/*
- * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import jalview.analysis.Rna;
-import jalview.analysis.WUSSParseException;
-
import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Map.Entry;
-import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
/**
* DOCUMENT ME!
*/
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<SimpleBP> 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
+ * @param rnaAnnotation
*/
- private void _updateRnaSecStr(CharSequence RNAannot)
+ private void _updateRnaSecStr(CharSequence rnaAnnotation)
{
- try {
- _rnasecstr = Rna.GetBasePairs(RNAannot);
- invalidrnastruc=-1;
- }
- catch (WUSSParseException px)
+ try
+ {
+ _rnasecstr = Rna.getHelixMap(rnaAnnotation);
+ invalidrnastruc = -1;
+ } catch (WUSSParseException px)
{
- invalidrnastruc=px.getProblemPos();
+ // DEBUG System.out.println(px);
+ invalidrnastruc = px.getProblemPos();
}
- if (invalidrnastruc>-1)
+ 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;
+ 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);
+ }
+
+ /**
+ * Get the RNA Secondary Structure SequenceFeature Array if present
+ */
+ public SequenceFeature[] getRnaSecondaryStructure()
+ {
+ return this._rnasecstr;
+ }
+
+ /**
+ * Check the RNA Secondary Structure is equivalent to one in given
+ * AlignmentAnnotation param
+ */
+ public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that)
+ {
+ return rnaSecondaryStructureEquivalent(that, true);
+ }
+
+ public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that,
+ boolean compareType)
+ {
+ SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
+ SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
+ if (thisSfArray == null || thatSfArray == null)
+ {
+ return thisSfArray == null && thatSfArray == null;
+ }
+ if (thisSfArray.length != thatSfArray.length)
+ {
+ return false;
+ }
+ Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
+ // like this
+ Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
+ // like this
+ for (int i = 0; i < thisSfArray.length; i++)
+ {
+ SequenceFeature thisSf = thisSfArray[i];
+ SequenceFeature thatSf = thatSfArray[i];
+ if (compareType)
+ {
+ if (thisSf.getType() == null || thatSf.getType() == null)
+ {
+ if (thisSf.getType() == null && thatSf.getType() == null)
+ {
+ continue;
+ }
+ else
+ {
+ return false;
+ }
+ }
+ if (!thisSf.getType().equals(thatSf.getType()))
+ {
+ return false;
+ }
+ }
+ if (!(thisSf.getBegin() == thatSf.getBegin()
+ && thisSf.getEnd() == thatSf.getEnd()))
+ {
+ return false;
+ }
+ }
+ return true;
+
}
- public java.util.Hashtable sequenceMapping;
- /** DOCUMENT ME!! */
+ /**
+ * map of positions in the associated annotation
+ */
+ private Map<Integer, Annotation> sequenceMapping;
+
+ /**
+ * lower range for quantitative data
+ */
public float graphMin;
- /** DOCUMENT ME!! */
+ /**
+ * Upper range for quantitative data
+ */
public float graphMax;
/**
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"))
public AlignmentAnnotation(String label, String description,
Annotation[] annotations)
{
+ setAnnotationId();
// always editable?
editable = true;
this.label = label;
char firstChar = 0;
for (int i = 0; i < annotations.length; i++)
{
+ // DEBUG System.out.println(i + ": " + annotations[i]);
if (annotations[i] == null)
{
continue;
if (annotations[i].secondaryStructure == 'H'
|| annotations[i].secondaryStructure == 'E')
{
+ // DEBUG System.out.println( "/H|E/ '" +
+ // annotations[i].secondaryStructure + "'");
hasIcons |= true;
}
else
// Check for RNA secondary structure
{
- //System.out.println(annotations[i].secondaryStructure);
+ // DEBUG System.out.println( "/else/ '" +
+ // annotations[i].secondaryStructure + "'");
+ // TODO: 2.8.2 should this ss symbol validation check be a function in
+ // RNA/ResidueProperties ?
+ // allow for DSSP extended code:
+ // https://www.wikidoc.org/index.php/Secondary_structure#The_DSSP_code
+ // GHITEBS as well as C and X (for missing?)
