package org.cipres.kepler.sandbox;

import java.io.File;

import org.cipres.util.CipresFile;

public class PhyloFileUtils {

	//for creating actor to translate NexusToPhylip
	public static File NexusToPhylip(File inputNexusFile, String outputPhylipFilename)
	throws Exception {	
		if(!inputNexusFile.canRead()){
			throw new Exception("Cannot Read " + inputNexusFile.getAbsolutePath());
		}
		String commands = 
			" EXECUTE " + inputNexusFile.getAbsolutePath() + ";" 
			+ " EXPORT File=" + outputPhylipFilename
			+ " FORMAT=PHYLIP TREES=YES REPLACE=YES;\n";
		ServiceRunner.paupExecute(commands);
		return new File(outputPhylipFilename);
	}
	
	//for creating actor to translate PhylipToNexus
	public static File PhylipToNexus(File inputPhylipFile, String outputNexusFilename)
	throws Exception {	
		if(!inputPhylipFile.canRead()){
			throw new Exception("Cannot Read " + inputPhylipFile.getAbsolutePath());
		}
		String commands = 
			" TONEXUS FORMAT=PHYLIP FromFile=" + inputPhylipFile.getAbsolutePath() 
			+ " ToFile=" + outputNexusFilename + " REPLACE=YES;\n"
			+ " EXECUTE" + outputNexusFilename + ";"
			+ " SAVETREES File=" + outputNexusFilename
			+ " FORMAT=NEXUS APPEND=YES;";
		ServiceRunner.paupExecute(commands);
		return new File(outputNexusFilename);
	}	
	
	
    //THIS NEXT METHOD SHOULD BE USED BY THE CLUSTAL ACTOR
	public static File removeSymbolsFromNexus(File inputNexusFile)
	throws Exception {	
		CipresFile cfIn = new CipresFile(inputNexusFile.getAbsolutePath());
		CipresFile cfOut = new CipresFile(KeplerTest.CLUSTAL_NEXUS_OUT);
		String content = cfIn.getContent();
		//find beginnning of symbols statement
		int pos1 = content.toLowerCase().indexOf("symbols");
		//find end of symbols statement (will be the 2nd quotation mark after "symbols")
		int pos2 = content.indexOf("\"", pos1);
		pos2 = content.indexOf("\"", pos2+1);
		String symbolsString  = content.substring(pos1, pos2);
		cfOut.fillFromString(content.substring(0,pos1) + 
				content.substring(pos1 + symbolsString.length() + 1, content.length()));
		return new File(cfOut.getAbsolutePath());
	}

	
}