1. mzR
  2. src
  3. cramp.cpp
Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
Showing1 changed files
src/cramp.cpp
History View file @e3f79ff5f7
1 1 
deleted file mode 100644
... ... 
@@ -1,402 +0,0 @@
1 
-/***************************************************************************
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-cramp.cpp
3 
-
4 
-***************************************************************************
5 
-cramp.hpp -- renamed cramp.h to avoid R checker warning
6 
-
7 
-  A C++ wrapper for the RAMP code.
8 
-
9 
-  Use this library to parse an mzXML file in a non-sequential way, by
10 
-  taking advantage of the index element.
11 
-
12 
-  (C) 2004 by Brian Pratt, Insilicos LLC
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-
14 
-  Based on mzXML2Other, which has this copyright:
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-	 -------------------
16 
-	 begin					 : Wed Apr 2
17 
-	 copyright				 : (C) 2002 by Pedrioli Patrick, ISB, Proteomics
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-	 email					 : ppatrick@student.ethz.ch
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- ***************************************************************************/
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-
21 
-/***************************************************************************
22 
-*																								  *
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-*	 This program is free software; you can redistribute it and/or modify  *
24 
-*	 it under the terms of the GNU Library or "Lesser" General Public 	  *
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-*	 License (LGPL) as published by the Free Software Foundation;			  *
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-*	 either version 2 of the License, or (at your option) any later		  *
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-*	 version.																				  *
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-*																								  *
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-***************************************************************************/
30 
-
31 
-#include<Rcpp.h>
32 
-
33 
-// Taken from http://tolstoy.newcastle.edu.au/R/e2/devel/06/11/1242.html
34 
-// and http://stackoverflow.com/questions/11588765/using-rcpp-with-windows-specific-includes
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-// Undefine the Realloc macro, which is defined by both R and by Windows stuff
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-// Also need to undefine the Free macro
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-#if defined(__MINGW32__)
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-#undef Realloc
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-#undef Free
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-#endif
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-
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-#include <stdlib.h>
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-#include <iostream>
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-#include <fstream>
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-#include "stdio.h"
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-#if !defined(_MSC_VER) && !defined(__MINGW32__)
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-#include "sys/errno.h"
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-#endif
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-#include "cramp.h"
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-#include<R.h>
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-
52 
-#if defined(__MINGW32__)
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-#include <windows.h>
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-#endif
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-
56 
-/**
57 
- * This function performs a non-sequential parsing operation on an indexed
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- * msxml file.
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- *
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- * @param fileName: Name of the msxml file
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- * @param startSCan: Number of the scan we want to read from
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- * @param what: -HEADER will return num, msLevel and retentionTime
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- *              -SCAN will return only the peaks
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- *              -ALL will return everything found in scan, precursorMz and peaks
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- *
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- * @return pData is dynamically allocate and becomes property of the caller, who
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- *         is responsible for its deallocation!!
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- */
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-
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-
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-
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-cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
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-    m_filename(fileName), m_declaredScansOnly(declaredScansOnly), m_runInfo()
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-{
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-    m_handle = rampOpenFile(fileName);
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-    m_scanOffsets = NULL;
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-    m_runInfo = NULL;
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-    m_lastScan = 0;
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-    if (!OK())
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-    {
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-        // HENRY -- I would prefer this to be silent, and let the caller deals with it
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-        // cout << "Error: Could not open file " << fileName << ": " << strerror(errno) << endl;
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-        // END HENRY
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-    }
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-    else
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-    {
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-
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-        m_runInfo = getRunInfo();
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-
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-        // HENRY -- always read index to set scan count, since scan count
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-        // declared at the top of the mzXML file is unreliable now that
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-        // there are missing scans.
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-        // This will also set the structs m_scanOffsets, and the value m_lastScan
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-
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-        //      if (m_runInfo->m_data.scanCount < 0) { // undeclared scan count
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-        // this will provoke reading of index, which sets scan count
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-        rampScanInfo* tmp = getScanHeaderInfo ( 1 );
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-        delete(tmp); // was free - but see https://github.com/sneumann/mzR/issues/52
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-        // }
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-        // END HENRY
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-    }
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-}
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-
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-cRamp::~cRamp()
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-{
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-    rampCloseFile(m_handle);
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-
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-    // NB: these pointers may be null on file open failure,
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-    // but free/delete of NULL is OK per C++ standard
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-    free(m_scanOffsets);
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-    delete m_runInfo; // was free() - but allocated with new
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-}
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-
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-//
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-// here are the private guts
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-//
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-rampInfo* cRamp::do_ramp( ramp_fileoffset_t arg , eWhatToRead	what )
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-{
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-
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-    switch( what )
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-    {
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-    case RAMP_RUNINFO:
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-    case RAMP_HEADER:
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-    case RAMP_PEAKS:
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-    case RAMP_INSTRUMENT:
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-        break; // OK
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-    default:
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-        Rf_error("unknown read type!\n");
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-        return NULL;
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-        break;
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-    }
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-
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-    rampInfo* returnPtr=NULL;
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-
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-    if ((RAMP_RUNINFO != what) && (RAMP_INSTRUMENT != what) && !m_scanOffsets)
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-    {
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-        int iLastScan = 0;
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-        // we need the index to get anything besides the header
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-        //      std::cerr << "in: getIndexOffset(m_handle);!\n";
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-        ramp_fileoffset_t indexOffset = getIndexOffset(m_handle);
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-        //      std::cerr << "out: getIndexOffset(m_handle);!\n";
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-
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-        // std::cerr << "in: readIndex();!\n";
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-        m_scanOffsets = readIndex(m_handle, indexOffset, &iLastScan);
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-        //std::cerr << "out: readIndex();!\n";
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-        if (iLastScan >= m_runInfo->m_data.scanCount)
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-        {
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-            if (!m_declaredScansOnly)
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-            {
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-                m_runInfo->m_data.scanCount = iLastScan;
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-            }
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-            else     // get rid of all the fake entries created
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-            {
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-
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-                //  std::cerr << "get rid of all the fake entries created\n";
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-                for (int n=1; n<=iLastScan; n++) // ramp is 1 based
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-                {
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-                    if (m_scanOffsets[n]==-1)
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-                    {
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-                        // find a run of fakes
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-                        int m;
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-                        for (m=n+1; (m<=iLastScan)&&(m_scanOffsets[m]==-1); m++);
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-                        if (m<=iLastScan)
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-                        {
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-                            memmove(m_scanOffsets+n,m_scanOffsets+m,
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-                                    sizeof(ramp_fileoffset_t)*((iLastScan-m)+1));
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-                        }
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-                        iLastScan-=(m-n);
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-                    }
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-                }
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-            }
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-        }
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-        // HENRY - store last scan explicitly.
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-        m_lastScan = iLastScan;
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-        // END HENRY
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-    }
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-
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-
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-    // HENRY -- arg is out of bounds. instead of creating havoc in RAMP, let's just kill it here.
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-    if (RAMP_RUNINFO != what && (RAMP_INSTRUMENT != what) && (arg > m_runInfo->m_data.scanCount || arg < 1))
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-    {
