src/jalview/structure/StructureViewSettings.java

   1 package jalview.structure;
   2
   3 public class StructureViewSettings
   4 {
   5   private String dbRefType;
   6
   7   /**
   8    * set to true to add derived sequence annotations (temp factor read from
   9    * file, or computed secondary structure) to the alignment
  10    */
  11   private static boolean visibleChainAnnotation = false;
  12
  13   /**
  14    * Set true to predict secondary structure (using JMol for protein, Annotate3D
  15    * for RNA)
  16    */
  17   private static boolean predictSecStr = false;
  18
  19   /**
  20    * Set true (with predictSecondaryStructure=true) to predict secondary
  21    * structure using an external service (currently Annotate3D for RNA only)
  22    */
  23   private static boolean externalSecondaryStructure = false;
  24
  25   private static boolean showSeqFeatures = true;
  26
  27   public static void addSettings(boolean addAlignmentAnnotations,
  28           boolean predictSecStr, boolean externalSecStr)
  29   {
  30     StructureViewSettings.visibleChainAnnotation = addAlignmentAnnotations;
  31     StructureViewSettings.predictSecStr = predictSecStr;
  32     StructureViewSettings.externalSecondaryStructure = externalSecStr;
  33     StructureViewSettings.showSeqFeatures = true;
  34   }
  35
  36   public static boolean isVisibleChainAnnotation()
  37   {
  38     return visibleChainAnnotation;
  39   }
  40
  41   public static void setVisibleChainAnnotation(
  42           boolean visibleChainAnnotation)
  43   {
  44     StructureViewSettings.visibleChainAnnotation = visibleChainAnnotation;
  45   }
  46
  47   public static boolean isPredictSecondaryStructure()
  48   {
  49     return predictSecStr;
  50   }
  51
  52   public static void setPredictSecondaryStructure(
  53           boolean predictSecondaryStructure)
  54   {
  55     StructureViewSettings.predictSecStr = predictSecondaryStructure;
  56   }
  57
  58   public static boolean isExternalSecondaryStructure()
  59   {
  60     return externalSecondaryStructure;
  61   }
  62
  63   public static void setExternalSecondaryStructure(
  64           boolean externalSecondaryStructure)
  65   {
  66     StructureViewSettings.externalSecondaryStructure = externalSecondaryStructure;
  67   }
  68
  69   public static boolean isShowSeqFeatures()
  70   {
  71     return showSeqFeatures;
  72   }
  73
  74   public static void setShowSeqFeatures(boolean showSeqFeatures)
  75   {
  76     StructureViewSettings.showSeqFeatures = showSeqFeatures;
  77   }
  78
  79 }