/*
- * 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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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.SecStrConsensus.SimpleBP;
+
import jalview.analysis.WUSSParseException;
import java.util.ArrayList;
+ public ArrayList<SimpleBP> bps=null;
/**
* RNA secondary structure contact positions
*/
*/
private void _updateRnaSecStr(CharSequence RNAannot)
{
- try
- {
- _rnasecstr = Rna.GetBasePairs(RNAannot);
- invalidrnastruc = -1;
- } catch (WUSSParseException px)
+ try {
+ _rnasecstr = Rna.GetBasePairs(RNAannot);
+ bps = Rna.GetModeleBP(RNAannot);
+ invalidrnastruc=-1;
+ }
+ catch (WUSSParseException px)
{
- invalidrnastruc = px.getProblemPos();
+ // DEBUG System.out.println(px);
+ invalidrnastruc=px.getProblemPos();
}
if (invalidrnastruc > -1)
{
return NO_GRAPH;
}
}
-
+ // JBPNote: what does this do ?
+ public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
+ {
+ bps = Rna.GetModeleBP(RNAannot);
+ }
/**
* Creates a new AlignmentAnnotation object.
*
|| annotations[i].secondaryStructure == 'B'
|| annotations[i].secondaryStructure == 'C'
|| annotations[i].secondaryStructure == 'D'
- || annotations[i].secondaryStructure == '1'
+ || annotations[i].secondaryStructure == 'E'
|| annotations[i].secondaryStructure == 'F'
|| annotations[i].secondaryStructure == 'G'
- || annotations[i].secondaryStructure == '2'
+ || annotations[i].secondaryStructure == 'H'
|| annotations[i].secondaryStructure == 'I'
|| annotations[i].secondaryStructure == 'J'
|| annotations[i].secondaryStructure == 'K'
// &&
// annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
firstChar != ' '
- && firstChar != 'H'
- && firstChar != 'E'
+ && firstChar != '$'
+ && firstChar != 'ยต' // JBPNote should explicitly express as unicode number to avoid source code translation problems
&& firstChar != '('
&& firstChar != '['
&& firstChar != '>'
&& firstChar != 'B'
&& firstChar != 'C'
&& firstChar != 'D'
- && firstChar != '1'
+ && firstChar != 'E'
&& firstChar != 'F'
&& firstChar != 'G'
- && firstChar != '2'
+ && firstChar != 'H'
&& firstChar != 'I'
&& firstChar != 'J'
&& firstChar != 'K'