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Further structure accessing feature
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentAnnotation.java
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
9037008
..
ad07680
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-37,7
+37,7
@@
public class AlignmentAnnotation
public boolean autoCalculated = false;
public String annotationId;
public boolean autoCalculated = false;
public String annotationId;
-
+
public SequenceI sequenceRef;
/** DOCUMENT ME!! */
public SequenceI sequenceRef;
/** DOCUMENT ME!! */
@@
-53,6
+53,8
@@
public class AlignmentAnnotation
* RNA secondary structure contact positions
*/
public SequenceFeature[] _rnasecstr = null;
* RNA secondary structure contact positions
*/
public SequenceFeature[] _rnasecstr = null;
+
+ public String rnaStructure;
/**
* Updates the _rnasecstr field Determines the positions that base pair and
/**
* Updates the _rnasecstr field Determines the positions that base pair and
@@
-64,6
+66,8
@@
public class AlignmentAnnotation
{
_rnasecstr = Rna.GetBasePairs(RNAannot);
Rna.HelixMap(_rnasecstr);
{
_rnasecstr = Rna.GetBasePairs(RNAannot);
Rna.HelixMap(_rnasecstr);
+
+ setRNAStruc(RNAannot);
if (_rnasecstr != null && _rnasecstr.length > 0)
{
if (_rnasecstr != null && _rnasecstr.length > 0)
{
@@
-73,7
+77,7
@@
public class AlignmentAnnotation
}
// System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
}
}
// System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
}
-
+
public java.util.Hashtable sequenceMapping;
/** DOCUMENT ME!! */
public java.util.Hashtable sequenceMapping;
/** DOCUMENT ME!! */
@@
-304,7
+308,15
@@
public class AlignmentAnnotation
annotationId = this.hashCode() + "";
}
annotationId = this.hashCode() + "";
}
- /**
+ public void setRNAStruc(String string) {
+ rnaStructure=string;
+}
+
+ public String getRNAStruc(){
+ return rnaStructure;
+ }
+
+/**
* Creates a new AlignmentAnnotation object.
*
* @param label
* Creates a new AlignmentAnnotation object.
*
* @param label