From 67b813a6274ce28d9c56a0fceb4d755144d3e9cf Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 18 Mar 2010 10:38:13 +0000 Subject: [PATCH] disabled simple blast parser for 2.4.1 release --- src/jalview/io/AppletFormatAdapter.java | 6 +++--- src/jalview/io/IdentifyFile.java | 4 +++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index b494dff..76b87f8 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -38,7 +38,7 @@ public class AppletFormatAdapter */ public static final String[] READABLE_FORMATS = new String[] { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", - "PDB", "JnetFile", "SimpleBLAST" }; + "PDB", "JnetFile"}; //, "SimpleBLAST" }; /** * List of valid format strings for use by callers of the formatSequences @@ -66,14 +66,14 @@ public class AppletFormatAdapter * corresponding to READABLE_FNAMES */ public static final String[] READABLE_EXTENSIONS = new String[] - { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar", ".blast" }; + { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar"}; //, ".blast" }; /** * List of readable formats by application in order corresponding to * READABLE_EXTENSIONS */ public static final String[] READABLE_FNAMES = new String[] - { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", "SimpleBLAST" }; + { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview"};// , "SimpleBLAST" }; public static String INVALID_CHARACTERS = "Contains invalid characters"; diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index bf5f665..2679b48 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -209,7 +209,7 @@ public class IdentifyFile reply = "PDB"; break; } - // TODO comment out SimpleBLAST identification for Jalview 2.4.1 + /*// TODO comment out SimpleBLAST identification for Jalview 2.4.1 else if (!lineswereskipped && data.indexOf("BLAST")<4) { reply = "SimpleBLAST"; @@ -217,6 +217,8 @@ public class IdentifyFile } // end comments for Jalview 2.4.1 + * + */ else if (!lineswereskipped && data.charAt(0) != '*' && data.charAt(0) != ' ' && data.indexOf(":") < data.indexOf(",")) // && -- 1.7.10.2