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 private static String currentDefaultFormat = DBRefSource.PDB;
30 public enum StructureFormat
35 private static StructureFormat currentDefaultFormat = StructureFormat.PDB;
37 public static void addSettings(boolean addAlignmentAnnotations,
38 boolean predictSecStr, boolean externalSecStr)
40 StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
41 StructureImportSettings.predictSecStr = predictSecStr;
42 StructureImportSettings.externalSecondaryStructure = externalSecStr;
43 StructureImportSettings.showSeqFeatures = true;
46 public static boolean isVisibleChainAnnotation()
48 return visibleChainAnnotation;
51 public static void setVisibleChainAnnotation(
52 boolean visibleChainAnnotation)
54 StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
57 public static boolean isPredictSecondaryStructure()
62 public static void setPredictSecondaryStructure(
63 boolean predictSecondaryStructure)
65 StructureImportSettings.predictSecStr = predictSecondaryStructure;
68 public static boolean isExternalSecondaryStructure()
70 return externalSecondaryStructure;
73 public static void setExternalSecondaryStructure(
74 boolean externalSecondaryStructure)
76 StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
79 public static boolean isShowSeqFeatures()
81 return showSeqFeatures;
84 public static void setShowSeqFeatures(boolean showSeqFeatures)
86 StructureImportSettings.showSeqFeatures = showSeqFeatures;
89 public static String getCurrentDefaultFormat()
91 return currentDefaultFormat.toString();
94 public static void setCurrentDefaultFormat(String currentDefaultFormat)
96 StructureImportSettings.currentDefaultFormat = StructureFormat
97 .valueOf(currentDefaultFormat);
100 public static boolean isProcessHETATMs()
102 return processHETATMs;
105 public static void setProcessHETATMs(boolean processHETATMs)
107 StructureImportSettings.processHETATMs = processHETATMs;