[Sashimi-commit] ReAdW Base64.cpp, NONE, 1.1 Base64.h, NONE, 1.1 SHA1.cpp, NONE, 1.1 SHA1.h, NONE,

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Update of /cvsroot/sashimi/ReAdW
In directory sc8-pr-cvs8.sourceforge.net:/tmp/cvs-serv31246

Modified Files:
	ReAdW.cpp ReAdW.dsp ReAdW.h StdAfx.cpp StdAfx.h resource.h 
	xml_out.cpp xml_out.h xrawfile2.cpp xrawfile2.h 
Added Files:
	Base64.cpp Base64.h SHA1.cpp SHA1.h 
Removed Files:
	base64.cpp base64.h sha1.cpp sha1.h 
Log Message:
renamed base64 to Base64, sha1 to SHA1 in prep for unifying shared code amnong converters

--- NEW FILE: SHA1.h ---
/*---------------------------------------------------------------------------
##  File:
##      @@(#) sha1.h
##  Author:
##      Dominik Reichl <Dom...@ti...>
##
##*****************************************************************************
##
##   This program is free software; you can redistribute it and/or modify  
##   it under the terms of the GNU Library or "Lesser" General Public      
##   License (LGPL) as published by the Free Software Foundation;          
##   either version 2 of the License, or (at your option) any later        
##   version.                                                              
##
##*****************************************************************************
##
## Changes
##
##  $Log: SHA1.h,v $
##  Revision 1.1  2006/09/29 17:32:07  spacepod
##  renamed base64 to Base64, sha1 to SHA1 in prep for unifying shared code amnong converters
##
##  Revision 1.2  2004/08/30 19:11:15  brendanx
##  Fix line endings.
##
##  Revision 1.1.1.1  2004/03/28 21:47:05  ppatrick
##  Initial import.
##
##
##
##---------------------------------------------------------------------------*/
/*
	100% free public domain implementation of the SHA-1
	algorithm by Dominik Reichl <Dom...@ti...>

	=== Test Vectors (from FIPS PUB 180-1) ===

	"abc"
		A9993E36 4706816A BA3E2571 7850C26C 9CD0D89D

	"abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq"
		84983E44 1C3BD26E BAAE4AA1 F95129E5 E54670F1

	A million repetitions of "a"
		34AA973C D4C4DAA4 F61EEB2B DBAD2731 6534016F
*/

#if !defined(___SHA1_H___)
#define ___SHA1_H___

#include <stdio.h> // Needed for file access
#include <memory.h> // Needed for memset and memcpy
#include <string> // Needed for strcat and strcpy

#define LITTLE_ENDIAN
#define MAX_FILE_READ_BUFFER 8000

class CSHA1
{
public:
	// Rotate x bits to the left
	#define ROL32(value, bits) (((value)<<(bits))|((value)>>(32-(bits))))

	#ifdef LITTLE_ENDIAN
		#define SHABLK0(i) (block->l[i] = (ROL32(block->l[i],24) & 0xFF00FF00) \
			| (ROL32(block->l[i],8) & 0x00FF00FF))
	#else
		#define SHABLK0(i) (block->l[i])
	#endif

	#define SHABLK(i) (block->l[i&15] = ROL32(block->l[(i+13)&15] ^ block->l[(i+8)&15] \
		^ block->l[(i+2)&15] ^ block->l[i&15],1))

	// SHA-1 rounds
	#define R0(v,w,x,y,z,i) { z+=((w&(x^y))^y)+SHABLK0(i)+0x5A827999+ROL32(v,5); w=ROL32(w,30); }
	#define R1(v,w,x,y,z,i) { z+=((w&(x^y))^y)+SHABLK(i)+0x5A827999+ROL32(v,5); w=ROL32(w,30); }
	#define R2(v,w,x,y,z,i) { z+=(w^x^y)+SHABLK(i)+0x6ED9EBA1+ROL32(v,5); w=ROL32(w,30); }
	#define R3(v,w,x,y,z,i) { z+=(((w|x)&y)|(w&x))+SHABLK(i)+0x8F1BBCDC+ROL32(v,5); w=ROL32(w,30); }
	#define R4(v,w,x,y,z,i) { z+=(w^x^y)+SHABLK(i)+0xCA62C1D6+ROL32(v,5); w=ROL32(w,30); }

	typedef union {
		unsigned char c[64];
		unsigned long l[16];
	} SHA1_WORKSPACE_BLOCK;

	// Two different formats for ReportHash(...)
	enum { REPORT_HEX = 0, REPORT_DIGIT = 1 };

	// Constructor and Destructor
	CSHA1();
	virtual ~CSHA1();

	unsigned long m_state[5];
	unsigned long m_count[2];
	unsigned char m_buffer[64];
	unsigned char m_digest[20];

	void Reset();

	// Update the hash value
	void Update(unsigned char* data, unsigned int len);
	bool HashFile(char *szFileName);

	// Finalize hash and report
	void Final();
	void ReportHash(char *szReport, unsigned char uReportType = REPORT_HEX);
	void GetHash(unsigned char *uDest);

private:
	// Private SHA-1 transformation
	void Transform(unsigned long state[5], unsigned char buffer[64]);
};

#endif // ___SHA1_H___

Index: xrawfile2.h
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/xrawfile2.h,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** xrawfile2.h	14 Dec 2004 22:25:40 -0000	1.4
--- xrawfile2.h	29 Sep 2006 17:32:07 -0000	1.5
***************
*** 1,2 ****
--- 1,4 ----
+ // -*- mode: c++ -*-
+ 
  /***************************************************************************
                               ReAdW
***************
*** 23,26 ****
--- 25,30 ----
  #define __XRAWFILE2

+ #include "StdAfx.h"
+ 
  // Machine generated IDispatch wrapper class(es) created with ClassWizard
  /////////////////////////////////////////////////////////////////////////////
***************
*** 165,167 ****
  };

! #endif //__XRAWFILE2
\ No newline at end of file
--- 169,171 ----
  };

! #endif //__XRAWFILE2

Index: ReAdW.cpp
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/ReAdW.cpp,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** ReAdW.cpp	20 Sep 2006 21:19:42 -0000	1.13
--- ReAdW.cpp	29 Sep 2006 17:32:07 -0000	1.14
***************
*** 1,21 ****
  /***************************************************************************
!                              ReAdW

  This program converts Xcalibur native data into mzXML format. The program 
  requires the XRawfile library from ThermoFinnigan to run.

