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965f716
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ignores blank lines read in and write out
author
amwaterhouse
<Andrew Waterhouse>
Fri, 27 May 2005 15:40:31 +0000
(15:40 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Fri, 27 May 2005 15:40:31 +0000
(15:40 +0000)
src/jalview/io/ClustalFile.java
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diff --git
a/src/jalview/io/ClustalFile.java
b/src/jalview/io/ClustalFile.java
index
4138a88
..
3594afa
100755
(executable)
--- a/
src/jalview/io/ClustalFile.java
+++ b/
src/jalview/io/ClustalFile.java
@@
-60,7
+60,8
@@
public class ClustalFile extends AlignFile {
headers.addElement(id);
\r
}
\r
\r
headers.addElement(id);
\r
}
\r
\r
- tempseq.append(str.nextToken());
\r
+ if(str.hasMoreTokens())
\r
+ tempseq.append(str.nextToken());
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
@@
-123,6
+124,7
@@
public class ClustalFile extends AlignFile {
return print(getSeqsAsArray());
\r
}
\r
public static String print(SequenceI[] s) {
\r
return print(getSeqsAsArray());
\r
}
\r
public static String print(SequenceI[] s) {
\r
+
\r
StringBuffer out = new StringBuffer("CLUSTAL\n\n");
\r
\r
int max = 0;
\r
StringBuffer out = new StringBuffer("CLUSTAL\n\n");
\r
\r
int max = 0;
\r
@@
-156,18
+158,20
@@
public class ClustalFile extends AlignFile {
int start = i*len;
\r
int end = start + len;
\r
\r
int start = i*len;
\r
int end = start + len;
\r
\r
- if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {
\r
- out.append(s[j].getSequence().substring(start,end) + "\n");
\r
- } else {
\r
- if (start < s[j].getSequence().length()) {
\r
- out.append(s[j].getSequence().substring(start) + "\n");
\r
- }
\r
+ if (end < s[j].getSequence().length() && start < s[j].getSequence().length() )
\r
+ out.append(s[j].getSequence().substring(start,end));
\r
+ else
\r
+ {
\r
+ if (start < s[j].getSequence().length())
\r
+ out.append(s[j].getSequence().substring(start));
\r
}
\r
}
\r
+ out.append("\n");
\r
j++;
\r
}
\r
out.append("\n");
\r
\r
}
\r
j++;
\r
}
\r
out.append("\n");
\r
\r
}
\r
+
\r
return out.toString();
\r
}
\r
\r
return out.toString();
\r
}
\r
\r