package jalview.structure;

import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;

/**
 * bean holding settings for structure IO. TODO: tests for validation of values
 * TODO: tests for race conditions (all fields are static, is that correct ?)
 * 
 * @author tcofoegbu
 *
 */
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 processSecStr = 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;

  public enum StructureParser
  {
    JMOL_PARSER, JALVIEW_PARSER
  }


  /**
   * Determines the default file format for structure files to be downloaded
   * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
   */
  private static PDBEntry.Type defaultStructureFileFormat = Type.PDB;

  /**
   * Determines the parser used for parsing PDB format file. Possible options
   * are : JMolParser|JalveiwParser
   */
  private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
  public static void addSettings(boolean addAlignmentAnnotations,
          boolean processSecStr, boolean externalSecStr)
  {
    StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
    StructureImportSettings.processSecStr = processSecStr;
    StructureImportSettings.externalSecondaryStructure = externalSecStr;
    StructureImportSettings.showSeqFeatures = true;
  }

  public static boolean isVisibleChainAnnotation()
  {
    return visibleChainAnnotation;
  }

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

  public static boolean isProcessSecondaryStructure()
  {
    return processSecStr;
  }

  public static void setProcessSecondaryStructure(
          boolean processSecondaryStructure)
  {
    StructureImportSettings.processSecStr = processSecondaryStructure;
  }

  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 getDefaultStructureFileFormat()
  {
    return defaultStructureFileFormat.toString();
  }

  public static void setDefaultStructureFileFormat(
          String defaultStructureFileFormat)
  {
    StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
            .valueOf(defaultStructureFileFormat.toUpperCase());
  }

  public static String getDefaultPDBFileParser()
  {
    return defaultPDBFileParser.toString();
  }

  public static void setDefaultPDBFileParser(
          StructureParser defaultPDBFileParser)
  {
    StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
  }

  public static void setDefaultPDBFileParser(String defaultPDBFileParser)
  {
    StructureImportSettings.defaultPDBFileParser = StructureParser
            .valueOf(defaultPDBFileParser.toUpperCase());
  }

}