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' // ambiguous on
+ // its own -- already checked above
+ || annotations[i].secondaryStructure == 'F'
+ // || annotations[i].secondaryStructure == 'G'
+ // || annotations[i].secondaryStructure == 'H' // ambiguous on
+ // its own -- already checked above
+ // || 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;
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 != '('
- && firstChar != '['
- && firstChar != '>'
- && firstChar != '{'
- && firstChar != 'A'
- && firstChar != 'B'
- && firstChar != 'C'
- && firstChar != 'D'
- && firstChar != '1'
- && firstChar != 'F'
- && firstChar != 'G'
- && firstChar != '2'
- && 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'
+ 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)
{
_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<mx;i++)
+ char[] string = new char[max - offset];
+ int mx = annotations.length;
+
+ 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);
}
};
-
- private long _lastrnaannot=-1;
- public String getRNAStruc(){
+
+ private long _lastrnaannot = -1;
+
+ public String getRNAStruc()
+ {
if (isrna)
{
String rnastruc = new AnnotCharSequence().toString();
- if (_lastrnaannot!=rnastruc.hashCode())
+ if (_lastrnaannot != rnastruc.hashCode())
{
// ensure rna structure contacts are up to date
- _lastrnaannot=rnastruc.hashCode();
+ _lastrnaannot = rnastruc.hashCode();
_updateRnaSecStr(rnastruc);
}
return rnastruc;
return null;
}
-/**
+ /**
* Creates a new AlignmentAnnotation object.
*
* @param label
public AlignmentAnnotation(String label, String description,
Annotation[] annotations, float min, float max, int graphType)
{
+ setAnnotationId();
// graphs are not editable
editable = graphType == 0;
if (annotations == null)
{
visible = false; // try to prevent renderer from displaying.
+ invalidrnastruc = -1;
return; // this is a non-annotation row annotation - ie a sequence score.
}
float min = graphMin;
float max = graphMax;
boolean drawValues = true;
-
+ _linecolour = null;
if (min == max)
{
min = 999999999;
{
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)
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "X";
+ annotations[i].displayCharacter = "";
}
}
}
*/
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.label = annotation.label;
this.padGaps = annotation.padGaps;
this.visible = annotation.visible;
- this.centreColLabels=annotation.centreColLabels;
- this.scaleColLabel=annotation.scaleColLabel;
- this.showAllColLabels=annotation.showAllColLabels;
+ 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<String, String> val : annotation.properties.entrySet())
+ {
+ properties.put(val.getKey(), val.getValue());
+ }
+ }
if (this.hasScore = annotation.hasScore)
{
this.score = annotation.score;
{
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++)
{
- annotations[i] = new Annotation(ann[i]);
+ if (ann[i] != null)
+ {
+ annotations[i] = new Annotation(ann[i]);
+ if (_linecolour != null)
+ {
+ _linecolour = annotations[i].colour;
+ }
+ }
}
- ;
- 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<Integer> 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)
}
}
}
- else
- {
- this.sequenceMapping = null;
- }
+ }
+ else
+ {
+ this.sequenceMapping = null;
}
}
// TODO: check if we need to do this: JAL-952
- //if (this.isrna=annotation.isrna)
+ // if (this.isrna=annotation.isrna)
{
// _rnasecstr=new SequenceFeature[annotation._rnasecstr];
}
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)
{
int epos = sequenceRef.findPosition(endRes);
if (sequenceMapping != null)
{
- Hashtable newmapping = new Hashtable();
- Enumeration e = sequenceMapping.keys();
- while (e.hasMoreElements())
+ Map<Integer, Annotation> newmapping = new HashMap<>();
+ Iterator<Integer> 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));
*
* @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++)
{
{
return;
}
- sequenceMapping = new java.util.Hashtable();
+ sequenceMapping = new HashMap<>();
int seqPos;
seqPos = i + startRes;
}
- sequenceMapping.put(new Integer(seqPos), annotations[i]);
+ sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
}
}
}
+ /**
+ * 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)
{
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 = Integer.valueOf(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;
}
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
}
/**
- * 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
{
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.
