package org.cipres.kepler.sandbox;

import java.io.File;
import java.io.IOException;
import javax.swing.JOptionPane;

import org.apache.log4j.Logger;
import org.cipres.datatypes.PhyloDataset;
import org.cipres.guigen.ServiceCommandPanel;
import org.cipres.kepler.DisplayObject;
import org.cipres.kepler.SubsetChooser;
import org.cipres.helpers.JRun;
import org.cipres.kepler.registry.*;
import org.cipres.util.CipresFile;
import org.cipres.CipresIDL.api1.DataMatrix;
import org.cipres.CipresIDL.api1.Tree;

import forester.atv.ATVjframe;

public class ServiceRunner {
	
	private static Logger logger = Logger.getLogger(ServiceRunner.class.getName());
	CipresKeplerRegistry reg = Globals.getInstance().getRegistry();
	
	public void editAlignment_Seaview(File inputNexusFile) throws InterruptedException, IOException {
		ActorInfo seaViewActor = reg.getActor("AlignmentEditor_Seaview");
		
		File appFile = new File(seaViewActor.getAppPath());
		
		String[] args = { inputNexusFile.getAbsolutePath() };
		JRun jrun = new JRun();
		jrun.setExecutable("open -a " + appFile.getName());
		jrun.setArguments(args);
		//jrun.setStandardOutputStream(System.out);
		jrun.setOutputFilename(reg.getDefaultStdOutDir() + "StdOut.log");
		jrun.setErrorFilename(reg.getDefaultStdErrDir() + "StdErr.log");
		jrun.setWorkingDirPath(appFile.getParent());
		jrun.setWaitForExecution(true);
		jrun.execute();
		
		
	}
	
	public void showTreeForester(File inputNexusFile)
	throws Exception {
		PhyloDataset pdTrees = new PhyloDataset();
		pdTrees.initialize(inputNexusFile);
		for(int i = 0; i< pdTrees.getTrees().length; i++){
			Tree tree = pdTrees.getTrees()[i];
			forester.tree.Tree displayedTree = new forester.tree.Tree(tree.m_newick);
			ATVjframe atvframe = new ATVjframe(displayedTree);
			atvframe.setTitle(tree.m_name + " from file " + inputNexusFile.getName());
			atvframe.showWhole();	
		}
		
	}
	
	public File runClustal() throws Exception {
		return runClustal(null, null);
	}

	public File runClustal(String inputFastaFilename, String outputNexusFileName)
	throws Exception {
		ActorInfo clustalActor = reg.getActor(KeplerTest.CLUSTAL_ACTOR_NAME);
		ServiceCommandPanel pnl = new ServiceCommandPanel(new File(clustalActor.getGuiXmlFile()));
		pnl.setDefaultInFileDirectory(reg.getDefaultInputFileDir());
		if(inputFastaFilename!=null){
			pnl.setParameterValue("infile", inputFastaFilename);
		}
		if(outputNexusFileName!=null){
			pnl.setParameterValue("outfile", outputNexusFileName);
		}
		pnl.showServicePanelAsDialog();
		
		File appFile = new File(clustalActor.getAppPath());
		String args[] = { pnl.getCmdBlock() };
		JRun jrun = new JRun();
		jrun.setExecutable(appFile.getAbsolutePath());
		jrun.setArguments(args);
		jrun.setStandardOutputStream(System.out);
		jrun.setOutputFilename(reg.getDefaultStdOutDir() + "StdOut.log");
		jrun.setErrorFilename(reg.getDefaultStdErrDir() + "StdErr.log");
		jrun.setWorkingDirPath(appFile.getParent());
		jrun.setWaitForExecution(true);

		System.out.println(jrun.execute());
		logger.info("Clustal Finished with exit code "
				+ jrun.getExitCode());

		File retFile = new File(pnl
				.getParameterValue("outfile"));
		
		return PhyloFileUtils.removeSymbolsFromNexus(retFile);

	}

	
	public File runPaupConsensusTrees(File inputNexusFile, File outputNexusFile) 
	throws Exception {
		ActorInfo paupActor = reg.getActor(KeplerTest.CONSENSUS_TREE_PAUP);
		//get paup commands using guigen
		ServiceCommandPanel pnl = new ServiceCommandPanel(
				new File(paupActor.getGuiXmlFile()));
		pnl.setParameterValue("infile",inputNexusFile.getAbsolutePath());
		pnl.setParameterValue("outfile",outputNexusFile.getAbsolutePath());
		pnl.showServicePanelAsDialog();
		
