From 921482b865982d9c0bc28d5d493cf04620bcde37 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Sun, 19 Sep 2010 08:14:46 +0000
Subject: [PATCH] changes for INDEXED_FASTA_FORMAT
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14753 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/SimpleDocumentEntry.java | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
index 41d77e236..c968bbf76 100644
--- a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
@@ -123,8 +123,8 @@ abstract public class SimpleDocumentEntry
final int MAX_LOOP = 9999;
while((new_line_group =
- LineGroup.readNextLineGroup(pushback_reader)) != null)
- {
+ LineGroup.readNextLineGroup(pushback_reader, this)) != null)
+ {
if(new_line_group instanceof SimpleDocumentFeature)
{
final SimpleDocumentFeature new_feature =
@@ -158,6 +158,9 @@ abstract public class SimpleDocumentEntry
}
else
addLineGroup(new_line_group);
+
+ if(new_line_group instanceof IndexFastaStream)
+ break;
}
pushback_reader.close();
@@ -443,7 +446,7 @@ abstract public class SimpleDocumentEntry
try
{
while((new_line_group =
- LineGroup.readNextLineGroup(pushback_reader)) != null)
+ LineGroup.readNextLineGroup(pushback_reader, this)) != null)
{
if(new_line_group instanceof MiscLineGroup)
new_line_groups.addElement(new_line_group);
--
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