import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
private AlignmentI getSearchResultFragmentAlignment() throws Exception
{
AlignmentI alf = new FormatAdapter().readFile(
- alignmentFragFile.getAbsolutePath(), FormatAdapter.FILE,
- "FASTA");
+ alignmentFragFile.getAbsolutePath(), DataSourceType.FILE,
+ FileFormat.Fasta);
return alf;
}
private AlignmentI getSearchResultAlignment() throws Exception
{
AlignmentI alf = new FormatAdapter().readFile(
- alignmentResultFile.getAbsolutePath(), FormatAdapter.FILE,
- "FASTA");
+ alignmentResultFile.getAbsolutePath(), DataSourceType.FILE,
+ FileFormat.Fasta);
return alf;
}
JSONParser jp = new JSONParser();
// read JSON in same way - via fileparse
Object hitfragment = jp.parse(new FileParse(hitTestFile,
- FormatAdapter.FILE).getReader());
+ DataSourceType.FILE).getReader());
Assert.assertTrue((hitfragment instanceof JSONObject),
"Didn't find a JSON object map in " + hitTestFile);
AlignmentI searchResult = getSearchResultFragmentAlignment();
"Didn't read search result alignment from " + alignmentFragFile);
HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
- hjsp.parseFrom(new FileParse(hmmerResultFile, FormatAdapter.FILE));
+ hjsp.parseFrom(new FileParse(hmmerResultFile, DataSourceType.FILE));
AlignmentAnnotation[] aa = searchResult.getSequenceAt(5)
.getAnnotation();
Assert.assertNotNull(aa);