!                              -------------------
!     begin				: Sat Mar 27
!     copyright			: (C) 2004 by Pedrioli Patrick, ISB, Proteomics
!     email				: ppa...@st...
  ***************************************************************************/

  /***************************************************************************
!  *                                                                         *
!  *   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 2 of the License, or     *
!  *   (at your option) any later version.                                   *
!  *                                                                         *
   ***************************************************************************/

--- 1,23 ----
+ // -*- mode: c++ -*-
+ 
  /***************************************************************************
! 							 ReAdW

  This program converts Xcalibur native data into mzXML format. The program 
  requires the XRawfile library from ThermoFinnigan to run.

! 							 -------------------
! 	begin				: Sat Mar 27
! 	copyright			: (C) 2004 by Pedrioli Patrick, ISB, Proteomics
! 	email				: ppa...@st...
  ***************************************************************************/

  /***************************************************************************
!  *									   *
!  *  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 2 of the License, or	   *
!  *  (at your option) any later version.					   *
!  *									   *
   ***************************************************************************/

***************
*** 63,77 ****
  	  cerr << std::endl << exeName << " version " << T2X_VERSION << std::endl << std::endl;
  	  cerr << "Usage: " << exeName << " [-c , -NoCompression , -NoRulers ] <raw file path> [<output file>]\n"
! 	       << "                 -c:              Centroid the data (meaningfull only\n"
! 	       << "                                  if RAW data is profile)\n"
! 	       << "                 -NoCompression:  Do not use zlib for comrpessing peaks.\n"
! 	       << "                 -NoRulers:       Do not attempt compression using m/z\n"
! 	       << "                                  ruler.\n"
  	       << endl
! 	       << "                                  output file: if not supplied, the raw filename will be used,\n"
! 	       << "                                               with the extension reset to .mzXML.\n"
  	       << endl
  	       << "              --------- By Patrick Pedrioli ------------\n";
!                 
  	  return -1;
  	}
--- 65,80 ----
  	  cerr << std::endl << exeName << " version " << T2X_VERSION << std::endl << std::endl;
  	  cerr << "Usage: " << exeName << " [-c , -NoCompression , -NoRulers ] <raw file path> [<output file>]\n"
! 	       << "  -c:              Centroid the data (meaningfull only\n"
! 	       << "                   if RAW data is profile)\n"
! 	       << "  -NoCompression:  Do not use zlib for comrpessing peaks.\n"
! 	       << "  -NoRulers:       Do not attempt compression using m/z\n"
! 	       << "                    ruler.\n"
  	       << endl
! 	       << "  output file:     Filename for mzXML output;\n"
! 	       << "                   if not supplied, the raw filename will be used,\n"
! 	       << "                   with the extension reset to .mzXML.\n"
  	       << endl
  	       << "              --------- By Patrick Pedrioli ------------\n";
! 				
  	  return -1;
  	}
***************
*** 84,90 ****

        for( fileArg = 1 ; fileArg < argc ; ++fileArg )
!         {
  	  if (*argv[fileArg] == '-')
!             {
  	      bDoCentroid = ( NULL != strchr( argv[fileArg] , 'c' ) );
  	      if( strstr( argv[fileArg] , "NoCompression" ) )
--- 87,93 ----

        for( fileArg = 1 ; fileArg < argc ; ++fileArg )
! 	{
  	  if (*argv[fileArg] == '-')
! 	    {
  	      bDoCentroid = ( NULL != strchr( argv[fileArg] , 'c' ) );
  	      if( strstr( argv[fileArg] , "NoCompression" ) )
***************
*** 96,103 ****
  		  bDoRulers = false;
  		}
!             }
!         }
        fileArg -= 2;
!         
        int outputFileArg = fileArg + 1;

--- 99,106 ----
  		  bDoRulers = false;
  		}
! 	    }
! 	}
        fileArg -= 2;
! 		
        int outputFileArg = fileArg + 1;

***************
*** 120,124 ****
        cout << "Processing scans\n";
        for( scanNum = firstScan ; scanNum <= lastScan ; scanNum++ )
! 	{
  	  XmlWriter.writeScan( scanNum );
  	}
--- 123,128 ----
        cout << "Processing scans\n";
        for( scanNum = firstScan ; scanNum <= lastScan ; scanNum++ )
! 	{
! 	  //cout << "scan " << scanNum << std::endl;
  	  XmlWriter.writeScan( scanNum );
  	}

Index: ReAdW.dsp
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/ReAdW.dsp,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** ReAdW.dsp	6 Jun 2006 22:11:30 -0000	1.11
--- ReAdW.dsp	29 Sep 2006 17:32:07 -0000	1.12
***************
*** 33,43 ****
  # PROP BASE Use_MFC 0
  # PROP BASE Use_Debug_Libraries 0
! # PROP BASE Output_Dir "ReAdW___Win32_Release"
! # PROP BASE Intermediate_Dir "ReAdW___Win32_Release"
  # PROP BASE Target_Dir ""
  # PROP Use_MFC 0
  # PROP Use_Debug_Libraries 0
! # PROP Output_Dir "ReAdW___Win32_Release"
! # PROP Intermediate_Dir "ReAdW___Win32_Release"
  # PROP Target_Dir ""
  # ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
--- 33,43 ----
  # PROP BASE Use_MFC 0
  # PROP BASE Use_Debug_Libraries 0
! # PROP BASE Output_Dir "Release"
! # PROP BASE Intermediate_Dir "Release"
  # PROP BASE Target_Dir ""
  # PROP Use_MFC 0
  # PROP Use_Debug_Libraries 0
! # PROP Output_Dir "Release"
! # PROP Intermediate_Dir "Release"
  # PROP Target_Dir ""
  # ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
***************
*** 49,54 ****
  # ADD BSC32 /nologo
  LINK32=link.exe
! # ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib  kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386
! # ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib  kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386

  !ELSEIF  "$(CFG)" == "ReAdW - Win32 Debug"
--- 49,54 ----
  # ADD BSC32 /nologo
  LINK32=link.exe
! # ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386
! # ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386

  !ELSEIF  "$(CFG)" == "ReAdW - Win32 Debug"
***************
*** 56,77 ****
  # PROP BASE Use_MFC 0
  # PROP BASE Use_Debug_Libraries 1
! # PROP BASE Output_Dir "ReAdW___Win32_Debug"
! # PROP BASE Intermediate_Dir "ReAdW___Win32_Debug"
  # PROP BASE Target_Dir ""
! # PROP Use_MFC 0
  # PROP Use_Debug_Libraries 1
! # PROP Output_Dir "ReAdW___Win32_Debug"
! # PROP Intermediate_Dir "ReAdW___Win32_Debug"
  # PROP Target_Dir ""
! # ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /GZ  /c
! # ADD CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /GZ  /c
  # ADD BASE RSC /l 0x409 /d "_DEBUG"
! # ADD RSC /l 0x409 /d "_DEBUG"
  BSC32=bscmake.exe
  # ADD BASE BSC32 /nologo
  # ADD BSC32 /nologo
  LINK32=link.exe
! # ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib  kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept
! # ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib  kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept

