import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
assertEquals(0, chainA.seqend); // not set
assertEquals(18, chainA.sequence.getStart());
assertEquals(314, chainA.sequence.getEnd());
assertEquals(0, chainA.seqend); // not set
assertEquals(18, chainA.sequence.getStart());
assertEquals(314, chainA.sequence.getEnd());
assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|A", chainA.sequence.getName());
assertNull(chainA.sequence.getAnnotation());
assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|A", chainA.sequence.getName());
assertNull(chainA.sequence.getAnnotation());
PDBChain chainC = pf.getChains().get(2);
assertEquals(18, chainC.sequence.getStart());
assertEquals(314, chainC.sequence.getEnd());
PDBChain chainC = pf.getChains().get(2);
assertEquals(18, chainC.sequence.getStart());
assertEquals(314, chainC.sequence.getEnd());
assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|C", chainC.sequence.getName());
assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|C", chainC.sequence.getName());
{
PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
DataSourceType.FILE);
{
PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
DataSourceType.FILE);
- assertEquals("E", anns[2].annotations[18].displayCharacter);
- assertEquals("H", anns[2].annotations[23].displayCharacter);
+ assertEquals('E', anns[2].annotations[18].secondaryStructure);
+ assertEquals('H', anns[2].annotations[23].secondaryStructure);