From fe80a06d94b6b38bfdee7b8156b8d4de37f39692 Mon Sep 17 00:00:00 2001
From: alchemistmatt <matthew.monroe@pnnl.gov>
Date: Mon, 9 Apr 2018 18:29:36 -0700
Subject: [PATCH] Allow the FASTA file to have extension .faa

---
 .../edu/ucsd/msjava/msdbsearch/CompactFastaSequence.java    | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/main/java/edu/ucsd/msjava/msdbsearch/CompactFastaSequence.java b/src/main/java/edu/ucsd/msjava/msdbsearch/CompactFastaSequence.java
index d264244e..cf999646 100644
--- a/src/main/java/edu/ucsd/msjava/msdbsearch/CompactFastaSequence.java
+++ b/src/main/java/edu/ucsd/msjava/msdbsearch/CompactFastaSequence.java
@@ -99,8 +99,10 @@ private CompactFastaSequence(String filepath, String alphabet) {
         String basepath = filepath.substring(0, filepath.length() - extension.length() - 1);
 
         this.baseFilepath = basepath;
-        if (!extension.equalsIgnoreCase("fasta") && !extension.equalsIgnoreCase("fa")) {
-            System.err.println("Input error: not a fasta file");
+        if (!extension.equalsIgnoreCase("fasta") &&
+            !extension.equalsIgnoreCase("fa") &&
+            !extension.equalsIgnoreCase("faa")) {
+            System.err.println("Input error: not a fasta file (extension must be .fasta or .fa or .faa)");
             System.exit(-1);
         }