  !ENDIF 
--- 56,79 ----
  # PROP BASE Use_MFC 0
  # PROP BASE Use_Debug_Libraries 1
! # PROP BASE Output_Dir "Debug"
! # PROP BASE Intermediate_Dir "Debug"
  # PROP BASE Target_Dir ""
! # PROP Use_MFC 2
  # PROP Use_Debug_Libraries 1
! # PROP Output_Dir "Debug"
! # PROP Intermediate_Dir "Debug"
! # PROP Ignore_Export_Lib 0
  # PROP Target_Dir ""
! # ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /GZ /c
! # ADD CPP /nologo /MDd /W3 /Gm /GX /ZI /Od /I "../../../common/zlib/include" /I "../../../common" /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /D "_AFXDLL" /FR /FD /GZ /c
! # SUBTRACT CPP /YX
  # ADD BASE RSC /l 0x409 /d "_DEBUG"
! # ADD RSC /l 0x409 /fo"ReAdW.res" /d "_DEBUG" /d "_AFXDLL"
  BSC32=bscmake.exe
  # ADD BASE BSC32 /nologo
  # ADD BSC32 /nologo
  LINK32=link.exe
! # ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept
! # ADD LINK32 ws2_32.lib zlib1.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept /libpath:"../../../common/zlib/lib"

  !ENDIF 
***************
*** 84,96 ****
--- 86,150 ----

  # PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+ # Begin Source File
+ 
+ SOURCE=.\ReAdW.cpp
+ # End Source File
+ # Begin Source File
+ 
+ SOURCE=.\StdAfx.cpp
+ # End Source File
+ # Begin Source File
+ 
+ SOURCE=.\xml_out.cpp
+ # End Source File
+ # Begin Source File
+ 
+ SOURCE=.\xrawfile2.cpp
+ # End Source File
  # End Group
  # Begin Group "Header Files"

  # PROP Default_Filter "h;hpp;hxx;hm;inl"
+ # Begin Source File
+ 
+ SOURCE=.\ReAdW.h
+ # End Source File
+ # Begin Source File
+ 
+ SOURCE=.\resource.h
+ # End Source File
+ # Begin Source File
+ 
+ SOURCE=.\StdAfx.h
+ # End Source File
+ # Begin Source File
+ 
+ SOURCE=.\xml_out.h
+ # End Source File
+ # Begin Source File
+ 
+ SOURCE=.\xrawfile2.h
+ # End Source File
  # End Group
  # Begin Group "Resource Files"

  # PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+ # Begin Source File
+ 
+ SOURCE=.\fish.ico
+ # End Source File
+ # Begin Source File
+ 
+ SOURCE=.\ReAdW.rc
+ # End Source File
  # End Group
+ # Begin Source File
+ 
+ SOURCE=..\..\..\common\Base64.cpp
+ # End Source File
+ # Begin Source File
+ 
+ SOURCE=..\..\..\common\SHA1.cpp
+ # End Source File
  # End Target
  # End Project

--- sha1.cpp DELETED ---

--- NEW FILE: Base64.cpp ---
/* downloaded from web */

#include "stdafx.h"
#include <string.h>
#include <stdio.h>
#include <math.h>
//#include <winsock.h>

#include "base64.h"

inline int getPosition( char buf );

static const unsigned char *b64_tbl = (const unsigned char*) "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
static const unsigned char b64_pad = '=';

/* base64 encode a group of between 1 and 3 input chars into a group of  4 output chars */
static void encode_group (unsigned char output[],
                          const unsigned char input[],
                          int n)
{
   unsigned char ingrp[3];

   ingrp[0] = n > 0 ? input[0] : 0;
   ingrp[1] = n > 1 ? input[1] : 0;
   ingrp[2] = n > 2 ? input[2] : 0;

   /* upper 6 bits of ingrp[0] */
   output[0] = n > 0 ? b64_tbl[ingrp[0] >> 2] : b64_pad;

   /* lower 2 bits of ingrp[0] | upper 4 bits of ingrp[1] */
   output[1] = n > 0 ? b64_tbl[((ingrp[0] & 0x3) << 4) | (ingrp[1] >> 4)] : b64_pad;

   /* lower 4 bits of ingrp[1] | upper 2 bits of ingrp[2] */
   output[2] = n > 1 ? b64_tbl[((ingrp[1] & 0xf) << 2) | (ingrp[2] >> 6)] : b64_pad;

   /* lower 6 bits of ingrp[2] */
   output[3] = n > 2 ? b64_tbl[ingrp[2] & 0x3f] : b64_pad;

}

int b64_encode (char *dest,
                const unsigned char *src,
                int len)
{
   int outsz = 0;

   while (len > 0)
   {
      encode_group ((unsigned char*)dest + outsz, src, len > 3 ? 3 : len);
      len -= 3;
      src += 3;
      outsz += 4;
   }

   return outsz;
}

/* base64 decode a group of 4 input chars into a group of between 0 and
 * 3 output chars */
static void decode_group (unsigned char output[],
                          const unsigned char input[],
                          int *n)
{
   unsigned char *t1, *t2;
   *n = 0;

   if (input[0] == '=')
      return;

   t1 = (unsigned char*) strchr ((const char*)b64_tbl, input[0]);
   t2 = (unsigned char*) strchr ((const char*)b64_tbl, input[1]);

   output[(*n)++] = ((t1 - b64_tbl) << 2) | ((t2 - b64_tbl) >> 4);

   if (input[2] == '=')
      return;

   t1 = (unsigned char*) strchr ((const char*)b64_tbl, input[2]);

   output[(*n)++] = ((t2 - b64_tbl) << 4) | ((t1 - b64_tbl) >> 2);

   if (input[3] == '=')
      return;

   t2 = (unsigned char*) strchr ((const char*)b64_tbl, input[3]);

   output[(*n)++] = ((t1 - b64_tbl) << 6) | (t2 - b64_tbl);

   return;
}

inline int getPosition( char buf )
{

  if( buf > 96 )		// [a-z]
    return (buf - 71);
  else if( buf > 64 )		// [A-Z]
    return (buf - 65);
  else if( buf > 47 )		// [0-9]
    return (buf + 4);
  else if( buf == 43 )
    return 63;
  else				// buf == '/'
    return 64;
}

void b64_decode_mio ( char *dest,  char *src )
{
   char *temp;

  temp = dest;

  while (*src)
    {
      int register a;
      int register b;
      int t1,t2,t3,t4;

      t1 = src[0];
      t2 = src[1];
      t3 = src[2];
      t4 = src[3];

      if (t1 == 61 )		// if == '='
	return;

      if( t1 > 96 )		// [a-z]
	a = (t1 - 71);
      else if( t1 > 64 )		// [A-Z]
	a = (t1 - 65);
      else if( t1 > 47 )		// [0-9]
	a = (t1 + 4);
      else if( t1 == 43 )
	a = 62;
      else				// src[0] == '/'
	a = 63;     

      if( t2 > 96 )		// [a-z]
	b = (t2 - 71);
      else if( t2 > 64 )		// [A-Z]
	b = (t2 - 65);
      else if( t2 > 47 )		// [0-9]
	b = (t2 + 4);
      else if( t2 == 43 )
	b = 62;
      else				// src[0] == '/'
	b = 63;     