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-        return (NULL);
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-    }
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-
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-    if (m_scanOffsets || (RAMP_RUNINFO == what) || (RAMP_INSTRUMENT == what))
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-    {
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-        ramp_fileoffset_t scanOffset=-1;
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-        if (RAMP_RUNINFO == what || RAMP_INSTRUMENT == what)
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-        {
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-            scanOffset = 0; // read from head of file
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-        }
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-        else
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-        {
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-            scanOffset = m_scanOffsets[arg]; // ramp is one-based
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-        }
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-
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-        if (scanOffset >= 0)
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-        {
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-
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-            // -----------------------------------------------------------------------
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-            // And now we can parse the info we were looking for
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-            // -----------------------------------------------------------------------
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-
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-
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-            // Ok now we have to copy everything in our structure
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-            switch( what )
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-            {
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-            case RAMP_RUNINFO:
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-                //	   std::cerr << "in: rampRunInfo( m_handle )\n";
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-                returnPtr = new rampRunInfo( m_handle );
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-                //  std::cerr << "out: rampRunInfo( m_handle )\n";
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-                break;
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-            case RAMP_HEADER:
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-                //  std::cerr <<  "in: rampScanInfo( m_handle, scanOffset, (int)arg )\n" ;
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-                returnPtr = new rampScanInfo( m_handle, scanOffset, (int)arg );
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-                //std::cerr <<  "out: rampScanInfo( m_handle, scanOffset, (int)arg )\n" ;
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-                if (returnPtr)
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-                {
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-#ifdef HAVE_PWIZ_MZML_LIB
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-                    if (!m_handle->mzML) // rampadapter already set this for us
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-#endif
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-                        ((rampScanInfo *)returnPtr)->m_data.filePosition = scanOffset; // for future reference
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-
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-                    // HENRY -- error checking here
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-                    if (((rampScanInfo*)returnPtr)->m_data.acquisitionNum < 0)
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-                    {
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-                        // something failed in RAMP, possibly because it's a missing scan
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-                        delete ((rampScanInfo*)returnPtr);
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-                        returnPtr = NULL;
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-                    }
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-                }
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-                break;
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-            case RAMP_PEAKS:
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-                returnPtr = new rampPeakList( m_handle, scanOffset);
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-
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-                // HENRY -- error checking here
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-                if (returnPtr && ((rampPeakList*)returnPtr)->getPeakCount() <= 0)
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-                {
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-                    // something failed in RAMP, possibly because it's a missing scan
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-                    delete ((rampPeakList*)returnPtr);
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-                    returnPtr = NULL;
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-                }
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-                break;
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-
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-                // HENRY -- add the instrument info reading functionality (present in RAMP, but not provided in cRAMP before)
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-            case RAMP_INSTRUMENT:
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-                //	   std::cerr <<  "in: rampInstrumentInfo(m_handle)\n" ;
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-                returnPtr = new rampInstrumentInfo(m_handle);
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-                //std::cerr <<  "out: rampInstrumentInfo(m_handle)\n" ;
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-                if (((rampInstrumentInfo*)returnPtr)->m_instrumentStructPtr == NULL)
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-                {
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-                    delete ((rampInstrumentInfo*)returnPtr);
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-                    returnPtr = NULL;
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-                }
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-                break;
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-            }
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-
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-        }
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-    }
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-
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-
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-
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-    return returnPtr;
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-}
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-
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-
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-/**
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- * This function performs a non-sequential parsing operation on an indexed
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- * msxml file to obtain minimal info on the msRun contained in the file.
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-
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- *
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- * @return rapRunInfo* is dynamically allocate and becomes property of the caller, who
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- *         is responsible for its deallocation!!
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- */
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-
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-rampRunInfo* cRamp::getRunInfo (  )
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-{
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-    rampRunInfo* result;
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-    if (m_runInfo)   // did we derive this already?
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-    {
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-        result = new rampRunInfo(*m_runInfo);
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-    }
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-    else
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-    {
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-        result = (rampRunInfo*) do_ramp(0, RAMP_RUNINFO);
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-    }
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-    return result;
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-}
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-
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-/**
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- * This function performs a non-sequential parsing operation on an indexed
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- * msxml file to obtain minimal header info for a numbered scan (thus minimizing parse time).
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- *
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- * @param fileName: Name of the msxml file
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- * @param startSCan: Number of the scan we want to read from
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- * @return rapHeaderInfo* is dynamically allocate and becomes property of the caller, who
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- *         is responsible for its deallocation!! returns just the minimal header info num, msLevel and retentionTime
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- */
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-
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-rampScanInfo* cRamp::getScanHeaderInfo ( int whichScan  )
301 
-{
302 
-    return (rampScanInfo*) do_ramp((ramp_fileoffset_t)whichScan, RAMP_HEADER);
303 
-}
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-
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-
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-/**
307 
- * This function performs a non-sequential parsing operation on an indexed
308 
- * msxml file to obtain peak info for a numbered scan.
309 
- *
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- * @param fileName: Name of the msxml file
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- * @param startSCan: Number of the scan we want to read from
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- * @return rapPeakList* is dynamically allocate and becomes property of the caller, who
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- *         is responsible for its deallocation!! returns everything found in scan, precursorMz and peaks
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- */
315 
-
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-rampPeakList* cRamp::getPeakList ( int whichScan )
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-{
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-    return (rampPeakList*) do_ramp((ramp_fileoffset_t)whichScan, RAMP_PEAKS);
319 
-}
320 
-
321 
-// HENRY - provides instrument info getting method
322 
-rampInstrumentInfo* cRamp::getInstrumentInfo ()
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-{
324 
-    return (rampInstrumentInfo*) do_ramp(0, RAMP_INSTRUMENT);
325 
-}
326 
-// END HENRY
327 
-
328 
-
329 
-// HENRY - sequential access parser that skips over missing scans. This version only reads scan header.
330 
-bool cRampIterator::nextScan(rampScanInfo** scanInfo)
331 
-{
332 
-    while (++m_currentScan <= m_cramp.getLastScan() && m_cramp.getScanOffset(m_currentScan) <= 0);
333 
-    if (m_currentScan > m_cramp.getLastScan())
334 
-    {
335 
-        return (false);
336 
-    }
337 
-
338 
-    *scanInfo = (rampScanInfo*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_HEADER);
339 
-    return (true);
340 
-}
341 
-// END HENRY
342 
-
343 
-// HENRY - sequential access parser that skips over missing scans. This version reads both scan header and peak list.
344 
-bool cRampIterator::nextScan(rampScanInfo** scanInfo, rampPeakList** peakList)
345 
-{
346 
-    while (++m_currentScan <= m_cramp.getLastScan() && m_cramp.getScanOffset(m_currentScan) <= 0);
347 
-    if (m_currentScan > m_cramp.getLastScan())
348 
-    {
349 
-        return (false);
350 
-    }
351 
-
352 
-    *scanInfo = (rampScanInfo*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_HEADER);
353 
-    *peakList = (rampPeakList*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_PEAKS);
354 
-
355 
-    return (true);
356 
-
357 
-}
358 
-// END HENRY
359 
-
360 
-// HENRY - resets the sequential access parser to the first scan.
361 
-void cRampIterator::reset()
362 
-{
363 
-    m_currentScan = 1;
364 
-}
365 
-// END HENRY
366 
-
367 
-/**
368 
- * populate from a file handle
369 
- **/
370 
-rampPeakList::rampPeakList(RAMPFILE *handle, ramp_fileoffset_t index)
371 
-{
372 
-    init();
373 
-    m_peaksCount = readPeaksCount(handle,index);
374 
-    m_pPeaks = (rampPeakInfoStruct *)readPeaks(handle,index);
375 
-}
376 
-
377 
-/**
378 
- * populate from a file handle
379 
- **/
380 
-rampScanInfo::rampScanInfo(RAMPFILE *handle, ramp_fileoffset_t index, int seqNum)
381 
-{
382 
-    init();
383 
-    readHeader(handle,index,&m_data);
384 
-    m_data.seqNum = seqNum;
385 
-}
386 
-
387 
-/**
388 
- * populate from a file handle
389 
- **/
390 
-rampRunInfo::rampRunInfo(RAMPFILE *handle)
391 
-{
392 
-    init();
393 
-    readMSRun(handle,&m_data);
394 
-}
395 
-
396 
-// HENRY - provides instrument info reading functionality
397 
-rampInstrumentInfo::rampInstrumentInfo(RAMPFILE *handle)
398 
-{
399 
-    init();
400 
-    m_instrumentStructPtr = getInstrumentStruct(handle);
401 
-}
402 
-// END HENRY
Browse code

