/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.structure.StructureImportSettings;
import java.io.IOException;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBfileTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testIsRna()
{
* Constructor with file path performs parse()
*/
PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb",
- AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
assertEquals("3W5V", pf.getId());
// verify no alignment annotations created
public void testParse_withAnnotations_noSS() throws IOException
{
PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
- AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
assertEquals(4, anns.length);
public void testParse_withJmol_noAnnotations() throws IOException
{
PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
- AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
/*
* alignment annotations _are_ created anyway (in
throws IOException
{
PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
- AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
/*
* Alignment annotations for TempFactor, SecStruct, per sequence (chain)
// TODO requires a mock for Annotate3D processing
// and/or run as an integration test
PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb",
- AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
}
/**
return al.getAlignmentAnnotation();
}
- // @formatter:on
-
@BeforeMethod(alwaysRun = true)
public void setUp()
{