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;
acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
- List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> set1 = new ArrayList<>();
set1.add(acf1);
set1.add(acf2);
- List<AlignedCodonFrame> set2 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> set2 = new ArrayList<>();
set2.add(acf2);
set2.add(acf3);
assertEquals(1, pmap.getSeqs().size());
assertEquals("4IM2|A", pmap.getSeqs().get(0).getName());
- List<int[]> structuremap1 = new ArrayList(
+ List<int[]> structuremap1 = new ArrayList<>(
sm.getMapping(P4IM2_MISSING)[0]
.getPDBResNumRanges(seq.getStart(), seq.getEnd()));
// positional mapping to atoms for color by structure is still wrong, even
// though panel looks correct.
- StructureMappingcommandSet smcr[] = JmolCommands
- .getColourBySequenceCommand(apssm,
+ String[] smcr = new JmolCommands().colourBySequence(apssm,
new String[]
{ pdbe.getFile() },
new SequenceI[][]
new SequenceRenderer(alf.alignPanel.getAlignViewport()),
alf.alignPanel);
// Expected - all residues are white
- for (StructureMappingcommandSet smm : smcr)
+ for (String c : smcr)
{
- for (String c : smm.commands)
- {
- System.out.println(c);
- }
+ assertTrue(c.contains("color[255,255,255]"));
+ System.out.println(c);
}
}
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" +