merge conflicts

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@121284 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 23/09/2016 08:43:32
Showing1 changed files
src/cramp.cpp
History View file @8516f59b6f
... ... 
@@ -95,7 +95,7 @@ cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
95 95 
         //      if (m_runInfo->m_data.scanCount < 0) { // undeclared scan count
96 96 
         // this will provoke reading of index, which sets scan count
97 97 
         rampScanInfo* tmp = getScanHeaderInfo ( 1 );
98 
-        free(tmp);
98 
+        delete(tmp); // was free - but see https://github.com/sneumann/mzR/issues/52
99 99 
         // }
100 100 
         // END HENRY
101 101 
     }
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 130 commits.

Commit information:

Commit id: 289dc240065888efcaa22ae75951e81f94fc800f

Fix package description after merge

Committed by: Steffen Neumann
Author Name: Steffen Neumann
Commit date: 2014-09-28 17:21:35 +0200
Author date: 2014-09-28 17:21:35 +0200

Commit id: 88248e8d6d86bb54dc260f0c55608dd1a949ade4

merged gsoc into master

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-27 08:49:45 +0100
Author date: 2014-09-27 08:49:45 +0100

Commit id: bb01e0fe0b4f04335925472a7c2b91bd22b57755

included KK's segfault patch and fixed unit test accordingly

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-27 08:44:50 +0100
Author date: 2014-09-27 08:44:50 +0100

Commit id: 708bd0b8ac4b2b5bae9a9b91588a260f2eeefb46

add message about pwiz backend in Bioc 3.1

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-25 01:20:52 +0100
Author date: 2014-09-25 01:20:52 +0100

Commit id: 4c1410ec3c8f153ad0a4b04722cad5a7d77cfd4c

restoring ramp as default backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-25 01:06:21 +0100
Author date: 2014-09-25 01:06:21 +0100

Commit id: c5d60529934813456555934bbeed29502100b41b

show pwiz method

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 21:09:38 +0100
Author date: 2014-09-21 21:09:38 +0100

Commit id: 20bfbfa1db25ec247f2313804d9b73c086a2d920

add close,mzRpwiz-method alias

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 21:04:48 +0100
Author date: 2014-09-21 21:04:48 +0100

Commit id: f80ecdc2a7f14c311b42ad279c62307a6e0aad30

test that close(pwiz) works

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 20:45:50 +0100
Author date: 2014-09-21 20:45:50 +0100

Commit id: d18dc8b0c7197c72b1bb2a70e7becfe983ced9a1

fixed signature for pwiz close method

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 20:44:41 +0100
Author date: 2014-09-21 20:44:41 +0100

Commit id: c0d7451e6b31068cde89f08ac5037a1509857cc5

fix codoc mismatch

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 19:02:00 +0100
Author date: 2014-09-21 19:02:00 +0100

Commit id: 14974a3d0890a7e2a1a7179aaa483e20a5700ef9

add close for pwiz backend to news

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:58:06 +0100
Author date: 2014-09-21 18:58:06 +0100

Commit id: c9d2bbb339c0ecdc9870dbd7a59bfbb94ef67f73

dummy close for pwiz backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:56:48 +0100
Author date: 2014-09-21 18:56:48 +0100

Commit id: 6d608b453328d6c751dc828d2586b016eb17b095

more close calls to remove for pwiz backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:52:55 +0100
Author date: 2014-09-21 18:52:55 +0100

Commit id: 5650801e07df64e2d74302ec98a31938bb62f11f

no isInitialised with pwiz

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:41:57 +0100
Author date: 2014-09-21 18:41:57 +0100

Commit id: 2a3d0eeb24673eb74c3ffa38fefb1883f9bee15d

no close with pwiz

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:46:38 +0100
Author date: 2014-09-21 17:46:38 +0100

Commit id: b3ae014569b6e46ccb6b396dfb9320dd7ba8fb16

bump version to avoid confusions

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:30:28 +0100
Author date: 2014-09-21 17:30:28 +0100

Commit id: a1bd596ffbeef73b4b505342f45742f9997e33d1

using pwiz as default raw data backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:29:02 +0100
Author date: 2014-09-21 17:29:02 +0100

Commit id: 51b4ea21d9cf034d54b0911bf281af3a937375de

Steffen's changes in v 1.11.11

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 16:21:14 +0100
Author date: 2014-09-20 16:21:14 +0100

Commit id: 81cde1ca48974585c9d6f51927087a922b13dd89

add new length to doc header

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 16:06:46 +0100
Author date: 2014-09-20 16:06:46 +0100

Commit id: 3fe883cb7ecad4867908fb907374a4df63b50a1f

show and length mzRident methods

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 15:56:26 +0100
Author date: 2014-09-20 15:56:26 +0100

Commit id: 3efb44e00fb94cdf0eb8207634218cbb47ab1b54

VignetteBuilder: knitr

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-27 01:03:36 +0100
Author date: 2014-08-27 01:03:36 +0100

Commit id: 73b0f902dfaa53f359318708f0606dc1f4677057

BiocStyle vig

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-26 23:59:29 +0100
Author date: 2014-08-26 23:59:29 +0100

Commit id: 185f281d07ed7b4a7f093eaf7b61271a88c85e20

update readme

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-26 23:20:02 +0100
Author date: 2014-08-26 23:20:02 +0100

Commit id: d5cc992e128594d331592b2bd57871fabf6737c9

update to build

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:41:17 +0100
Author date: 2014-08-17 22:41:17 +0100

Commit id: 27318416c94859102a061838a1a3f83d378414e3

bump to 1.99

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:12:44 +0100
Author date: 2014-08-17 22:12:44 +0100

Commit id: 13caefb4d4b469f0406ed96509ea4cebce8235b0

pulled from https://github.com/thirdwing/mzR

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:00:57 +0100
Author date: 2014-08-17 22:00:57 +0100

Commit id: 14822efb6c2238eda371718043bec9cc8fb27558

doc

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-16 22:06:51 -0400
Author date: 2014-08-16 22:06:51 -0400

Commit id: 323424443efac769c436fb87128fad64a0358187

R_init_mzR.c

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-10 00:46:14 -0400
Author date: 2014-08-10 00:46:14 -0400

Commit id: a91c0601e674efbb6949331a53ea9c6af53a4ba5

vignettes

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-06 21:03:23 -0400
Author date: 2014-08-06 21:03:23 -0400

Commit id: 4607e0a595f60a083d1eb90b804348ac5a8c1fb4

update with msdata

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-05 12:33:40 -0400
Author date: 2014-08-05 12:33:40 -0400

Commit id: cc09a790eda22b7d64226116ada89bad9089e0b2

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-04 22:29:15 -0400
Author date: 2014-08-04 22:29:15 -0400

Commit id: fac511ee0f7841791bbf5380f2c948fd045b3adb

unit test against mzID

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-04 22:16:03 -0400
Author date: 2014-08-04 22:16:03 -0400

Commit id: 449952e31fe354b2589d8a723a4f8a842812ede6

enzymes() returns data.frame

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:29:59 -0400
Author date: 2014-08-03 16:29:59 -0400

Commit id: 874fba33e8029023d5e3bbd168dc998d51544c9d

writing support dropped

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:14:26 -0400
Author date: 2014-08-03 16:14:26 -0400

Commit id: 338f3e80dd8f98419555ab1a4aa443e14d089f24

modifications()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:02:20 -0400
Author date: 2014-08-03 16:02:20 -0400

Commit id: 34ee62ee27e7b012b9ce2bd696d63e5f80185200

psms() update

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 15:41:36 -0400
Author date: 2014-08-03 15:41:36 -0400

Commit id: b8bdea9a1e2a7ab3410eea5c26566ef74e488d95

score()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 14:14:53 -0400
Author date: 2014-08-03 14:14:53 -0400

Commit id: a42f1195b3f0b40c28aa2acfb782e517633206c9

psms()

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-03 13:54:34 -0400
Author date: 2014-08-03 13:54:34 -0400

Commit id: 6c2a87019e3b328dbecc1a965d3e41e6539e0d90

para() update, numeric correction

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-02 23:57:41 -0400
Author date: 2014-08-02 23:57:41 -0400

Commit id: 119edf40600beb8e3b8e8006a0d955a887d06b1d

update para()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-30 10:54:40 -0400
Author date: 2014-07-30 10:54:40 -0400

Commit id: 69ac718d0418f2ab3ba824a735975ae6c04aec00

update database()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-30 10:38:42 -0400
Author date: 2014-07-30 10:38:42 -0400

Commit id: f7818556b2e1e3296a727eca6d2853a8b7a16b12

clean

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 21:35:59 -0400
Author date: 2014-07-29 21:35:59 -0400

Commit id: f67403a92b6beca4128c36b42367414463234253

database()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 21:33:07 -0400
Author date: 2014-07-29 21:33:07 -0400

Commit id: 8b0255a9c7da6ccc6c7796f49f608b792bac0dfe

para()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 20:33:14 -0400
Author date: 2014-07-29 20:33:14 -0400

Commit id: 183afed91ad6beb07fffb5cbe4673773619d938b

Rd

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-29 00:36:40 -0400
Author date: 2014-07-29 00:36:40 -0400

