+/*
+ * 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.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
+import jalview.gui.JvOptionPane;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.io.File;
+import java.util.List;
import org.junit.Assert;
import org.testng.annotations.AfterClass;
public class AnnotatedPDBFileInputTest
{
- AlignmentI al;
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
- String pdbStr = "examples/1gaq.txt";
+ AlignmentI al;
String pdbId;
- @BeforeMethod(alwaysRun = true)
+ /**
+ * Ensure 'process secondary structure from PDB and add annotations' are set
+ * in preferences, and load PDB example file 1gaq
+ *
+ * @throws Exception
+ */
+ @BeforeMethod(alwaysRun = true)
public void setup() throws Exception
{
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
Cache.applicationProperties.setProperty("ADD_SS_ANN",
Boolean.TRUE.toString());
FileLoader loader = new FileLoader(false);
- AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
- FormatAdapter.FILE);
+ AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
+ DataSourceType.FILE);
al = af.getViewport().getAlignment();
pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
.get(0).getId();
+ StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void checkNoDuplicates()
{
// not strictly a requirement, but strange things may happen if multiple
{
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]);
}
}
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" }, enabled = false)
public void checkPDBannotationSource()
{
-
+ Assert.fail(
+ "This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
for (SequenceI asq : al.getSequences())
{
for (AlignmentAnnotation aa : asq.getAnnotation())
{
System.out.println("CalcId: " + aa.getCalcId());
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ if (StructureImportSettings.getDefaultPDBFileParser()
+ .equals(StructureParser.JALVIEW_PARSER))
+ {
+ assertTrue(mc_view.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
}
}
}
/**
* Check sequence features have been added
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void checkPDBSequenceFeatures()
{
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- StructureMapping[] mappings = ssm.getMapping("1gaq");
- // suspect we really want to make assertions on sequence features
- // in these mappings' sequencess
/*
* 1GAQ/A
*/
- SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
- assertEquals(296, sf.length);
- assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqA", sf[0].getDescription());
- assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqA", sf[295].getDescription());
+ List<SequenceFeature> sf = al.getSequenceAt(0).getSequenceFeatures();
+ SequenceFeatures.sortFeatures(sf, true);
+ assertEquals(296, sf.size());
+ assertEquals("RESNUM", sf.get(0).getType());
+ assertEquals("GLU: 19 1gaqA", sf.get(0).getDescription());
+ assertEquals("RESNUM", sf.get(295).getType());
+ assertEquals("TYR: 314 1gaqA", sf.get(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("RESNUM", sf[97].getType());
- assertEquals("ALA: 98 1gaqB", sf[97].getDescription());
+ SequenceFeatures.sortFeatures(sf, true);
+ assertEquals(98, sf.size());
+ assertEquals("RESNUM", sf.get(0).getType());
+ assertEquals("ALA: 1 1gaqB", sf.get(0).getDescription());
+ assertEquals("RESNUM", sf.get(97).getType());
+ assertEquals("ALA: 98 1gaqB", sf.get(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("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqC", sf[295].getDescription());
+ SequenceFeatures.sortFeatures(sf, true);
+ assertEquals(296, sf.size());
+ assertEquals("RESNUM", sf.get(0).getType());
+ assertEquals("GLU: 19 1gaqC", sf.get(0).getDescription());
+ assertEquals("RESNUM", sf.get(295).getType());
+ assertEquals("TYR: 314 1gaqC", sf.get(295).getDescription());
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void checkAnnotationWiring()
{
assertTrue(al.getAlignmentAnnotation() != null);
break;
}
}
- assertTrue(
- "Couldn't find sequence associated annotation "
- + aa.label
- + " on the sequence it is associated with.\nSequence associated editing will fail.",
+ assertTrue("Couldn't find sequence associated annotation "
+ + aa.label
+ + " on the sequence it is associated with.\nSequence associated editing will fail.",
found);
}
}
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[]
- { "-props",
- "test/jalview/io/testProps.jvprops" });
+ jalview.bin.Jalview
+ .main(new String[]
+ { "-props", "test/jalview/io/testProps.jvprops" });
}
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testJalviewProjectRelocationAnnotation() throws Exception
{
String inFile = "examples/1gaq.txt";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
+ AlignFrame af = new jalview.io.FileLoader()
+ .LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
+ af.saveAlignment(tfile, FileFormat.Jalview);
assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
+ af.isSaveAlignmentSuccessful());
af.closeMenuItem_actionPerformed(true);
af = null;
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
assertTrue("Failed to import new project", af != null);
for (SequenceI asq : af.getViewport().getAlignment().getSequences())
{
sq = sq.getDatasetSequence();
}
assertNotNull(sq.getAllPDBEntries());
- assertEquals("Expected only one PDB ID", sq.getAllPDBEntries().size(), 1);
+ assertEquals("Expected only one PDB ID", 1,
+ sq.getAllPDBEntries().size());
for (PDBEntry pdbentry : sq.getAllPDBEntries())
{
- System.err.println("PDB Entry " + pdbentry.getId() + " "
- + pdbentry.getFile());
+ System.err.println(
+ "PDB Entry " + pdbentry.getId() + " " + pdbentry.getFile());
boolean exists = false, found = false;
for (AlignmentAnnotation ana : sq.getAnnotation())
{
System.err.println("CalcId " + ana.getCalcId());
if (ana.getCalcId() != null
- && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
+ && mc_view.PDBfile.isCalcIdHandled(ana.getCalcId()))
{
exists = true;
- if (MCview.PDBfile.isCalcIdForFile(ana,
- pdbentry.getId()))
+ if (mc_view.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
{
found = true;
}
}
if (exists)
{
- assertTrue("Couldn't find any annotation for " + pdbentry.getId()
- + " (file handle " + pdbentry.getFile() + ")", found);
+ assertTrue(
+ "Couldn't find any annotation for " + pdbentry.getId()
+ + " (file handle " + pdbentry.getFile() + ")",
+ found);
}
}
}
git://source.jalview.org / jalview.git / blobdiff