+/*
+ * 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.structure;
import static org.testng.Assert.assertEquals;
public class AtomSpecTest
{
@Test
- public void testFromChimeraAtomSpec_chimera()
+ public void testFromChimeraAtomSpec()
{
- AtomSpec as = AtomSpec.fromChimeraAtomspec("#1:12.B", false);
+ AtomSpec as = AtomSpec.fromChimeraAtomspec("#1:12.B");
assertEquals(as.getModelNumber(), 1);
assertEquals(as.getPdbResNum(), 12);
assertEquals(as.getChain(), "B");
assertNull(as.getPdbFile());
// no model - default to zero
- as = AtomSpec.fromChimeraAtomspec(":13.C", false);
+ as = AtomSpec.fromChimeraAtomspec(":13.C");
assertEquals(as.getModelNumber(), 0);
assertEquals(as.getPdbResNum(), 13);
assertEquals(as.getChain(), "C");
assertNull(as.getPdbFile());
// model.submodel
- as = AtomSpec.fromChimeraAtomspec("#3.2:15", false);
+ as = AtomSpec.fromChimeraAtomspec("#3.2:15");
assertEquals(as.getModelNumber(), 3);
assertEquals(as.getPdbResNum(), 15);
assertEquals(as.getChain(), "");
String spec = "3:12.B";
try
{
- as = AtomSpec.fromChimeraAtomspec(spec, false);
+ as = AtomSpec.fromChimeraAtomspec(spec);
fail("Expected exception for " + spec);
} catch (IllegalArgumentException e)
{
spec = "#3:12-14.B";
try
{
- as = AtomSpec.fromChimeraAtomspec(spec, false);
+ as = AtomSpec.fromChimeraAtomspec(spec);
fail("Expected exception for " + spec);
} catch (IllegalArgumentException e)
{
spec = "";
try
{
- as = AtomSpec.fromChimeraAtomspec(spec, false);
+ as = AtomSpec.fromChimeraAtomspec(spec);
fail("Expected exception for " + spec);
} catch (IllegalArgumentException e)
{
spec = null;
try
{
- as = AtomSpec.fromChimeraAtomspec(spec, false);
+ as = AtomSpec.fromChimeraAtomspec(spec);
fail("Expected exception for " + spec);
} catch (NullPointerException e)
{
}
@Test
- public void testFromChimeraAtomSpec_chimeraX()
+ public void testFromChimeraXAtomSpec()
{
- AtomSpec as = AtomSpec.fromChimeraAtomspec("#1/B:12", true);
+ AtomSpec as = AtomSpec.fromChimeraXAtomspec("#1/B:12");
assertEquals(as.getModelNumber(), 1);
assertEquals(as.getPdbResNum(), 12);
assertEquals(as.getChain(), "B");
assertNull(as.getPdbFile());
-
+
// no model - default to zero
- as = AtomSpec.fromChimeraAtomspec("/C:13", true);
+ as = AtomSpec.fromChimeraXAtomspec("/C:13");
assertEquals(as.getModelNumber(), 0);
assertEquals(as.getPdbResNum(), 13);
assertEquals(as.getChain(), "C");
assertNull(as.getPdbFile());
-
+
// model.submodel
- as = AtomSpec.fromChimeraAtomspec("#3.2/:15", true);
+ as = AtomSpec.fromChimeraXAtomspec("#3.2/:15");
assertEquals(as.getModelNumber(), 3);
assertEquals(as.getPdbResNum(), 15);
assertEquals(as.getChain(), "");
assertNull(as.getPdbFile());
-
+
String spec = "3:12.B";
try
{
- as = AtomSpec.fromChimeraAtomspec(spec, true);
+ as = AtomSpec.fromChimeraXAtomspec(spec);
fail("Expected exception for " + spec);
} catch (IllegalArgumentException e)
{
// ok
}
-
+
spec = "#3:12-14.B";
try
{
- as = AtomSpec.fromChimeraAtomspec(spec, true);
+ as = AtomSpec.fromChimeraXAtomspec(spec);
fail("Expected exception for " + spec);
} catch (IllegalArgumentException e)
{
// ok
}
-
+
spec = "";
try
{
- as = AtomSpec.fromChimeraAtomspec(spec, true);
+ as = AtomSpec.fromChimeraXAtomspec(spec);
fail("Expected exception for " + spec);
} catch (IllegalArgumentException e)
{
// ok
}
-
+
spec = null;
try
{
- as = AtomSpec.fromChimeraAtomspec(spec, true);
+ as = AtomSpec.fromChimeraXAtomspec(spec);
fail("Expected exception for " + spec);
} catch (NullPointerException e)
{