1 package jalview.structure;
3 public class StructureViewSettings
5 private String dbRefType;
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 public static void addSettings(boolean addAlignmentAnnotations,
28 boolean predictSecStr, boolean externalSecStr)
30 StructureViewSettings.visibleChainAnnotation = addAlignmentAnnotations;
31 StructureViewSettings.predictSecStr = predictSecStr;
32 StructureViewSettings.externalSecondaryStructure = externalSecStr;
33 StructureViewSettings.showSeqFeatures = true;
36 public static boolean isVisibleChainAnnotation()
38 return visibleChainAnnotation;
41 public static void setVisibleChainAnnotation(
42 boolean visibleChainAnnotation)
44 StructureViewSettings.visibleChainAnnotation = visibleChainAnnotation;
47 public static boolean isPredictSecondaryStructure()
52 public static void setPredictSecondaryStructure(
53 boolean predictSecondaryStructure)
55 StructureViewSettings.predictSecStr = predictSecondaryStructure;
58 public static boolean isExternalSecondaryStructure()
60 return externalSecondaryStructure;
63 public static void setExternalSecondaryStructure(
64 boolean externalSecondaryStructure)
66 StructureViewSettings.externalSecondaryStructure = externalSecondaryStructure;
69 public static boolean isShowSeqFeatures()
71 return showSeqFeatures;
74 public static void setShowSeqFeatures(boolean showSeqFeatures)
76 StructureViewSettings.showSeqFeatures = showSeqFeatures;