package org.cipres.kepler.testcase;

import org.cipres.CipresIDL.api1.DataMatrix;
import org.cipres.CipresIDL.api1.Tree;
import org.cipres.datatypes.PhyloDataset;

public class TestPhyloDataReaderActor {

    // tree structure
    private Tree _tree = null;
        
    // data matrix
    private DataMatrix _dataMatrix = null;
        
    // taxa info
    private String[] _taxaInfo = null;
        
    // phylodataset used to store and parse the input data
    private PhyloDataset _phyloDataset;
    
    // set the Nexus data to initialize the phylodataset
    public void setNexusData(String nexusContent) {
        try {
            _phyloDataset = new PhyloDataset();
            // initialize the phylodataset with the input data
            _phyloDataset.initialize( nexusContent );
        } catch (Exception ex) {
            ex.printStackTrace();
            if (_phyloDataset!= null)
                _phyloDataset = null;
        }
        
        _tree = _phyloDataset.getFirstTree();                           
        _dataMatrix = _phyloDataset.getDataMatrix();
        _taxaInfo = _phyloDataset.getTaxaInfo();
    }
    
    // get the first tree in the phylodataset
    public Tree getTree() { 
        return _tree;
    }
    
    // get the data matrix from the phylodataset
    public DataMatrix getDataMatrix() {
        return _dataMatrix;
    }
    
    // get the taxa info from the phylodataset
    public String[] getTaxaInfo() {
        return _taxaInfo;
    }
}