      *temp++ = ( a << 2) | ( b >> 4);

      if (t3 == 61)
	return;

      if( t3 > 96 )		// [a-z]
	a = (t3 - 71);
      else if( t3 > 64 )		// [A-Z]
	a = (t3 - 65);
      else if( t3 > 47 )		// [0-9]
	a = (t3 + 4);
      else if( t3 == 43 )
	a = 62;
      else				// src[0] == '/'
	a = 63;     

      *temp++ = ( b << 4) | ( a >> 2);

      if (t4 == 61)
	return;

      if( t4 > 96 )		// [a-z]
	b = (t4 - 71);
      else if( t4 > 64 )		// [A-Z]
	b = (t4 - 65);
      else if( t4 > 47 )		// [0-9]
	b = (t4 + 4);
      else if( t4 == 43 )
	b = 62;
      else				// src[0] == '/'
	b = 63;    

      *temp++ = ( a << 6) | ( b );

      src += 4;
    }
}

Index: ReAdW.h
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/ReAdW.h,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ReAdW.h	30 Aug 2004 19:11:15 -0000	1.2
--- ReAdW.h	29 Sep 2006 17:32:07 -0000	1.3
***************
*** 1,2 ****
--- 1,4 ----
+ // -*- mode: c++ -*-
+ 
  /***************************************************************************
                               ReAdW

--- NEW FILE: Base64.h ---
#ifndef _BASE64_H
#define _BASE64_H

int b64_encode (char *dest,
		const unsigned char *src,
		int len);
void b64_decode_mio (char *dest, char *src);

#endif /* BASE64_H */

Index: StdAfx.h
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/StdAfx.h,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** StdAfx.h	14 Jul 2006 14:59:44 -0000	1.5
--- StdAfx.h	29 Sep 2006 17:32:07 -0000	1.6
***************
*** 1,2 ****
--- 1,4 ----
+ // -*- mode: c++ -*-
+ 
  // stdafx.h : include file for standard system include files,
  //  or project specific include files that are used frequently, but
***************
*** 30,33 ****
--- 32,37 ----
  #include <string>

+ 
+ 
  #include "zlib.h"

--- base64.cpp DELETED ---

Index: xrawfile2.cpp
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/xrawfile2.cpp,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** xrawfile2.cpp	14 Dec 2004 22:25:40 -0000	1.4
--- xrawfile2.cpp	29 Sep 2006 17:32:07 -0000	1.5
***************
*** 1,2 ****
--- 1,4 ----
+ // -*- mode: c++ -*-
+ 
  /***************************************************************************
                               ReAdW

Index: StdAfx.cpp
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/StdAfx.cpp,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** StdAfx.cpp	30 Aug 2004 19:11:15 -0000	1.2
--- StdAfx.cpp	29 Sep 2006 17:32:07 -0000	1.3
***************
*** 1,2 ****
--- 1,4 ----
+ // -*- mode: c++ -*-
+ 
  // stdafx.cpp : source file that includes just the standard includes
  //	Thermo2mzXML.pch will be the pre-compiled header

Index: xml_out.cpp
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/xml_out.cpp,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** xml_out.cpp	20 Sep 2006 21:19:42 -0000	1.34
--- xml_out.cpp	29 Sep 2006 17:32:07 -0000	1.35
***************
*** 1,2 ****
--- 1,4 ----
+ // -*- mode: c++ -*-
+ 
  /***************************************************************************
                               ReAdW
***************
*** 192,196 ****
    }
    m_Csha1.Final();
!   m_Csha1.ReportHash( m_pReport, CSHA1::REPORT_HEX );

--- 194,198 ----
    }
    m_Csha1.Final();
!   m_Csha1.ReportHash( m_pReport, SHA1::REPORT_HEX );

***************
*** 348,351 ****
--- 350,385 ----
  void XmlOut::m_prepareScan() {

+   /*
+     pull out 'filter' line
+     
+     extract ms level from filter line
+ 
+     close previous scan if required
+ 
+     extract polarity from filter line
+ 
+     extract scan type (zoom, survey) from filter line
+ 
+     get # peaks (numPackets /  2)
+ 
+     if level > 1, get precursor Mz and Ce
+ 
+       first use DLL call
+         otherwise, extract from filter line (presumably less accurate)
+ 
+       try to get precursor charge state
+ 
+       get precursor intensity
+         flip through prev scan, looking for +/- 0.05 expected mass
+ 
+       get m/z pairs, intensity
+       
+       compress if requested
+         then convert to b64
+ 
+       otherwise, just convert to b64
+ 
+    */
+ 
    char	lf = 0xA;

***************
*** 356,359 ****
--- 390,395 ----
    /*
      Get the scan filter
+     
+     For example, "ITMS + c NSI Full ms [ 300.00-2000.00]
    */
    m_bstrFilter = NULL;
***************
*** 366,369 ****
--- 402,408 ----
    /*
      extract the msLevel
+     
+     The level is the character after the 'ms' in the filter string;
+     ' ' is a level 1/survey scan
    */
    char* msLevel = strstr( szTemp , "ms" );
***************
*** 558,561 ****
--- 597,603 ----
      }

+ 
+     // CE: RT of the survey scan from which the precursor was selected
+ 
      // and then the CE
      VariantClear( &varValue );
***************
*** 564,571 ****
      if( m_xRawfile.GetTrailerExtraValueForScanNum(m_scanNum, "API Source CID Energy:" , &varValue ) ) {
        // First try to use the OCX
!       if( varValue.vt == VT_R4 )
  	m_CE = varValue.fltVal;
!       else if ( varValue.vt != VT_ERROR )
  	cerr << "Unexpected type when looking for CE\n";
      }

