From: kiramt <k.mourao@dundee.ac.uk>
Date: Fri, 16 Feb 2018 10:16:28 +0000 (+0000)
Subject: JAL-2909 Removed buggy CIGAR parsing code which was not used
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c471de0bd58af67bc91d413f3bf1209c4113a601;p=jalview.git

JAL-2909 Removed buggy CIGAR parsing code which was not used
---

diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index 4e7e03f..a44d74b 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -191,76 +191,6 @@ public abstract class CigarBase
   }
 
   /**
-   * turn a cigar string into a series of operation range pairs
-   * 
-   * @param cigarString
-   *          String
-   * @return object[] {char[] operation, int[] range}
-   * @throws java.lang.Exception
-   *           for improperly formated cigar strings or ones with unknown
-   *           operations
-   */
-  public static Object[] parseCigarString(String cigarString)
-          throws Exception
-  {
-    int ops = 0;
-    for (int i = 0, l = cigarString.length(); i < l; i++)
-    {
-      char c = cigarString.charAt(i);
-      if (c == M || c == (M - _case_shift) || c == I
-              || c == (I - _case_shift) || c == D || c == (D - _case_shift))
-      {
-        ops++;
-      }
-    }
-    char[] operation = new char[ops];
-    int[] range = new int[ops];
-    int op = 0;
-    int i = 0, l = cigarString.length();
-    while (i < l)
-    {
-      char c;
-      int j = i;
-      do
-      {
-        c = cigarString.charAt(j++);
-      } while (c >= '0' && c <= '9' && j < l);
-      if (j >= l && c >= '0' && c <= '9')
-      {
-        throw new Exception(MessageManager
-                .getString("exception.unterminated_cigar_string"));
-      }
-      try
-      {
-        String rangeint = cigarString.substring(i, j - 1);
-        range[op] = Integer.parseInt(rangeint);
-        i = j;
-      } catch (Exception e)
-      {
-        throw new Error(MessageManager
-                .getString("error.implementation_bug_parse_cigar_string"));
-      }
-      if (c >= 'a' && c <= 'z')
-      {
-        c -= _case_shift;
-      }
-      if ((c == M || c == I || c == D))
-      {
-        operation[op++] = c;
-      }
-      else
-      {
-        throw new Exception(MessageManager.formatMessage(
-                "exception.unexpected_operation_cigar_string_pos",
-                new String[]
-                { new StringBuffer(c).toString(),
-                    Integer.valueOf(i).toString(), cigarString }));
-      }
-    }
-    return new Object[] { operation, range };
-  }
-
-  /**
    * add an operation to cigar string
    * 
    * @param op
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index c2a6a9c..afe10fc 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -467,25 +467,6 @@ public class SeqCigar extends CigarSimple
   }
 
   /**
-   * Create a cigar object from a cigar string like '[<I|D|M><range>]+' Will
-   * fail if the given seq already contains gaps (JBPNote: future implementation
-   * will fix)
-   * 
-   * @param seq
-   *          SequenceI object resolvable to a dataset sequence
-   * @param cigarString
-   *          String
-   * @return Cigar
-   */
-  public static SeqCigar parseCigar(SequenceI seq, String cigarString)
-          throws Exception
-  {
-    Object[] opsandrange = parseCigarString(cigarString);
-    return new SeqCigar(seq, (char[]) opsandrange[0],
-            (int[]) opsandrange[1]);
-  }
-
-  /**
    * create an alignment from the given array of cigar sequences and gap
    * character, and marking the given segments as visible in the given
    * hiddenColumns.
diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index 89169d6..57f1156 100644
--- a/test/jalview/datamodel/SeqCigarTest.java
+++ b/test/jalview/datamodel/SeqCigarTest.java
@@ -90,11 +90,6 @@ public class SeqCigarTest
     assertEquals("Failed to recover ungapped sequence cigar operations",
             "42M", cs_null);
     testCigar_string(s_gapped, ex_cs_gapped);
-    SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
-    assertEquals("Failed parseCigar", ex_cs_gapped,
-            gen_sgapped.getCigarstring());
-
-    testSeqRecovery(gen_sgapped, s_gapped);
 
     /*
      * Test dataset resolution