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JAL-2600 Tidies
[jalview.git]
/
src
/
jalview
/
io
/
ClustalFile.java
diff --git
a/src/jalview/io/ClustalFile.java
b/src/jalview/io/ClustalFile.java
index
f7a45de
..
5d58d42
100755
(executable)
--- a/
src/jalview/io/ClustalFile.java
+++ b/
src/jalview/io/ClustalFile.java
@@
-37,9
+37,10
@@
public class ClustalFile extends AlignFile
{
}
{
}
- public ClustalFile(String inFile, String type) throws IOException
+ public ClustalFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public ClustalFile(FileParse source) throws IOException
}
public ClustalFile(FileParse source) throws IOException
@@
-196,13
+197,7
@@
public class ClustalFile extends AlignFile
}
@Override
}
@Override
- public String print()
- {
- return print(getSeqsAsArray());
- // TODO: locaRNA style aln output
- }
-
- public String print(SequenceI[] s)
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
{
StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
@@
-213,7
+208,7
@@
public class ClustalFile extends AlignFile
while ((i < s.length) && (s[i] != null))
{
while ((i < s.length) && (s[i] != null))
{
- String tmp = printId(s[i]);
+ String tmp = printId(s[i], jvsuffix);
if (s[i].getSequence().length > max)
{
if (s[i].getSequence().length > max)
{
@@
-244,7
+239,8
@@
public class ClustalFile extends AlignFile
while ((j < s.length) && (s[j] != null))
{
while ((j < s.length) && (s[j] != null))
{
- out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+ out.append(new Format("%-" + maxid + "s").form(printId(s[j],
+ jvsuffix) + " "));
int start = i * len;
int end = start + len;
int start = i * len;
int end = start + len;