From 59ed6b28645515af88ce1d9b6f16e317d9f37ea8 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 15 Nov 2013 09:39:00 +0000
Subject: [PATCH] remove unused option and fix embl submission option
---
uk/ac/sanger/artemis/io/GffToEMBL.java | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GffToEMBL.java b/uk/ac/sanger/artemis/io/GffToEMBL.java
index 0b2825c76..838247b40 100644
--- a/uk/ac/sanger/artemis/io/GffToEMBL.java
+++ b/uk/ac/sanger/artemis/io/GffToEMBL.java
@@ -227,7 +227,6 @@ class GffToEMBL
System.out.println("-s\tspace separated list of sequences to read and write out");
System.out.println("-o\toutput directory");
System.out.println("-f\t[y|n] flatten the gene model, default is y");
- System.out.println("-l\tlocation of EMBL mapping files (qualifier_mapping and key_mapping)");
System.out.println("-z\t[y|n] gzip output, default is y");
System.out.println("-a\t[y|n] for EMBL submission format change to n, default is y");
System.exit(0);
@@ -236,8 +235,8 @@ class GffToEMBL
boolean gzip = true;
boolean emblSubmission = true;
boolean flatten = true;
- Vector<String> files = null;
- String outDir = null;
+ Vector<String> files = new java.util.Vector<String>();;
+ String outDir = System.getProperty("user.dir"); // working directory
for(int i=0; i<args.length; i++)
{
String s = args[i];
@@ -248,7 +247,7 @@ class GffToEMBL
}
else if(s.equals("-a"))
{
- if(i + 1 < args.length && args[i + 1].toLowerCase().equals("n"))
+ if(i + 1 < args.length && args[i + 1].toLowerCase().equals("y"))
emblSubmission = false;
}
else if(s.equals("-f"))
@@ -263,8 +262,6 @@ class GffToEMBL
}
else if(args[i].toLowerCase().equals("-s"))
{
- if(files == null)
- files = new java.util.Vector<String>();
for(int j = i + 1; j < args.length; j++)
{
if(args[j].startsWith("-"))
@@ -274,10 +271,12 @@ class GffToEMBL
}
}
- if(outDir == null)
+ final File outDirFile = new File(outDir);
+ if(!outDirFile.exists() && !outDirFile.mkdir())
{
- File f = new File(files.get(0));
- outDir = f.getParentFile().getAbsolutePath();
+ JOptionPane.showMessageDialog(null, "Problems writing to "+
+ outDirFile.getAbsolutePath(), "Error", JOptionPane.ERROR_MESSAGE);
+ System.exit(0);
}
for(String fn: files)
--
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