--- 606,617 ----
      if( m_xRawfile.GetTrailerExtraValueForScanNum(m_scanNum, "API Source CID Energy:" , &varValue ) ) {
        // First try to use the OCX
!       if( varValue.vt == VT_R4 ) {
! 	// VT_R4: OLE float type
  	m_CE = varValue.fltVal;
!       }
!       // JMT: !!! missing R8 !!!
!       else if ( varValue.vt != VT_ERROR ) {
  	cerr << "Unexpected type when looking for CE\n";
+       }
      }

***************
*** 610,614 ****
--- 656,671 ----

      long scanNum = m_scanNum;
+ 
+ 
+ 
+ 
+     /**
+       find the precursor mass/charge and intensity info
+     */
      if( m_numPakets != 0 ) {
+ 
+       // jmt: the goal is to get the parent scan's info: I don't know if this
+       // is sequentially the previous scan number, or the scan's
+       // parent, somehow wrapped in this scan?
        m_xRawfile.GetPrevMassListFromScanNum(&scanNum,
  					    szFilter,			// filter
***************
*** 622,634 ****
  					    &nArraySize);		// arraySize

        if( nArraySize ) {
  	// Get a pointer to the SafeArray
  	SAFEARRAY FAR* psa = varMassList.parray;
- 
  	DataPeak* pDataPeaks = NULL;
  	SafeArrayAccessData( psa, (void**)(&pDataPeaks) );
  	m_precursorIntensity = 0;

  	// Find most intense peak around precursorMz
  	for( long j=0; j<nArraySize; j++ ) {
  	  double dMass = pDataPeaks[j].dMass;
--- 679,699 ----
  					    &nArraySize);		// arraySize

+       // nArraySize: (presuming) number of mass/intensity pairs for this scan
+       // if empty, no precursor scan
        if( nArraySize ) {
+ 	
  	// Get a pointer to the SafeArray
  	SAFEARRAY FAR* psa = varMassList.parray;
  	DataPeak* pDataPeaks = NULL;
+ 	// use our pDataPeaks array to access the SafeArray data.
  	SafeArrayAccessData( psa, (void**)(&pDataPeaks) );
  	m_precursorIntensity = 0;

+ 
  	// Find most intense peak around precursorMz
+ 	/*
+ 	  the goal is to search the precursor's scan info to get the
+ 	  m/z and intensity
+ 	*/
  	for( long j=0; j<nArraySize; j++ ) {
  	  double dMass = pDataPeaks[j].dMass;
***************
*** 641,645 ****
  	      }
  	    }
! 	  }	
  	  if( dMass - m_precursorMz > 0.05 ) {
  	    break;
--- 706,710 ----
  	      }
  	    }
! 	  }
  	  if( dMass - m_precursorMz > 0.05 ) {
  	    break;
***************
*** 651,655 ****

! 	// jmt: check this?
  	VariantClear( &varMassList );	
  	// Delete all memory associated with the variant and
--- 716,720 ----

! 
  	VariantClear( &varMassList );	
  	// Delete all memory associated with the variant and
***************
*** 734,739 ****
        }

        // We add 5 bytes for the the trailing == and the /0
!       m_pEncoded = (char *) new char [(  (((2 * nArraySize) * sizeof(uint32_t) + (int)ceil(( nArraySize * 2 * sizeof(uint32_t)) * 0.1) + 12) / 3) * 4 + 5)];
        //m_pEncoded = (char *) new char [(  (((2 * nArraySize) * sizeof(float) + ceil(( nArraySize * 2 * sizeof(float)) * 0.1) + 12) / 3) * 4 + 5)];
        //m_pEncodedPrevScan = (char *) new char [(  (((2 * nArraySize) * sizeof(float)) / 3) * 4 + 5)];
--- 799,809 ----
        }

+ 
+       // we now allocate m_pEncoded after the network data is base64
+       // converted and we know the size of the converted string
+ 
+ 
        // We add 5 bytes for the the trailing == and the /0
!       // m_pEncoded = (char *) new char [(  (((2 * nArraySize) * sizeof(uint32_t) + (int)ceil(( nArraySize * 2 * sizeof(uint32_t)) * 0.1) + 12) / 3) * 4 + 5)];
        //m_pEncoded = (char *) new char [(  (((2 * nArraySize) * sizeof(float) + ceil(( nArraySize * 2 * sizeof(float)) * 0.1) + 12) / 3) * 4 + 5)];
        //m_pEncodedPrevScan = (char *) new char [(  (((2 * nArraySize) * sizeof(float)) / 3) * 4 + 5)];
***************
*** 851,863 ****
  	  // Using the vectors is a little more complicated and slow, 
  	  // but the conversion does not work directly

! 	  *dMass = (float) pDataPeaks[j].dMass;
! 	  *dIntensity = (float) pDataPeaks[j].dIntensity;
! 
! 	  // Convert form host to network
! 	  (unsigned int) ((unsigned int *)pDataNetwork)[n] = (unsigned int) htonl( *(unsigned int*) dMass );
! 	  n++;
! 	  (unsigned int) ((unsigned int *)pDataNetwork)[n] = (unsigned int) htonl( *(unsigned int*) dIntensity );
! 	  n++;
  	}
        }
--- 921,977 ----
  	  // Using the vectors is a little more complicated and slow, 
  	  // but the conversion does not work directly
+ 
+               // convert from double to float
+               float mz  = (float) pDataPeaks[j].dMass;
+               float intensity = (float) pDataPeaks[j].dIntensity;
+               
+               // get the 4 bytes that represent a float:
+               // get the addr of the float, treat it as a uint32 ptr, and dereference
+               uint32_t mzBytes = (*(uint32_t *)(&mz) );
+               
+               // pretend that peakDataNework stores 4-byte unsigned ints, rather
+               // than 4-byte floats, for the sake of the conversion
+               ( (uint32_t *) pDataNetwork)[n] = htonl(mzBytes);
+               //printf("%f, %8.8X, %8.8X; ", mz, mzBytes, ( (uint32_t *) pDataNetwork)[n] );
+               n++;
+               
+               
+               // Convert from host to network
+               //(unsigned int) ((unsigned int *)pDataNetwork)[n] = (unsigned int) htonl( *(unsigned int*) dMass );
+               
+               
+ 	  //n++;
+ 
+               // convert from double to float
+               
+               //float intensity = (float) pDataPeaks[j].dIntensity;
+               
+               // get the 4 bytes that represent a float:
+               // get the addr of the float, treat it as a uint32 ptr, and dereference
+               uint32_t intensityBytes = (*(uint32_t *)(&intensity) );
+               
+               // pretend that peakDataNework stores 4-byte unsigned ints, rather
+               // than 4-byte floats, for the sake of the conversion
+               ( (uint32_t *) pDataNetwork)[n] = htonl(intensityBytes);
+               //printf("%f, %8.8X, %8.8X; ", intensity, intensityBytes, ( (uint32_t *) pDataNetwork)[n] );
+               n++;
+               
+               
+               // Convert from host to network
+               //(unsigned int) ((unsigned int *)pDataNetwork)[n] = (unsigned int) htonl( *(unsigned int*) dMass );
+              
+               
+ 
+               // sanity check
+               uint32_t mb2;
+               uint32_t ib2;
+               mb2 = ntohl(( (uint32_t *) pDataNetwork)[n-2]);
+               ib2 = ntohl(( (uint32_t *) pDataNetwork)[n-1]);
+               //printf("%f, %f\n\n", (*(float*)(&mb2)), (*(float*)(&ib2))  );
+ 

