package jalview.ext.forester.io;

import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.ext.archaeopteryx.Tree;
import jalview.ext.treeviewer.TreeI;
import jalview.ext.treeviewer.TreeParserI;
import jalview.io.AlignmentFileReaderI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;

import java.io.IOException;

import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.phylogeny.Phylogeny;

public class ForesterParser implements TreeParserI, AlignmentFileReaderI
{
  private final PhylogenyParser parser;

  protected ForesterParser(PhylogenyParser foresterParser, FileParse source)
  {
    parser = foresterParser;
  }

  @Override
  public TreeI[] parse() throws IOException
  {
    Phylogeny[] foresterTrees = parser.parse();
    TreeI[] jalviewTrees = new TreeI[foresterTrees.length];

    for (int i = 0; i < foresterTrees.length; i++)
    {
      jalviewTrees[i] = new Tree(foresterTrees[i]);
    }
    return jalviewTrees;

  }

  @Override
  public void setSource(Object source) throws IOException
  {
    parser.setSource(source);

  }

  @Override
  public String getName()
  {
    return parser.getName();
  }

  @Override
  public SequenceI[] getSeqsAsArray()
  {
    // TODO Auto-generated method stub
    return null;
  }

  @Override
  public void addAnnotations(AlignmentI al)
  {
    // TODO Auto-generated method stub

  }

  @Override
  public void addGroups(AlignmentI al)
  {
    // TODO Auto-generated method stub

  }

  @Override
  public void setSeqs(SequenceI[] sequencesArray)
  {
    // TODO Auto-generated method stub

  }

  @Override
  public boolean hasWarningMessage()
  {
    // TODO Auto-generated method stub
    return false;
  }

  @Override
  public String getWarningMessage()
  {
    // TODO Auto-generated method stub
    return null;
  }

  @Override
  public String getInFile()
  {
    // TODO Auto-generated method stub
    return null;
  }

  @Override
  public DataSourceType getDataSourceType()
  {
    // TODO Auto-generated method stub
    return null;
  }

  @Override
  public FeatureSettingsModelI getFeatureColourScheme()
  {
    // TODO Auto-generated method stub
    return null;
  }

  public static ForesterParser createNexusParser(FileParse source)
  {
    return new ForesterParser(new NexusPhylogeniesParser(), source);
  }

  public static ForesterParser createPhyloXmlParser(FileParse source)
  {
    // support non-xsd validating?
    return new ForesterParser(
            PhyloXmlParser.createPhyloXmlParserXsdValidating(), source);
  }
}