package org.cipres.kepler.sandbox;

import java.io.*;

import javax.swing.JOptionPane;

import org.cipres.kepler.registry.*;
import org.cipres.CipresIDL.api1.MatrixAlign;
import org.cipres.guigen.ServiceCommandPanel;
import org.cipres.helpers.CipresServiceDialog;
import org.cipres.helpers.RegistryEntryWrapper;


public class KeplerTest {

	public final static String SEP = System.getProperty("file.separator");
	
	//THE FOLLOWING WILL BE DEDUCED WHEN USER SELECTS ACTOR	
	public final static String CLUSTAL_ACTOR_NAME = "SequenceAlign_Clustal";
	public final static String INFER_TREE_PARS_PAUP = "InferTreeByParsimony_Paup";
	public final static String CONSENSUS_TREE_PAUP = "ConsensusTree_Paup";
	
    //THESE ARE SET FOR CONVENIENCE FOR TESTING BUT WILL EVENTUALLY BE GENERATED
	//AUTOMATICALLY BY APPLICATION
	public final static String HOME_DIR = System.getProperty("user.home") + SEP;
	public final static String TEMP_DIR = HOME_DIR + "temp" + SEP;
	public final static String PAUP_NEXUS_OUT = TEMP_DIR + "paup_output.nex";
	public final static String NEXUS_SUBSET_TAXA_OUT = TEMP_DIR + "subsetter_taxa_output.nex";
	public final static String NEXUS_SUBSET_TREES_OUT = TEMP_DIR + "subsetter_trees_output.nex";
	public final static String PAUP_CMD_FILE = TEMP_DIR + "paup_cmds.nex";
	public final static String PAUP_TREES_OUT = TEMP_DIR + "paup_trees.nex";
	//public final static String CLUSTAL_FASTA_IN = FILES_DIR + "zfish_nt_12T.fasta";
	//public final static String CLUSTAL_FASTA_IN = FILES_DIR + "globin.pep";
	public final static String CLUSTAL_NEXUS_OUT = TEMP_DIR + "clustal_output.nex";
	public final static String PROTEIN_NEXUS = TEMP_DIR + "protein.nex";
	public final static String NEXUS_TO_PHYLIP = TEMP_DIR + "NexusToPhylip.phylip";
	public final static String PHYLIP_TO_NEXUS = TEMP_DIR + "PhylipToNexus.nex";
	public final static String CONTREE_OUTPUT = TEMP_DIR + "ConTreesNexus.nex";
	public static String TEST_NEXUS;

	public static void main(String[] args) {

		try {
			CipresKeplerRegistry reg = Globals.getInstance().getRegistry();
			ServiceRunner serviceRunner = new ServiceRunner();	
             //for testing fasta->clustal->subsetter->TreeInfer->ConTree->NexToPhylip->PhylipToNex
			if(args[0].equalsIgnoreCase("0")){	
				//run Clustal on fasta file
				File clustalNexFileOutput = new File(CLUSTAL_NEXUS_OUT);
				String clustalFastaInput = Globals.getInstance().getSampleFilesDir() + "zfish_nt_12T.fasta";
				clustalNexFileOutput = serviceRunner.runClustal(clustalFastaInput, CLUSTAL_NEXUS_OUT);
				
				//take clustal output and send to Subsetter
				File nexSubsetterOutput = new File(NEXUS_SUBSET_TAXA_OUT);
				nexSubsetterOutput = serviceRunner.subsetNexusByTaxa(clustalNexFileOutput, new File(NEXUS_SUBSET_TAXA_OUT));
				
				//Take subset nexus file and send to paup for tree inference
				File paupInferNexFileOutput = serviceRunner.runPaupInfer( 
						nexSubsetterOutput, 
						new File(PAUP_NEXUS_OUT), null);
				
				//Take inference output trees and send to tree Subsetter
				//Can't use this until bug in ReadNexusServer is fixed
				File treeSubsetterOutput = new File(NEXUS_SUBSET_TREES_OUT);
				treeSubsetterOutput = serviceRunner.subsetTrees(paupInferNexFileOutput,treeSubsetterOutput);
				
