src/trackParser/ReadAndParse.java
//The readIn method relies on the parseIt method below. It assigns the read-in file to the private RegionObject

The readIn method relies on the parseIt method below. It assigns the read-in file to the private RegionObject
The readIn method relies on the parseIt method below . It assigns the read - in file to the private RegionObject
public void readIn(String someFile)
	{
		try 
		{
			String firstLine = null;
			ArrayList<RegionObject> tempAR = new ArrayList<RegionObject>();
			ImportFile f1 = new ImportFile();
			f1.setFileName(someFile);
			FileReader f1a = new FileReader(f1.returnFile());
			BufferedReader in0 = new BufferedReader(f1a);
			firstLine = in0.readLine();
			this.parseIt(firstLine);
			firstLine = in0.readLine();
			while (firstLine != null)
			{
				String[] strArray = firstLine.split("\t");
				RegionObject vnishh = new RegionObject(strArray[indexEnsemblTranscriptID], strArray[indexContig], strArray[indexSense].charAt(0), strArray[indexExonStarts], strArray[indexExonEnds]);
				/*/BEGIN TS CODE//
				System.out.println(strArray[indexEnsemblTranscriptID] + " is the EnsembleTranscriptID.\n" + strArray[indexContig] + " is the indexContig.\n"  + strArray[indexSense].charAt(0) + " is the sense.\n"  + strArray[indexExonStarts] + " is the ExonStarts.\n"  + strArray[indexExonEnds] + " is the ExonEnds.\n"  + "...all being dumped into the new RegionObject");
				//END TS CODE/*/
				tempAR.add(vnishh);
				/*/Begin TS code//
				System.out.println("Added the item to the temp array.");
				System.out.println(vnishh);
				//END TS CODE/*/
				firstLine = in0.readLine();
			}
			for (RegionObject r: tempAR)
				{
					parseFurther(r);
				}
			in0.close();
			/*/Begin TS Code//
			System.out.println("If all the above worked, now remove the TS code and print out all of eR");
			System.out.println(eR.size() + " is the size of the eR array ");
			for(ExonObject e: eR)
			{
				System.out.println(e.getContig());
				System.out.println(e.getexonStart());
				System.out.println(e.getexonEnd());
			}
			System.out.println("If all the above worked, eR was printed");
			System.out.println(eR.size() + " is the size of the eR array");
			//END TS CODE/*/
			makeFileBed(eR);
		} 
		catch (IOException e) 
		{
			System.out.println("Something went wrong when attempting to read in the file using readIn method of ReadAndParse Class.");
			e.printStackTrace();
		}
	}
public void readIn ( String someFile ) { try { String firstLine = null ; ArrayList < RegionObject > tempAR = new ArrayList < RegionObject > ( ) ; ImportFile f1 = new ImportFile ( ) ; f1 . setFileName ( someFile ) ; FileReader f1a = new FileReader ( f1 . returnFile ( ) ) ; BufferedReader in0 = new BufferedReader ( f1a ) ; firstLine = in0 . readLine ( ) ; this . parseIt ( firstLine ) ; firstLine = in0 . readLine ( ) ; while ( firstLine != null ) { String [ ] strArray = firstLine . split ( "\t" ) ; RegionObject vnishh = new RegionObject ( strArray [ indexEnsemblTranscriptID ] , strArray [ indexContig ] , strArray [ indexSense ] . charAt ( 0 ) , strArray [ indexExonStarts ] , strArray [ indexExonEnds ] ) ; /*/BEGIN TS CODE//
				System.out.println(strArray[indexEnsemblTranscriptID] + " is the EnsembleTranscriptID.\n" + strArray[indexContig] + " is the indexContig.\n"  + strArray[indexSense].charAt(0) + " is the sense.\n"  + strArray[indexExonStarts] + " is the ExonStarts.\n"  + strArray[indexExonEnds] + " is the ExonEnds.\n"  + "...all being dumped into the new RegionObject");
				//END TS CODE/*/ tempAR . add ( vnishh ) ; /*/Begin TS code//
				System.out.println("Added the item to the temp array.");
				System.out.println(vnishh);
				//END TS CODE/*/ firstLine = in0 . readLine ( ) ; } for ( RegionObject r : tempAR ) { parseFurther ( r ) ; } in0 . close ( ) ; /*/Begin TS Code//
			System.out.println("If all the above worked, now remove the TS code and print out all of eR");
			System.out.println(eR.size() + " is the size of the eR array ");
			for(ExonObject e: eR)
			{
				System.out.println(e.getContig());
				System.out.println(e.getexonStart());
				System.out.println(e.getexonEnd());
			}
			System.out.println("If all the above worked, eR was printed");
			System.out.println(eR.size() + " is the size of the eR array");
			//END TS CODE/*/ makeFileBed ( eR ) ; } catch ( IOException e ) { System . out . println ( "Something went wrong when attempting to read in the file using readIn method of ReadAndParse Class." ) ; e . printStackTrace ( ) ; } }
The readIn method relies on the parseIt method below.
The readIn method relies on the parseIt method below .
//Variables used within this method only
 //import a file
 //stream the file
 //characterize / parse the file based on first line properties
 //For all in tempAR second level parse