Commit id: 73d380115e205eedc211869d6eace3564b3fc1cf

modified: vignettes/mzR.Rnw

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-27 00:49:10 -0400
Author date: 2014-07-27 00:49:10 -0400

Commit id: 93214634ff41a9da84019320dfe6314cb7f94422

score

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-26 19:42:34 -0400
Author date: 2014-07-26 19:42:34 -0400

Commit id: cbdee47033cf10927b0dc33a02208c9ff9d89771

same header info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-22 12:45:46 -0400
Author date: 2014-07-22 12:45:46 -0400

Commit id: 1e6ebe39851ecddedf01daa2c69fcd1f2dba906c

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: inst/unitTests/runit.backends.R modified: man/metadata.Rd modified: man/mzR-class.Rd

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-18 00:40:10 -0400
Author date: 2014-07-18 00:40:10 -0400

Commit id: 0ed92085be5af56a78cdf0f1732a356c48d7a0f9

1.11.10

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-17 21:31:27 -0400
Author date: 2014-07-17 21:31:27 -0400

Commit id: b6e254b2cca93778bfcdc549b75052d0b19bb2bb

fixed

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-16 01:40:10 -0400
Author date: 2014-07-16 01:40:10 -0400

Commit id: 096aa2a6f5aebb5b99bc2e22a0fb023b1353b141

Merge pull request #3 from lgatto/master

fix backend checking
Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-07-15 21:20:15 -0400
Author date: 2014-07-15 21:20:15 -0400

Commit id: 6d8623c47c0b53e6805b9757c178c4639319a29d

fix backend checking

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-07-15 23:32:46 +0100
Author date: 2014-07-15 23:32:46 +0100

Commit id: 9060e3435a76ace952d915c3bb993e04ac93f12a

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-14 10:52:41 -0400
Author date: 2014-07-14 10:52:41 -0400

Commit id: 068ec46671400a2db3bfb10f001f30599b8495e8

modified: ChangeLog

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 17:29:16 -0400
Author date: 2014-07-12 17:29:16 -0400

Commit id: a8f42c9de00ed64470733eb5c63567e99d40e867

more info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 14:57:33 -0400
Author date: 2014-07-12 14:57:33 -0400

Commit id: 4a88ad7c2c8ec911c44a45d16dedced9530505c2

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 14:13:29 -0400
Author date: 2014-07-12 14:13:29 -0400

Commit id: 935d44c5a52b895fe6ff663c062e006e4f25fab0

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 13:52:33 -0400
Author date: 2014-07-12 13:52:33 -0400

Commit id: f1c05ff287215f385938a116042d09bcea2aae88

modified: R/methods-mzRident.R modified: man/mzR-class.Rd modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 11:20:58 -0400
Author date: 2014-07-12 11:20:58 -0400

Commit id: ca620536203355349c7267ad15a2ab6a2d248319

pass R CMD check

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-12 00:36:08 -0400
Author date: 2014-07-12 00:36:08 -0400

Commit id: add1d1c98fe60955953036641671527337e89363

modified: R/methods-mzRident.R modified: man/metadata.Rd modified: man/mzR-class.Rd modified: src/Makevars modified: src/Makevars.win

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 23:48:02 -0400
Author date: 2014-07-11 23:48:02 -0400

Commit id: 050051489df378a26aa97cccfefbf7ebe4102ef5

pepInfo()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 18:10:10 -0400
Author date: 2014-07-11 18:10:10 -0400

Commit id: f093e39599ea2357c91816b7ff9de102f33e8e68

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 15:12:28 -0400
Author date: 2014-07-11 15:12:28 -0400

Commit id: 3dc85db859c4d36040d3edb9ceb57074b0476f2d

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 14:49:47 -0400
Author date: 2014-07-11 14:49:47 -0400

Commit id: ab1261cb3bfe1c02de5f7a053e6de5223686488d

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 13:47:12 -0400
Author date: 2014-07-11 13:47:12 -0400

Commit id: 01a4a2be981724624719580cd8e4f0866091f295

version

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 01:48:50 -0400
Author date: 2014-07-11 01:48:50 -0400

Commit id: 5f49d13b736cebd65484a5993cdcce253853d4e7

remove mz5

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 01:41:00 -0400
Author date: 2014-07-11 01:41:00 -0400

Commit id: fb3dbe2f1bf007cd033fd803426d4be2e362b3e2

Update H5public.h

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-07-07 08:46:19 -0400
Author date: 2014-07-07 08:46:19 -0400

Commit id: 2446f08fdadd11c38a1cb54dddfe1e52b1a7bca9

modified: src/pwiz/utility/chemistry/Chemistry.hpp modified: src/pwiz/utility/misc/Std.hpp modified: src/pwiz/utility/misc/sha1calc.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 19:41:41 -0400
Author date: 2014-07-04 19:41:41 -0400

Commit id: b7c28c0db06b2dc9f8f5a7dcd218b7581ffd8121

compiled

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 18:05:54 -0400
Author date: 2014-07-04 18:05:54 -0400

Commit id: 1ffe5c024dafd51c2342f4d1dd930cb8d67d8041

modified: DESCRIPTION modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 10:09:46 -0400
Author date: 2014-07-04 10:09:46 -0400

Commit id: 06e03716f187508072c33d3f0e9e79e135b22c05

modified: src/Makevars modified: src/hdf5/src/H5public.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 22:32:09 -0400
Author date: 2014-07-03 22:32:09 -0400

Commit id: 488ed2bd55151ece46c8cb5ac1df11f73b7c47a3

modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 21:48:39 -0400
Author date: 2014-07-03 21:48:39 -0400

Commit id: 06f4d0a3832e47ad4a69e53d7b9b751dbb9f2770

modified: src/hdf5/src/H5public.h modified: src/pwiz/utility/misc/SHA1.cpp modified: src/pwiz/utility/misc/SHA1.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 21:47:50 -0400
Author date: 2014-07-03 21:47:50 -0400

Commit id: ff58989379a67f20ac8797ba437d430d8b5a2d62

modified: src/RcppIdent.cpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-30 09:42:05 -0400
Author date: 2014-06-30 09:42:05 -0400

Commit id: 58dfa68675768c13950299c43229c1b0f1f1824b

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 21:17:18 -0400
Author date: 2014-06-28 21:17:18 -0400

Commit id: 6c228ae30c477e76add7e3ea805e386f1a0d862d

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 20:16:55 -0400
Author date: 2014-06-28 20:16:55 -0400

Commit id: 464d4e83a9e06732f7c3f1a0172a9cb2bbd53943

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 17:21:01 -0400
Author date: 2014-06-28 17:21:01 -0400

Commit id: ed36541a5fc99192f9df55222f2a2d9a6352ae33

idInfo

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 17:02:20 -0400
Author date: 2014-06-28 17:02:20 -0400

Commit id: 1ed6dceee93d2f57a66a94b15774212403d42200

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 15:19:47 -0400
Author date: 2014-06-28 15:19:47 -0400

Commit id: 47b2a99876650729a329ebeebc174d9873919667

modified: DESCRIPTION

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 13:12:13 -0400
Author date: 2014-06-28 13:12:13 -0400

Commit id: ecad541c1e2d92f7be63433c5bf362d7b7f955b2

mzid supported done

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 13:04:27 -0400
Author date: 2014-06-28 13:04:27 -0400

Commit id: 684340ce7ee5b8fadbd4dfa839e3b0d7ba9b1c91

mzid file support

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-28 01:02:19 -0400
Author date: 2014-06-28 01:02:19 -0400

Commit id: 7382b1321539a2838ae75da6f9c1ff9cbe98bb6b

mzid

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 23:38:36 -0400
Author date: 2014-06-27 23:38:36 -0400

Commit id: 5423b4c653762d90ce6d4bf7dcf1d591a2a9987f

modified: R/methods-mzRpwiz.R modified: R/zzz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 23:27:36 -0400
Author date: 2014-06-27 23:27:36 -0400

Commit id: 9e20328e920207328eb68b9fa59c198d0d634a0f

Update AllGenerics.R

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-27 22:52:37 -0400
Author date: 2014-06-27 22:52:37 -0400

