import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
import jalview.io.StructureFile;
import org.testng.Assert;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class Mapping
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.initLogger();
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
/*
* more test data
int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[]
{ 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
- StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
- jalview.io.FormatAdapter.FILE);
+ DataSourceType.FILE);
assertTrue(pmap != null);
SequenceI protseq = pmap.getSeqsAsArray()[0];
AlignmentAnnotation pstra = protseq
"EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
Sequence sq1 = new Sequence(sq);
String inFile;
- StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
// Associate the 1GAQ pdb file with the subsequence 'imported' from another
// source
StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
new String[]
- { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
+ { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
assertTrue("PDB File couldn't be found", pde != null);
StructureMapping[] mp = ssm.getMapping(inFile);
assertTrue("No mappings made.", mp != null && mp.length > 0);
AlignFrame seqf = new FileLoader(false)
.LoadFileWaitTillLoaded(
">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
- FormatAdapter.PASTE, "FASTA");
+ DataSourceType.PASTE, FileFormat.Fasta);
SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
- StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
new String[] { null }, "examples/3W5V.pdb",
- jalview.io.FormatAdapter.FILE);
+ DataSourceType.FILE);
if (pmap == null)
{
AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
@Test(groups = { "Functional" })
public void compareTransferredToRefPDBAnnot() throws Exception
{
- StructureViewSettings.setShowSeqFeatures(true);
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
+ StructureImportSettings.setShowSeqFeatures(true);
AlignFrame ref = new FileLoader(false)
.LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
- jalview.io.FormatAdapter.FILE);
+ DataSourceType.FILE);
SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0);
SequenceI newseq = new Sequence(refseq.getName() + "Copy",
refseq.getSequenceAsString());
// make it harder by shifting the copy vs the reference
newseq.setStart(refseq.getStart() + 25);
newseq.setEnd(refseq.getLength() + 25 + refseq.getStart());
- StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
ssm.setProcessSecondaryStructure(true);
ssm.setAddTempFacAnnot(true);
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
- jalview.io.FormatAdapter.FILE);
+ DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals("Original and copied sequence of different lengths.",
refseq.getLength(), newseq.getLength());