Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
- // ##### Does this need to happen? Follow
- // openStructureFileForSequence() below
- /*
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(structureFile.getAbsolutePath(),
- DataSourceType.FILE, seq, true, Desktop.instance);
- */
-
// open structure view
AlignmentPanel ap = af.alignPanel;
if (headless)
Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
true);
TFType tft = notempfac ? null : TFType.DEFAULT;
- /*
- String tftString = subVals.get("tempfac");
- ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
- af, structureFilepath);
- if (tftString == null && tftAv != null)
- {
- tftString = tftAv.getSubVals().getContent();
- }
- */
if (tftString != null && !notempfac)
{
// get kind of temperature factor annotation
import java.io.IOException;
import org.json.simple.parser.ParseException;
-import org.junit.Assert;
+import org.testng.Assert;
import org.testng.FileAssert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.structure.StructureMapping;
new Sequence("Dummy/1-2000", "ASDASDA"),
EBIAlfaFold.parseJSONtoPAEContactMatrix(
new FileInputStream(paeFile)));
- Assert.assertNotEquals("No data from " + paeFile, cm.getMax(), 0);
+ Assert.assertNotEquals(cm.getMax(), 0.0f, "No data from " + paeFile);
}
@Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")
FileAssert.assertFile(new File(paeFile),
"Test file '" + paeFile + "' doesn't seem to exist");
}
+ SequenceI seq = new Sequence("Dummy/1-2000",
+ "ASDASDAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ AlignFrame af = new AlignFrame(al, seq.getLength(), 1);
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
+ StructureMapping sm = new StructureMapping(seq, pdbFile, null, null,
+ null, null);
+ ssm.addStructureMapping(sm);
StructureMapping[] smArray = ssm.getMapping(pdbFile);
{
boolean done = EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(
smArray, paeInput, "label");
- Assert.assertTrue(
- "Import of '" + paeFile + "' didn't complete successfully",
- done);
+ Assert.assertTrue(done,
+ "Import of '" + paeFile + "' didn't complete successfully");
} catch (IOException | ParseException e)
{
e.printStackTrace();
}
+ }
+ @DataProvider(name = "getPDBandPAEfiles")
+ public Object[][] getPDBandPAEfiles()
+ {
+ return new String[][] {
+ //
+ /*
+ */
+ { "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
+ "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json" },
+ /*
+ { "examples/AlphaFold/AF-A0A1U8FD60-F1-model_v4.pdb",
+ "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
+ { "examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb",
+ "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
+ { "examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb",
+ "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_2023.json" },
+ */
+ };
}
+
}