X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=b8c12c6260c98bd49487350de11ae96b8944b845;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=576201a63c4d199f3216345fac56840ba289c329;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java index 576201a..b8c12c6 100644 --- a/test/jalview/io/AnnotatedPDBFileInputTest.java +++ b/test/jalview/io/AnnotatedPDBFileInputTest.java @@ -1,17 +1,29 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.io; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertTrue; -import java.io.File; - -import org.junit.Assert; -import org.testng.annotations.AfterClass; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; - import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; @@ -19,20 +31,30 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; +import jalview.structure.StructureImportSettings; +import jalview.structure.StructureImportSettings.StructureParser; + +import java.io.File; + +import org.testng.annotations.AfterClass; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.BeforeMethod; +import org.testng.annotations.Test; public class AnnotatedPDBFileInputTest { AlignmentI al; - String pdbStr = "examples/1gaq.txt"; - String pdbId; - @BeforeMethod + /** + * 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", @@ -40,14 +62,17 @@ public class AnnotatedPDBFileInputTest Cache.applicationProperties.setProperty("ADD_SS_ANN", Boolean.TRUE.toString()); FileLoader loader = new FileLoader(false); - AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr, + AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt", FormatAdapter.FILE); al = af.getViewport().getAlignment(); - pdbId = al.getSequenceAt(0).getDatasetSequence().getPDBId() + pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries() .get(0).getId(); + StructureImportSettings.setDefaultStructureFileFormat("PDB"); + // StructureImportSettings + // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER); } - @Test + @Test(groups = { "Functional" }) public void checkNoDuplicates() { // not strictly a requirement, but strange things may happen if multiple @@ -60,14 +85,13 @@ public class AnnotatedPDBFileInputTest { 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 + @Test(groups = { "Functional" }) public void checkPDBannotationSource() { @@ -77,7 +101,11 @@ public class AnnotatedPDBFileInputTest { System.out.println("CalcId: " + aa.getCalcId()); - assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId)); + if (StructureImportSettings.getDefaultPDBFileParser().equals( + StructureParser.JALVIEW_PARSER)) + { + assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId)); + } } } } @@ -85,23 +113,18 @@ public class AnnotatedPDBFileInputTest /** * Check sequence features have been added */ - @Test + @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("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 @@ -109,9 +132,9 @@ public class AnnotatedPDBFileInputTest 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 @@ -119,12 +142,12 @@ public class AnnotatedPDBFileInputTest 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 + @Test(groups = { "Functional" }) public void checkAnnotationWiring() { assertTrue(al.getAlignmentAnnotation() != null); @@ -156,24 +179,24 @@ public class AnnotatedPDBFileInputTest /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - jalview.bin.Jalview.main(new String[] - { "-props", "test/src/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 + @Test(groups = { "Functional" }) public void testJalviewProjectRelocationAnnotation() throws Exception { @@ -197,9 +220,10 @@ public class AnnotatedPDBFileInputTest { sq = sq.getDatasetSequence(); } - assertNotNull(sq.getPDBId()); - assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1); - for (PDBEntry pdbentry : sq.getPDBId()) + assertNotNull(sq.getAllPDBEntries()); + assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries() + .size()); + for (PDBEntry pdbentry : sq.getAllPDBEntries()) { System.err.println("PDB Entry " + pdbentry.getId() + " " + pdbentry.getFile()); @@ -211,8 +235,7 @@ public class AnnotatedPDBFileInputTest && MCview.PDBfile.isCalcIdHandled(ana.getCalcId())) { exists = true; - if (MCview.PDBfile.isCalcIdForFile(ana, - pdbentry.getId())) + if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId())) { found = true; }