From 0bec4854366c4bc4608ed0d7dc1506fc6afe2285 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Fri, 8 Jul 2016 17:16:54 +0100 Subject: [PATCH] JAL-1919 Fixed failing tests, enabled HETATM processing from structure file to be configurable. Minor refactorings (StructureViewSettings class renamed to StructureImportSettings, fileName variables of AlignFile class renamed to dataObject since in realty it could be a file, url or pasted string) --- src/MCview/PDBChain.java | 4 +-- src/MCview/PDBfile.java | 8 +++-- src/jalview/bin/Cache.java | 7 ++-- src/jalview/ext/jmol/JmolParser.java | 6 ++-- src/jalview/io/AlignFile.java | 18 +++++------ src/jalview/io/AppletFormatAdapter.java | 18 +++++------ src/jalview/io/StructureFile.java | 22 ++++++------- ...wSettings.java => StructureImportSettings.java} | 34 +++++++++++++------- src/jalview/ws/dbsources/Pdb.java | 8 ++--- test/MCview/PDBChainTest.java | 4 +-- test/jalview/ext/jmol/JmolParserTest.java | 33 +++++++++++++++++-- test/jalview/gui/AlignViewportTest.java | 8 ++--- test/jalview/io/AnnotatedPDBFileInputTest.java | 2 ++ test/jalview/structure/Mapping.java | 2 +- .../structure/StructureSelectionManagerTest.java | 2 +- test/jalview/ws/PDBSequenceFetcherTest.java | 6 ++-- 16 files changed, 113 insertions(+), 69 deletions(-) rename src/jalview/structure/{StructureViewSettings.java => StructureImportSettings.java} (66%) diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 248cf29..885521b 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -30,7 +30,7 @@ import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.StructureMapping; -import jalview.structure.StructureViewSettings; +import jalview.structure.StructureImportSettings; import java.awt.Color; import java.util.List; @@ -423,7 +423,7 @@ public class PDBChain // System.out.println("PDB Sequence is :\nSequence = " + seq); // System.out.println("No of residues = " + residues.size()); - if (StructureViewSettings.isShowSeqFeatures()) + if (StructureImportSettings.isShowSeqFeatures()) { for (i = 0, iSize = resFeatures.size(); i < iSize; i++) { diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 9a9b6f6..9acc2e7 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -25,6 +25,7 @@ import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; import jalview.io.FileParse; import jalview.io.StructureFile; +import jalview.structure.StructureImportSettings; import jalview.util.MessageManager; import java.io.IOException; @@ -46,10 +47,10 @@ public class PDBfile extends StructureFile } public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr, - boolean externalSecStr, String file, String protocol) + boolean externalSecStr, String dataObject, String protocol) throws IOException { - super(false, file, protocol); + super(false, dataObject, protocol); addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr); doParse(); } @@ -131,7 +132,8 @@ public class PDBfile extends StructureFile break; } if (line.indexOf("ATOM") == 0 - || (line.indexOf("HETATM") == 0 && !terFlag)) + || (StructureImportSettings.isProcessHETATMs() + && line.indexOf("HETATM") == 0 && !terFlag)) { terFlag = false; diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index dde67de..cf251dc 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -21,7 +21,7 @@ package jalview.bin; import jalview.datamodel.DBRefSource; -import jalview.structure.StructureViewSettings; +import jalview.structure.StructureImportSettings; import jalview.ws.dbsources.das.api.DasSourceRegistryI; import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; import jalview.ws.sifts.SiftsSettings; @@ -426,9 +426,12 @@ public class Cache System.out .println("Jalview Version: " + codeVersion + codeInstallation); - StructureViewSettings.setCurrentDefaultFormat(jalview.bin.Cache + StructureImportSettings.setCurrentDefaultFormat(jalview.bin.Cache .getDefault( "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT)); + + StructureImportSettings.setProcessHETATMs(jalview.bin.Cache.getDefault( + "PROCESS_HETATM", false)); // jnlpVersion will be null if we're using InstallAnywhere // Dont do this check if running in headless mode if (jnlpVersion == null diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index 309e196..c514503 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -27,7 +27,7 @@ import jalview.datamodel.SequenceI; import jalview.io.FileParse; import jalview.io.StructureFile; import