+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
import static org.testng.AssertJUnit.assertEquals;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.io.File;
-import org.junit.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
al = af.getViewport().getAlignment();
pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
.get(0).getId();
+ StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
{
for (int q = p + 1; q < avec.length; q++)
{
- Assert.assertNotEquals("Found a duplicate annotation row "
- + avec[p].label, avec[p], avec[q]);
+ assertTrue("Found a duplicate annotation row "
+ + avec[p].label, avec[p] != avec[q]);
}
}
}
{
System.out.println("CalcId: " + aa.getCalcId());
+ if (StructureImportSettings.getDefaultPDBFileParser().equals(
+ StructureParser.JALVIEW_PARSER))
+ {
assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
}
}
}
SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqA", sf[0].getDescription());
+ assertEquals("GLU:19 1gaqA", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqA", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqA", sf[295].getDescription());
/*
* 1GAQ/B
sf = al.getSequenceAt(1).getSequenceFeatures();
assertEquals(98, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("ALA: 1 1gaqB", sf[0].getDescription());
+ assertEquals("ALA:1 1gaqB", sf[0].getDescription());
assertEquals("RESNUM", sf[97].getType());
- assertEquals("ALA: 98 1gaqB", sf[97].getDescription());
+ assertEquals("ALA:98 1gaqB", sf[97].getDescription());
/*
* 1GAQ/C
sf = al.getSequenceAt(2).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqC", sf[0].getDescription());
+ assertEquals("GLU:19 1gaqC", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqC", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqC", sf[295].getDescription());
}
@Test(groups = { "Functional" })
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);