X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=b8c12c6260c98bd49487350de11ae96b8944b845;hb=528c0f1815bc67b54618ad5b16c2162946974caf;hp=acc2cb8161cb5888cb0cafe5e27b76fefb0ddd21;hpb=cd47f700cdf7aef86873db26ce3dc97a20c672c7;p=jalview.git diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java index acc2cb8..b8c12c6 100644 --- a/test/jalview/io/AnnotatedPDBFileInputTest.java +++ b/test/jalview/io/AnnotatedPDBFileInputTest.java @@ -1,32 +1,78 @@ +/* + * 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.junit.Assert.assertNotEquals; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertTrue; + +import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +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.Before; -import org.junit.Test; +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/2GIS.pdb"; - @Before + String pdbId; + + /** + * 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", + Boolean.TRUE.toString()); + 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().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 @@ -39,14 +85,13 @@ public class AnnotatedPDBFileInputTest { for (int q = p + 1; q < avec.length; q++) { - 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() { @@ -56,12 +101,53 @@ public class AnnotatedPDBFileInputTest { System.out.println("CalcId: " + aa.getCalcId()); - assertTrue(MCview.PDBfile.isCalcIdForFile(aa.getCalcId(), pdbStr)); + if (StructureImportSettings.getDefaultPDBFileParser().equals( + StructureParser.JALVIEW_PARSER)) + { + assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId)); + } } } } - @Test + /** + * Check sequence features have been added + */ + @Test(groups = { "Functional" }) + public void checkPDBSequenceFeatures() + { + /* + * 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()); + + /* + * 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()); + + /* + * 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()); + } + + @Test(groups = { "Functional" }) public void checkAnnotationWiring() { assertTrue(al.getAlignmentAnnotation() != null); @@ -89,4 +175,78 @@ public class AnnotatedPDBFileInputTest } } } + + /** + * @throws java.lang.Exception + */ + @BeforeClass(alwaysRun = true) + public static void setUpBeforeClass() throws Exception + { + jalview.bin.Jalview.main(new String[] { "-props", + "test/jalview/io/testProps.jvprops" }); + } + + /** + * @throws java.lang.Exception + */ + @AfterClass(alwaysRun = true) + public static void tearDownAfterClass() throws Exception + { + jalview.gui.Desktop.instance.closeAll_actionPerformed(null); + + } + + @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); + assertTrue("Didn't read input file " + inFile, af != null); + assertTrue("Failed to store as a project.", + af.saveAlignment(tfile, "Jalview")); + af.closeMenuItem_actionPerformed(true); + af = null; + af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, + FormatAdapter.FILE); + assertTrue("Failed to import new project", af != null); + for (SequenceI asq : af.getViewport().getAlignment().getSequences()) + { + SequenceI sq = asq; + while (sq.getDatasetSequence() != null) + { + sq = sq.getDatasetSequence(); + } + 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()); + 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())) + { + exists = true; + if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId())) + { + found = true; + } + } + } + if (exists) + { + assertTrue("Couldn't find any annotation for " + pdbentry.getId() + + " (file handle " + pdbentry.getFile() + ")", found); + } + } + } + } }