jalview.schemes.ResidueProperties; -import jalview.structure.StructureViewSettings; +import jalview.structure.StructureImportSettings; import jalview.util.MessageManager; import java.io.IOException; @@ -186,7 +186,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener prot.add(chainseq); } - if (StructureViewSettings.isPredictSecondaryStructure()) + if (StructureImportSettings.isPredictSecondaryStructure()) { createAnnotation(chainseq, chain, ms.at); } @@ -208,7 +208,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener { // System.out.println("Seq Id : " + atom.getSeqID()); // System.out.println("To String : " + atom.toString()); - if (atom.isHetero()) + if (!StructureImportSettings.isProcessHETATMs() && atom.isHetero()) { continue; } diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 984eff6..5760fbe 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -89,14 +89,14 @@ public abstract class AlignFile extends FileParse /** * Constructor which parses the data from a file of some specified type. * - * @param inFile - * Filename to read from. + * @param dataObject + * Filename, URL or Pasted String to read from. * @param type - * What type of file to read from (File, URL) + * What type of file to read from (File, URL, Pasted String) */ - public AlignFile(String inFile, String type) throws IOException + public AlignFile(String dataObject, String type) throws IOException { - this(true, inFile, type); + this(true, dataObject, type); } /** @@ -105,16 +105,16 @@ public abstract class AlignFile extends FileParse * * @param parseImmediately * if false, need to call 'doParse()' to begin parsing data - * @param inFile - * Filename to read from. + * @param dataObject + * Filename, URL or Pasted String to read from. * @param type * What type of file to read from (File, URL) * @throws IOException */ - public AlignFile(boolean parseImmediately, String inFile, String type) + public AlignFile(boolean parseImmediately, String dataObject, String type) throws IOException { - super(inFile, type); + super(dataObject, type); initData(); if (parseImmediately) { diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 42a8ead..fb414f4 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -26,7 +26,7 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; -import jalview.structure.StructureViewSettings; +import jalview.structure.StructureImportSettings; import jalview.util.MessageManager; import java.io.File; @@ -280,11 +280,11 @@ public class AppletFormatAdapter { // TODO obtain config value from preference settings. // Set value to 'true' to test PDB processing with Jmol: JAL-1213 - boolean isParseWithJMOL = !StructureViewSettings + boolean isParseWithJMOL = !StructureImportSettings .getCurrentDefaultFormat().equalsIgnoreCase("PDB"); if (isParseWithJMOL) { - StructureViewSettings.addSettings(annotFromStructure, + StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, inFile, @@ -292,9 +292,9 @@ public class AppletFormatAdapter } else { - StructureViewSettings.addSettings(annotFromStructure, + StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); - StructureViewSettings.setShowSeqFeatures(true); + StructureImportSettings.setShowSeqFeatures(true); alignFile = new MCview.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, inFile, type); @@ -302,7 +302,7 @@ public class AppletFormatAdapter } else if (format.equals("mmCIF")) { - StructureViewSettings.addSettings(annotFromStructure, + StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, inFile, type); @@ -436,21 +436,21 @@ public class AppletFormatAdapter boolean isParseWithJMOL = false; if (isParseWithJMOL) { - StructureViewSettings.addSettings(annotFromStructure, + StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, source); } else { - StructureViewSettings.setShowSeqFeatures(true); + StructureImportSettings.setShowSeqFeatures(true); alignFile = new MCview.