Commit id: 19731b9e51b72027eb02ee6be5aa7343c5b12ace

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRpwiz.R modified: man/metadata.Rd modified: man/mzR-class.Rd modified: man/openMSfile.Rd modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h modified: src/RcppPwizModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 22:03:31 -0400
Author date: 2014-06-27 22:03:31 -0400

Commit id: 94ac2b4ba810d0f820a9266be782667e375ede9a

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 10:15:58 -0400
Author date: 2014-06-27 10:15:58 -0400

Commit id: 1259a8db48d4f7aa9ffe403dd5ee574bbfd238fb

modified: R/zzz.R modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-27 00:44:31 -0400
Author date: 2014-06-27 00:44:31 -0400

Commit id: 9791bc574989cdefe279071dbf3a47232e1d8c86

identadata src

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-27 00:22:35 -0400
Author date: 2014-06-27 00:22:35 -0400

Commit id: ede49e01e23c6586777d72fdd0dfef4bd40729f2

software info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 22:20:57 -0400
Author date: 2014-06-26 22:20:57 -0400

Commit id: 431b2b42a93ff52a05d82801d1830ba81c72f18f

writeMSfile()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 21:53:11 -0400
Author date: 2014-06-26 21:53:11 -0400

Commit id: 53a7a31378bd42adcf779cd1fbe9e2d052a507d7

deleted: src/hdf5/c++/src/H5 deleted: src/hdf5/c++/src/H5DataTy deleted: src/pwiz/data/common/BinaryIndexSt deleted: src/pwiz/data/common/ParamT deleted: src/pwiz/data/m deleted: src/pwiz/data/msdata/BinaryDataEnc deleted: src/pwiz/data/msdata/Chroma deleted: src/pwiz/data/msdata/MSNu deleted: src/pwiz/data/msdata/Seri deleted: src/pwiz/data/msdata/Serializer deleted: src/pwiz/data/msdata/Serializer_mz deleted: src/pwiz/data/msdata/Sp deleted: src/pwiz/data/msdata/Spec deleted: src/pwiz/data/msdata/mz5/Refer deleted: src/pwiz/utility/mis deleted: src/pwiz/utility/misc/IntegerS

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 19:04:22 -0400
Author date: 2014-06-26 19:04:22 -0400

Commit id: 359a40045162a49d94d68f0d60f2c6bb43970a2c

modified: NAMESPACE modified: R/AllGenerics.R modified: R/io.R modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h modified: src/RcppPwizModule.cpp new file: src/boost/filesystem/src/operations new file: src/hdf5/c++/src/H5 new file: src/hdf5/c++/src/H5DataTy new file: src/pwiz/data/common/BinaryIndexSt new file: src/pwiz/data/common/ParamT new file: src/pwiz/data/m new file: src/pwiz/data/msdata/BinaryDataEnc new file: src/pwiz/data/msdata/Chroma new file: src/pwiz/data/msdata/MSNu new file: src/pwiz/data/msdata/Seri new file: src/pwiz/data/msdata/Serializer new file: src/pwiz/data/msdata/Serializer_mz new file: src/pwiz/data/msdata/Sp new file: src/pwiz/data/msdata/Spec new file: src/pwiz/data/msdata/mz5/Refer new file: src/pwiz/utility/mis new file: src/pwiz/utility/misc/IntegerS

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 19:00:48 -0400
Author date: 2014-06-26 19:00:48 -0400

Commit id: 2ce04488e7a8e623a7dfd2b9408da0b9dd5059a4

modified: inst/unitTests/runit.backends.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 15:59:21 -0400
Author date: 2014-06-26 15:59:21 -0400

Commit id: 3103fd4fa92ddd63700c8b5940344db44e97be09

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 13:33:44 -0400
Author date: 2014-06-26 13:33:44 -0400

Commit id: 329f7c1201360f5ebf5703d4837b25ae332e7a85

modified: man/metadata.Rd modified: man/mzR-class.Rd modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 11:35:13 -0400
Author date: 2014-06-26 11:35:13 -0400

Commit id: 0adf852da9ccec69103038ca96b30e8715d3c898

modified: inst/unitTests/runit.backends.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 11:20:03 -0400
Author date: 2014-06-26 11:20:03 -0400

Commit id: 219b5287ca5531577b4a6c80f403957ddef5ab94

modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-26 01:33:43 -0400
Author date: 2014-06-26 01:33:43 -0400

Commit id: 14316dcb1c16ca922d9962ed9ecdaac324e1a151

deleted: src/R_init_mzR.c modified: src/RcppPwiz.cpp deleted: src/ramp_base64.cpp deleted: src/ramp_base64.h

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-26 01:04:14 -0400
Author date: 2014-06-26 01:04:14 -0400

Commit id: efb21501a1b05b680b3d35aa124216f9977b5993

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 23:44:07 -0400
Author date: 2014-06-25 23:44:07 -0400

Commit id: 4e9e1dec2879178547d681603aec46259a6a9978

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:54:26 -0400
Author date: 2014-06-25 22:54:26 -0400

Commit id: 0e7fc23b1ff7508fed6331c0e517a8dc6fa33a0c

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:28:24 -0400
Author date: 2014-06-25 22:28:24 -0400

Commit id: 9ad55a2cdd89791bf75ad23f0ee91b3fc70624ad

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:13:35 -0400
Author date: 2014-06-25 22:13:35 -0400

Commit id: c9fecd83ebf31f142c22030f4593fe5ac675323a

modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 23:31:33 -0400
Author date: 2014-06-24 23:31:33 -0400

Commit id: 4edf517724950d6771fd19c979a460711baa5891

modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 23:01:49 -0400
Author date: 2014-06-24 23:01:49 -0400

Commit id: 22ca998b6b6d3a7496f293f44909436a5b7d8ad0

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 21:31:58 -0400
Author date: 2014-06-24 21:31:58 -0400

Commit id: 6beb4ce5c49cafa644766e23453ed6d10bb89c34

modified: man/metadata.Rd modified: man/mzR-class.Rd

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-22 12:02:07 -0400
Author date: 2014-06-22 12:02:07 -0400

Commit id: dc5e65d93bb67d1b4a1488b90099946e22eed13c

deleted: .travis.yml

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-22 11:26:02 -0400
Author date: 2014-06-22 11:26:02 -0400

Commit id: be53359804d6c7416c715c3eb259fb931c6c117a

modified: .travis.yml modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:33:37 -0400
Author date: 2014-06-21 21:33:37 -0400

Commit id: 1afd9887dac232f3e72fe9d20d44a72b42e28461

deleted: .Rinstignore

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:27:46 -0400
Author date: 2014-06-21 21:27:46 -0400

Commit id: bd4c954bd246787137eb0d961a91bb80b774cb6a

new file: .Rbuildignore new file: .travis.yml

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:25:47 -0400
Author date: 2014-06-21 21:25:47 -0400

Commit id: 3bc8fcca8002a62458a2b2dd1c6b7cf6a8cfab9f

fixed error on windows and snow leopard

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:18:50 -0400
Author date: 2014-06-21 21:18:50 -0400

Commit id: ed9c622443eb992cf3322d687312e3f56bf8be72

Update Makevars.win

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-15 00:55:16 +0800
Author date: 2014-06-15 00:55:16 +0800

Commit id: bf8c7bd931cd93b5db6d84c9c1bf323ea7702e74

new file: src/boost/signals/connection.hpp new file: src/boost/signals/detail/config.hpp new file: src/boost/signals/detail/gen_signal_N.pl new file: src/boost/signals/detail/named_slot_map.hpp new file: src/boost/signals/detail/signal_base.hpp new file: src/boost/signals/detail/signals_common.hpp new file: src/boost/signals/detail/slot_call_iterator.hpp new file: src/boost/signals/signal0.hpp new file: src/boost/signals/signal1.hpp new file: src/boost/signals/signal10.hpp new file: src/boost/signals/signal2.hpp new file: src/boost/signals/signal3.hpp new file: src/boost/signals/signal4.hpp new file: src/boost/signals/signal5.hpp new file: src/boost/signals/signal6.hpp new file: src/boost/signals/signal7.hpp new file: src/boost/signals/signal8.hpp new file: src/boost/signals/signal9.hpp new file: src/boost/signals/signal_template.hpp new file: src/boost/signals/slot.hpp new file: src/boost/signals/trackable.hpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-14 12:52:52 -0400
Author date: 2014-06-14 12:52:52 -0400

