/*
- * 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 2.8.1)
+ * 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.
- *
+ *
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import jalview.analysis.Rna;
+import jalview.analysis.WUSSParseException;
import java.util.Enumeration;
import java.util.Hashtable;
public boolean autoCalculated = false;
public String annotationId;
-
+
public SequenceI sequenceRef;
/** DOCUMENT ME!! */
* RNA secondary structure contact positions
*/
public SequenceFeature[] _rnasecstr = null;
-
- public String rnaStructure;
+
+ /**
+ * 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
*
* @param RNAannot
*/
- private void _updateRnaSecStr(String RNAannot)
+ private void _updateRnaSecStr(CharSequence RNAannot)
{
- _rnasecstr = Rna.GetBasePairs(RNAannot);
+ try
+ {
+ _rnasecstr = Rna.GetBasePairs(RNAannot);
+ invalidrnastruc = -1;
+ } catch (WUSSParseException px)
+ {
+ invalidrnastruc = px.getProblemPos();
+ }
+ if (invalidrnastruc > -1)
+ {
+ return;
+ }
Rna.HelixMap(_rnasecstr);
-
- setRNAStruc(RNAannot);
+ // 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 boolean centreColLabels = false;
+ private boolean isrna;
+
/*
* (non-Javadoc)
*
void areLabelsSecondaryStructure()
{
boolean nonSSLabel = false;
- boolean isrna = false;
+ isrna = false;
StringBuffer rnastring = new StringBuffer();
char firstChar = 0;
{
if (isrna)
{
- _updateRnaSecStr(rnastring.toString());
+ _updateRnaSecStr(new AnnotCharSequence());
}
}
annotationId = this.hashCode() + "";
}
- public void setRNAStruc(String string) {
- rnaStructure=string;
-}
-
- public String getRNAStruc(){
- return rnaStructure;
+ /**
+ * 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
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)
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;
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)
}
}
}
+ // 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 (seqname && this.sequenceRef != null)
{
+ 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 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