package jalview.io;

import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;

import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

public enum FileFormat implements FileFormatI
{
  Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new FastaFile(inFile, sourceType);
    }

    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new FastaFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new FastaFile();
    }
  },
  Pfam("PFAM", "pfam", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new PfamFile(inFile, sourceType);
    }

    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new PfamFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new PfamFile();
    }
  },
  Stockholm("Stockholm", "sto,stk", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new StockholmFile(inFile, sourceType);
    }
    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new StockholmFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new StockholmFile();
    }

  },

  PIR("PIR", "pir", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new PIRFile(inFile, sourceType);
    }
    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new PIRFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new PIRFile();
    }
  },
  BLC("BLC", "BLC", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new BLCFile(inFile, sourceType);
    }    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new BLCFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new BLCFile();
    }
  },
  AMSA("AMSA", "amsa", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new AMSAFile(inFile, sourceType);
    }

    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new AMSAFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new BLCFile();
    }
  },
  Html("HTML", "html", true, false)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new HtmlFile(inFile, sourceType);
    }    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new HtmlFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new HtmlFile();
    }

    @Override
    public boolean isComplexAlignFile()
    {
      return true;
    }

  },
  Rnaml("RNAML", "xml,rnaml", true, false)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new RnamlFile(inFile, sourceType);
    }    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new RnamlFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new RnamlFile();
    }

  },
  Json("JSON","json", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new JSONFile(inFile, sourceType);
    }    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new JSONFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new JSONFile();
    }

    @Override
    public boolean isComplexAlignFile()
    {
      return true;
    }

  },
  Pileup("PileUp", "pileup", false, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new PileUpfile(inFile, sourceType);
    }    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new PileUpfile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new PileUpfile();
    }

  },
  MSF("MSF", "msf", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new MSFfile(inFile, sourceType);
    }    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new MSFfile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new MSFfile();
    }

  },
  Clustal("Clustal", "aln", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new ClustalFile(inFile, sourceType);
    }    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new ClustalFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new ClustalFile();
    }
  },
  Phylip("PHYLIP", "phy", true, true)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new PhylipFile(inFile, sourceType);
    }

    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new PhylipFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new PhylipFile();
    }
  },
  Jnet("JnetFile", "", false, false)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      JPredFile af = new JPredFile(inFile, sourceType);
      af.removeNonSequences();
      return af;
    }

    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      JPredFile af = new JPredFile(source);
      af.removeNonSequences();
      return af;
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return null; // todo is this called?
    }

  },
  Features("GFF or Jalview features", "gff2,gff3", false, false)
  {
    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new FeaturesFile(true, inFile, sourceType);
    }

    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new FeaturesFile(source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new FeaturesFile();
    }
  },
  PDB("PDB", "", false, false)
  {

    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      // TODO obtain config value from preference settings.
      // Set value to 'true' to test PDB processing with Jmol: JAL-1213
      boolean isParseWithJMOL = StructureImportSettings
              .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
      if (isParseWithJMOL)
      {
        return new JmolParser(
                StructureImportSettings.isVisibleChainAnnotation(),
                StructureImportSettings.isProcessSecondaryStructure(),
                StructureImportSettings.isExternalSecondaryStructure(),
                inFile,
                sourceType);
      }
      else
      {
        StructureImportSettings.setShowSeqFeatures(true);
        return new MCview.PDBfile(
                StructureImportSettings.isVisibleChainAnnotation(),
                StructureImportSettings.isProcessSecondaryStructure(),
                StructureImportSettings.isExternalSecondaryStructure(),
                inFile,
                sourceType);
      }
    }

    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      boolean isParseWithJMOL = StructureImportSettings
              .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
      if (isParseWithJMOL)
      {
        return new JmolParser(
                StructureImportSettings.isVisibleChainAnnotation(),
                StructureImportSettings.isProcessSecondaryStructure(),
                StructureImportSettings.isExternalSecondaryStructure(),
                source);
      }
      else
      {
        StructureImportSettings.setShowSeqFeatures(true);
        return new MCview.PDBfile(
                StructureImportSettings.isVisibleChainAnnotation(),
                StructureImportSettings.isProcessSecondaryStructure(),
                StructureImportSettings.isExternalSecondaryStructure(),
                source);
      }
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new JmolParser(); // todo or null?
    }
  },
  MMCif("mmCIF", "cif", false, false)
  {

    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return new JmolParser(
              StructureImportSettings.isVisibleChainAnnotation(),
              StructureImportSettings.isProcessSecondaryStructure(),
              StructureImportSettings.isExternalSecondaryStructure(),
              inFile, sourceType);
    }

    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return new JmolParser(
              StructureImportSettings.isVisibleChainAnnotation(),
              StructureImportSettings.isProcessSecondaryStructure(),
              StructureImportSettings.isExternalSecondaryStructure(),
              source);
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return new JmolParser(); // todo or null?
    }
  },
  Jalview("Jalview", "jar,jvp", true, false)
  {

    @Override
    public AlignmentFileI getAlignmentFile(String inFile,
            DataSourceType sourceType) throws IOException
    {
      return null;
    }

    @Override
    public AlignmentFileI getAlignmentFile(FileParse source)
            throws IOException
    {
      return null;
    }

    @Override
    public AlignmentFileI getAlignmentFile()
    {
      return null;
    }
  };

  /**
   * A lookup map of enums by upper-cased name
   */
  private static Map<String, FileFormat> names;
  static
  {
    names = new HashMap<String, FileFormat>();
    for (FileFormat format : FileFormat.values())
    {
      names.put(format.toString().toUpperCase(), format);
    }
  }

  private boolean writable;

  private boolean readable;

  private String extensions;

  private String name;

  /**
   * Answers a list of writeable file formats (as string, corresponding to the
   * toString() and forName() methods)
   * 
   * @return
   */
  public static List<String> getWritableFormats()
  {
    List<String> l = new ArrayList<String>();
    for (FileFormatI ff : values())
    {
      if (ff.isWritable())
      {
        l.add(ff.toString());
      }
    }
    return l;
  }

  /**
   * Answers a list of readable file formats (as string, corresponding to the
   * toString() and forName() methods)
   * 
   * @return
   */
  public static List<String> getReadableFormats()
  {
    List<String> l = new ArrayList<String>();
    for (FileFormatI ff : values())
    {
      if (ff.isReadable())
      {
        l.add(ff.toString());
      }
    }
    return l;
  }

  @Override
  public boolean isComplexAlignFile()
  {
    return false;
  }

  @Override
  public String getShortDescription()
  {
    return toString();
  }

  /**
   * Returns the file format with the given name, or null if format is null or
   * invalid. Unlike valueOf(), this is not case-sensitive, to be kind to
   * writers of javascript.
   * 
   * @param format
   * @return
   */
  public static FileFormatI forName(String format)
  {
    // or could store format.getShortDescription().toUpperCase()
    // in order to decouple 'given name' from enum name
    return format == null ? null : names.get(format.toUpperCase());
  }

  @Override
  public boolean isReadable()
  {
    return readable;
  }

  @Override
  public boolean isWritable()
  {
    return writable;
  }

  /**
   * Constructor
   * 
   * @param shortName
   * @param extensions
   *          comma-separated list of file extensions associated with the format
   * @param isReadable
   * @param isWritable
   */
  private FileFormat(String shortName, String extensions,
          boolean isReadable, boolean isWritable)
  {
    this.name = shortName;
    this.extensions = extensions;
    this.readable = isReadable;
    this.writable = isWritable;
  }

  @Override
  public String getExtensions()
  {
    return extensions;
  }

  @Override
  public String toString()
  {
    return name;
  }
}