Commit id: 5ac3655c7e81f429859eb6b509208f8ec785e1f9

modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-07 11:42:14 -0400
Author date: 2014-06-07 11:42:14 -0400

Commit id: f9f42e3d83adbaf98a201e50866821bc0e43598a

modified: ChangeLog modified: src/RcppPwiz.cpp modified: src/hdf5/src/H5FDmulti.c

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-07 11:24:01 -0400
Author date: 2014-06-07 11:24:01 -0400

Commit id: d8d6f92e46efa93f8234e542b1c4f8f98cee59e5

modified: R/zzz.R.in

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 17:28:36 -0400
Author date: 2014-06-06 17:28:36 -0400

Commit id: e64a8bb7bb7988047466848e5b449038ae9460b3

modified: R/zzz.R modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 16:40:29 -0400
Author date: 2014-06-06 16:40:29 -0400

Commit id: 0a44cc02ea9b5417ac51f60632fc1b6100c6d160

modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 16:01:08 -0400
Author date: 2014-06-06 16:01:08 -0400

Commit id: 4d19d457031e0ae9af343a44774f5deebae01cc8

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 14:16:37 -0400
Author date: 2014-06-06 14:16:37 -0400

Commit id: effcb581a573e13b7b7cc9b459ef2dec4885b4be

modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-06 04:33:43 -0400
Author date: 2014-06-06 04:33:43 -0400

Commit id: 028f6748d4cf81d47569edcd67fe25064b084e60

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-04 23:21:43 -0400
Author date: 2014-06-04 23:21:43 -0400

Commit id: d95b557d2c637630ca784889cd0ef1f56b8423d5

Update methods-mzRpwiz.R

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:51:47 -0400
Author date: 2014-06-04 21:51:47 -0400

Commit id: aad52653c2ceb33655364d5a39c0559225746cfb

Update RcppPwizModule.cpp

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:50:32 -0400
Author date: 2014-06-04 21:50:32 -0400

Commit id: 4fda90cc08feb731aeb65c6015a033fbe46c372e

Update RcppPwiz.cpp

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:48:06 -0400
Author date: 2014-06-04 21:48:06 -0400

Commit id: 660d2e984fabdd20997ff8b648d361c7d9aae711

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-02 13:07:57 -0400
Author date: 2014-06-02 13:07:57 -0400

Commit id: ec6bbdf496a57f2f39b2e4c3bbada75a060e5bbe

modified: src/boost_aux/boost/utility/singleton.hpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-02 09:21:07 -0400
Author date: 2014-06-02 09:21:07 -0400

Commit id: a093954cb779467026288c7f51cca083e0a20661

modified: src/pwiz/data/msdata/ramp/ramp.cpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-05-29 07:36:21 -0400
Author date: 2014-05-29 07:36:21 -0400

Commit id: 4510a1cda50ee8f1f43b667297918dcffed45af2

modified: src/Makevars modified: src/cramp.h modified: src/pwiz/data/msdata/ramp/ramp.cpp deleted: src/ramp.cpp deleted: src/ramp.h modified: src/rampR.cpp deleted: src/ramp_base64.cpp deleted: src/ramp_base64.h

Committed by: qkou
Author Name: qkou
Commit date: 2014-05-28 20:17:42 -0400
Author date: 2014-05-28 20:17:42 -0400


