package jalview.structure;
-import jalview.datamodel.DBRefSource;
-
+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
{
/**
* Set true to predict secondary structure (using JMol for protein, Annotate3D
* for RNA)
*/
- private static boolean predictSecStr = false;
+ private static boolean processSecStr = false;
/**
* Set true (with predictSecondaryStructure=true) to predict secondary
private static boolean showSeqFeatures = true;
- public static final String JMOL_PARSER = "JMolParser";
-
- public static final String JALVIEW_PARSER = "JalViewParser";
-
- public static final String MMCIF = "mmCIF";
+ public enum StructureParser
+ {
+ JMOL_PARSER, JALVIEW_PARSER
+ }
- public static final String PDB = "PDB";
/**
* Determines the default file format for structure files to be downloaded
* from the PDB sequence fetcher. Possible options include: PDB|mmCIF
*/
- private static String defaultStructureFileFormat = DBRefSource.PDB;
+ private static PDBEntry.Type defaultStructureFileFormat = Type.PDB;
/**
* Determines the parser used for parsing PDB format file. Possible options
* are : JMolParser|JalveiwParser
*/
- private static String defaultPDBFileParser = JMOL_PARSER;
+ private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
public static void addSettings(boolean addAlignmentAnnotations,
- boolean predictSecStr, boolean externalSecStr)
+ boolean processSecStr, boolean externalSecStr)
{
StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
- StructureImportSettings.predictSecStr = predictSecStr;
+ StructureImportSettings.processSecStr = processSecStr;
StructureImportSettings.externalSecondaryStructure = externalSecStr;
StructureImportSettings.showSeqFeatures = true;
}
StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
}
- public static boolean isPredictSecondaryStructure()
+ public static boolean isProcessSecondaryStructure()
{
- return predictSecStr;
+ return processSecStr;
}
- public static void setPredictSecondaryStructure(
- boolean predictSecondaryStructure)
+ public static void setProcessSecondaryStructure(
+ boolean processSecondaryStructure)
{
- StructureImportSettings.predictSecStr = predictSecondaryStructure;
+ StructureImportSettings.processSecStr = processSecondaryStructure;
}
public static boolean isExternalSecondaryStructure()
public static String getDefaultStructureFileFormat()
{
- return defaultStructureFileFormat;
+ return defaultStructureFileFormat.toString();
}
public static void setDefaultStructureFileFormat(
String defaultStructureFileFormat)
{
- StructureImportSettings.defaultStructureFileFormat = defaultStructureFileFormat;
+ StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
+ .valueOf(defaultStructureFileFormat);
}
public static String getDefaultPDBFileParser()
{
- return defaultPDBFileParser;
+ return defaultPDBFileParser.toString();
}
- public static void setDefaultPDBFileParser(String defaultPDBFileParser)
+ public static void setDefaultPDBFileParser(
+ StructureParser defaultPDBFileParser)
{
StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
}
+ public static void setDefaultPDBFileParser(String defaultPDBFileParser)
+ {
+ StructureImportSettings.defaultPDBFileParser = StructureParser
+ .valueOf(defaultPDBFileParser);
+ }
+
}