*/
package jalview.structure;
+import jalview.bin.Instance;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
*/
public class StructureImportSettings
{
+
+ private StructureImportSettings()
+ {
+ // singleton
+ }
+
+ private static StructureImportSettings getInstance()
+ {
+ Instance j = Instance.getInstance();
+ return (j.structureImportSettings == null
+ ? j.structureImportSettings = new StructureImportSettings()
+ : j.structureImportSettings);
+ }
+
/**
* set to true to add derived sequence annotations (temp factor read from
* file, or computed secondary structure) to the alignment
*/
- private static boolean visibleChainAnnotation = false;
+ private boolean visibleChainAnnotation = false;
/**
* Set true to predict secondary structure (using JMol for protein, Annotate3D
* for RNA)
*/
- private static boolean processSecStr = false;
+ private boolean processSecStr = false;
/**
* Set true (with predictSecondaryStructure=true) to predict secondary
* structure using an external service (currently Annotate3D for RNA only)
*/
- private static boolean externalSecondaryStructure = false;
+ private boolean externalSecondaryStructure = false;
- private static boolean showSeqFeatures = true;
+ private boolean showSeqFeatures = true;
public enum StructureParser
{
* 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;
+ private 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;
+ private StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
public static void addSettings(boolean addAlignmentAnnotations,
boolean processSecStr, boolean externalSecStr)
{
- StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
- StructureImportSettings.processSecStr = processSecStr;
- StructureImportSettings.externalSecondaryStructure = externalSecStr;
- StructureImportSettings.showSeqFeatures = true;
+ StructureImportSettings s = getInstance();
+ s.visibleChainAnnotation = addAlignmentAnnotations;
+ s.processSecStr = processSecStr;
+ s.externalSecondaryStructure = externalSecStr;
+ s.showSeqFeatures = true;
}
public static boolean isVisibleChainAnnotation()
{
- return visibleChainAnnotation;
+ return getInstance().visibleChainAnnotation;
}
public static void setVisibleChainAnnotation(
boolean visibleChainAnnotation)
{
- StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
+ getInstance().visibleChainAnnotation = visibleChainAnnotation;
}
public static boolean isProcessSecondaryStructure()
{
- return processSecStr;
+ return getInstance().processSecStr;
}
public static void setProcessSecondaryStructure(
boolean processSecondaryStructure)
{
- StructureImportSettings.processSecStr = processSecondaryStructure;
+ getInstance().processSecStr = processSecondaryStructure;
}
public static boolean isExternalSecondaryStructure()
{
- return externalSecondaryStructure;
+ return getInstance().externalSecondaryStructure;
}
public static void setExternalSecondaryStructure(
boolean externalSecondaryStructure)
{
- StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
+ getInstance().externalSecondaryStructure = externalSecondaryStructure;
}
public static boolean isShowSeqFeatures()
{
- return showSeqFeatures;
+ return getInstance().showSeqFeatures;
}
public static void setShowSeqFeatures(boolean showSeqFeatures)
{
- StructureImportSettings.showSeqFeatures = showSeqFeatures;
+ getInstance().showSeqFeatures = showSeqFeatures;
}
public static PDBEntry.Type getDefaultStructureFileFormat()
{
- return defaultStructureFileFormat;
+ return getInstance().defaultStructureFileFormat;
}
public static void setDefaultStructureFileFormat(
String defaultStructureFileFormat)
{
- StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
+ getInstance().defaultStructureFileFormat = PDBEntry.Type
.valueOf(defaultStructureFileFormat.toUpperCase());
}
public static String getDefaultPDBFileParser()
{
- return defaultPDBFileParser.toString();
+ return getInstance().defaultPDBFileParser.toString();
}
public static void setDefaultPDBFileParser(
StructureParser defaultPDBFileParser)
{
- StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
+ getInstance().defaultPDBFileParser = defaultPDBFileParser;
}
public static void setDefaultPDBFileParser(String defaultPDBFileParser)
{
- StructureImportSettings.defaultPDBFileParser = StructureParser
+ getInstance().defaultPDBFileParser = StructureParser
.valueOf(defaultPDBFileParser.toUpperCase());
}