1 package jalview.structure;
3 import jalview.datamodel.DBRefSource;
5 public class StructureViewSettings
7 private String dbRefType;
10 * set to true to add derived sequence annotations (temp factor read from
11 * file, or computed secondary structure) to the alignment
13 private static boolean visibleChainAnnotation = false;
16 * Set true to predict secondary structure (using JMol for protein, Annotate3D
19 private static boolean predictSecStr = false;
22 * Set true (with predictSecondaryStructure=true) to predict secondary
23 * structure using an external service (currently Annotate3D for RNA only)
25 private static boolean externalSecondaryStructure = false;
27 private static boolean showSeqFeatures = true;
29 private static String currentDefaultFormat = DBRefSource.PDB;
31 public static void addSettings(boolean addAlignmentAnnotations,
32 boolean predictSecStr, boolean externalSecStr)
34 StructureViewSettings.visibleChainAnnotation = addAlignmentAnnotations;
35 StructureViewSettings.predictSecStr = predictSecStr;
36 StructureViewSettings.externalSecondaryStructure = externalSecStr;
37 StructureViewSettings.showSeqFeatures = true;
40 public static boolean isVisibleChainAnnotation()
42 return visibleChainAnnotation;
45 public static void setVisibleChainAnnotation(
46 boolean visibleChainAnnotation)
48 StructureViewSettings.visibleChainAnnotation = visibleChainAnnotation;
51 public static boolean isPredictSecondaryStructure()
56 public static void setPredictSecondaryStructure(
57 boolean predictSecondaryStructure)
59 StructureViewSettings.predictSecStr = predictSecondaryStructure;
62 public static boolean isExternalSecondaryStructure()
64 return externalSecondaryStructure;
67 public static void setExternalSecondaryStructure(
68 boolean externalSecondaryStructure)
70 StructureViewSettings.externalSecondaryStructure = externalSecondaryStructure;
73 public static boolean isShowSeqFeatures()
75 return showSeqFeatures;
78 public static void setShowSeqFeatures(boolean showSeqFeatures)
80 StructureViewSettings.showSeqFeatures = showSeqFeatures;
83 public static String getCurrentDefaultFormat()
85 return currentDefaultFormat;
88 public static void setCurrentDefaultFormat(String currentDefaultFormat)
90 StructureViewSettings.currentDefaultFormat = currentDefaultFormat;