From f8df2bd2d7768ca0751aabc9a166a56d9865c3f4 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 21 Mar 2013 09:21:52 +0000
Subject: [PATCH] set amino acids to uppercase
---
uk/ac/sanger/artemis/sequence/AminoAcidSequence.java | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java b/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
index 2b18c1ea1..aed54a527 100644
--- a/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
+++ b/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
@@ -1056,7 +1056,7 @@ public class AminoAcidSequence
/**
* The number of amino acid symbols, not including stop codons: 20.
**/
- public final static int amino_acid_symbol_count = 20;
+ //private final static int amino_acid_symbol_count = 20;
public static void setGeneCode()
@@ -1072,8 +1072,8 @@ public class AminoAcidSequence
{
for(int i = 0 ; i < 64 ; ++i)
{
- final char new_table_char =
- ((String)(options_file_table.elementAt(i))).charAt(0);
+ final char new_table_char = Character.toUpperCase(
+ ((String)(options_file_table.elementAt(i))).charAt(0));
if(isLegalCodon (new_table_char))
codon_translation_array[i] = new_table_char;
--
GitLab