		//this command has paup:
		//1. import input and write to output
		//2. execute contree and append trees to output
		paupExecute("EXECUTE " + inputNexusFile.getAbsolutePath() + ";"
				+ " EXPORT File=" + pnl.getParameterValue("outfile")
				+ " FORMAT = NEXUS TREES=NO REPLACE=YES;"
				+ " CLEARTREES NOWARN=YES;"
				+ " SET WARNRESET=NO; "
				+ pnl.getCmdBlock() +
				" TreeFile =" + pnl.getParameterValue("outfile") 
				+ " APPEND=YES;");
		
		//PhyloDataset pdTrees = new PhyloDataset();
		//pdTrees.initialize(new cipresFile(pnl.getParameterValue("outfile")));	
		
		//pdTrees.writeToNexus(outputNexusFile);
		return new File(pnl.getParameterValue("outfile"));
		
	}
	
	public File runPaupInfer(File inputNexusFile, File outputNexusFile, 
			String PaupCommands) 
	throws Exception {
		ActorInfo paupActor = reg.getActor(KeplerTest.INFER_TREE_PARS_PAUP);
		String outFilePath;
	
		if(PaupCommands == null) {
			//get paup commands using guigen
			ServiceCommandPanel pnl = new ServiceCommandPanel(
					new File(paupActor.getGuiXmlFile()));
			pnl.setParameterValue("infile",inputNexusFile.getAbsolutePath());
			pnl.setParameterValue("outfile",outputNexusFile.getAbsolutePath());
			pnl.showServicePanelAsDialog();
			PaupCommands = pnl.getCmdBlock();
			outFilePath = pnl.getParameterValue("outfile");
		}
		else {
			outFilePath = outputNexusFile.getAbsolutePath();
		}
		
		//if path to output file is > 64 chars paup will throw an error
		//so, we have give paup only the filename, which causes it to write to
		//its own dir, then rename the file to the location specified by the
		//outFilePath
		File outfile =  new File(outFilePath);		
		File paupApp = new File(paupActor.getAppPath());
		File paupOut = new File(paupApp.getParent() 
				+ Globals.getInstance().getDirSep()
				+ outfile.getName());
		 String commands = 
			PaupCommands 
			+ "\n EXPORT File=" + outfile.getName()
			+ " FORMAT=NEXUS REPLACE=YES;\n"
			+ " SAVETREES File=" + outfile.getName()
			+ " FORMAT=NEXUS BRLENS=YES MAXDECIMALS=2"
			+ " APPEND=YES;";
		paupExecute(commands);
		//now move outfile to its proper location
		//outfile is currently located in same dir as paup
		if(!outfile.getAbsolutePath().equalsIgnoreCase(paupOut.getAbsolutePath())){
			paupOut.renameTo(outfile);
		}
	
		return new File(outFilePath);
		
	}
	
	public static void paupExecute(String commands) throws Exception{
		CipresFile cmdFile = new CipresFile(KeplerTest.PAUP_CMD_FILE);
		cmdFile.fillFromString("#NEXUS\nBEGIN PAUP;\n" + 
				commands + " QUIT;\nEND;");	
		logger.info("Running paupExecute on commands" + commands);
		CipresKeplerRegistry registry = Globals.getInstance().getRegistry();
		ActorInfo paupActor = registry.getActor(KeplerTest.CONSENSUS_TREE_PAUP);
		
		//run paup
		File appFile = new File(paupActor.getAppPath());
		String args[] = { cmdFile.getAbsolutePath() };
		JRun jrun = new JRun();
		jrun.setExecutable(appFile.getAbsolutePath());
		jrun.setArguments(args);
		jrun.setStandardOutputStream(System.out);
		jrun.setOutputFilename(registry.getDefaultStdOutDir() + "StdOut.log");
		jrun.setErrorFilename(registry.getDefaultStdErrDir() + "StdErr.log");
		jrun.setWorkingDirPath(appFile.getParent());
		jrun.setWaitForExecution(true);
		System.out.println(jrun.execute());
		System.out.println("Paup Finished with exit code " + jrun.getExitCode());
	}
	