* @param colSel
*/
public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
- ColumnSelection colSel)
+ HiddenColumns hidden)
{
this(alignmentAnnotation);
if (annotations == null)
{
return;
}
- colSel.makeVisibleAnnotation(this);
+ makeVisibleAnnotation(hidden);
}
public void setPadGaps(boolean padgaps, char gapchar)
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);
+ }
}
}
}
{
if (seqname && this.sequenceRef != null)
{
- int i=description.toLowerCase().indexOf("<html>");
- if (i>-1)
+ int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
+ if (i > -1)
{
// move the html tag to before the sequence reference.
- return "<html>"+sequenceRef.getName()+" : "+description.substring(i+6);
+ return "<html>" + sequenceRef.getName() + " : "
+ + description.substring(i + 6);
}
return sequenceRef.getName() + " : " + description;
}
public boolean isValidStruc()
{
- return invalidrnastruc==-1;
+ return invalidrnastruc == -1;
}
+
public long getInvalidStrucPos()
{
return invalidrnastruc;
/**
* machine readable ID string indicating what generated this annotation
*/
- protected String calcId="";
+ protected String calcId = "";
+
+ /**
+ * properties associated with the calcId
+ */
+ protected Map<String, String> 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;
{
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<Integer, Annotation> mapForsq = new HashMap<>();
+ if (sequenceMapping != null)
+ {
+ if (sp2sq != null)
+ {
+ for (Entry<Integer, Annotation> 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<Integer, int[]> mapping,
+ int from, int to, int idxoffset)
+ {
+ if (mapping != null)
+ {
+ Map<Integer, Annotation> old = sequenceMapping;
+ Map<Integer, Annotation> 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<String> 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;
+ }
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
+ {
+ if (annotations != null)
+ {
+ makeVisibleAnnotation(0, annotations.length, hiddenColumns);
+ }
+ }
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ public void makeVisibleAnnotation(int start, int end,
+ HiddenColumns hiddenColumns)
+ {
+ if (annotations != null)
+ {
+ if (hiddenColumns.hasHiddenColumns())
+ {
+ removeHiddenAnnotation(start, end, hiddenColumns);
+ }
+ else
+ {
+ restrict(start, end);
+ }
+ }
+ }
+
+ /**
+ * The actual implementation of deleting hidden annotation columns
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ private void removeHiddenAnnotation(int start, int end,
+ HiddenColumns hiddenColumns)
+ {
+ // mangle the alignmentAnnotation annotation array
+ ArrayList<Annotation[]> annels = new ArrayList<>();
+ Annotation[] els = null;
+
+ int w = 0;
+
+ Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
+ end + 1, false);
+
+ int copylength;
+ int annotationLength;
+ while (blocks.hasNext())
+ {
+ int[] block = blocks.next();
+ annotationLength = block[1] - block[0] + 1;
+
+ if (blocks.hasNext())
+ {
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
+ }
+ else
+ {
+ if (annotationLength + block[0] <= annotations.length)
+ {
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
+ }
+ else
+ {
+ // copy to the end of the annotation row
+ copylength = annotations.length - block[0];
+ }
+ }
+
+ els = new Annotation[annotationLength];
+ annels.add(els);
+ System.arraycopy(annotations, block[0], els, 0, copylength);
+ w += annotationLength;
+ }
+
+ if (w != 0)
+ {
+ annotations = new Annotation[w];
+
+ w = 0;
+ for (Annotation[] chnk : annels)
+ {
+ System.arraycopy(chnk, 0, annotations, w, chnk.length);
+ w += chnk.length;
+ }
+ }
+ }
+
+ public static Iterable<AlignmentAnnotation> findAnnotations(
+ Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
+ String label)
+ {
+
+ ArrayList<AlignmentAnnotation> 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<AlignmentAnnotation> list,
+ String calcId)
+ {
+
+ if (calcId != null && !"".equals(calcId))
+ {
+ for (AlignmentAnnotation a : list)
+ {
+ if (a.getCalcId() == calcId)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ public static Iterable<AlignmentAnnotation> findAnnotation(
+ List<AlignmentAnnotation> list, String calcId)
+ {
+
+ List<AlignmentAnnotation> 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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff