From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 16 May 2017 14:38:33 +0000 (+0100)
Subject: JAL-2505 refactored method removed
X-Git-Tag: Release_2_10_3b1~269
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=516567645c306018e92e4556a8c120b3b2cdbc60;p=jalview.git

JAL-2505 refactored method removed
---

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 6bb123a..34233f0 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -215,86 +215,6 @@ public class Rna
    */
 
   /**
-   * Figures out which helix each position belongs to and stores the helix
-   * number in the 'featureGroup' member of a SequenceFeature Based off of RALEE
-   * code ralee-helix-map.
-   * 
-   * @param pairs
-   *          Array of SequenceFeature (output from Rna.GetBasePairs)
-   */
-  protected static void computeHelixMap(SequenceFeature[] pairs)
-  {
-
-    int helix = 0; // Number of helices/current helix
-    int lastopen = 0; // Position of last open bracket reviewed
-    int lastclose = 9999999; // Position of last close bracket reviewed
-
-    int open; // Position of an open bracket under review
-    int close; // Position of a close bracket under review
-    int j; // Counter
-
-    Map<Integer, Integer> helices = new HashMap<Integer, Integer>();
-    // Keep track of helix number for each position
-
-    // Go through each base pair and assign positions a helix
-    for (int i = 0; i < pairs.length; i++)
-    {
-
-      open = pairs[i].getBegin();
-      close = pairs[i].getEnd();
-
-      // System.out.println("open " + open + " close " + close);
-      // System.out.println("lastclose " + lastclose + " lastopen " + lastopen);
-
-      // we're moving from right to left based on closing pair
-      /*
-       * catch things like <<..>>..<<..>> |
-       */
-      if (open > lastclose)
-      {
-        helix++;
-      }
-
-      /*
-       * catch things like <<..<<..>>..<<..>>>> |
-       */
-      j = pairs.length - 1;
-      while (j >= 0)
-      {
-        int popen = pairs[j].getBegin();
-
-        // System.out.println("j " + j + " popen " + popen + " lastopen "
-        // +lastopen + " open " + open);
-        if ((popen < lastopen) && (popen > open))
-        {
-          if (helices.containsValue(popen)
-                  && ((helices.get(popen)) == helix))
-          {
-            continue;
-          }
-          else
-          {
-            helix++;
-            break;
-          }
-        }
-
-        j -= 1;
-      }
-
-      // Put positions and helix information into the hashtable
-      helices.put(open, helix);
-      helices.put(close, helix);
-
-      // Record helix as featuregroup
-      pairs[i].setFeatureGroup(Integer.toString(helix));
-
-      lastopen = open;
-      lastclose = close;
-    }
-  }
-
-  /**
    * Answers true if the character is a recognised symbol for RNA secondary
    * structure. Currently accepts a-z, A-Z, ()[]{}<>.
    *