Sequence File Handler Java Code 07-16-2014d1122

2015-01-13

Sequence File Handler Java Code 07-16-2014d1122

fasta file handler
protein dna sequence file handler code
import fasta file sequences
export sequences to fasta file

code



import java.util.ArrayList;








public class SequenceFileHandler {





	UsefulTools useful_tools = new UsefulTools();


	ArrayList names = new ArrayList();


	ArrayList sequences = new ArrayList();


	String current_line = "";


	


	


	public ArrayList getNames()


	{


		return names;

public ArrayList getSequences()



		return sequences;

public ArrayList getSequencesFromFile(String file_path)



		


		ArrayList lines = useful_tools.storeTextFiletoArrayList(file_path);


		boolean contains_greater_than_sign = false;


		for(int i=0; i<lines.size();i++)


		{


			String current_line = lines.get(i).toString();


			if(current_line.indexOf(">")!=-1)


			{


				contains_greater_than_sign = true;

}

//if it contains a greater than sign, then this is a fasta file and the names and sequences should be collected accordingly
//otherwise, each line without a space is a sequence, and the name should be some arbitrary name
if(contains_greater_than_sign)



			boolean title_found = false;


			


			for(int i=0; i<lines.size(); i++)


			{


				current_line = lines.get(i).toString();


				if(!title_found)


				{


					if(current_line.indexOf(">")!=-1 && current_line.length()>0)


					{


						title_found = true;


						names.add(current_line.replaceAll(">(.+)", "$1"));

}
else if(title_found)



					current_line = lines.get(i).toString();


					//make sure there are no spaces


					if(useful_tools.getMatchesRegEx(current_line, "\\s")==0 && current_line.length()>0)


					


					{


						


						sequences.add(current_line);


						title_found = false;

}
}
}
else



			int sequence_count = 0;


			//each line without a space should be a sequence


			for(int i=0; i<lines.size(); i++)


			{


				current_line = lines.get(i).toString();


				if(useful_tools.getMatchesRegEx(current_line, "\\s")==0 && current_line.length()>0)


				{


					


					sequences.add(current_line);


					sequence_count++;


					names.add("seq"+sequence_count);

}
}
return sequences;
}

/*
* this function expects sequences separated by commas
*/
public void createFastaFromSequences(String sequences, String directory, String filename)



		createFastaFromSequences(useful_tools.stringWithCommasToArrayList(sequences), directory, filename);

public void createFastaFromSequences(ArrayList sequences, String directory, String filename)



		String output_string = "";


		for(int i=0; i<sequences.size(); i++)


		{


			output_string+=">seq"+(i+1)+"\r\n"+sequences.get(i).toString()+"\r\n";

useful_tools.createTextFile(directory, filename, output_string);
}
}

}