src/trackParser/ReadAndParse.java
//The parseIt method looks for select headers in the first line

The parseIt method looks for select headers in the first line
The parseIt method looks for select headers in the first line
public void parseIt(String headString)
	{
		String[] labels = headString.split("\t");
		int numberItems = labels.length;
		for (int i = 0; i < numberItems; i++)
		{
			/*/Begin TS Code
			System.out.println("The labels index i is: " + i +". And the string is: " + labels[i]);
			//End TS code/*/
			if(labels[i].equals("name")) 
			{
				indexEnsemblTranscriptID = i;
				/*/Begin TS Code
				System.out.println("i is: " + i +". And assigned to: " + "indexEnsemblTranscriptID");
				//End TS code/*/
			}
			else if(labels[i].equals("chrom"))
			{
				indexContig = i;
				/*/Begin TS Code
				System.out.println("i is: " + i +". And assigned to: " + "indexContig");
				//End TS code/*/
			}
			else if(labels[i].equals("strand"))
			{
				indexSense = i;
				/*/Begin TS Code//
				System.out.println("i is: " + i +". And assigned to: " + "indexSense");
				//End TS code/*/
			}
			else if(labels[i].equals("exonStarts"))
			{
				indexExonStarts = i;
				/*/Begin TS Code
				System.out.println("i is: " + i +". And assigned to: " + "indexExonStarts");
				//End TS code/*/
			}
			else if(labels[i].equals("exonEnds"))
			{
				indexExonEnds = i;
				/*/Begin TS Code
				System.out.println("i is: " + i +". And assigned to: " + "indexExonEnds");
				//End TS code/*/
			}
			else
			{
				/*/Begin TS Code
				System.out.println("i is: " + i +". And went unassigned");
				//End TS code/*/
			}
		}
	}
public void parseIt ( String headString ) { String [ ] labels = headString . split ( "\t" ) ; int numberItems = labels . length ; for ( int i = 0 ; i < numberItems ; i ++ ) { /*/Begin TS Code
			System.out.println("The labels index i is: " + i +". And the string is: " + labels[i]);
			//End TS code/*/ if ( labels [ i ] . equals ( "name" ) ) { indexEnsemblTranscriptID = i ; /*/Begin TS Code
				System.out.println("i is: " + i +". And assigned to: " + "indexEnsemblTranscriptID");
				//End TS code/*/ } else if ( labels [ i ] . equals ( "chrom" ) ) { indexContig = i ; /*/Begin TS Code
				System.out.println("i is: " + i +". And assigned to: " + "indexContig");
				//End TS code/*/ } else if ( labels [ i ] . equals ( "strand" ) ) { indexSense = i ; /*/Begin TS Code//
				System.out.println("i is: " + i +". And assigned to: " + "indexSense");
				//End TS code/*/ } else if ( labels [ i ] . equals ( "exonStarts" ) ) { indexExonStarts = i ; /*/Begin TS Code
				System.out.println("i is: " + i +". And assigned to: " + "indexExonStarts");
				//End TS code/*/ } else if ( labels [ i ] . equals ( "exonEnds" ) ) { indexExonEnds = i ; /*/Begin TS Code
				System.out.println("i is: " + i +". And assigned to: " + "indexExonEnds");
				//End TS code/*/ } else { /*/Begin TS Code
				System.out.println("i is: " + i +". And went unassigned");
				//End TS code/*/ } } }
The parseIt method looks for select headers in the first line
The parseIt method looks for select headers in the first line