1 package jalview.structure;
4 public class StructureImportSettings
7 * set to true to add derived sequence annotations (temp factor read from
8 * file, or computed secondary structure) to the alignment
10 private static boolean visibleChainAnnotation = false;
13 * Set true to predict secondary structure (using JMol for protein, Annotate3D
16 private static boolean processSecStr = false;
19 * Set true (with predictSecondaryStructure=true) to predict secondary
20 * structure using an external service (currently Annotate3D for RNA only)
22 private static boolean externalSecondaryStructure = false;
24 private static boolean showSeqFeatures = true;
26 private static boolean processHETATMs = false;
28 public enum StructureFormat
33 private static StructureFormat currentDefaultFormat = StructureFormat.PDB;
35 public static void addSettings(boolean addAlignmentAnnotations,
36 boolean processSecStr, boolean externalSecStr)
38 StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
39 StructureImportSettings.processSecStr = processSecStr;
40 StructureImportSettings.externalSecondaryStructure = externalSecStr;
41 StructureImportSettings.showSeqFeatures = true;
44 public static boolean isVisibleChainAnnotation()
46 return visibleChainAnnotation;
49 public static void setVisibleChainAnnotation(
50 boolean visibleChainAnnotation)
52 StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
55 public static boolean isProcessSecondaryStructure()
60 public static void setProcessSecondaryStructure(
61 boolean processSecondaryStructure)
63 StructureImportSettings.processSecStr = processSecondaryStructure;
66 public static boolean isExternalSecondaryStructure()
68 return externalSecondaryStructure;
71 public static void setExternalSecondaryStructure(
72 boolean externalSecondaryStructure)
74 StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
77 public static boolean isShowSeqFeatures()
79 return showSeqFeatures;
82 public static void setShowSeqFeatures(boolean showSeqFeatures)
84 StructureImportSettings.showSeqFeatures = showSeqFeatures;
87 public static String getCurrentDefaultFormat()
89 return currentDefaultFormat.toString();
92 public static void setCurrentDefaultFormat(String currentDefaultFormat)
94 StructureImportSettings.currentDefaultFormat = StructureFormat
95 .valueOf(currentDefaultFormat);
98 public static boolean isProcessHETATMs()
100 return processHETATMs;
103 public static void setProcessHETATMs(boolean processHETATMs)
105 StructureImportSettings.processHETATMs = processHETATMs;