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
JAL-2416 order score models by order of addition rather than name
[jalview.git]
/
src
/
jalview
/
io
/
MSFfile.java
diff --git
a/src/jalview/io/MSFfile.java
b/src/jalview/io/MSFfile.java
index
7e46978
..
f379724
100755
(executable)
--- a/
src/jalview/io/MSFfile.java
+++ b/
src/jalview/io/MSFfile.java
@@
-58,7
+58,7
@@
public class MSFfile extends AlignFile
* @throws IOException
* DOCUMENT ME!
*/
* @throws IOException
* DOCUMENT ME!
*/
- public MSFfile(String inFile, String type) throws IOException
+ public MSFfile(String inFile, DataSourceType type) throws IOException
{
super(inFile, type);
}
{
super(inFile, type);
}
@@
-216,7
+216,8
@@
public class MSFfile extends AlignFile
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public String print(SequenceI[] sqs)
+ @Override
+ public String print(SequenceI[] sqs, boolean jvSuffix)
{
boolean is_NA = Comparison.isNucleotide(sqs);
{
boolean is_NA = Comparison.isNucleotide(sqs);
@@
-307,7
+308,7
@@
public class MSFfile extends AlignFile
while ((i < s.length) && (s[i] != null))
{
while ((i < s.length) && (s[i] != null))
{
- nameBlock[i] = new String(" Name: " + printId(s[i]) + " ");
+ nameBlock[i] = new String(" Name: " + printId(s[i], jvSuffix) + " ");
idBlock[i] = new String("Len: "
+ maxLenpad.form(s[i].getSequence().length) + " Check: "
idBlock[i] = new String("Len: "
+ maxLenpad.form(s[i].getSequence().length) + " Check: "
@@
-359,7
+360,7
@@
public class MSFfile extends AlignFile
while ((j < s.length) && (s[j] != null))
{
while ((j < s.length) && (s[j] != null))
{
- String name = printId(s[j]);
+ String name = printId(s[j], jvSuffix);
out.append(new Format("%-" + maxid + "s").form(name + " "));
out.append(new Format("%-" + maxid + "s").form(name + " "));
@@
-407,15
+408,4
@@
public class MSFfile extends AlignFile
return out.toString();
}
return out.toString();
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public String print()
- {
- return print(getSeqsAsArray());
- }
}
}