/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
*
*/
package jalview.datamodel;
+import jalview.analysis.Rna;
+import jalview.analysis.WUSSParseException;
+
+import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* DOCUMENT ME!
*
/** 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;
*/
public boolean centreColLabels = false;
+ private boolean isrna;
+
/*
* (non-Javadoc)
*
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++)
{
{
hasIcons |= true;
}
+ else
+ // Check for RNA secondary structure
+ {
+ //System.out.println(annotations[i].secondaryStructure);
+ 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')
+ {
+ hasIcons |= true;
+ isrna |= true;
+ }
+ }
- if (annotations[i].displayCharacter == null)
+ // System.out.println("displaychar " + annotations[i].displayCharacter);
+
+ if (annotations[i].displayCharacter == null
+ || annotations[i].displayCharacter.length() == 0)
{
+ rnastring.append('.');
continue;
}
if (annotations[i].displayCharacter.length() == 1)
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'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
}
}
}
+ else
+ {
+ rnastring.append(annotations[i].displayCharacter.charAt(1));
+ }
if (annotations[i].displayCharacter.length() > 0)
{
}
}
+ 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 < mx; i++)
+ {
+ String dc;
+ string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter
+ .trim()).length() < 1) ? '.' : dc.charAt(0);
+ }
+ return new String(string);
+ }
+ };
+
+ private long _lastrnaannot = -1;
+
+ public String getRNAStruc()
+ {
+ if (isrna)
+ {
+ String rnastruc = new AnnotCharSequence().toString();
+ if (_lastrnaannot != rnastruc.hashCode())
+ {
+ // ensure rna structure contacts are up to date
+ _lastrnaannot = rnastruc.hashCode();
+ _updateRnaSecStr(rnastruc);
+ }
+ return rnastruc;
+ }
+ return null;
+ }
+
+ /**
* Creates a new AlignmentAnnotation object.
*
* @param label
* checks graphMin and graphMax, secondary structure symbols, sets graphType
* appropriately, sets null labels to the empty string if appropriate.
*/
- private void validateRangeAndDisplay()
+ public void validateRangeAndDisplay()
{
if (annotations == null)
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 = "";
+ annotations[i].displayCharacter = "X";
}
}
}
this.label = annotation.label;
this.padGaps = annotation.padGaps;
this.visible = annotation.visible;
+ this.centreColLabels = annotation.centreColLabels;
+ this.scaleColLabel = annotation.scaleColLabel;
+ this.showAllColLabels = annotation.showAllColLabels;
+ this.calcId = annotation.calcId;
if (this.hasScore = annotation.hasScore)
{
this.score = annotation.score;
}
}
}
+ // TODO: check if we need to do this: JAL-952
+ // if (this.isrna=annotation.isrna)
+ {
+ // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+ }
validateRangeAndDisplay(); // construct hashcodes, etc.
}
{
if (annotations[i] == null)
annotations[i] = new Annotation(String.valueOf(gapchar), null,
- ' ', 0f);
+ ' ', 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().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;
}
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 = "";
+
+ /**
+ * 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;
+ }
+
+ public void setCalcId(String calcId)
+ {
+ this.calcId = calcId;
+ }
}
git://source.jalview.org / jalview.git / blobdiff