X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=1583f84ab14e0f90569ba4e543fc404dec149e06;hb=28787d9646cca5dd77190930f59b7ff32cf995b4;hp=800e70ac7bdab45720fb1db9466e692776a8f2f4;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git
diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 800e70a..1583f84 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,13 +1,13 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
@@ -15,14 +15,12 @@
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
-
/* Author: Lauren Michelle Lui
* Methods are based on RALEE methods http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/
* */
package jalview.analysis;
-import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Stack;
import java.util.Vector;
@@ -31,7 +29,8 @@ import jalview.datamodel.SequenceFeature;
public class Rna
{
- static Hashtable pairHash = new Hashtable();
+ static Hashtable pairHash = new Hashtable();
+
/**
* Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
* positions in "stack" vector. When a close bracket is reached, pair this
@@ -44,7 +43,8 @@ public class Rna
* @return Array of SequenceFeature; type = RNA helix, begin is open base
* pair, end is close base pair
*/
- public static SequenceFeature[] GetBasePairs(CharSequence line) throws WUSSParseException
+ public static SequenceFeature[] GetBasePairs(CharSequence line)
+ throws WUSSParseException
{
Stack stack = new Stack();
Vector pairs = new Vector();
@@ -70,7 +70,6 @@ public class Rna
Object temp = stack.pop();
pairs.addElement(temp);
pairs.addElement(i);
- //System.out.println(pairs);
}
i++;
@@ -84,30 +83,29 @@ public class Rna
{
int begin = Integer.parseInt(pairs.elementAt(p).toString());
int end = Integer.parseInt(pairs.elementAt(p + 1).toString());
-
- outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
+
+ outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
end, "");
- //pairHash.put(begin, end);
+ // pairHash.put(begin, end);
}
return outPairs;
}
-
-
+
/**
* Function to get the end position corresponding to a given start position
- * @param indice - start position of a base pair
+ *
+ * @param indice
+ * - start position of a base pair
* @return - end position of a base pair
*/
- /*makes no sense at the moment :(
- public int findEnd(int indice){
- //TODO: Probably extend this to find the start to a given end?
- //could be done by putting everything twice to the hash
- ArrayList pair = new ArrayList();
- return pairHash.get(indice);
- }*/
-
+ /*
+ * makes no sense at the moment :( public int findEnd(int indice){ //TODO:
+ * Probably extend this to find the start to a given end? //could be done by
+ * putting everything twice to the hash ArrayList pair = new
+ * ArrayList(); return pairHash.get(indice); }
+ */
/**
* Figures out which helix each position belongs to and stores the helix
@@ -191,4 +189,3 @@ public class Rna
}
}
}
-