/*
* 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
*
* 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.
*
* 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 .
*/
package jalview.datamodel;
import jalview.analysis.Rna;
import jalview.analysis.WUSSParseException;
import java.util.Enumeration;
import java.util.Hashtable;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
public class AlignmentAnnotation
{
/**
* If true, this annotations is calculated every edit, eg consensus, quality
* or conservation graphs
*/
public boolean autoCalculated = false;
public String annotationId;
public SequenceI sequenceRef;
/** DOCUMENT ME!! */
public String label;
/** DOCUMENT ME!! */
public String description;
/** DOCUMENT ME!! */
public Annotation[] annotations;
/**
* RNA secondary structure contact positions
*/
public SequenceFeature[] _rnasecstr = null;
/**
* position of annotation resulting in invalid WUSS parsing or -1
*/
private long invalidrnastruc=-1;
/**
* 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 {
_rnasecstr = Rna.GetBasePairs(RNAannot);
invalidrnastruc=-1;
}
catch (WUSSParseException 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;
}
// System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
}
public java.util.Hashtable sequenceMapping;
/** DOCUMENT ME!! */
public float graphMin;
/** DOCUMENT ME!! */
public float graphMax;
/**
* Score associated with label and description.
*/
public double score = Double.NaN;
/**
* flag indicating if annotation has a score.
*/
public boolean hasScore = false;
public GraphLine threshold;
// Graphical hints and tips
/** Can this row be edited by the user ? */
public boolean editable = false;
/** Indicates if annotation has a graphical symbol track */
public boolean hasIcons; //
/** Indicates if annotation has a text character label */
public boolean hasText;
/** is the row visible */
public boolean visible = true;
public int graphGroup = -1;
/** Displayed height of row in pixels */
public int height = 0;
public int graph = 0;
public int graphHeight = 40;
public boolean padGaps = false;
public static final int NO_GRAPH = 0;
public static final int BAR_GRAPH = 1;
public static final int LINE_GRAPH = 2;
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()
*/
protected void finalize() throws Throwable
{
sequenceRef = null;
groupRef = null;
super.finalize();
}
public static int getGraphValueFromString(String string)
{
if (string.equalsIgnoreCase("BAR_GRAPH"))
{
return BAR_GRAPH;
}
else if (string.equalsIgnoreCase("LINE_GRAPH"))
{
return LINE_GRAPH;
}
else
{
return NO_GRAPH;
}
}
/**
* Creates a new AlignmentAnnotation object.
*
* @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)
{
// always editable?
editable = true;
this.label = label;
this.description = description;
this.annotations = annotations;
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')
{
hasIcons |= true;
}
else
// Check for RNA secondary structure
{
if (annotations[i].secondaryStructure == 'S')
{
hasIcons |= true;
isrna |= true;
}
}
// 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)
{
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 != 'S'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
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 (nonSSLabel)
{
hasIcons = false;
for (int j = 0; j < annotations.length; j++)
{
if (annotations[j] != null
&& annotations[j].secondaryStructure != ' ')
{
annotations[j].displayCharacter = String
.valueOf(annotations[j].secondaryStructure);
annotations[j].secondaryStructure = ' ';
}
}
}
else
{
if (isrna)
{
_updateRnaSecStr(new AnnotCharSequence());
}
}
annotationId = this.hashCode() + "";
}
/**
