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JAL-2999 release date for 2.10.4b1 set for 27th May 2018
[jalview.git]
/
src
/
jalview
/
io
/
PileUpfile.java
diff --git
a/src/jalview/io/PileUpfile.java
b/src/jalview/io/PileUpfile.java
index
7b5ce0d
..
f7f718b
100755
(executable)
--- a/
src/jalview/io/PileUpfile.java
+++ b/
src/jalview/io/PileUpfile.java
@@
-92,7
+92,7
@@
public class PileUpfile extends MSFfile
i++;
}
i++;
}
- out.append(" MSF: " + s[0].getSequence().length
+ out.append(" MSF: " + s[0].getLength()
+ " Type: P Check: " + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
+ " Type: P Check: " + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
@@
-151,8
+151,8
@@
public class PileUpfile extends MSFfile
int start = (i * 50) + (k * 10);
int end = start + 10;
int start = (i * 50) + (k * 10);
int end = start + 10;
- if ((end < s[j].getSequence().length)
- && (start < s[j].getSequence().length))
+ int length = s[j].getLength();
+ if ((end < length) && (start < length))
{
out.append(s[j].getSequence(start, end));
{
out.append(s[j].getSequence(start, end));
@@
-167,7
+167,7
@@
public class PileUpfile extends MSFfile
}
else
{
}
else
{
- if (start < s[j].getSequence().length)
+ if (start < length)
{
out.append(s[j].getSequenceAsString().substring(start));
out.append(newline);
{
out.append(s[j].getSequenceAsString().substring(start));
out.append(newline);