package jalview.structure;
-
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+
+/**
+ * bean holding settings for structure IO. TODO: tests for validation of values
+ *
+ * @author tcofoegbu
+ *
+ */
public class StructureImportSettings
{
/**
private static boolean processHETATMs = false;
- public enum StructureFormat
+ public enum StructureParser
{
- PDB, MMCIF
- };
+ JMOL_PARSER, JALVIEW_PARSER
+ }
- private static StructureFormat currentDefaultFormat = StructureFormat.PDB;
+ /**
+ * Determines the default file format for structure files to be downloaded
+ * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
+ */
+ private static PDBEntry.Type defaultStructureFileFormat = Type.PDB;
+
+ /**
+ * 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)
{
StructureImportSettings.showSeqFeatures = showSeqFeatures;
}
- public static String getCurrentDefaultFormat()
+ public static String getDefaultStructureFileFormat()
{
- return currentDefaultFormat.toString();
+ return defaultStructureFileFormat.toString();
}
- public static void setCurrentDefaultFormat(String currentDefaultFormat)
+ public static void setDefaultStructureFileFormat(
+ String defaultStructureFileFormat)
{
- StructureImportSettings.currentDefaultFormat = StructureFormat
- .valueOf(currentDefaultFormat);
+ StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
+ .valueOf(defaultStructureFileFormat);
}
public static boolean isProcessHETATMs()
StructureImportSettings.processHETATMs = processHETATMs;
}
+ 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);
+ }
+
}