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, source); } } else if (format.equals("mmCIF")) { - StructureViewSettings.addSettings(annotFromStructure, + StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, source); diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java index 6a236fd..6970ffa 100644 --- a/src/jalview/io/StructureFile.java +++ b/src/jalview/io/StructureFile.java @@ -9,7 +9,7 @@ import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; -import jalview.structure.StructureViewSettings; +import jalview.structure.StructureImportSettings; import java.awt.Color; import java.io.IOException; @@ -67,19 +67,19 @@ public abstract class StructureFile extends AlignFile public void xferSettings() { - this.visibleChainAnnotation = StructureViewSettings + this.visibleChainAnnotation = StructureImportSettings .isVisibleChainAnnotation(); - this.predictSecondaryStructure = StructureViewSettings + this.predictSecondaryStructure = StructureImportSettings .isPredictSecondaryStructure(); - this.externalSecondaryStructure = StructureViewSettings + this.externalSecondaryStructure = StructureImportSettings .isExternalSecondaryStructure(); } - public StructureFile(boolean parseImmediately, String inFile, String type) + public StructureFile(boolean parseImmediately, String dataObject, String type) throws IOException { - super(parseImmediately, inFile, type); + super(parseImmediately, dataObject, type); } public StructureFile(boolean a, FileParse fp) throws IOException @@ -270,11 +270,11 @@ public abstract class StructureFile extends AlignFile predictSecondaryStructure, externalSecondaryStructure, new FileParse(getDataName(), type) }; - StructureViewSettings.setShowSeqFeatures(false); - StructureViewSettings.setVisibleChainAnnotation(false); - StructureViewSettings + StructureImportSettings.setShowSeqFeatures(false); + StructureImportSettings.setVisibleChainAnnotation(false); + StructureImportSettings .setPredictSecondaryStructure(predictSecondaryStructure); - StructureViewSettings + StructureImportSettings .setExternalSecondaryStructure(externalSecondaryStructure); Object jmf = constructor.newInstance(args); AlignmentI al = new Alignment((SequenceI[]) cl.getMethod( @@ -297,7 +297,7 @@ public abstract class StructureFile extends AlignFile } catch (ClassNotFoundException q) { } - StructureViewSettings.setShowSeqFeatures(true); + StructureImportSettings.setShowSeqFeatures(true); } public PDBChain findChain(String id) throws Exception diff --git a/src/jalview/structure/StructureViewSettings.java b/src/jalview/structure/StructureImportSettings.java similarity index 66% rename from src/jalview/structure/StructureViewSettings.java rename to src/jalview/structure/StructureImportSettings.java index 5880d0f..b23fd53 100644 --- a/src/jalview/structure/StructureViewSettings.java +++ b/src/jalview/structure/StructureImportSettings.java @@ -2,10 +2,8 @@ package jalview.structure; import jalview.datamodel.DBRefSource; -public class StructureViewSettings +public class StructureImportSettings { - private String dbRefType; - /** * set to true to add derived sequence annotations (temp factor read from * file, or computed secondary structure) to the alignment @@ -26,15 +24,17 @@ public class StructureViewSettings private static boolean showSeqFeatures = true; + private static boolean processHETATMs = false; + private static String currentDefaultFormat = DBRefSource.PDB; public static void addSettings(boolean addAlignmentAnnotations, boolean predictSecStr, boolean externalSecStr) { - StructureViewSettings.visibleChainAnnotation = addAlignmentAnnotations; - StructureViewSettings.predictSecStr = predictSecStr; - StructureViewSettings.externalSecondaryStructure = externalSecStr; - StructureViewSettings.showSeqFeatures = true; + StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations; + StructureImportSettings.predictSecStr = predictSecStr; + StructureImportSettings.externalSecondaryStructure = externalSecStr; + StructureImportSettings.showSeqFeatures = true; } public static boolean isVisibleChainAnnotation() @@ -45,7 +45,7 @@ public class StructureViewSettings public static void setVisibleChainAnnotation( boolean visibleChainAnnotation) { - StructureViewSettings.visibleChainAnnotation = visibleChainAnnotation; + StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation; } public static boolean isPredictSecondaryStructure() @@ -56,7 +56,7 @@ public class StructureViewSettings public static void setPredictSecondaryStructure( boolean predictSecondaryStructure) { - StructureViewSettings.predictSecStr = predictSecondaryStructure; + StructureImportSettings.predictSecStr = predictSecondaryStructure; } public static boolean isExternalSecondaryStructure() @@ -67,7 +67,7 @@ public class StructureViewSettings public static void setExternalSecondaryStructure( boolean externalSecondaryStructure) { - StructureViewSettings.externalSecondaryStructure = externalSecondaryStructure; + StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure; } public static boolean isShowSeqFeatures() @@ -77,7 +77,7 @@ public class StructureViewSettings public static void setShowSeqFeatures(boolean showSeqFeatures) { - StructureViewSettings.showSeqFeatures = showSeqFeatures; + StructureImportSettings.showSeqFeatures = showSeqFeatures; } public static String getCurrentDefaultFormat() @@ -87,7 +87,17 @@ public class StructureViewSettings public static void setCurrentDefaultFormat(String currentDefaultFormat) { - StructureViewSettings.currentDefaultFormat = currentDefaultFormat; + StructureImportSettings.currentDefaultFormat = currentDefaultFormat; + } + + public static boolean isProcessHETATMs() + { + return processHETATMs; + } + + public static void setProcessHETATMs(boolean processHETATMs) + { + StructureImportSettings.processHETATMs = processHETATMs; } } diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index d3a6238..d945699 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -30,7 +30,7 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.io.FormatAdapter; import jalview.io.PDBFeatureSettings; -import jalview.structure.StructureViewSettings; +import jalview.structure.StructureImportSettings; import jalview.util.MessageManager; import jalview.ws.ebi.EBIFetchClient; @@ -132,12 +132,12 @@ public class Pdb extends EbiFileRetrievedProxy stopQuery(); return null; } - String ext = StructureViewSettings.getCurrentDefaultFormat() + String ext = StructureImportSettings.getCurrentDefaultFormat() .equalsIgnoreCase("mmcif") ? ".cif" : ".xml"; EBIFetchClient ebi = new EBIFetchClient(); file = ebi.fetchDataAsFile("pdb:" + id, - StructureViewSettings.getCurrentDefaultFormat().toLowerCase(), + StructureImportSettings.getCurrentDefaultFormat().toLowerCase(), ext) .getAbsolutePath(); stopQuery(); @@ -150,7 +150,7 @@ public class Pdb extends EbiFileRetrievedProxy pdbAlignment = new FormatAdapter().readFile(file, jalview.io.AppletFormatAdapter.FILE, - StructureViewSettings.getCurrentDefaultFormat()); + StructureImportSettings.getCurrentDefaultFormat()); if (pdbAlignment != null) { List toremove = new ArrayList(); diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java index ff745ac..0406128 100644 --- a/test/MCview/PDBChainTest.java +++ b/test/MCview/PDBChainTest.java @@ -32,7 +32,7 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; import jalview.schemes.TaylorColourScheme; -import jalview.structure.StructureViewSettings; +import jalview.structure.StructureImportSettings; import java.awt.Color; import java.util.Vector; @@ -56,7 +56,7 @@ public class PDBChainTest public void setUp() { System.out.println("setup"); - StructureViewSettings.setShowSeqFeatures(true); + StructureImportSettings.setShowSeqFeatures(true); c = new PDBChain("1GAQ", "A"); } diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java index 7ac1579..0627a4a 100644 --- a/test/jalview/ext/jmol/JmolParserTest.java +++ b/test/jalview/ext/jmol/JmolParserTest.java @@ -30,6 +30,7 @@ import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.io.AppletFormatAdapter; import jalview.io.FileLoader; +import jalview.structure.StructureImportSettings; import java.util.Vector; @@ -55,7 +56,7 @@ public class JmolParserTest //@formatter:off // a modified and very cut-down extract of 4UJ4 - String pdbWithChainBreak = + String pastePDBDataWithChainBreak = "HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" + // chain B has missing residues; these should all go in the same sequence: "ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" + @@ -105,6 +106,31 @@ public class JmolParserTest @Test(groups = { "Functional" }) public void testFileParser() throws Exception { + StructureImportSettings.setProcessHETATMs(false); + for (String pdbStr : testFile) + { + PDBfile mctest = new PDBfile(false, false, false, pdbStr, + AppletFormatAdapter.FILE); + JmolParser jtest = new JmolParser(false, false, false, pdbStr, + jalview.io.AppletFormatAdapter.FILE); + Vector seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs(); + + assertTrue( + "No sequences extracted from testfile\n" + + (jtest.hasWarningMessage() ? jtest.getWarningMessage() + : "(No warnings raised)"), seqs != null + && seqs.size() > 0); + for (SequenceI sq : seqs) + { + assertEquals("JMol didn't process " + pdbStr + + " to the same sequence as MCView", + sq.getSequenceAsString(), mcseqs.remove(0) + .getSequenceAsString()); + AlignmentI