From 18cf107f9621eeb45039cbed6f533d5012d2d0fc Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 26 Jan 2011 15:14:27 +0000
Subject: [PATCH] fix for reading fasta with java less than 1.6
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15370 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/IndexFastaStream.java | 31 +++++++++++++++----
1 file changed, 25 insertions(+), 6 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/IndexFastaStream.java b/uk/ac/sanger/artemis/io/IndexFastaStream.java
index e02f58d0c..9408bd348 100644
--- a/uk/ac/sanger/artemis/io/IndexFastaStream.java
+++ b/uk/ac/sanger/artemis/io/IndexFastaStream.java
@@ -47,12 +47,6 @@ public class IndexFastaStream extends StreamSequence
private FastaSequenceIndex fastaIndex;
private int len;
private String contig;
- static {
- ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".dna");
- ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".seq");
- ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".fas");
- ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".ffn");
- }
public IndexFastaStream(Entry entry)
{
@@ -111,7 +105,19 @@ public class IndexFastaStream extends StreamSequence
else
fastaIndexFile = new File(fasta.getName() + ".fai");
if (fastaIndexFile.exists())
+ {
+ try
+ {
+ setExtensions();
+ }
+ catch(UnsupportedClassVersionError e)
+ {
+ System.err.println("Java version "+System.getProperty("java.version")+
+ " does not support indexed fasta - use Java 1.6 or higher.");
+ return false;
+ }
return true;
+ }
}
}
catch(Exception e)
@@ -121,6 +127,19 @@ public class IndexFastaStream extends StreamSequence
return false;
}
+ /**
+ * Add to supported FASTA allowed suffixes.
+ */
+ private static void setExtensions()
+ {
+ if(ReferenceSequenceFileFactory.FASTA_EXTENSIONS.contains(".dna"))
+ return;
+ ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".dna");
+ ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".seq");
+ ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".fas");
+ ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".ffn");
+ }
+
public void setContigByIndex(int seqIndex)
{
/*ReferenceSequence ref = getReferenceSequence(seqIndex);
--
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