From e82bc564d96e699e5ab535c18f45190916821e3f Mon Sep 17 00:00:00 2001
From: andrewjpage <andrewjpage@gmail.com>
Date: Tue, 31 Jul 2012 12:05:48 +0100
Subject: [PATCH] novel combination marked as new st

---
 modules/MLST/Spreadsheet/Row.pm | 2 +-
 t/Output/SpreadsheetRow.t       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/MLST/Spreadsheet/Row.pm b/modules/MLST/Spreadsheet/Row.pm
index 993b90f..f31e8a7 100644
--- a/modules/MLST/Spreadsheet/Row.pm
+++ b/modules/MLST/Spreadsheet/Row.pm
@@ -33,7 +33,7 @@ sub _build__common_cells
   my @common_cells = (
     $self->compare_alleles->sequence_filename_root,
     $self->sequence_type_obj->sequence_type_or_nearest,
-    ($self->compare_alleles->new_st ? "New ST" : ''),
+    ($self->compare_alleles->new_st || defined($self->sequence_type_obj->nearest_sequence_type) ? "New ST" : ''),
     ($self->compare_alleles->contamination ? "Contamination" : ''),
   );
   return \@common_cells;
diff --git a/t/Output/SpreadsheetRow.t b/t/Output/SpreadsheetRow.t
index 813f0e4..97f63e0 100644
--- a/t/Output/SpreadsheetRow.t
+++ b/t/Output/SpreadsheetRow.t
@@ -71,8 +71,8 @@ $sequence_type_obj = MLST::SequenceType->new(
   sequence_names    => $compare_alleles->found_sequence_names
 );
 ok(($spreadsheet_row_obj = MLST::Spreadsheet::Row->new(sequence_type_obj => $sequence_type_obj, compare_alleles => $compare_alleles)),'create a valid spreadsheet row obj with contamination');
-is_deeply($spreadsheet_row_obj->allele_numbers_row, ['contigs', 4,'','Contamination',3,3,1], 'valid allele_number row with contamination');
-is_deeply($spreadsheet_row_obj->genomic_row, ['contigs', 4,'','Contamination','GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCACTGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGACATTATGGATGCTGGCAAACTGGTTACCGACGAACTGGTGATCGCGCTGGTTAAAGGGCGCATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCCGCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGTACCGGACGAACTGATCGTTGACCGTATCGTCGGTCGCCGCGTTCACGCGCCGTCTGGTCGTGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGTAAAGACGACGTTACCGGTGAAGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTACGTAAACGTCTGGTTGAATACCATCAGATGACAGCACCGCTGATCGGCTACTACTCCAAAGAAGCTGAAGCGGGTA',
+is_deeply($spreadsheet_row_obj->allele_numbers_row, ['contigs', 4,'New ST','Contamination',3,3,1], 'valid allele_number row with contamination');
+is_deeply($spreadsheet_row_obj->genomic_row, ['contigs', 4,'New ST','Contamination','GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCACTGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGACATTATGGATGCTGGCAAACTGGTTACCGACGAACTGGTGATCGCGCTGGTTAAAGGGCGCATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCCGCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGTACCGGACGAACTGATCGTTGACCGTATCGTCGGTCGCCGCGTTCACGCGCCGTCTGGTCGTGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGTAAAGACGACGTTACCGGTGAAGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTACGTAAACGTCTGGTTGAATACCATCAGATGACAGCACCGCTGATCGGCTACTACTCCAAAGAAGCTGAAGCGGGTA',
 'ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCGGGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACAAAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTAACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTGCCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGCGTGGCGATTTCGTCATGTTCGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTACTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCCTGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCAACTCGTGT',
 'CGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACCGGCGAGCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGTGCAGTAGACGTTATCGTCGTTGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCACATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAAGCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTTCGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCTCGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCGCGTGAAAGTGGTGAAGAACAAAATCGCTGCACCGTTTAAACAGGCTGAATTTCAGATCCTCTACGGCGAAGGTATCAACTTCTACGGCGA'],
  'valid genomic row with contamination');