package org.cipres.kepler.testcase;

// import org.cipres.kepler.registry.Globals;

public class TestRecIDCM3Workflow {

    /** 
     * test input file name
     * You may want to change it to the path of your test nexus file
     */
    public final static String TEST_NEXUS_INFILE = "C://work//Cipres-Kepler//dist//jar//cipres//help//sampleFiles//TestNexusFile.nex";

    /**
     * @main test program
     */
    public static void main(String[] args) {
        // Step 1: initializer
    	// TODO: this is never read
        //TestInitializerActor initializer = new TestInitializerActor();
        
        // Step 2: nexus file reader
        TestNexusFileReaderActor nexusFileReader = new TestNexusFileReaderActor();
        if (args.length > 0)
            nexusFileReader.setNexusFileName(args[1]);
        else
            nexusFileReader.setNexusFileName(TEST_NEXUS_INFILE);
        
        // Step 3: phylodataset
        TestPhyloDataReaderActor phyloDataReader = new TestPhyloDataReaderActor();
        phyloDataReader.setNexusData(nexusFileReader.getNexusFileContent());
        
        // Branch 1: Step 3.1.1 : tree parser for the original tree
        TestTreeParserActor treeParserOriginal = new TestTreeParserActor();
        treeParserOriginal.setTree(phyloDataReader.getTree());
        
        // Branch 1: Step 3.1.2 : display original tree info
        System.out.println("Original tree score: "+treeParserOriginal.getTreeScore());
        System.out.println("Original tree expression: "+treeParserOriginal.getTreeNewick());
        System.out.println("Display original tree with TreeViz:");
        TestTreeVizForesterActor treeVizOriginal = new TestTreeVizForesterActor();
        treeVizOriginal.setTreeNewick(treeParserOriginal.getTreeNewick());
        treeVizOriginal.showTree();
        
        // Branch 2: Step 3.2.1 : RecIDCM3
        TestRecIDCM3Actor recIDCM3 = new TestRecIDCM3Actor();
        recIDCM3.setDataMatrix(phyloDataReader.getDataMatrix());
        recIDCM3.setTree(phyloDataReader.getTree());
        
        // Branch 2: Step 3.2.2 : tree parser for the improved tree
        TestTreeParserActor treeParserImproved = new TestTreeParserActor();
        treeParserImproved.setTree(recIDCM3.getFinalTree());
        
        // Branch 2: Step 3.2.3 : display improved tree info
        System.out.println("Improved tree name: "+treeParserImproved.getTreeName());
        System.out.println("Improved tree score: "+treeParserImproved.getTreeScore());
        System.out.println("Improved tree leaf set: "+treeParserImproved.getTreeLeafSet());
        System.out.println("Improved tree expression: "+treeParserImproved.getTreeNewick());
        System.out.println("Display improved tree with TreeViz:");
        TestTreeVizForesterActor treeVizImproved = new TestTreeVizForesterActor();
        treeVizImproved.setTreeNewick(treeParserImproved.getTreeNewick());
        treeVizImproved.showTree();
        
        System.out.println("Workflow is finished!");

    }

}