! 	  //(unsigned int) ((unsigned int *)pDataNetwork)[n] = (unsigned int) htonl( *(unsigned int*) dIntensity );
!          //printf("%f, %8.8X, %8.8X\n", *dIntensity, *(unsigned int *)dIntensity, (unsigned int) ((unsigned int *)pDataNetwork)[n]);
! 	  //n++;
  	}
        }
***************
*** 899,915 ****
  	m_compressedLen = comprLen;

! 	int encodedLength = b64_encode( m_pEncoded, (const unsigned char *) compr, 
! 					comprLen);
! 
! 	m_pEncoded[encodedLength] = '\0';

  	free( compr );
        }
!       else {
! 	// no zlib compression;
  	// do base64 encoding directly
! 	int encodedLength = b64_encode( m_pEncoded, (const unsigned char *) pDataNetwork, 
! 					n * sizeof(float) ); // This one is for m/z increments peaks element
! 	m_pEncoded[encodedLength] = '\0';
        }

--- 1013,1038 ----
  	m_compressedLen = comprLen;

! 	Base64 base64Encoder;
! 	int encodedLength = base64Encoder.b64_encode( (const unsigned char *) compr, 
! 						      comprLen);
! 	// copy encoded bytes to m_pEncoded
! 	unsigned char* encodedByteArray = base64Encoder.getOutputBuffer();
! 	for (int bc=0; bc<=encodedLength; bc++) { // <= to get the \0
! 	  m_pEncoded[bc] = encodedByteArray[bc];
! 	}
! 	// this is now done in Base64::b64_encode:
! 	// m_pEncoded[encodedLength] = '\0';
! 	base64Encoder.freeOutputBuffer();

  	free( compr );
        }
!       else { // no zlib compression;
  	// do base64 encoding directly
! 	Base64 base64Encoder;
! 	int encodedLength = base64Encoder.b64_encode( (const unsigned char *) pDataNetwork, 
! 						      (nArraySize*2) * sizeof(float) ); // This one is for m/z increments peaks element
! 	m_pEncoded = new char[strlen((const char*)base64Encoder.getOutputBuffer()) + 1]; // +1 for \0
! 	strcpy(m_pEncoded, (const char*)base64Encoder.getOutputBuffer());
! 	base64Encoder.freeOutputBuffer();
        }

***************
*** 1029,1033 ****
  		<< "        peaksCount=\"" << m_numPakets/2 << "\"" << lf
  		<< "        polarity=\"" << m_polarity << "\"" << lf
! 		<< "        scanType=\"" << m_scanType << "\"" << lf
  		<< "        retentionTime=\"PT" << m_RT*60 << "S\"" << lf;
    if( m_msLevel > 1 ) {
--- 1152,1156 ----
  		<< "        peaksCount=\"" << m_numPakets/2 << "\"" << lf
  		<< "        polarity=\"" << m_polarity << "\"" << lf
! 		//<< "        scanType=\"" << m_scanType << "\"" << lf
  		<< "        retentionTime=\"PT" << m_RT*60 << "S\"" << lf;
    if( m_msLevel > 1 ) {
***************
*** 1051,1073 ****

    m_fout	<< "    <peaks precision=\"32\"" << lf
! 		<< "           byteOrder=\"network\"" << lf;

    if( m_isRulers ) {
!     m_fout  << "           contentType=\"m/z ruler\"" << lf;
    }
!   else {
!     m_fout  << "           contentType=\"m/z-int\"" << lf;
    }

    if( m_doCompression ) {
!     m_fout  << "           compressionType=\"zlib\"" << lf
  	    << "           compressedLen=\"" << m_compressedLen;
    }
! 
!   m_fout << "\">"	<< m_pEncoded
  	 << "</peaks>" << lf;

    // We don't close the scan element untill we are sure if the next
!   // scan will be dependent on this one or not We save the params we
    // are going to need to see if the next scan element will be a
    // children of the current one
--- 1174,1201 ----

    m_fout	<< "    <peaks precision=\"32\"" << lf
! 		<< "           byteOrder=\"network\"";

    if( m_isRulers ) {
!     m_fout  << lf << "           contentType=\"m/z ruler\"" ;
    }
!   else {
!          // JMT TEMP TESTING
!     m_fout  << lf << "           pairOrder=\"m/z-int\"";
! // JMT
! 
!     //m_fout  << lf << "           contentType=\"m/z-int\"";
    }

    if( m_doCompression ) {
!     m_fout  << lf << "           compressionType=\"zlib\"" << lf
  	    << "           compressedLen=\"" << m_compressedLen;
    }
! 
!   m_fout << ">"; 
!   m_fout << m_pEncoded
  	 << "</peaks>" << lf;

    // We don't close the scan element untill we are sure if the next
!   // scan will be dependent on this one or not.  We save the params we
    // are going to need to see if the next scan element will be a
    // children of the current one
***************
*** 1164,1168 ****
    }
    m_Csha1.Final();
!   m_Csha1.ReportHash( m_pReport, CSHA1::REPORT_HEX );

    m_fout << m_pReport << "</sha1>" << lf;
--- 1292,1296 ----
    }
    m_Csha1.Final();
!   m_Csha1.ReportHash( m_pReport, SHA1::REPORT_HEX );

    m_fout << m_pReport << "</sha1>" << lf;

Index: xml_out.h
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/xml_out.h,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** xml_out.h	20 Sep 2006 18:43:26 -0000	1.14
--- xml_out.h	29 Sep 2006 17:32:07 -0000	1.15
***************
*** 1,2 ****
--- 1,4 ----
+ // -*- mode: c++ -*-
+ 
  /***************************************************************************
                               ReAdW
***************
*** 32,37 ****

  #include "xrawfile2.h"
! #include "sha1.h"
! #include "base64.h"

  #define LITTLE_ENDIAN
--- 34,39 ----

  #include "xrawfile2.h"
! #include "SHA1.h"
! #include "Base64.h"

