package jalview.json.binding.biojson.v1;


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

import com.github.reinert.jjschema.Attributes;

@Attributes(title="BioJSON", description="A specification for the representation and exchange of bioinformatics data")
public class AlignmentPojo
{
  @Attributes(required = true, description = "Serial version identifier for <b>BioJSON</b> schema")
  private String svid = "1.0";

  @Attributes(
    required = true,
    minItems = 1,
    	    description = "An array of Sequences which makes up the Alignment")
  private List<SequencePojo> seqs = new ArrayList<SequencePojo>();

  @Attributes(
    required = false,
    minItems = 0,
    maxItems = 2147483647,
    exclusiveMaximum = true,
    description = "Alignment annotations stores symbols and graphs usually rendered </br>below the alignment.")
  private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();

  @Attributes(
    required = false,
    minItems = 0,
    maxItems = 2147483647,
    description = "A sequence group is a region of an alignment which could <br>span across multiple columns and rows. These can be treated as<br> a sub-alignments.")
  private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();

  @Attributes(
    required = false,
    minItems = 0,
    maxItems = 2147483647,
    description = "Sequence features are associated with sequences rather than <br>alignments. A sequence feature can span across multiple <br>sequences in an alignment. They indicate features generated <br>by the same analysis process or retrieved from the same database <br>(such as Uniprot features).")
  private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();

  @Attributes(
    required = false,
    enums = { "None", "User Defined", "Clustal", "Zappo", "Taylor",
        "Nucleotide", "Pyrimidine", "Purine", "Turn", "Helix", "Strand",
        "Buried", "Hydro", "T-Coffee Scores", "RNA Interaction type",
        "Blosum62", "RNA Helices", "% Identity" },
    description = "The <a href=\"colour_schemes.html\">Colour Scheme</a> applied to the alignment")
  private String colourScheme;
  
  @Attributes(required = true, maxItems = 1, description = "This is an array of key=value pairs for storing custom application <br>specific settings")
  Map<String, Object> appSettings = new HashMap<String, Object>();

  public AlignmentPojo()
  {
  }

  public List<SequencePojo> getSeqs()
  {
    return seqs;
  }

  public void setSeqs(ArrayList<SequencePojo> seqs)
  {
    this.seqs = seqs;
  }

  public Map<String, Object> getAppSettings()
  {
    return appSettings;
  }

  public void setAppSettings(Map<String, Object> appSettings)
  {
    this.appSettings = appSettings;
  }

  public List<AlignmentAnnotationPojo> getAlignAnnotation()
  {
    return alignAnnotation;
  }

  public void setAlignAnnotation(
          List<AlignmentAnnotationPojo> alignAnnotation)
  {
    this.alignAnnotation = alignAnnotation;
  }

  public List<SequenceGrpPojo> getSeqGroups()
  {
    return seqGroups;
  }

  public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
  {
    this.seqGroups = seqGroups;
  }

  public List<SequenceFeaturesPojo> getSeqFeatures()
  {
    return seqFeatures;
  }

  public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
  {
    this.seqFeatures = seqFeatures;
  }

  public String getSvid()
  {
    return svid;
  }

  public void setGlobalColorScheme(String globalColorScheme)
  {
    this.appSettings.put("globalColorScheme", globalColorScheme);
  }

  public String getColourScheme()
  {
    return colourScheme;
  }

  public void setColourScheme(String colourScheme)
  {
    this.colourScheme = colourScheme;
  }

}