    //Works, but not real uselss until bug in ReadNexusServer is fixed
	public File subsetTrees(File inputNexusFile, File outputNexusFile)
			throws Exception {

		PhyloDataset pdIn = new PhyloDataset();
		pdIn.initialize(inputNexusFile);
		
		if(pdIn.getTrees()==null){
			JOptionPane.showMessageDialog(null, "There are no trees to subset");
			return inputNexusFile;
		}
		
		DisplayObject[] displayObjects = new DisplayObject[pdIn.getTrees().length];
		Tree tree = null;
		String treeName;
		int j;
		for (int i = 0; i < pdIn.getTrees().length; i++) {
			tree = pdIn.getTrees()[i];
			if(tree.m_name==null || tree.m_name.trim().length()==0){
				j = i + 1;
				treeName = "Tree" + j;
			}
			else {
				treeName = tree.m_name;
			}			
			displayObjects[i] = new DisplayObject(new Integer(i), treeName);
		}

		SubsetChooser sc = new SubsetChooser(displayObjects);
		DisplayObject[] displayObjectsSubset = sc.showSubsetChooserAsDialog();

		// create new PhyloDataset comprised of the subset and write it to nexus
		PhyloDataset pdOut;
		Integer jInt;
		Tree[] treesOut = new Tree[displayObjectsSubset.length];
		for (int i = 0; i < displayObjectsSubset.length; i++) {
			jInt = (Integer) displayObjectsSubset[i].getObject();
			j = jInt.intValue();
			treesOut[i] = pdIn.getTrees()[j];
		}


		pdOut = new PhyloDataset(null, treesOut, pdIn.getTaxaInfo());

		pdOut.writeToNexus(outputNexusFile);
		return outputNexusFile;
	}
	
	
	public File subsetNexusByTaxa(File inputNexusFile, File outputNexusFile)
			throws Exception {

		PhyloDataset pdIn = new PhyloDataset();
		pdIn.initialize(inputNexusFile);
		
		if(pdIn.getTaxaInfo()==null){
			JOptionPane.showMessageDialog(null, "There are no taxa to subset");
			return inputNexusFile;
		}
		
		DisplayObject[] displayObjects = new DisplayObject[pdIn.getTaxaInfo().length];
		for (int i = 0; i < pdIn.getTaxaInfo().length; i++) {
			displayObjects[i] = new DisplayObject(new Integer(i), pdIn
					.getTaxaInfo()[i]);
		}
		
		SubsetChooser sc = new SubsetChooser(displayObjects);
		DisplayObject[] displayObjectsSubset = sc.showSubsetChooserAsDialog();

		// create new PhyloDataset comprised of the subset and write it to nexus
		PhyloDataset pdOut;
		DataMatrix dmIn = pdIn.getDataMatrix();
		DataMatrix dmOut = new DataMatrix();		
		String[] taxa = new String[displayObjectsSubset.length];
		short[][] matrix = new short[displayObjectsSubset.length][pdIn
				.getDataMatrix().m_numCharacters];
		Integer jInt;
		int j = 0;
		for (int i = 0; i < displayObjectsSubset.length; i++) {
			jInt = (Integer) displayObjectsSubset[i].getObject();
			j = jInt.intValue();
			taxa[i] = pdIn.getTaxaInfo()[j];
			for (int k = 0; k < dmIn.m_matrix[0].length; k++) {
				matrix[i][k] = dmIn.m_matrix[j][k];
			}
		}

		dmOut.m_matrix = matrix;
		dmOut.m_symbols = dmIn.m_symbols;
		dmOut.m_charStateLookup = dmIn.m_charStateLookup;
		dmOut.m_datatype = dmIn.m_datatype;
		dmOut.m_numCharacters = dmIn.m_numCharacters;
		dmOut.m_numStates = dmIn.m_numStates;
		dmOut.m_charStateLookup = dmIn.m_charStateLookup;

		pdOut = new PhyloDataset(dmOut, pdIn.getTrees(), taxa);

		pdOut.writeToNexus(outputNexusFile);
		return outputNexusFile;
	}
	
		
}