+/*
+ * 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 jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+/**
+ * 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
+ *
+ */
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;
- private static boolean processHETATMs = false;
-
- private static String currentDefaultFormat = DBRefSource.PDB;
- public enum StructureFormat
+ public enum StructureParser
{
- PDB, MMCIF
- };
+ JMOL_PARSER, JALVIEW_PARSER
+ }
+
+ /**
+ * 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 static StructureFormat currentDefaultFormat = StructureFormat.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 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()
StructureImportSettings.showSeqFeatures = showSeqFeatures;
}
- public static String getCurrentDefaultFormat()
+ public static String getDefaultStructureFileFormat()
+ {
+ return defaultStructureFileFormat.toString();
+ }
+
+ public static void setDefaultStructureFileFormat(
+ String defaultStructureFileFormat)
{
- return currentDefaultFormat.toString();
+ StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
+ .valueOf(defaultStructureFileFormat.toUpperCase());
}
- public static void setCurrentDefaultFormat(String currentDefaultFormat)
+ public static String getDefaultPDBFileParser()
{
- StructureImportSettings.currentDefaultFormat = StructureFormat
- .valueOf(currentDefaultFormat);
+ return defaultPDBFileParser.toString();
}
- public static boolean isProcessHETATMs()
+ public static void setDefaultPDBFileParser(
+ StructureParser defaultPDBFileParser)
{
- return processHETATMs;
+ StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
}
- public static void setProcessHETATMs(boolean processHETATMs)
+ public static void setDefaultPDBFileParser(String defaultPDBFileParser)
{
- StructureImportSettings.processHETATMs = processHETATMs;
+ StructureImportSettings.defaultPDBFileParser = StructureParser
+ .valueOf(defaultPDBFileParser.toUpperCase());
}
}