
{
@@ -99,11 +111,51 @@ 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
+ */
+ public java.util.Hashtable sequenceMapping;
/** DOCUMENT ME!! */
public float graphMin;
@@ -202,11 +254,13 @@ 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.
*
@@ -254,37 +308,39 @@ 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 == '1'
- || annotations[i].secondaryStructure == 'F'
- || annotations[i].secondaryStructure == 'G'
- || annotations[i].secondaryStructure == '2'
- || 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;
@@ -315,8 +371,8 @@ public class AlignmentAnnotation
// &&
// annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
firstChar != ' '
- && firstChar != 'H'
- && firstChar != 'E'
+ && firstChar != '$'
+ && firstChar != 0xCE
&& firstChar != '('
&& firstChar != '['
&& firstChar != '>'
@@ -325,10 +381,10 @@ public class AlignmentAnnotation
&& firstChar != 'B'
&& firstChar != 'C'
&& firstChar != 'D'
- && firstChar != '1'
+ && firstChar != 'E'
&& firstChar != 'F'
&& firstChar != 'G'
- && firstChar != '2'
+ && firstChar != 'H'
&& firstChar != 'I'
&& firstChar != 'J'
&& firstChar != 'K'
@@ -437,11 +493,10 @@ 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);
}
public String toString()
@@ -451,9 +506,8 @@ 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);
}
@@ -597,7 +651,9 @@ 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;
@@ -616,6 +672,14 @@ 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;
@@ -624,9 +688,9 @@ 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++)
{
@@ -639,24 +703,26 @@ 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 Hashtable();
+ Enumeration pos = annotation.sequenceMapping.keys();
+ while (pos.hasMoreElements())
{
- Integer p = null;
- sequenceMapping = new Hashtable();
- Enumeration pos = annotation.sequenceMapping.keys();
- while (pos.hasMoreElements())
+ // could optimise this!
+ p = (Integer) pos.nextElement();
+ 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)
@@ -666,10 +732,10 @@ public class AlignmentAnnotation
}
}
}
- else
- {
- this.sequenceMapping = null;
- }
+ }
+ else
+ {
+ this.sequenceMapping = null;
}
}
// TODO: check if we need to do this: JAL-952
@@ -695,13 +761,21 @@ 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)
{
@@ -863,7 +937,9 @@ public class AlignmentAnnotation
public void adjustForAlignment()
{
if (sequenceRef == null)
+ {
return;
+ }
if (annotations == null)
{
@@ -889,7 +965,7 @@ public class AlignmentAnnotation
{
position = sequenceRef.findIndex(a) - 1;
- temp[position] = (Annotation) sequenceMapping.get(index);
+ temp[position] = sequenceMapping.get(index);
}
}
@@ -910,8 +986,10 @@ public class AlignmentAnnotation
if (annotations[i] == null)
{
if (i + 1 < iSize)
+ {
System.arraycopy(annotations, i + 1, annotations, i, iSize - i
- 1);
+ }
iSize--;
}
else
@@ -942,10 +1020,14 @@ 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.
@@ -1045,11 +1127,15 @@ 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);
+ }
}
}
}
@@ -1093,6 +1179,11 @@ 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
*/
@@ -1107,4 +1198,157 @@ 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[]
+ Hashtable mapForsq = new Hashtable();
+ 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)
+ {
+ Hashtable old = sequenceMapping, remap = new Hashtable();
+ 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.EMPTY_LIST;
+ }
+ return properties.keySet();
+ }
}