X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=c0038a1905c9c9830ef613c20b9ad39882b1dea6;hb=c3f8260b41c41ceca04c86f3fe56059e4704d834;hp=d07f28c59c628928d517bb9b9742b1c0c4103488;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java index d07f28c..c0038a1 100644 --- a/test/jalview/io/AnnotatedPDBFileInputTest.java +++ b/test/jalview/io/AnnotatedPDBFileInputTest.java @@ -30,12 +30,16 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.SequenceFeatures; import jalview.gui.AlignFrame; +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; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; @@ -44,6 +48,13 @@ import org.testng.annotations.Test; public class AnnotatedPDBFileInputTest { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + AlignmentI al; String pdbId; @@ -91,18 +102,19 @@ public class AnnotatedPDBFileInputTest } } - @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()); - if (StructureImportSettings.getDefaultPDBFileParser().equals( - StructureParser.JALVIEW_PARSER)) + if (StructureImportSettings.getDefaultPDBFileParser() + .equals(StructureParser.JALVIEW_PARSER)) { assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId)); } @@ -119,32 +131,35 @@ public class AnnotatedPDBFileInputTest /* * 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 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" })