translation source code

[Jared Roach]

	Well, here's C translation source code I wrote as an XFCN for HyperCard
for the Macintosh, so you would be able to dispense with most of it for 
whatever you wanted it for, most likely.  I include the whole code just to 
put it into context.  Please don't hesitate to ask for clarification.  
Note that my elegance and experience in programming C probably falls 
somewhere in the middle of the lowest percentile, so be warned!
	The XFCN parts of the code are shareware by Mark Hanrek.

//  DNA2Prot XFCN by Jared Roach  © August 1996
//  This program translates DNA sequences
//  The XFCN shell was downloaded form the Web and is © 1992 Mark Hanrek


//***************************************************************************************
//	 Hanrek XCMD Shell 1.2
//
//   ©1992 Mark Hanrek & The Information Workshop.  All Rights Reserved.
//
//	 Note: 	Do all your programming between the bold black lines below. 
//			Put additional functions you create into the "Support Functions" 
//			section below that.  Put function prototypes into ExampleXFCN.h.
//

/******************************************************************* Includes ********/

#include "SetUpA4.h"
#include "HyperXCmd.h"
#include "SuperCard.h"
#include "StandardFunctions.h"
#include "string.h"

/******************************************************************* Main Entry ******/

pascal void main( XCmdPtr paramPtr )	// No need to ever change any of this...
{
	RememberA0();
	SetUpA4();
	InitializeReturnInfo( paramPtr );
	ExternalHandler( paramPtr );
	RestoreA4();
}	




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//
//	DNA2ProtXFCN HyperTalk Syntax:
//  put 1 into frame (should be 1,2, or 3)
//  put 1 into flag
//  
//  put cd fld "Sequence" into seq
//  
//  put DNA2ProtXFCN( seq, frame, flag ) into cd fld "output"
//  
//

#include "DNA2ProtXFCN.h"

void ExternalHandler( XCmdPtr paramPtr )
{
	short	i=0;
	short	k=0;
	short	q=0;
	short	p=0;
	short	nFrame;
	short	nProtLength;
	
	
	char 	pBase;
	char 	pResidue;
	char 	pSeq[3000];
	char 	pProtSeq[1000];
	
	
 	size_t 	nSeqLength;
 	short 	nFlagVariable = 0;
	
	
	ParamToCString( 0, pSeq );			// the first parameter is the sequence
	ParamToShort( 1, &nFrame ); 			
	ParamToShort( 2, &nFlagVariable ); 			
	
	nSeqLength=strlen(pSeq); 
	nProtLength = (nSeqLength-nFrame+1)/3;
	
	
	
	if ( nSeqLength < 1 )
		return;
	
	k = nFrame-1;		
	q = nProtLength*3+k;
		
