1 package jalview.structure;
3 import jalview.datamodel.DBRefSource;
5 public class StructureImportSettings
8 * set to true to add derived sequence annotations (temp factor read from
9 * file, or computed secondary structure) to the alignment
11 private static boolean visibleChainAnnotation = false;
14 * Set true to predict secondary structure (using JMol for protein, Annotate3D
17 private static boolean predictSecStr = false;
20 * Set true (with predictSecondaryStructure=true) to predict secondary
21 * structure using an external service (currently Annotate3D for RNA only)
23 private static boolean externalSecondaryStructure = false;
25 private static boolean showSeqFeatures = true;
27 private static boolean processHETATMs = false;
29 public static final String JMOL_PARSER = "JMolParser";
31 public static final String JALVIEW_PARSER = "JalViewParser";
33 public static final String MMCIF = "mmCIF";
35 public static final String PDB = "PDB";
38 * Determines the default file format for structure files to be downloaded
39 * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
41 private static String defaultStructureFileFormat = DBRefSource.PDB;
44 * Determines the parser used for parsing PDB format file. Possible options
45 * are : JMolParser|JalveiwParser
47 private static String defaultPDBFileParser = JMOL_PARSER;
48 public static void addSettings(boolean addAlignmentAnnotations,
49 boolean predictSecStr, boolean externalSecStr)
51 StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
52 StructureImportSettings.predictSecStr = predictSecStr;
53 StructureImportSettings.externalSecondaryStructure = externalSecStr;
54 StructureImportSettings.showSeqFeatures = true;
57 public static boolean isVisibleChainAnnotation()
59 return visibleChainAnnotation;
62 public static void setVisibleChainAnnotation(
63 boolean visibleChainAnnotation)
65 StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
68 public static boolean isPredictSecondaryStructure()
73 public static void setPredictSecondaryStructure(
74 boolean predictSecondaryStructure)
76 StructureImportSettings.predictSecStr = predictSecondaryStructure;
79 public static boolean isExternalSecondaryStructure()
81 return externalSecondaryStructure;
84 public static void setExternalSecondaryStructure(
85 boolean externalSecondaryStructure)
87 StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
90 public static boolean isShowSeqFeatures()
92 return showSeqFeatures;
95 public static void setShowSeqFeatures(boolean showSeqFeatures)
97 StructureImportSettings.showSeqFeatures = showSeqFeatures;
100 public static String getDefaultStructureFileFormat()
102 return defaultStructureFileFormat;
105 public static void setDefaultStructureFileFormat(
106 String defaultStructureFileFormat)
108 StructureImportSettings.defaultStructureFileFormat = defaultStructureFileFormat;
111 public static boolean isProcessHETATMs()
113 return processHETATMs;
116 public static void setProcessHETATMs(boolean processHETATMs)
118 StructureImportSettings.processHETATMs = processHETATMs;
121 public static String getDefaultPDBFileParser()
123 return defaultPDBFileParser;
126 public static void setDefaultPDBFileParser(String defaultPDBFileParser)
128 StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;