/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*/
public static final String[] READABLE_EXTENSIONS = new String[]
{ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto" }; // ,
+ "sto,stk" }; // ,
// ".blast"
// };
AlignFile afile = null;
String inFile;
+
/**
- * character used to write newlines
+ * character used to write newlines
*/
protected String newline = System.getProperty("line.separator");
+
public void setNewlineString(String nl)
{
newline = nl;
}
+
public String getNewlineString()
{
return newline;
}
+
/**
* check that this format is valid for reading
*
{
String protocol = FILE;
String ft = file.toLowerCase().trim();
- if (ft.indexOf("http:") ==0 || ft.indexOf("https:") ==0 || ft.indexOf("file:") == 0)
+ if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+ || ft.indexOf("file:") == 0)
{
protocol = URL;
}