+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.structure;
+import java.util.Locale;
+
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.util.MessageManager;
/**
* bean holding settings for structure IO. TODO: tests for validation of values
+ * TODO: tests for race conditions (all fields are static, is that correct ?)
*
* @author tcofoegbu
*
JMOL_PARSER, JALVIEW_PARSER
}
+ public static enum TFType
+ {
+ DEFAULT, PLDDT;
+
+ @Override
+ public String toString()
+ {
+ return MessageManager.getString(
+ "label.tftype_" + this.name().toLowerCase(Locale.ROOT));
+ }
+ }
/**
* Determines the default file format for structure files to be downloaded
* are : JMolParser|JalveiwParser
*/
private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
+
+ private static TFType temperatureFactorType;
+
public static void addSettings(boolean addAlignmentAnnotations,
boolean processSecStr, boolean externalSecStr)
{
return visibleChainAnnotation;
}
+ public static void setTemperatureFactorType(TFType t)
+ {
+ StructureImportSettings.temperatureFactorType = t;
+ }
+
public static void setVisibleChainAnnotation(
boolean visibleChainAnnotation)
{
StructureImportSettings.showSeqFeatures = showSeqFeatures;
}
- public static String getDefaultStructureFileFormat()
+ public static PDBEntry.Type getDefaultStructureFileFormat()
{
- return defaultStructureFileFormat.toString();
+ return defaultStructureFileFormat;
}
public static void setDefaultStructureFileFormat(
String defaultStructureFileFormat)
{
StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
- .valueOf(defaultStructureFileFormat);
+ .valueOf(defaultStructureFileFormat.toUpperCase(Locale.ROOT));
}
public static String getDefaultPDBFileParser()
public static void setDefaultPDBFileParser(String defaultPDBFileParser)
{
StructureImportSettings.defaultPDBFileParser = StructureParser
- .valueOf(defaultPDBFileParser);
+ .valueOf(defaultPDBFileParser.toUpperCase(Locale.ROOT));
+ }
+
+ public static TFType getTemperatureFactorType()
+ {
+ return temperatureFactorType;
}
}