private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
.toString();
+ private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString();
/*
* a date formatter using a fixed (rather than the user's) locale;
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
.getDefault(
"PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
-
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+ // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
if (jnlpVersion == null
* Determines the parser used for parsing PDB format file. Possible options
* are : JMolParser|JalveiwParser
*/
+ private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
public static void addSettings(boolean addAlignmentAnnotations,
boolean processSecStr, boolean externalSecStr)
{
.valueOf(defaultStructureFileFormat.toUpperCase());
}
+ public static String getDefaultPDBFileParser()
+ {
+ return defaultPDBFileParser.toString();
+ }
+
+ public static void setDefaultPDBFileParser(
+ StructureParser defaultPDBFileParser)
+ {
+ StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
+ }
+
+ public static void setDefaultPDBFileParser(String defaultPDBFileParser)
+ {
+ StructureImportSettings.defaultPDBFileParser = StructureParser
+ .valueOf(defaultPDBFileParser.toUpperCase());
+ }
}
import jalview.io.AppletFormatAdapter;
import jalview.io.FileLoader;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.util.Vector;
Cache.applicationProperties.setProperty("ADD_SS_ANN",
Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ StructureImportSettings
+ .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.io.File;
{
System.out.println("CalcId: " + aa.getCalcId());
- // if (StructureImportSettings.getDefaultPDBFileParser().equals(
- // StructureParser.JALVIEW_PARSER))
- // {
- // assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
- // }
+ if (StructureImportSettings.getDefaultPDBFileParser().equals(
+ StructureParser.JALVIEW_PARSER))
+ {
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
}
}
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ StructureImportSettings
+ .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
testRetrieveProteinSeqFromPDB();
}