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JAL-1569 test for open/close RNA parenthesis character
author
Jim Procter
<jprocter@dundee.ac.uk>
Sun, 23 Nov 2014 16:37:33 +0000
(16:37 +0000)
committer
Jim Procter
<jprocter@dundee.ac.uk>
Sun, 23 Nov 2014 16:37:33 +0000
(16:37 +0000)
src/jalview/schemes/ResidueProperties.java
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diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
aca75b7
..
8acf1f2
100755
(executable)
--- a/
src/jalview/schemes/ResidueProperties.java
+++ b/
src/jalview/schemes/ResidueProperties.java
@@
-1699,7
+1699,9
@@
public class ResidueProperties
* Used by getRNASecStrucState
*
*/
* Used by getRNASecStrucState
*
*/
- public static Hashtable toRNAssState;
+ public static Hashtable<String, String> toRNAssState;
+
+ public static boolean RNAcloseParen[] = new boolean[255];
static
{
toRNAssState = new Hashtable<String, String>();
static
{
toRNAssState = new Hashtable<String, String>();
@@
-1763,7
+1765,15
@@
public class ResidueProperties
toRNAssState.put("y", "Y");
toRNAssState.put("Z", "Z");
toRNAssState.put("z", "Z");
toRNAssState.put("y", "Y");
toRNAssState.put("Z", "Z");
toRNAssState.put("z", "Z");
-
+ for (int p = 0; p < RNAcloseParen.length; p++)
+ {
+ RNAcloseParen[p] = false;
+ }
+ for (String k : toRNAssState.keySet())
+ {
+ RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k)
+ .charAt(0);
+ }
}
/**
}
/**
@@
-1784,7
+1794,8
@@
public class ResidueProperties
String ssc = ssstring.substring(i, i + 1);
if (toRNAssState.containsKey(ssc))
{
String ssc = ssstring.substring(i, i + 1);
if (toRNAssState.containsKey(ssc))
{
- ss.append((String) toRNAssState.get(ssc));
+ // valid ss character - so return it
+ ss.append(ssc); // (String) toRNAssState.get(ssc));
}
else
{
}
else
{
@@
-1794,6
+1805,11
@@
public class ResidueProperties
return ss.toString();
}
return ss.toString();
}
+ public static boolean isCloseParenRNA(char dc)
+ {
+ return RNAcloseParen[dc];
+ }
+
// main method generates perl representation of residue property hash
// / cut here
public static void main(String[] args)
// main method generates perl representation of residue property hash
// / cut here
public static void main(String[] args)