import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
* alignment with reference to mappings
*/
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nCAGT\n", FormatAdapter.PASTE);
+ ">Seq1\nCAGT\n", DataSourceType.PASTE);
SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
AlignedCodonFrame acf1 = new AlignedCodonFrame();
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+ ">Seq1\nRSVQ\n", DataSourceType.PASTE);
AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+ ">Seq2\nDGEL\n", DataSourceType.PASTE);
SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+ ">Seq1\nRSVQ\n", DataSourceType.PASTE);
AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+ ">Seq2\nDGEL\n", DataSourceType.PASTE);
SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", FormatAdapter.FILE);
+ "examples/uniref50.fa", DataSourceType.FILE);
AlignmentAnnotation[] anns = af.viewport.getAlignment()
.getAlignmentAnnotation();
assertNotNull("No annotations found", anns);
Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
Boolean.TRUE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", FormatAdapter.FILE);
+ "examples/uniref50.fa", DataSourceType.FILE);
ColourSchemeI cs = new PIDColourScheme();
af.getViewport().setGlobalColourScheme(cs);
assertFalse(cs.conservationApplied());
public void testSetGetHasSearchResults()
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", FormatAdapter.FILE);
+ "examples/uniref50.fa", DataSourceType.FILE);
SearchResultsI sr = new SearchResults();
SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);