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refactor to use model API
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
707eee8
..
04977e8
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-1,6
+1,6
@@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-43,6
+43,8
@@
public class Alignment implements AlignmentI
public static final int PROTEIN = 0;
public static final int NUCLEOTIDE = 1;
public static final int PROTEIN = 0;
public static final int NUCLEOTIDE = 1;
+
+ public boolean hasRNAStructure = false;
/** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
/** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
@@
-732,6
+734,10
@@
public class Alignment implements AlignmentI
*/
public void addAnnotation(AlignmentAnnotation aa, int pos)
{
*/
public void addAnnotation(AlignmentAnnotation aa, int pos)
{
+ if(aa.getRNAStruc()!= null){
+ hasRNAStructure=true;
+ }
+
int aSize = 1;
if (annotations != null)
{
int aSize = 1;
if (annotations != null)
{
@@
-832,6
+838,11
@@
public class Alignment implements AlignmentI
return false;
}
}
return false;
}
}
+
+ public boolean hasRNAStructure(){
+ //TODO can it happen that structure is removed from alignment?
+ return hasRNAStructure;
+ }
public void setDataset(Alignment data)
{
public void setDataset(Alignment data)
{