package jalview.structure;


public class StructureImportSettings
{
  /**
   * set to true to add derived sequence annotations (temp factor read from
   * file, or computed secondary structure) to the alignment
   */
  private static boolean visibleChainAnnotation = false;

  /**
   * Set true to predict secondary structure (using JMol for protein, Annotate3D
   * for RNA)
   */
  private static boolean predictSecStr = false;

  /**
   * Set true (with predictSecondaryStructure=true) to predict secondary
   * structure using an external service (currently Annotate3D for RNA only)
   */
  private static boolean externalSecondaryStructure = false;

  private static boolean showSeqFeatures = true;

  private static boolean processHETATMs = false;

  public enum StructureFormat
  {
    PDB, MMCIF
  };

  private static StructureFormat currentDefaultFormat = StructureFormat.PDB;

  public static void addSettings(boolean addAlignmentAnnotations,
          boolean predictSecStr, boolean externalSecStr)
  {
    StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
    StructureImportSettings.predictSecStr = predictSecStr;
    StructureImportSettings.externalSecondaryStructure = externalSecStr;
    StructureImportSettings.showSeqFeatures = true;
  }

  public static boolean isVisibleChainAnnotation()
  {
    return visibleChainAnnotation;
  }

  public static void setVisibleChainAnnotation(
          boolean visibleChainAnnotation)
  {
    StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
  }

  public static boolean isPredictSecondaryStructure()
  {
    return predictSecStr;
  }

  public static void setPredictSecondaryStructure(
          boolean predictSecondaryStructure)
  {
    StructureImportSettings.predictSecStr = predictSecondaryStructure;
  }

  public static boolean isExternalSecondaryStructure()
  {
    return externalSecondaryStructure;
  }

  public static void setExternalSecondaryStructure(
          boolean externalSecondaryStructure)
  {
    StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
  }

  public static boolean isShowSeqFeatures()
  {
    return showSeqFeatures;
  }

  public static void setShowSeqFeatures(boolean showSeqFeatures)
  {
    StructureImportSettings.showSeqFeatures = showSeqFeatures;
  }

  public static String getCurrentDefaultFormat()
  {
    return currentDefaultFormat.toString();
  }

  public static void setCurrentDefaultFormat(String currentDefaultFormat)
  {
    StructureImportSettings.currentDefaultFormat = StructureFormat
            .valueOf(currentDefaultFormat);
  }

  public static boolean isProcessHETATMs()
  {
    return processHETATMs;
  }

  public static void setProcessHETATMs(boolean processHETATMs)
  {
    StructureImportSettings.processHETATMs = processHETATMs;
  }

}