X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=0fcf43dc0ca1ff782c1482d516ac8c055c67bd08;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=ea13922c13e1602da45d59a057fa163da415b9f8;hpb=28787d9646cca5dd77190930f59b7ff32cf995b4;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index ea13922..0fcf43d 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,6 +1,6 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
@@ -14,10 +14,13 @@
* 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 .
+ * 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;
@@ -55,6 +58,7 @@ public class AlignmentAnnotation
+ public ArrayList bps=null;
/**
* RNA secondary structure contact positions
*/
@@ -73,13 +77,15 @@ public class AlignmentAnnotation
*/
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)
{
@@ -197,7 +203,11 @@ public class AlignmentAnnotation
return NO_GRAPH;
}
}
-
+ // JBPNote: what does this do ?
+ public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
+ {
+ bps = Rna.GetModeleBP(RNAannot);
+ }
/**
* Creates a new AlignmentAnnotation object.
*
@@ -254,10 +264,10 @@ public class AlignmentAnnotation
|| 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'
@@ -306,8 +316,8 @@ public class AlignmentAnnotation
// &&
// annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
firstChar != ' '
- && firstChar != 'H'
- && firstChar != 'E'
+ && firstChar != '$'
+ && firstChar != '�' // JBPNote should explicitly express as unicode number to avoid source code translation problems
&& firstChar != '('
&& firstChar != '['
&& firstChar != '>'
@@ -316,10 +326,10 @@ public class AlignmentAnnotation
&& firstChar != 'B'
&& firstChar != 'C'
&& firstChar != 'D'
- && firstChar != '1'
+ && firstChar != 'E'
&& firstChar != 'F'
&& firstChar != 'G'
- && firstChar != '2'
+ && firstChar != 'H'
&& firstChar != 'I'
&& firstChar != 'J'
&& firstChar != 'K'