git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Dont add pdb format here
[jalview.git]
/
src
/
jalview
/
io
/
MSFfile.java
diff --git
a/src/jalview/io/MSFfile.java
b/src/jalview/io/MSFfile.java
index
179204e
..
bae4342
100755
(executable)
--- a/
src/jalview/io/MSFfile.java
+++ b/
src/jalview/io/MSFfile.java
@@
-70,7
+70,7
@@
public class MSFfile extends AlignFile
/**
\r
* DOCUMENT ME!
\r
*/
\r
/**
\r
* DOCUMENT ME!
\r
*/
\r
- public void parse()
\r
+ public void parse() throws IOException
\r
{
\r
int i = 0;
\r
boolean seqFlag = false;
\r
{
\r
int i = 0;
\r
boolean seqFlag = false;
\r
@@
-147,9
+147,6
@@
public class MSFfile extends AlignFile
String head = headers.elementAt(i).toString();
\r
String seq = seqhash.get(head).toString();
\r
\r
String head = headers.elementAt(i).toString();
\r
String seq = seqhash.get(head).toString();
\r
\r
- int start = -1;
\r
- int end = -1;
\r
-
\r
if (maxLength < head.length())
\r
{
\r
maxLength = head.length();
\r
if (maxLength < head.length())
\r
{
\r
maxLength = head.length();
\r
@@
-157,8
+154,17
@@
public class MSFfile extends AlignFile
\r
// Replace ~ with a sensible gap character
\r
seq = seq.replace('~', '-');
\r
\r
// Replace ~ with a sensible gap character
\r
seq = seq.replace('~', '-');
\r
+ if (!isValidProteinSequence(seq))
\r
+ {
\r
+ throw new IOException(AppletFormatAdapter.
\r
+ INVALID_CHARACTERS
\r
+ + " : " + head
\r
+ + " : " + invalidCharacter);
\r
+ }
\r
+
\r
\r
Sequence newSeq = parseId(head);
\r
\r
Sequence newSeq = parseId(head);
\r
+
\r
newSeq.setSequence(seq);
\r
\r
seqs.addElement(newSeq);
\r
newSeq.setSequence(seq);
\r
\r
seqs.addElement(newSeq);
\r