  #define LITTLE_ENDIAN
***************
*** 132,139 ****
    // variables
    IXRawfile m_xRawfile;			// Create an instance fo the COleDispatchDriver object
!   __int64*	m_index;
    char*	m_xmlName;
!   BOOL    m_doCompression;
!   BOOL    m_doRulers;
    BOOL	m_doCentroid;
    int		m_fieldCorrection;
--- 134,141 ----
    // variables
    IXRawfile m_xRawfile;			// Create an instance fo the COleDispatchDriver object
!   __int64*  m_index;
    char*	m_xmlName;
!   BOOL  m_doCompression;
!   BOOL  m_doRulers;
    BOOL	m_doCentroid;
    int		m_fieldCorrection;
***************
*** 144,150 ****
    long	m_firstScan;
    long	m_lastScan;
!   double	m_startTime;
!   double	m_endTime;
!   CSHA1	m_Csha1;
    char	m_pReport[1024];		// sha1 hash
    BSTR	m_bstrInstModel;
--- 146,152 ----
    long	m_firstScan;
    long	m_lastScan;
!   double m_startTime;
!   double m_endTime;
!   SHA1	m_Csha1;
    char	m_pReport[1024];		// sha1 hash
    BSTR	m_bstrInstModel;
***************
*** 152,157 ****

    // Scan information
!   bool    m_isRulers;
!   int     m_compressedLen;
    long	m_scanNum;
    BSTR	m_bstrFilter;
--- 154,159 ----

    // Scan information
!   bool m_isRulers;
!   int m_compressedLen;
    long	m_scanNum;
    BSTR	m_bstrFilter;
***************
*** 160,180 ****
    char*	m_scanType;
    long	m_numPakets;
!   double	m_RT;
!   double	m_lowMass;
!   double	m_highMass ;
!   double	m_TIC;
!   double	m_basePeakMass;
!   double	m_basePeakIntensity;
    long	m_channel;
    long	m_uniformTime;
!   double	m_frequency;
!   double	m_CE;	// RT of the survey scan from which the precursor was selected
!   double	m_precursorIntensity;
!   double	m_precursorMz;
!   int     m_precursorCharge;
!   char	*m_pEncoded , *m_pEncodedPrevScan;

    std::ofstream m_fout;
!   int	m_idxFout;

    static int M_accurateMasses;
--- 162,182 ----
    char*	m_scanType;
    long	m_numPakets;
!   double m_RT;
!   double m_lowMass;
!   double m_highMass ;
!   double m_TIC;
!   double m_basePeakMass;
!   double m_basePeakIntensity;
    long	m_channel;
    long	m_uniformTime;
!   double m_frequency;
!   double m_CE;	// RT of the survey scan from which the precursor was selected
!   double m_precursorIntensity;
!   double m_precursorMz;
!   int m_precursorCharge;
!   char *m_pEncoded , *m_pEncodedPrevScan;

    std::ofstream m_fout;
!   int m_idxFout;

    static int M_accurateMasses;

--- base64.h DELETED ---

Index: resource.h
===================================================================
RCS file: /cvsroot/sashimi/ReAdW/resource.h,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** resource.h	30 Aug 2004 19:11:15 -0000	1.3
--- resource.h	29 Sep 2006 17:32:07 -0000	1.4
***************
*** 1,2 ****
--- 1,4 ----
+ // -*- mode: c++ -*-
+ 
  //{{NO_DEPENDENCIES}}
  // Microsoft Visual C++ generated include file.

--- NEW FILE: SHA1.cpp ---
/*---------------------------------------------------------------------------
##  File:
##      @@(#) sha1.cpp
##  Author:
##      Dominik Reichl <Dom...@ti...>
##        - Modified by Patrick Pedrioli
##
##  Description:
##    A generic sha1 hash.
##
##*****************************************************************************
##
##   This program is free software; you can redistribute it and/or modify  
##   it under the terms of the GNU Library or "Lesser" General Public      
##   License (LGPL) as published by the Free Software Foundation;          
##   either version 2 of the License, or (at your option) any later        
##   version.                                                              
##
##*****************************************************************************
##
## Changes
##
##  $Log: SHA1.cpp,v $
##  Revision 1.1  2006/09/29 17:32:07  spacepod
##  renamed base64 to Base64, sha1 to SHA1 in prep for unifying shared code amnong converters
##
##  Revision 1.2  2004/08/30 19:11:15  brendanx
##  Fix line endings.
##
##  Revision 1.1.1.1  2004/03/28 21:47:05  ppatrick
##  Initial import.
##
##
##
##---------------------------------------------------------------------------*/
/*
	100% free public domain implementation of the SHA-1
	algorithm by Dominik Reichl <Dom...@ti...>

	=== Test Vectors (from FIPS PUB 180-1) ===

	"abc"
		A9993E36 4706816A BA3E2571 7850C26C 9CD0D89D

	"abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq"
		84983E44 1C3BD26E BAAE4AA1 F95129E5 E54670F1

	A million repetitions of "a"
		34AA973C D4C4DAA4 F61EEB2B DBAD2731 6534016F
*/

#include "stdafx.h"
#include "sha1.h"

#ifdef _DEBUG
#define new DEBUG_NEW
#undef THIS_FILE
static char THIS_FILE[] = __FILE__;
#endif

CSHA1::CSHA1()
{
	Reset();
}

CSHA1::~CSHA1()
{
	Reset();
}

void CSHA1::Reset()
{
	// SHA1 initialization constants
	m_state[0] = 0x67452301;
	m_state[1] = 0xEFCDAB89;
	m_state[2] = 0x98BADCFE;
	m_state[3] = 0x10325476;
	m_state[4] = 0xC3D2E1F0;

	m_count[0] = 0;
	m_count[1] = 0;
}

void CSHA1::Transform(unsigned long state[5], unsigned char buffer[64])
{
	unsigned long a = 0, b = 0, c = 0, d = 0, e = 0;

	SHA1_WORKSPACE_BLOCK* block;
	static unsigned char workspace[64];
	block = (SHA1_WORKSPACE_BLOCK *)workspace;
	memcpy(block, buffer, 64);

	// Copy state[] to working vars
	a = state[0];
	b = state[1];
	c = state[2];
	d = state[3];
	e = state[4];