* 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);
}
public 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)
{
String dc;
return ((index+offset<0) || (index+offset)>=max || annotations[index+offset]==null || (dc=annotations[index+offset].displayCharacter.trim()).length()<1)
? '.' : dc.charAt(0);
}
public String toString()
{
char[] string=new char[max-offset];
int mx=annotations.length;
for (int i=offset;i 1)
{
drawValues = false;
}
if (annotations[i].value > max)
{
max = annotations[i].value;
}
if (annotations[i].value < min)
{
min = annotations[i].value;
}
}
// 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;
}
}
}
graphMin = min;
graphMax = max;
areLabelsSecondaryStructure();
if (!drawValues && graphType != NO_GRAPH)
{
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] != null)
{
annotations[i].displayCharacter = "";
}
}
}
}
/**
* Copy constructor creates a new independent annotation row with the same
* associated sequenceRef
*
* @param annotation
*/
public AlignmentAnnotation(AlignmentAnnotation annotation)
{
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;
this.hasText = annotation.hasText;
this.height = annotation.height;
this.label = annotation.label;
this.padGaps = annotation.padGaps;
this.visible = annotation.visible;
if (this.hasScore = annotation.hasScore)
{
this.score = annotation.score;
}
if (annotation.threshold != null)
{
threshold = new GraphLine(annotation.threshold);
}
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 (annotation.sequenceRef != null)
{
this.sequenceRef = annotation.sequenceRef;
if (annotation.sequenceMapping != null)
{
Integer p = null;
sequenceMapping = new Hashtable();
Enumeration pos = annotation.sequenceMapping.keys();
while (pos.hasMoreElements())
{
// 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)
{
sequenceMapping.put(p, annotations[i]);
}
}
}
}
else
{
this.sequenceMapping = null;
}
}
}
validateRangeAndDisplay(); // construct hashcodes, etc.
}
/**
* 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)
{
// 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)
return;
Annotation[] temp = new Annotation[endRes - startRes + 1];
if (startRes < annotations.length)
{
System.arraycopy(annotations, startRes, temp, 0, endRes - startRes
+ 1);
}
if (sequenceRef != null)
{
// Clip the mapping, if it exists.
int spos = sequenceRef.findPosition(startRes);
int epos = sequenceRef.findPosition(endRes);
if (sequenceMapping != null)
{
Hashtable newmapping = new Hashtable();
Enumeration e = sequenceMapping.keys();
while (e.hasMoreElements())
{
Integer pos = (Integer) e.nextElement();
if (pos.intValue() >= spos && pos.intValue() <= epos)
{
newmapping.put(pos, sequenceMapping.get(pos));
}
}
sequenceMapping.clear();
sequenceMapping = newmapping;
}
}
annotations = temp;
}
/**
* set the annotation row to be at least length Annotations
*
* @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)
{
return true; // annotation row is correct - null == not visible and
// undefined length
}
if (annotations.length < length)
{
Annotation[] na = new Annotation[length];
System.arraycopy(annotations, 0, na, 0, annotations.length);
annotations = na;
return true;
}
return annotations.length > length;
}
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
public String toString()
{
StringBuffer buffer = new StringBuffer();
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] != null)
{
if (graph != 0)
{
buffer.append(annotations[i].value);
}
else if (hasIcons)
{
buffer.append(annotations[i].secondaryStructure);
}
else
{
buffer.append(annotations[i].displayCharacter);
}
}
buffer.append(", ");
}
// TODO: remove disgusting hack for 'special' treatment of consensus line.
