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JAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create tests and IdentifyFile routi...
author
Jim Procter
<jprocter@issues.jalview.org>
Mon, 3 Aug 2020 13:07:03 +0000
(14:07 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Mon, 3 Aug 2020 13:07:03 +0000
(14:07 +0100)
src/jalview/io/FileFormat.java
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diff --git
a/src/jalview/io/FileFormat.java
b/src/jalview/io/FileFormat.java
index
e94e1ce
..
298c40d
100644
(file)
--- a/
src/jalview/io/FileFormat.java
+++ b/
src/jalview/io/FileFormat.java
@@
-21,6
+21,7
@@
package jalview.io;
import jalview.datamodel.AlignmentI;
package jalview.io;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
@@
-243,6
+244,22
@@
public enum FileFormat implements FileFormatI
return new PhylipFile();
}
},
return new PhylipFile();
}
},
+ GenBank("GenBank/ENA Flatfile","gb",false,false)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ // Always assume we import from EMBL for now
+ return new EmblFlatFile(source, DBRefSource.EMBL);
+ }
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return null;
+ }
+ }
+ ,
Jnet("JnetFile", "", false, false)
{
@Override
Jnet("JnetFile", "", false, false)
{
@Override
@@
-407,8
+424,8
@@
public enum FileFormat implements FileFormatI
* @param shortName
* @param extensions
* comma-separated list of file extensions associated with the format
* @param shortName
* @param extensions
* comma-separated list of file extensions associated with the format
- * @param isReadable
- * @param isWritable
+ * @param isReadable - can be recognised by IdentifyFile and imported with the given reader
+ * @param isWritable - can be exported with the returned writer
*/
private FileFormat(String shortName, String extensions,
boolean isReadable, boolean isWritable)
*/
private FileFormat(String shortName, String extensions,
boolean isReadable, boolean isWritable)