	// 4 rounds of 20 operations each. Loop unrolled.
	R0(a,b,c,d,e, 0); R0(e,a,b,c,d, 1); R0(d,e,a,b,c, 2); R0(c,d,e,a,b, 3);
	R0(b,c,d,e,a, 4); R0(a,b,c,d,e, 5); R0(e,a,b,c,d, 6); R0(d,e,a,b,c, 7);
	R0(c,d,e,a,b, 8); R0(b,c,d,e,a, 9); R0(a,b,c,d,e,10); R0(e,a,b,c,d,11);
	R0(d,e,a,b,c,12); R0(c,d,e,a,b,13); R0(b,c,d,e,a,14); R0(a,b,c,d,e,15);
	R1(e,a,b,c,d,16); R1(d,e,a,b,c,17); R1(c,d,e,a,b,18); R1(b,c,d,e,a,19);
	R2(a,b,c,d,e,20); R2(e,a,b,c,d,21); R2(d,e,a,b,c,22); R2(c,d,e,a,b,23);
	R2(b,c,d,e,a,24); R2(a,b,c,d,e,25); R2(e,a,b,c,d,26); R2(d,e,a,b,c,27);
	R2(c,d,e,a,b,28); R2(b,c,d,e,a,29); R2(a,b,c,d,e,30); R2(e,a,b,c,d,31);
	R2(d,e,a,b,c,32); R2(c,d,e,a,b,33); R2(b,c,d,e,a,34); R2(a,b,c,d,e,35);
	R2(e,a,b,c,d,36); R2(d,e,a,b,c,37); R2(c,d,e,a,b,38); R2(b,c,d,e,a,39);
	R3(a,b,c,d,e,40); R3(e,a,b,c,d,41); R3(d,e,a,b,c,42); R3(c,d,e,a,b,43);
	R3(b,c,d,e,a,44); R3(a,b,c,d,e,45); R3(e,a,b,c,d,46); R3(d,e,a,b,c,47);
	R3(c,d,e,a,b,48); R3(b,c,d,e,a,49); R3(a,b,c,d,e,50); R3(e,a,b,c,d,51);
	R3(d,e,a,b,c,52); R3(c,d,e,a,b,53); R3(b,c,d,e,a,54); R3(a,b,c,d,e,55);
	R3(e,a,b,c,d,56); R3(d,e,a,b,c,57); R3(c,d,e,a,b,58); R3(b,c,d,e,a,59);
	R4(a,b,c,d,e,60); R4(e,a,b,c,d,61); R4(d,e,a,b,c,62); R4(c,d,e,a,b,63);
	R4(b,c,d,e,a,64); R4(a,b,c,d,e,65); R4(e,a,b,c,d,66); R4(d,e,a,b,c,67);
	R4(c,d,e,a,b,68); R4(b,c,d,e,a,69); R4(a,b,c,d,e,70); R4(e,a,b,c,d,71);
	R4(d,e,a,b,c,72); R4(c,d,e,a,b,73); R4(b,c,d,e,a,74); R4(a,b,c,d,e,75);
	R4(e,a,b,c,d,76); R4(d,e,a,b,c,77); R4(c,d,e,a,b,78); R4(b,c,d,e,a,79);

	// Add the working vars back into state[]
	state[0] += a;
	state[1] += b;
	state[2] += c;
	state[3] += d;
	state[4] += e;

	// Wipe variables
	a = 0; b = 0; c = 0; d = 0; e = 0;
}

// Use this function to hash in binary data and strings
void CSHA1::Update(unsigned char* data, unsigned int len)
{
	unsigned long i = 0, j = 0;

	j = (m_count[0] >> 3) & 63;

	if((m_count[0] += len << 3) < (len << 3)) m_count[1]++;

	m_count[1] += (len >> 29);

	if((j + len) > 63)
	{
		memcpy(&m_buffer[j], data, (i = 64 - j));
		Transform(m_state, m_buffer);

		for (; i+63 < len; i += 64)
		{
			Transform(m_state, &data[i]);
		}

		j = 0;
	}
	else i = 0;

	memcpy(&m_buffer[j], &data[i], len - i);
}

// Hash in file contents
bool CSHA1::HashFile(char *szFileName)
{
	unsigned long ulFileSize = 0, ulRest = 0, ulBlocks = 0;
	unsigned long i = 0;
	unsigned char uData[MAX_FILE_READ_BUFFER];
	FILE *fIn = NULL;

	if((fIn = fopen(szFileName, "rb")) == NULL) return(false);

	fseek(fIn, 0, SEEK_END);
	ulFileSize = ftell(fIn);
	fseek(fIn, 0, SEEK_SET);

	ulRest = ulFileSize % MAX_FILE_READ_BUFFER;
	ulBlocks = ulFileSize / MAX_FILE_READ_BUFFER;

	for(i = 0; i < ulBlocks; i++)
	{
		fread(uData, 1, MAX_FILE_READ_BUFFER, fIn);
		Update(uData, MAX_FILE_READ_BUFFER);
	}

	if(ulRest != 0)
	{
		fread(uData, 1, ulRest, fIn);
		Update(uData, ulRest);
	}

	fclose(fIn);
	fIn = NULL;

	return(true);
}

void CSHA1::Final()
{
	unsigned long i = 0, j = 0;
	unsigned char finalcount[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };

	for (i = 0; i < 8; i++)
		finalcount[i] = (unsigned char)((m_count[(i >= 4 ? 0 : 1)]
			>> ((3 - (i & 3)) * 8) ) & 255); // Endian independent

	Update((unsigned char *)"\200", 1);

	while ((m_count[0] & 504) != 448)
		Update((unsigned char *)"\0", 1);

	Update(finalcount, 8); // Cause a SHA1Transform()

	for (i = 0; i < 20; i++)
	{
		m_digest[i] = (unsigned char)((m_state[i >> 2] >> ((3 - (i & 3)) * 8) ) & 255);
	}

	// Wipe variables for security reasons
	i = 0; j = 0;
	memset(m_buffer, 0, 64);
	memset(m_state, 0, 20);
	memset(m_count, 0, 8);
	memset(finalcount, 0, 8);

	Transform(m_state, m_buffer);
}

// Get the final hash as a pre-formatted string
void CSHA1::ReportHash(char *szReport, unsigned char uReportType)
{
	unsigned char i = 0;
	char szTemp[4];

	if(uReportType == REPORT_HEX)
	{
		for(i = 0; i < 20; i++)
		{
			sprintf(szTemp, "%02x", m_digest[i]);
			strcat(szReport, szTemp);
		}
	}
	else if(uReportType == REPORT_DIGIT)
	{
		sprintf(szTemp, "%u", m_digest[0]);
		strcat(szReport, szTemp);

		for(i = 1; i < 20; i++)
		{
			sprintf(szTemp, " %u", m_digest[i]);
			strcat(szReport, szTemp);
		}
	}
	else strcpy(szReport, "Error: Unknown report type!");
}

// Get the raw message digest
void CSHA1::GetHash(unsigned char *uDest)
{
	memcpy(uDest, m_digest, 20);
}

--- sha1.h DELETED ---