				//Take tree Subsetter output and create consensus tree(s)
				File paupContreeNexFileOutput = serviceRunner.runPaupConsensusTrees(
						paupInferNexFileOutput, 
						new File(CONTREE_OUTPUT));
				
				paupContreeNexFileOutput.getAbsoluteFile();
				//translate paup output to phylip
				File NexToPhylip = PhyloFileUtils.NexusToPhylip(paupContreeNexFileOutput, NEXUS_TO_PHYLIP);
				
				//translate the phylip back to paup
				PhyloFileUtils.PhylipToNexus(NexToPhylip, PHYLIP_TO_NEXUS);
				
				System.exit(0);
			}

             // for testing ActorIterator
			if(args[0].equalsIgnoreCase("1")){
				ActorInfo actor = reg.getActor(INFER_TREE_PARS_PAUP);
				ActorIterator actorIterator = new ActorIterator(
						new File(actor.getGuiXmlFile()));
				File nexusIn = new File(Globals.getInstance().getSampleFilesDir() 
						+ "TestNexusFile.nex");
				actorIterator.setParameterValueInAll("infile",nexusIn.getAbsolutePath());
				actorIterator.setOutfileParamInAll(actor.getActorName());
				actorIterator.setVisible(true);
				ServiceCommandPanel[] pnls = actorIterator.getServiceCommandPanels();
				if(pnls!=null) {  //null returned if user clicks 'Cancel'
					//run paup_infer on each set of commands and send to forester to viz tree(s)
					File paupInferNexFileOutput;
					for (int i = 0; i < pnls.length; i++) {
						paupInferNexFileOutput = serviceRunner.runPaupInfer(
								new File(pnls[i].getParameterValue("infile")), 
								new File(pnls[i].getParameterValue("outfile")), 
								pnls[i].getCmdBlock());	
						serviceRunner.showTreeForester(paupInferNexFileOutput);
					}
				}
				System.exit(0);
			}
			
			//for testing registry editor
			if(args[0].equalsIgnoreCase("2")){
				//Print out current default InputFileDir
				System.out.println("InputFileDir = " + reg.getDefaultInputFileDir());
				//edit and get edited registry
				reg = CipresKeplerRegistry.EditRegistry();
				//Print out the default stdOutDir from the edited registry
				System.out.println("InputFileDir = " + reg.getDefaultInputFileDir());
				
				System.exit(0);
			}
			
             //for testing TreeViz
			if(args[0].equalsIgnoreCase("3")){
				File f = new File(Globals.getInstance().getSampleFilesDir() + "TestNexusFile.nex");
				serviceRunner.showTreeForester(f);
				//System.exit(0);
			}
			
			 //for testing Seaview
			if(args[0].equalsIgnoreCase("4")){
				File f = new File(Globals.getInstance().getSampleFilesDir() + "TestNexusFile.nex");
				serviceRunner.editAlignment_Seaview(f);
				//System.exit(0);
			}
			
			if (args[0].equalsIgnoreCase("5")) {
				RegistryEntryWrapper clustalWrapper = null;
				try {
					// get RecIDCM3 algorithm wrapper
					clustalWrapper = Globals.getInstance().getRegistry().getCipresService(MatrixAlign.class);
					// use GuiGen to get users' settings
					CipresServiceDialog dialog = clustalWrapper
							.getServiceDialog(null);
					//int status = dialog.showAndInitialize();
					int status = dialog.show();
					if (status == CipresServiceDialog.OK) {
						String cmds = dialog.getPanel().getCmdBlock();
						MatrixAlign service = (MatrixAlign) clustalWrapper
								.getService();
						// set the tree and matrix into the CORBA service
						
						org.omg.CORBA.StringHolder reply = new org.omg.CORBA.StringHolder();
						boolean executeSucceeded = false;
						service.getScore();
						executeSucceeded = service.execute(cmds, reply);
						System.out.println(executeSucceeded);

					} else if (status == CipresServiceDialog.ERROR) {
						JOptionPane.showMessageDialog(null,
								"error initializing service");
					}

				} catch (Exception e) {
					e.printStackTrace();
				} finally {
					if (clustalWrapper != null) {
						// release the RecIDCM3 service
						clustalWrapper.releaseService();
					}
					System.exit(0);
				}
			}
			
		} catch (Exception e) {
			e.printStackTrace();
		} finally {
			//System.exit(0);
		}
	}


}