From f8b26651e6c79267dc26ed55a00846691daf9563 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 22 Feb 2011 15:15:16 +0000
Subject: [PATCH] wrap sequence string
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15584 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/IOUtils.java | 26 +++++++++++++------
1 file changed, 18 insertions(+), 8 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 7a84c4dc5..420adf44d 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -181,14 +181,14 @@ class IOUtils
"Warning", JOptionPane.WARNING_MESSAGE);
return;
}
-
+
MarkerRange marker = selection.getMarkerRange();
Range range = marker.getRawRange();
int direction = ( marker.isForwardMarker() ? Bases.FORWARD : Bases.REVERSE);
FeatureVector features = entryGroup.getAllFeatures();
FileWriter writer = null;
String fastaFiles = "";
-
+
String name = entryGroup.getActiveEntries().elementAt(0).getName();
int sbeg = range.getStart();
int send = range.getEnd();
@@ -196,7 +196,6 @@ class IOUtils
StringBuffer buffSeq = null;
try
{
-
if(!view)
{
File newfile = new File(
@@ -222,16 +221,14 @@ class IOUtils
if(view) // sequence viewer
{
- buffSeq.append(">");
- buffSeq.append(header.toString());
- buffSeq.append("\n");
- buffSeq.append(basesStr);
+ buffSeq.append(">").append(header.toString()).append("\n");
+ wrapString(basesStr, buffSeq);
buffSeq.append("\n");
}
else // write to file
writeSequence(writer, header.toString(), basesStr);
}
-
+
if(writer != null)
writer.close();
}
@@ -397,6 +394,19 @@ class IOUtils
return basesStr;
}
+
+ private static void wrapString(String bases, StringBuffer buff)
+ {
+ final int SEQUENCE_LINE_BASE_COUNT = 60;
+ for(int k=0; k<bases.length(); k+=SEQUENCE_LINE_BASE_COUNT)
+ {
+ int end = k + SEQUENCE_LINE_BASE_COUNT;
+ if(end > bases.length())
+ end = bases.length();
+ buff.append ( bases.substring(k,end) ).append("\n");
+ }
+ }
+
private static void writeSequence(FileWriter writer, String header, String bases) throws IOException
{
writer.write (">" + header + "\n");
--
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