src/jalview/structure/StructureImportSettings.java

   1 package jalview.structure;
   2
   3 import jalview.datamodel.DBRefSource;
   4
   5 public class StructureImportSettings
   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   private static boolean processHETATMs = false;
  28
  29   private static String currentDefaultFormat = DBRefSource.PDB;
  30
  31   public static void addSettings(boolean addAlignmentAnnotations,
  32           boolean predictSecStr, boolean externalSecStr)
  33   {
  34     StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
  35     StructureImportSettings.predictSecStr = predictSecStr;
  36     StructureImportSettings.externalSecondaryStructure = externalSecStr;
  37     StructureImportSettings.showSeqFeatures = true;
  38   }
  39
  40   public static boolean isVisibleChainAnnotation()
  41   {
  42     return visibleChainAnnotation;
  43   }
  44
  45   public static void setVisibleChainAnnotation(
  46           boolean visibleChainAnnotation)
  47   {
  48     StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
  49   }
  50
  51   public static boolean isPredictSecondaryStructure()
  52   {
  53     return predictSecStr;
  54   }
  55
  56   public static void setPredictSecondaryStructure(
  57           boolean predictSecondaryStructure)
  58   {
  59     StructureImportSettings.predictSecStr = predictSecondaryStructure;
  60   }
  61
  62   public static boolean isExternalSecondaryStructure()
  63   {
  64     return externalSecondaryStructure;
  65   }
  66
  67   public static void setExternalSecondaryStructure(
  68           boolean externalSecondaryStructure)
  69   {
  70     StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
  71   }
  72
  73   public static boolean isShowSeqFeatures()
  74   {
  75     return showSeqFeatures;
  76   }
  77
  78   public static void setShowSeqFeatures(boolean showSeqFeatures)
  79   {
  80     StructureImportSettings.showSeqFeatures = showSeqFeatures;
  81   }
  82
  83   public static String getCurrentDefaultFormat()
  84   {
  85     return currentDefaultFormat;
  86   }
  87
  88   public static void setCurrentDefaultFormat(String currentDefaultFormat)
  89   {
  90     StructureImportSettings.currentDefaultFormat = currentDefaultFormat;
  91   }
  92
  93   public static boolean isProcessHETATMs()
  94   {
  95     return processHETATMs;
  96   }
  97
  98   public static void setProcessHETATMs(boolean processHETATMs)
  99   {
 100     StructureImportSettings.processHETATMs = processHETATMs;
 101   }
 102
 103 }