GenBank2Pdf.cs

// GenBank2Pdf.cs
// 
// Copyright (C) 2008 Jacob, jacobnix@gmail.com
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//


using System;
using System.IO;
using sharpPDF;
using sharpPDF.Enumerators;

namespace GenBank2Pdf
{
	public class ClsGenBank2Pdf
	{		
		string filename;
		string saveDirectory;	
		StreamReader sr;
		//StreamWriter sw;
		
		public void Load(string file)
		{
			this.filename = Path.GetFullPath(file);
			sr = File.OpenText(this.filename);
			saveDirectory = Path.GetDirectoryName(this.filename);	
		}
		
		public void GenBank2Pdf()
		{
			string line = "";
			short index = 0;		
			string[] tokensGenBankFlatFile = {"LOCUS","//"};
			char[] token = {' '};
			string ContigName = "";
			string BlockGenBankStart = "";
			string BlockGenBankEnd = "";
			string newPdfFile = "";
			pdfDocument pdfGenBankFile = null;
			pdfPage pdfGenBankFileFilePage = null;
			int pagePositionTextY = 0;
			
			Console.WriteLine("Parsing....");
			do 
			{
			  try {		
				line = sr.ReadLine();
				index = (short)line.IndexOf(tokensGenBankFlatFile[0]);
				if(index!=-1) { //found LOCUS?
				
					BlockGenBankStart = line;				 	
					line = line.Substring(5,(line.Length-5));
					line = line.Trim();
					index = (short)line.IndexOf(token[0]);
					ContigName = line.Substring(0,index);
					//start to generate a new PDF Gen Bank Flat File
					newPdfFile = saveDirectory + "/" + ContigName + ".pdf";
					pdfGenBankFile = new pdfDocument(ContigName,"Jacob Israel Cervantes Luevano");
					pdfGenBankFileFilePage = pdfGenBankFile.addPage();
					//sw = File.CreateText(newPdfFile);						
					//sw.WriteLine(BlockGenBankStart);
					pagePositionTextY = 150;	
					pdfGenBankFileFilePage.addText(BlockGenBankStart,5,pagePositionTextY,predefinedFont.csHelveticaBold,10);	
					Console.WriteLine("Extracting data block with identifier: {0} on file:{1}",ContigName,newPdfFile);
					continue;				
				}
				
				index = (short)line.IndexOf(tokensGenBankFlatFile[1]);
				if(index!=-1) { //found end block
					BlockGenBankEnd = line;
					//sw.WriteLine(BlockGenBankEnd);					
					//sw.Close();
					pagePositionTextY = pagePositionTextY + 10;
					pdfGenBankFileFilePage.addText(BlockGenBankEnd,5,pagePositionTextY,predefinedFont.csHelveticaBold,10);	
					pdfGenBankFile.createPDF(newPdfFile);
					pdfGenBankFile = null;
					pdfGenBankFileFilePage = null;	
					continue;	
				}				
					
				if(line != "" && line != " " && line != string.Empty) {
					//sw.WriteLine(line);
					pagePositionTextY = pagePositionTextY + 10;
					pdfGenBankFileFilePage.addText(line,5,pagePositionTextY,predefinedFont.csHelveticaBold,10);						                               
			    }    
			  }//end_try
			  catch(Exception e) {
					Console.WriteLine(e.Message);
			  }//end_try_catch
			}//end_while				
		    while(line!=null);
			sr.Close();
	    }		
 }
}