X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructure%2FMapping.java;h=181c27318978b3bde38acfceef7cafa8d0efda84;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=c057980b4b103a07885ef73420f22a3a1f7c2135;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java index c057980..181c273 100644 --- a/test/jalview/structure/Mapping.java +++ b/test/jalview/structure/Mapping.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 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.structure; import static org.testng.AssertJUnit.assertEquals; @@ -10,13 +30,12 @@ import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.io.FileLoader; import jalview.io.FormatAdapter; +import jalview.io.StructureFile; import org.testng.Assert; import org.testng.AssertJUnit; import org.testng.annotations.Test; -import MCview.PDBfile; - public class Mapping { @@ -27,8 +46,7 @@ public class Mapping * 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in * msd numbering, not pdb res numbering. */ - @Test(groups = - { "Functional" }, enabled = false) + @Test(groups = { "Functional" }, enabled = false) public void pdbEntryPositionMap() throws Exception { Assert.fail("This test intentionally left to fail"); @@ -44,15 +62,12 @@ public class Mapping // original numbers taken from // http://www.ebi.ac.uk/pdbe-srv/view/entry/1qcf/secondary.html // these are in numbering relative to the subsequence above - int coils[] = - { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[] - { 303, 315 }, sheets[] = new int[] - { 267, 268, 269, 270 }; + int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[] + { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 }; StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager(); - PDBfile pmap = ssm.setMapping(true, new SequenceI[] - { uprot }, new String[] - { "A" }, "test/jalview/ext/jmol/1QCF.pdb", + StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot }, + new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb", jalview.io.FormatAdapter.FILE); assertTrue(pmap != null); SequenceI protseq = pmap.getSeqsAsArray()[0]; @@ -110,8 +125,7 @@ public class Mapping } } - @Test(groups = - { "Functional" }, enabled = false) + @Test(groups = { "Functional" }, enabled = false) public void testPDBentryMapping() throws Exception { Assert.fail("This test intentionally left to fail"); @@ -123,9 +137,9 @@ public class Mapping StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager(); // Associate the 1GAQ pdb file with the subsequence 'imported' from another // source - PDBfile pde = ssm.setMapping(true, new SequenceI[] - { sq }, new String[] - { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE); + StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq }, + new String[] { "A" }, inFile = "examples/1gaq.txt", + jalview.io.FormatAdapter.FILE); assertTrue("PDB File couldn't be found", pde != null); StructureMapping[] mp = ssm.getMapping(inFile); assertTrue("No mappings made.", mp != null && mp.length > 0); @@ -196,8 +210,7 @@ public class Mapping Annotation a = transfer.annotations[tanpos], b = alan.annotations[p]; assertEquals("Non-equivalent annotation element at " + p + "(" + rseqpos + ")" + " expected at " + fpos + " (alIndex " - + tanpos + ")", - a == null ? a : a.toString(), + + tanpos + ")", a == null ? a : a.toString(), b == null ? b : b.toString()); System.out.print("(" + a + "|" + b + ")"); } @@ -212,7 +225,7 @@ public class Mapping * transform * */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void mapFer1From3W5V() throws Exception { AlignFrame seqf = new FileLoader(false) @@ -221,9 +234,8 @@ public class Mapping FormatAdapter.PASTE, "FASTA"); SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0); StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager(); - PDBfile pmap = ssm.setMapping(true, new SequenceI[] - { newseq }, new String[] - { null }, "examples/3W5V.pdb", + StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq }, + new String[] { null }, "examples/3W5V.pdb", jalview.io.FormatAdapter.FILE); if (pmap == null) { @@ -235,9 +247,10 @@ public class Mapping * compare reference annotation for imported pdb sequence to identical * seuqence with transferred annotation from mapped pdb file */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void compareTransferredToRefPDBAnnot() throws Exception { + StructureImportSettings.setShowSeqFeatures(true); AlignFrame ref = new FileLoader(false) .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb", jalview.io.FormatAdapter.FILE); @@ -250,9 +263,8 @@ public class Mapping StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager(); ssm.setProcessSecondaryStructure(true); ssm.setAddTempFacAnnot(true); - PDBfile pmap = ssm.setMapping(true, new SequenceI[] - { newseq }, new String[] - { null }, "test/jalview/ext/jmol/1QCF.pdb", + StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq }, + new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb", jalview.io.FormatAdapter.FILE); assertTrue(pmap != null); assertEquals("Original and copied sequence of different lengths.",