import jalview.analysis.AlignmentUtils;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.io.Jalview2xmlBase;
import jalview.io.StructureFile;
import jalview.util.MapList;
+import jalview.ws.DBRefFetcher;
import jalview.ws.sifts.SiftsSettings;
import java.util.ArrayList;
{
// for some reason 'BeforeMethod' (which should be inherited from
// Jalview2XmlBase isn't always called)...
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
try {
Thread.sleep(200);
} catch (Exception foo) {};
public void testAssociatedMappingToSubSeq() throws Exception
{
+ // currently this test fails if trimming is enabled
+ Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
+ Boolean.FALSE.toString());
String TEMP_FACTOR_AA="Temperature Factor";
String PDBID = "4IM2";
String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" +
PDBID);
AlignmentAnnotation subseq_tf=null;
- assertTrue(seq.getDBRefs() != null && seq.getDBRefs().length > 0);
+ assertTrue(seq.getDBRefs() != null && seq.getDBRefs().size() > 0);
if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
{