al = new Alignment(new SequenceI[] { sq }); + validateSecStrRows(al); + } + } + StructureImportSettings.setProcessHETATMs(true); for (String pdbStr : testFile) { PDBfile mctest = new PDBfile(false, false, false, pdbStr, @@ -173,14 +199,15 @@ public class JmolParserTest @Test(groups = { "Functional" }) public void testParse_missingResidues() throws Exception { - PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak, + PDBfile mctest = new PDBfile(false, false, false, + pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE); boolean annotFromStructure = false; boolean localSecondaryStruct = false; boolean serviceSecondaryStruct = false; JmolParser jtest = new JmolParser(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, - pdbWithChainBreak, + pastePDBDataWithChainBreak, jalview.io.AppletFormatAdapter.PASTE); Vector seqs = jtest.getSeqs(); Vector mcseqs = mctest.getSeqs(); diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index b39b2bd..c956da1 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -76,12 +76,12 @@ public class AlignViewportTest /* * Set up sequence pdb ids */ - PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb"); - PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb"); - PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb"); + PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"); + PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"); + PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb"); /* - * seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC + * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD */ al.getSequenceAt(0).getDatasetSequence() .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb")); diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java index 62d76a2..3524a88 100644 --- a/test/jalview/io/AnnotatedPDBFileInputTest.java +++ b/test/jalview/io/AnnotatedPDBFileInputTest.java @@ -31,6 +31,7 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; +import jalview.structure.StructureImportSettings; import java.io.File; @@ -65,6 +66,7 @@ public class AnnotatedPDBFileInputTest al = af.getViewport().getAlignment(); pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries() .get(0).getId(); + StructureImportSettings.setCurrentDefaultFormat("PDB"); } @Test(groups = { "Functional" }) diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java index 8674ed8..5ab43b5 100644 --- a/test/jalview/structure/Mapping.java +++ b/test/jalview/structure/Mapping.java @@ -250,7 +250,7 @@ public class Mapping @Test(groups = { "Functional" }) public void compareTransferredToRefPDBAnnot() throws Exception { - StructureViewSettings.setShowSeqFeatures(true); + StructureImportSettings.setShowSeqFeatures(true); AlignFrame ref = new FileLoader(false) .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb", jalview.io.FormatAdapter.FILE); diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java index 999d158..16f56a6 100644 --- a/test/jalview/structure/StructureSelectionManagerTest.java +++ b/test/jalview/structure/StructureSelectionManagerTest.java @@ -43,7 +43,7 @@ public class StructureSelectionManagerTest @BeforeMethod(alwaysRun = true) public void setUp() { - StructureViewSettings.setShowSeqFeatures(true); + StructureImportSettings.setShowSeqFeatures(true); ssm = new StructureSelectionManager(); } diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java index 27d2643..0c810a3 100644 --- a/test/jalview/ws/PDBSequenceFetcherTest.java +++ b/test/jalview/ws/PDBSequenceFetcherTest.java @@ -25,7 +25,7 @@ import static org.testng.AssertJUnit.assertTrue; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; -import jalview.structure.StructureViewSettings; +import jalview.structure.StructureImportSettings; import jalview.ws.seqfetcher.DbSourceProxy; import java.util.List; @@ -86,7 +86,7 @@ public class PDBSequenceFetcherTest { Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", Boolean.TRUE.toString()); - StructureViewSettings.setCurrentDefaultFormat("PDB"); + StructureImportSettings.setCurrentDefaultFormat("PDB"); testRetrieveProteinSeqFromPDB(); } @@ -96,7 +96,7 @@ public class PDBSequenceFetcherTest { Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", Boolean.TRUE.toString()); - StructureViewSettings.setCurrentDefaultFormat("mmCIF"); + StructureImportSettings.setCurrentDefaultFormat("mmCIF"); testRetrieveProteinSeqFromPDB(); } -- 1.7.10.2