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@94635 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 28/09/2014 18:06:01
Showing1 changed files
src/cramp.cpp
History View file @84a4b1664f
... ... 
@@ -2,14 +2,14 @@
2 2 
 cramp.cpp
3 3
4 4 
 ***************************************************************************
5 
-cramp.hpp -- renamed cramp.h to avoid R checker warning
5 
+cramp.hpp -- renamed cramp.h to avoid R checker warning
6 6
7 7 
   A C++ wrapper for the RAMP code.
8 8
9 9 
   Use this library to parse an mzXML file in a non-sequential way, by
10 
-  taking advantage of the index element.
10 
+  taking advantage of the index element.
11 11
12 
-  (C) 2004 by Brian Pratt, Insilicos LLC
12 
+  (C) 2004 by Brian Pratt, Insilicos LLC
13 13
14 14 
   Based on mzXML2Other, which has this copyright:
15 15 
 	 -------------------
... ... 
@@ -69,42 +69,46 @@ cramp.hpp -- renamed cramp.h to avoid R checker warning
69 69
70 70
71 71
72 
-cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
73 
-  m_filename(fileName), m_declaredScansOnly(declaredScansOnly), m_runInfo()
72 
+cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
73 
+    m_filename(fileName), m_declaredScansOnly(declaredScansOnly), m_runInfo()
74 74 
 {
75 
-   m_handle = rampOpenFile(fileName);
76 
-   m_scanOffsets = NULL;
77 
-   m_runInfo = NULL;
78 
-   m_lastScan = 0;
79 
-   if (!OK()) {
80 
-     // HENRY -- I would prefer this to be silent, and let the caller deals with it
81 
-     // cout << "Error: Could not open file " << fileName << ": " << strerror(errno) << endl;
82 
-     // END HENRY
83 
-   } else {
84 
-
85 
-      m_runInfo = getRunInfo();
86 
-
87 
-      // HENRY -- always read index to set scan count, since scan count
88 
-      // declared at the top of the mzXML file is unreliable now that
89 
-      // there are missing scans.
90 
-      // This will also set the structs m_scanOffsets, and the value m_lastScan
91 
-
92 
-      //      if (m_runInfo->m_data.scanCount < 0) { // undeclared scan count
93 
-         // this will provoke reading of index, which sets scan count
94 
-         rampScanInfo* tmp = getScanHeaderInfo ( 1 );
95 
-         free(tmp);
96 
-	 // }
97 
-      // END HENRY
98 
-   }
75 
+    m_handle = rampOpenFile(fileName);
76 
+    m_scanOffsets = NULL;
77 
+    m_runInfo = NULL;
78 
+    m_lastScan = 0;
79 
+    if (!OK())
80 
+    {
81 
+        // HENRY -- I would prefer this to be silent, and let the caller deals with it
82 
+        // cout << "Error: Could not open file " << fileName << ": " << strerror(errno) << endl;
83 
+        // END HENRY
84 
+    }
85 
+    else
86 
+    {
87 
+
88 
+        m_runInfo = getRunInfo();
89 
+
90 
+        // HENRY -- always read index to set scan count, since scan count
91 
+        // declared at the top of the mzXML file is unreliable now that
92 
+        // there are missing scans.
93 
+        // This will also set the structs m_scanOffsets, and the value m_lastScan
94 
+
95 
+        //      if (m_runInfo->m_data.scanCount < 0) { // undeclared scan count
96 
+        // this will provoke reading of index, which sets scan count
97 
+        rampScanInfo* tmp = getScanHeaderInfo ( 1 );
98 
+        free(tmp);
99 
+        // }
100 
+        // END HENRY
101 
+    }
99 102 
 }
100 103
101 
-cRamp::~cRamp() {
102 
-   rampCloseFile(m_handle);
103 
-
104 
-   // NB: these pointers may be null on file open failure,
105 
-   // but free/delete of NULL is OK per C++ standard
106 
-   free(m_scanOffsets);
107 
-   delete m_runInfo; // was free() - but allocated with new
104 
+cRamp::~cRamp()
105 
+{
106 
+    rampCloseFile(m_handle);
107 
+
108 
+    // NB: these pointers may be null on file open failure,
109 
+    // but free/delete of NULL is OK per C++ standard
110 
+    free(m_scanOffsets);
111 
+    delete m_runInfo; // was free() - but allocated with new
108 112 
 }
109 113
110 114 
 //
... ... 
@@ -112,157 +116,180 @@ cRamp::~cRamp() {
112 116 
 //
113 117 
 rampInfo* cRamp::do_ramp( ramp_fileoffset_t arg , eWhatToRead	what )
114 118 
 {
115 
-
116 
-   switch( what ) {
117 
-   case RAMP_RUNINFO:
118 
-   case RAMP_HEADER:
119 
-   case RAMP_PEAKS:
120 
-   case RAMP_INSTRUMENT:
121 
-      break; // OK
122 
-   default:
123 
-     Rf_error("unknown read type!\n");
124 
-      return NULL;
125 
-      break;
126 
-   }
127 
-
128 
-   rampInfo* returnPtr=NULL;
129 
-
130 
-   if ((RAMP_RUNINFO != what) && (RAMP_INSTRUMENT != what) && !m_scanOffsets) {
131 
-      int iLastScan = 0;
132 
-     // we need the index to get anything besides the header
133 
-      //      std::cerr << "in: getIndexOffset(m_handle);!\n";
134 
-      ramp_fileoffset_t indexOffset = getIndexOffset(m_handle);
135 
-      //      std::cerr << "out: getIndexOffset(m_handle);!\n";
136 
-
137 
-      // std::cerr << "in: readIndex();!\n";
138 
-      m_scanOffsets = readIndex(m_handle, indexOffset, &iLastScan);
139 
-      //std::cerr << "out: readIndex();!\n";
140 
-      if (iLastScan >= m_runInfo->m_data.scanCount) {
141 
-		 if (!m_declaredScansOnly) {
142 
-           m_runInfo->m_data.scanCount = iLastScan;
143 
-		 } else { // get rid of all the fake entries created
144 
-
145 
-		   //  std::cerr << "get rid of all the fake entries created\n";
146 
-			 for (int n=1;n<=iLastScan;n++) { // ramp is 1 based
147 
-				 if (m_scanOffsets[n]==-1) {
148 
-					// find a run of fakes
149 
-				    int m;
150 
-					for (m=n+1;(m<=iLastScan)&&(m_scanOffsets[m]==-1);m++);
151 
-					if (m<=iLastScan) {
152 
-						memmove(m_scanOffsets+n,m_scanOffsets+m,
153 
-						  sizeof(ramp_fileoffset_t)*((iLastScan-m)+1));
154 
-					}
155 
-					iLastScan-=(m-n);
156 
-				 }
157 
-			 }
158 
-		 }
159 
-      }
160 
-      // HENRY - store last scan explicitly.
161 
-      m_lastScan = iLastScan;
162 
-      // END HENRY
163 
-   }
164 
-
165 
-
166 
-   // HENRY -- arg is out of bounds. instead of creating havoc in RAMP, let's just kill it here.
167 
-   if (RAMP_RUNINFO != what && (RAMP_INSTRUMENT != what) && (arg > m_runInfo->m_data.scanCount || arg < 1)) {
168 
-     return (NULL);
169 
-   }
170 
-
171 
-   if (m_scanOffsets || (RAMP_RUNINFO == what) || (RAMP_INSTRUMENT == what)) {
172 
-      ramp_fileoffset_t scanOffset=-1;
173 
-      if (RAMP_RUNINFO == what || RAMP_INSTRUMENT == what) {
174 
-	scanOffset = 0; // read from head of file
175 
-      } else {
176 
-	scanOffset = m_scanOffsets[arg]; // ramp is one-based
177 
-      }
178 
-
179 
-      if (scanOffset >= 0) {
180 
-
181 
-         // -----------------------------------------------------------------------
182 
-         // And now we can parse the info we were looking for
183 
-         // -----------------------------------------------------------------------
184 
-
185 
-
186 
-         // Ok now we have to copy everything in our structure
187 
-         switch( what )
188 
-         {
189 
-         case RAMP_RUNINFO:
190 
-	   //	   std::cerr << "in: rampRunInfo( m_handle )\n";
191 
-            returnPtr = new rampRunInfo( m_handle );
192 
-	    //  std::cerr << "out: rampRunInfo( m_handle )\n";
193 
-            break;
194 
-         case RAMP_HEADER:
195 
-	   //  std::cerr <<  "in: rampScanInfo( m_handle, scanOffset, (int)arg )\n" ;
196 
-            returnPtr = new rampScanInfo( m_handle, scanOffset, (int)arg );
197 
-	    //std::cerr <<  "out: rampScanInfo( m_handle, scanOffset, (int)arg )\n" ;
198 
-            if (returnPtr) {
199 
-#ifdef HAVE_PWIZ_MZML_LIB
200 
-			   if (!m_handle->mzML) // rampadapter already set this for us
201 
-#endif
202 
-              ((rampScanInfo *)returnPtr)->m_data.filePosition = scanOffset; // for future reference
203 
-
204 
-              // HENRY -- error checking here
205 
-              if (((rampScanInfo*)returnPtr)->m_data.acquisitionNum < 0) {
206 
-                // something failed in RAMP, possibly because it's a missing scan
207 
-                delete ((rampScanInfo*)returnPtr);
208 
-                returnPtr = NULL;
209 
-              }
119 
+
120 
+    switch( what )
121 
+    {
122 
+    case RAMP_RUNINFO:
123 
+    case RAMP_HEADER:
124 
+    case RAMP_PEAKS:
125 
+    case RAMP_INSTRUMENT:
126 
+        break; // OK
127 
+    default:
128 
+        Rf_error("unknown read type!\n");
129 
+        return NULL;
130 
+        break;
131 
+    }
132 
+
133 
+    rampInfo* returnPtr=NULL;
134 
+
135 
+    if ((RAMP_RUNINFO != what) && (RAMP_INSTRUMENT != what) && !m_scanOffsets)
136 
+    {
137 
+        int iLastScan = 0;
138 
+        // we need the index to get anything besides the header
139 
+        //      std::cerr << "in: getIndexOffset(m_handle);!\n";
140 
+        ramp_fileoffset_t indexOffset = getIndexOffset(m_handle);
141 
+        //      std::cerr << "out: getIndexOffset(m_handle);!\n";
142 
+
143 
+        // std::cerr << "in: readIndex();!\n";
144 
+        m_scanOffsets = readIndex(m_handle, indexOffset, &iLastScan);
145 
+        //std::cerr << "out: readIndex();!\n";
146 
+        if (iLastScan >= m_runInfo->m_data.scanCount)
147 
+        {
148 
+            if (!m_declaredScansOnly)
149 
+            {
150 
+                m_runInfo->m_data.scanCount = iLastScan;
210 151 
             }
211 
-            break;
212 
-         case RAMP_PEAKS:
213 
-            returnPtr = new rampPeakList( m_handle, scanOffset);
214 
-
215 
-            // HENRY -- error checking here
216 
