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JAL-1236 CLUSTAL_HEADER property to configure the header for Clustal format files
author
Jim Procter
<jprocter@issues.jalview.org>
Fri, 13 Dec 2019 15:42:06 +0000
(15:42 +0000)
committer
Jim Procter
<jprocter@issues.jalview.org>
Fri, 13 Dec 2019 15:42:06 +0000
(15:42 +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
afb2009
..
537c154
100755
(executable)
--- a/
src/jalview/io/ClustalFile.java
+++ b/
src/jalview/io/ClustalFile.java
@@
-36,17
+36,28
@@
public class ClustalFile extends AlignFile
public ClustalFile()
{
public ClustalFile()
{
+ _initHeader();
}
public ClustalFile(String inFile, DataSourceType sourceType)
throws IOException
{
super(inFile, sourceType);
}
public ClustalFile(String inFile, DataSourceType sourceType)
throws IOException
{
super(inFile, sourceType);
+ _initHeader();
}
public ClustalFile(FileParse source) throws IOException
{
super(source);
}
public ClustalFile(FileParse source) throws IOException
{
super(source);
+ _initHeader();
+ }
+
+ private void _initHeader()
+ {
+ try {
+ clustalHeader = jalview.bin.Cache.getDefault("CLUSTAL_HEADER","CLUSTAL");
+ } catch (Error e) {};
+
}
@Override
}
@Override
@@
-196,11
+207,15
@@
public class ClustalFile extends AlignFile
}
}
}
}
}
}
-
+ /**
+ * clustal header - customise if needed
+ */
+ public String clustalHeader = "CLUSTAL";
+
@Override
public String print(SequenceI[] s, boolean jvsuffix)
{
@Override
public String print(SequenceI[] s, boolean jvsuffix)
{
- StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
+ StringBuffer out = new StringBuffer(clustalHeader + newline + newline);
int max = 0;
int maxid = 0;
int max = 0;
int maxid = 0;