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   public enum StructureFormat
  31   {
  32     PDB, MMCIF
  33   };
  34
  35   private static StructureFormat currentDefaultFormat = StructureFormat.PDB;
  36
  37   public static void addSettings(boolean addAlignmentAnnotations,
  38           boolean predictSecStr, boolean externalSecStr)
  39   {
  40     StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
  41     StructureImportSettings.predictSecStr = predictSecStr;
  42     StructureImportSettings.externalSecondaryStructure = externalSecStr;
  43     StructureImportSettings.showSeqFeatures = true;
  44   }
  45
  46   public static boolean isVisibleChainAnnotation()
  47   {
  48     return visibleChainAnnotation;
  49   }
  50
  51   public static void setVisibleChainAnnotation(
  52           boolean visibleChainAnnotation)
  53   {
  54     StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
  55   }
  56
  57   public static boolean isPredictSecondaryStructure()
  58   {
  59     return predictSecStr;
  60   }
  61
  62   public static void setPredictSecondaryStructure(
  63           boolean predictSecondaryStructure)
  64   {
  65     StructureImportSettings.predictSecStr = predictSecondaryStructure;
  66   }
  67
  68   public static boolean isExternalSecondaryStructure()
  69   {
  70     return externalSecondaryStructure;
  71   }
  72
  73   public static void setExternalSecondaryStructure(
  74           boolean externalSecondaryStructure)
  75   {
  76     StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
  77   }
  78
  79   public static boolean isShowSeqFeatures()
  80   {
  81     return showSeqFeatures;
  82   }
  83
  84   public static void setShowSeqFeatures(boolean showSeqFeatures)
  85   {
  86     StructureImportSettings.showSeqFeatures = showSeqFeatures;
  87   }
  88
  89   public static String getCurrentDefaultFormat()
  90   {
  91     return currentDefaultFormat.toString();
  92   }
  93
  94   public static void setCurrentDefaultFormat(String currentDefaultFormat)
  95   {
  96     StructureImportSettings.currentDefaultFormat = StructureFormat
  97             .valueOf(currentDefaultFormat);
  98   }
  99
 100   public static boolean isProcessHETATMs()
 101   {
 102     return processHETATMs;
 103   }
 104
 105   public static void setProcessHETATMs(boolean processHETATMs)
 106   {
 107     StructureImportSettings.processHETATMs = processHETATMs;
 108   }
 109
 110 }