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Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop
[jalview.git]
/
src
/
jalview
/
io
/
AnnotationFile.java
diff --git
a/src/jalview/io/AnnotationFile.java
b/src/jalview/io/AnnotationFile.java
index
69926b5
..
5266d08
100755
(executable)
--- a/
src/jalview/io/AnnotationFile.java
+++ b/
src/jalview/io/AnnotationFile.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
\r
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
\r
*
\r
* This file is part of Jalview.
\r
*
\r
*
\r
* This file is part of Jalview.
\r
*
\r
@@
-1018,7
+1018,7
@@
public class AnnotationFile
}
\r
}
\r
if (hasSymbols
\r
}
\r
}
\r
if (hasSymbols
\r
- && (token.equals("H") || token.equals("E") || token
\r
+ && (token.equals("H") || token.equals("E") || token.equals("S") || token
\r
.equals(" ")))
\r
{
\r
// Either this character represents a helix or sheet
\r
.equals(" ")))
\r
{
\r
// Either this character represents a helix or sheet
\r
@@
-1343,7
+1343,7
@@
public class AnnotationFile
sg.getStartRes(), sg.getEndRes() + 1);
\r
\r
c.calculate();
\r
sg.getStartRes(), sg.getEndRes() + 1);
\r
\r
c.calculate();
\r
- c.verdict(false, 25);
\r
+ c.verdict(false, 25); // TODO: refer to conservation percent threshold
\r
\r
sg.cs.setConservation(c);
\r
\r
\r
sg.cs.setConservation(c);
\r
\r