+/*
+ * 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;
-
-public class StructureImportSettings
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+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 implements ApplicationSingletonI
{
+
+ private StructureImportSettings()
+ {
+ // private singleton
+ }
+
+ private static StructureImportSettings getInstance()
+ {
+ return (StructureImportSettings) ApplicationSingletonProvider
+ .getInstance(StructureImportSettings.class);
+ }
+
/**
* 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 static boolean showSeqFeatures = true;
+ private boolean externalSecondaryStructure = false;
- private static boolean processHETATMs = false;
+ private boolean showSeqFeatures = true;
- 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 PDBEntry.Type defaultStructureFileFormat = Type.PDB;
+
+ /**
+ * Determines the parser used for parsing PDB format file. Possible options
+ * are : JMolParser|JalveiwParser
+ */
+ 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 getInstance().defaultStructureFileFormat;
}
- public static String getCurrentDefaultFormat()
+ public static void setDefaultStructureFileFormat(
+ String defaultStructureFileFormat)
{
- return currentDefaultFormat.toString();
+ getInstance().defaultStructureFileFormat = PDBEntry.Type
+ .valueOf(defaultStructureFileFormat.toUpperCase());
}
- public static void setCurrentDefaultFormat(String currentDefaultFormat)
+ public static String getDefaultPDBFileParser()
{
- StructureImportSettings.currentDefaultFormat = StructureFormat
- .valueOf(currentDefaultFormat);
+ return getInstance().defaultPDBFileParser.toString();
}
- public static boolean isProcessHETATMs()
+ public static void setDefaultPDBFileParser(
+ StructureParser defaultPDBFileParser)
{
- return processHETATMs;
+ getInstance().defaultPDBFileParser = defaultPDBFileParser;
}
- public static void setProcessHETATMs(boolean processHETATMs)
+ public static void setDefaultPDBFileParser(String defaultPDBFileParser)
{
- StructureImportSettings.processHETATMs = processHETATMs;
+ getInstance().defaultPDBFileParser = StructureParser
+ .valueOf(defaultPDBFileParser.toUpperCase());
}
}
git://source.jalview.org / jalview.git / blobdiff