if (label.indexOf("Consensus") == 0)
{
buffer.append("\n");
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] != null)
{
buffer.append(annotations[i].description);
}
buffer.append(", ");
}
}
return buffer.toString();
}
public void setThreshold(GraphLine line)
{
threshold = line;
}
public GraphLine getThreshold()
{
return threshold;
}
/**
* 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)
{
if (seqRef == null)
{
return;
}
sequenceRef = seqRef;
if (annotations == null)
{
return;
}
sequenceMapping = new java.util.Hashtable();
int seqPos;
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] != null)
{
if (alreadyMapped)
{
seqPos = seqRef.findPosition(i);
}
else
{
seqPos = i + startRes;
}
sequenceMapping.put(new Integer(seqPos), annotations[i]);
}
}
}
public void adjustForAlignment()
{
if (sequenceRef == null)
return;
if (annotations == null)
{
return;
}
int a = 0, aSize = sequenceRef.getLength();
if (aSize == 0)
{
// Its been deleted
return;
}
int position;
Annotation[] temp = new Annotation[aSize];
Integer index;
for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
{
index = new Integer(a);
if (sequenceMapping.containsKey(index))
{
position = sequenceRef.findIndex(a) - 1;
temp[position] = (Annotation) sequenceMapping.get(index);
}
}
annotations = temp;
}
/**
* 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 < iSize)
{
if (annotations[i] == null)
{
if (i + 1 < iSize)
System.arraycopy(annotations, i + 1, annotations, i, iSize - i
- 1);
iSize--;
}
else
{
i++;
}
}
Annotation[] ann = annotations;
annotations = new Annotation[i];
System.arraycopy(ann, 0, annotations, 0, i);
ann = null;
return iSize;
}
/**
* 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
* parameter to specify correspondence between current and new sequenceRef
*
* @param sequenceI
*/
public void setSequenceRef(SequenceI sequenceI)
{
if (sequenceI != null)
{
if (sequenceRef != null)
{
if (sequenceRef != sequenceI
&& !sequenceRef.equals(sequenceI)
&& sequenceRef.getDatasetSequence() != sequenceI
.getDatasetSequence())
{
// if sequenceRef isn't intersecting with sequenceI
// throw away old mapping and reconstruct.
sequenceRef = null;
if (sequenceMapping != null)
{
sequenceMapping = null;
// compactAnnotationArray();
}
createSequenceMapping(sequenceI, 1, true);
adjustForAlignment();
}
else
{
// Mapping carried over
sequenceRef = sequenceI;
}
}
else
{
// No mapping exists
createSequenceMapping(sequenceI, 1, true);
adjustForAlignment();
}
}
else
{
// throw away the mapping without compacting.
sequenceMapping = null;
sequenceRef = null;
}
}
/**
* @return the score
*/
public double getScore()
{
return score;
}
/**
* @param score
* the score to set
*/
public void setScore(double score)
{
hasScore = true;
this.score = score;
}
/**
*
* @return true if annotation has an associated score
*/
public boolean hasScore()
{
return hasScore || !Double.isNaN(score);
}
/**
* Score only annotation
*
* @param label
* @param description
* @param score
*/
public AlignmentAnnotation(String label, String description, double score)
{
this(label, description, null);
setScore(score);
}
/**
* copy constructor with edit based on the hidden columns marked in colSel
*
* @param alignmentAnnotation
* @param colSel
*/
public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
ColumnSelection colSel)
{
this(alignmentAnnotation);
if (annotations == null)
{
return;
}
colSel.makeVisibleAnnotation(this);
}
public void setPadGaps(boolean padgaps, char gapchar)
{
this.padGaps = padgaps;
if (padgaps)
{
hasText = true;
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] == null)
annotations[i] = new Annotation(String.valueOf(gapchar), null,
' ', 0f);
else if (annotations[i].displayCharacter == null
|| annotations[i].displayCharacter.equals(" "))
annotations[i].displayCharacter = String.valueOf(gapchar);
}
}
}
/**
* format description string for display
*
* @param seqname
* @return Get the annotation description string optionally prefixed by
* associated sequence name (if any)
*/
public String getDescription(boolean seqname)
{
if (seqname && this.sequenceRef != null)
{
int i=description.toLowerCase().indexOf("");
if (i>-1)
{
// move the html tag to before the sequence reference.
return ""+sequenceRef.getName()+" : "+description.substring(i+6);
}
return sequenceRef.getName() + " : " + description;
}
return description;
}
public boolean isValidStruc()
{
return invalidrnastruc==-1;
}
public long getInvalidStrucPos()
{
return invalidrnastruc;
}
/**
* machine readable ID string indicating what generated this annotation
*/
protected String calcId="";
public String getCalcId()
{
return calcId;
}
public void setCalcId(String calcId)
{
this.calcId = calcId;
}
}