  	for (i=k; i < q; ++i)	{
		pBase = pSeq[i];
  		if ( pBase == 'A' ) {
  			pBase = pSeq[++i];
  			if ( pBase == 'A' ) {
  				pBase = pSeq[++i];
  				if ( pBase == 'A' ) {
  					pResidue = 'K';
  				}
				else if ( pBase == 'C' ) {
  					pResidue = 'N';
  				}
				else if ( pBase == 'G' ) {
  					pResidue = 'K';  		
  				}
				else if ( pBase == 'T' ) {
  					pResidue = 'N';  		
  				}
				else  {									// case of N or other character 3rd base
					pResidue = 'X';
				}
  			}
			else if ( pBase == 'C' ) {
  				++i;
  				pResidue = 'T';							//all codons starting with AC are threonine
  			}
			else if ( pBase == 'G' ) {
  				pBase = pSeq[++i];
  				if ( pBase == 'A' ) {
  					pResidue = 'R';
  				}
				else if ( pBase == 'C' ) {
  					pResidue = 'S';
  				}
				else if ( pBase == 'G' ) {
  					pResidue = 'R';  		
  				}
				else if ( pBase == 'T' ) {
  					pResidue = 'S';  		
  				}
				else  {									// case of N or other character 3rd base
					pResidue = 'X';
				}  		
  			}
			else if ( pBase == 'T' ) {
  				pBase = pSeq[++i];
  				if ( pBase == 'A' ) {
  					pResidue = 'I';
  				}
				else if ( pBase == 'C' ) {
  					pResidue = 'I';
  				}
				else if ( pBase == 'G' ) {
  					pResidue = 'M';  		
  				}
				else if ( pBase == 'T' ) {
  					pResidue = 'I';  		
  				}
				else  {									// case of N or other character 3rd base
					pResidue = 'X';
				}  		
  			}
			else  {									// case of N or other character 2nd base
				++i;
				pResidue = 'X';
			}
  		}
		else if ( pBase == 'C' ) {
  			pBase = pSeq[++i];
  			if ( pBase == 'A' ) {
  				pBase = pSeq[++i];
  				if ( pBase == 'A' ) {
  					pResidue = 'Q';
  				}
				else if ( pBase == 'C' ) {
  					pResidue = 'H';
  				}
				else if ( pBase == 'G' ) {
  					pResidue = 'Q';  		
  				}
				else if ( pBase == 'T' ) {
  					pResidue = 'H';  		
  				}
				else  {									// case of N or other character 3rd base
					pResidue = 'X';
				}
  			}
			else if ( pBase == 'C' ) {
  				++i;
  				pResidue = 'P';							//all codons starting with CC are proline
  			}
			else if ( pBase == 'G' ) {
  				++i;
  				pResidue = 'R';							//all codons starting with CG are arginine
  			}
			else if ( pBase == 'T' ) {
  				++i;
  				pResidue = 'L';							//all codons starting with CT are leucine
  			}
			else  {									// case of N or other character 2nd base
				++i;
				pResidue = 'X';
			}  		
  		}
		else if ( pBase == 'G' ) {
  			pBase = pSeq[++i];
  			if ( pBase == 'A' ) {
  				pBase = pSeq[++i];
  				if ( pBase == 'A' ) {
  					pResidue = 'E';
  				}
				else if ( pBase == 'C' ) {
  					pResidue = 'D';
  				}
				else if ( pBase == 'G' ) {
  					pResidue = 'E';  		
  				}
				else if ( pBase == 'T' ) {
  					pResidue = 'D';  		
  				}
				else  {									// case of N or other character 3rd base
					pResidue = 'X';
				}
  			}
			else if ( pBase == 'C' ) {
  				++i;
  				pResidue = 'A';							//all codons starting with GC are alanine
  			}
			else if ( pBase == 'G' ) {
  				++i;
  				pResidue = 'G';							//all codons starting with GG are glycine
  			}
			else if ( pBase == 'T' ) {
  				++i;
  				pResidue = 'V';							//all codons starting with GT are valine
  			}
			else  {									// case of N or other character 2nd base
				++i;
				pResidue = 'X';
			}  		
  		}
		else if ( pBase == 'T' ) {
  			pBase = pSeq[++i];
  			if ( pBase == 'A' ) {
  				pBase = pSeq[++i];
  				if ( pBase == 'A' ) {
  					pResidue = ' ';
  				}
				else if ( pBase == 'C' ) {
  					pResidue = 'Y';
  				}
				else if ( pBase == 'G' ) {
  					pResidue = ' ';  		
  				}
				else if ( pBase == 'T' ) {
  					pResidue = 'Y';  		
  				}
				else  {									// case of N or other character 3rd base
					pResidue = 'Y';						//  I call uncertainty between tyrosine and stop: tyrosine
				}
  			}
			else if ( pBase == 'C' ) {
  				++i;
  				pResidue = 'S';							//all codons starting with TC are serine
  			}
			else if ( pBase == 'G' ) {
  				pBase = pSeq[++i];
  				if ( pBase == 'A' ) {
  					pResidue = ' ';
  				}
				else if ( pBase == 'C' ) {
  					pResidue = 'C';
  				}
				else if ( pBase == 'G' ) {
  					pResidue = 'W';  		
  				}
				else if ( pBase == 'T' ) {
  					pResidue = 'C';  		
  				}
				else  {									// case of N or other character 3rd base
					pResidue = 'X';
				}  		
  			}
			else if ( pBase == 'T' ) {
  				pBase = pSeq[++i];
  				if ( pBase == 'A' ) {
  					pResidue = 'L';
  				}
				else if ( pBase == 'C' ) {
  					pResidue = 'F';
  				}
				else if ( pBase == 'G' ) {
  					pResidue = 'L';  		
  				}
				else if ( pBase == 'T' ) {
  					pResidue = 'F';  		
  				}
				else  {									// case of N or other character 3rd base
					pResidue = 'X';
				}  		
  			}
			else  {									// case of N or other character 2nd base
				++i;
				pResidue = 'X';
			}  		
  		}
		else  {									// case of N or other character 1st base
			++i;
			++i;
			pResidue = 'X';
		}
		pProtSeq[p++]=pResidue;
	}
	
  	
  	
  	


	//Return Result
	for (i=0; i < p; ++i)
		AppendReturnInfo( kResult, "|b", pProtSeq[i] );
	AppendReturnInfo( kResult, "\r");
	
	
	
	if (nFlagVariable == 1)
		AppendReturnInfo( kResult, "\r DNA2Prot XFCN copyright Jared Roach 8/8/96 v0.01");
}