-            if (returnPtr && ((rampPeakList*)returnPtr)->getPeakCount() <= 0) {
217 
-              // something failed in RAMP, possibly because it's a missing scan
218 
-              delete ((rampPeakList*)returnPtr);
219 
-              returnPtr = NULL;
152 
+            else     // get rid of all the fake entries created
153 
+            {
154 
+
155 
+                //  std::cerr << "get rid of all the fake entries created\n";
156 
+                for (int n=1; n<=iLastScan; n++) // ramp is 1 based
157 
+                {
158 
+                    if (m_scanOffsets[n]==-1)
159 
+                    {
160 
+                        // find a run of fakes
161 
+                        int m;
162 
+                        for (m=n+1; (m<=iLastScan)&&(m_scanOffsets[m]==-1); m++);
163 
+                        if (m<=iLastScan)
164 
+                        {
165 
+                            memmove(m_scanOffsets+n,m_scanOffsets+m,
166 
+                                    sizeof(ramp_fileoffset_t)*((iLastScan-m)+1));
167 
+                        }
168 
+                        iLastScan-=(m-n);
169 
+                    }
170 
+                }
220 171 
             }
221 
-            break;
222 
-
223 
-         // HENRY -- add the instrument info reading functionality (present in RAMP, but not provided in cRAMP before)
224 
-         case RAMP_INSTRUMENT:
225 
-	   //	   std::cerr <<  "in: rampInstrumentInfo(m_handle)\n" ;
226 
-            returnPtr = new rampInstrumentInfo(m_handle);
227 
-	    //std::cerr <<  "out: rampInstrumentInfo(m_handle)\n" ;
228 
-            if (((rampInstrumentInfo*)returnPtr)->m_instrumentStructPtr == NULL) {
229 
-              delete ((rampInstrumentInfo*)returnPtr);
230 
-              returnPtr = NULL;
172 
+        }
173 
+        // HENRY - store last scan explicitly.
174 
+        m_lastScan = iLastScan;
175 
+        // END HENRY
176 
+    }
177 
+
178 
+
179 
+    // HENRY -- arg is out of bounds. instead of creating havoc in RAMP, let's just kill it here.
180 
+    if (RAMP_RUNINFO != what && (RAMP_INSTRUMENT != what) && (arg > m_runInfo->m_data.scanCount || arg < 1))
181 
+    {
182 
+        return (NULL);
183 
+    }
184 
+
185 
+    if (m_scanOffsets || (RAMP_RUNINFO == what) || (RAMP_INSTRUMENT == what))
186 
+    {
187 
+        ramp_fileoffset_t scanOffset=-1;
188 
+        if (RAMP_RUNINFO == what || RAMP_INSTRUMENT == what)
189 
+        {
190 
+            scanOffset = 0; // read from head of file
191 
+        }
192 
+        else
193 
+        {
194 
+            scanOffset = m_scanOffsets[arg]; // ramp is one-based
195 
+        }
196 
+
197 
+        if (scanOffset >= 0)
198 
+        {
199 
+
200 
+            // -----------------------------------------------------------------------
201 
+            // And now we can parse the info we were looking for
202 
+            // -----------------------------------------------------------------------
203 
+
204 
+
205 
+            // Ok now we have to copy everything in our structure
206 
+            switch( what )
207 
+            {
208 
+            case RAMP_RUNINFO:
209 
+                //	   std::cerr << "in: rampRunInfo( m_handle )\n";
210 
+                returnPtr = new rampRunInfo( m_handle );
211 
+                //  std::cerr << "out: rampRunInfo( m_handle )\n";
212 
+                break;
213 
+            case RAMP_HEADER:
214 
+                //  std::cerr <<  "in: rampScanInfo( m_handle, scanOffset, (int)arg )\n" ;
215 
+                returnPtr = new rampScanInfo( m_handle, scanOffset, (int)arg );
216 
+                //std::cerr <<  "out: rampScanInfo( m_handle, scanOffset, (int)arg )\n" ;
217 
+                if (returnPtr)
218 
+                {
219 
+#ifdef HAVE_PWIZ_MZML_LIB
220 
+                    if (!m_handle->mzML) // rampadapter already set this for us
221 
+#endif
222 
+                        ((rampScanInfo *)returnPtr)->m_data.filePosition = scanOffset; // for future reference
223 
+
224 
+                    // HENRY -- error checking here
225 
+                    if (((rampScanInfo*)returnPtr)->m_data.acquisitionNum < 0)
226 
+                    {
227 
+                        // something failed in RAMP, possibly because it's a missing scan
228 
+                        delete ((rampScanInfo*)returnPtr);
229 
+                        returnPtr = NULL;
230 
+                    }
231 
+                }
232 
+                break;
233 
+            case RAMP_PEAKS:
234 
+                returnPtr = new rampPeakList( m_handle, scanOffset);
235 
+
236 
+                // HENRY -- error checking here
237 
+                if (returnPtr && ((rampPeakList*)returnPtr)->getPeakCount() <= 0)
238 
+                {
239 
+                    // something failed in RAMP, possibly because it's a missing scan
240 
+                    delete ((rampPeakList*)returnPtr);
241 
+                    returnPtr = NULL;
242 
+                }
243 
+                break;
244 
+
245 
+                // HENRY -- add the instrument info reading functionality (present in RAMP, but not provided in cRAMP before)
246 
+            case RAMP_INSTRUMENT:
247 
+                //	   std::cerr <<  "in: rampInstrumentInfo(m_handle)\n" ;
248 
+                returnPtr = new rampInstrumentInfo(m_handle);
249 
+                //std::cerr <<  "out: rampInstrumentInfo(m_handle)\n" ;
250 
+                if (((rampInstrumentInfo*)returnPtr)->m_instrumentStructPtr == NULL)
251 
+                {
252 
+                    delete ((rampInstrumentInfo*)returnPtr);
253 
+                    returnPtr = NULL;
254 
+                }
255 
+                break;
231 256 
             }
232 
-            break;
233 
-         }
234 
-
235 
-      }
236 
-   }
237 
-
238 
-
239 
-
240 
-   return returnPtr;
257 
+
258 
+        }
259 
+    }
260 
+
261 
+
262 
+
263 
+    return returnPtr;
241 264 
 }
242 265
243 266
244 267 
 /**
245 268 
  * This function performs a non-sequential parsing operation on an indexed
246 
- * msxml file to obtain minimal info on the msRun contained in the file.
269 
+ * msxml file to obtain minimal info on the msRun contained in the file.
247 270
248 271 
  *
249 272 
  * @return rapRunInfo* is dynamically allocate and becomes property of the caller, who
250 273 
  *         is responsible for its deallocation!!
251 274 
  */
252 275
253 
-rampRunInfo* cRamp::getRunInfo (  ) {
254 
-   rampRunInfo* result;
255 
-   if (m_runInfo) { // did we derive this already?
256 
-      result = new rampRunInfo(*m_runInfo);
257 
-   } else {
258 
-      result = (rampRunInfo*) do_ramp(0, RAMP_RUNINFO);
259 
-   }
260 
-   return result;
276 
+rampRunInfo* cRamp::getRunInfo (  )
277 
+{
278 
+    rampRunInfo* result;
279 
+    if (m_runInfo)   // did we derive this already?
280 
+    {
281 
+        result = new rampRunInfo(*m_runInfo);
282 
+    }
283 
+    else
284 
+    {
285 
+        result = (rampRunInfo*) do_ramp(0, RAMP_RUNINFO);
286 
+    }
287 
+    return result;
261 288 
 }
262 289
263 290 
 /**
264 291 
  * This function performs a non-sequential parsing operation on an indexed
265 
- * msxml file to obtain minimal header info for a numbered scan (thus minimizing parse time).
292 
+ * msxml file to obtain minimal header info for a numbered scan (thus minimizing parse time).
266 293 
  *
267 294 
  * @param fileName: Name of the msxml file
268 295 
  * @param startSCan: Number of the scan we want to read from
... ... 
@@ -270,8 +297,9 @@ rampRunInfo* cRamp::getRunInfo (  ) {
270 297 
  *         is responsible for its deallocation!! returns just the minimal header info num, msLevel and retentionTime
271 298 
  */
272 299
273 
-rampScanInfo* cRamp::getScanHeaderInfo ( int whichScan  ) {
274 
-   return (rampScanInfo*) do_ramp((ramp_fileoffset_t)whichScan, RAMP_HEADER);
300 
+rampScanInfo* cRamp::getScanHeaderInfo ( int whichScan  )
301 
+{
302 
+    return (rampScanInfo*) do_ramp((ramp_fileoffset_t)whichScan, RAMP_HEADER);
275 303 
 }
276 304
277 305
... ... 
@@ -285,79 +313,90 @@ rampScanInfo* cRamp::getScanHeaderInfo ( int whichScan  ) {
285 313 
  *         is responsible for its deallocation!! returns everything found in scan, precursorMz and peaks
286 314 
  */
287 315
288 
-rampPeakList* cRamp::getPeakList ( int whichScan ) {
289 
-   return (rampPeakList*) do_ramp((ramp_fileoffset_t)whichScan, RAMP_PEAKS);
316 
+rampPeakList* cRamp::getPeakList ( int whichScan )
317 
+{
318 
+    return (rampPeakList*) do_ramp((ramp_fileoffset_t)whichScan, RAMP_PEAKS);
290 319 
 }
291 320
292 321 
 // HENRY - provides instrument info getting method
293 
-rampInstrumentInfo* cRamp::getInstrumentInfo () {
294 
-  return (rampInstrumentInfo*) do_ramp(0, RAMP_INSTRUMENT);
322 
+rampInstrumentInfo* cRamp::getInstrumentInfo ()
323 
+{
324 
+    return (rampInstrumentInfo*) do_ramp(0, RAMP_INSTRUMENT);
295 325 
 }
296 326 
 // END HENRY
297 327
298 328
299 329 
 // HENRY - sequential access parser that skips over missing scans. This version only reads scan header.
300 
-bool cRampIterator::nextScan(rampScanInfo** scanInfo) {
301 
-	while (++m_currentScan <= m_cramp.getLastScan() && m_cramp.getScanOffset(m_currentScan) <= 0);
302 
-  if (m_currentScan > m_cramp.getLastScan()) {
303 
-    return (false);
304 
-  }
305 
-
306 
-  *scanInfo = (rampScanInfo*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_HEADER);
307 
-  return (true);
330 
+bool cRampIterator::nextScan(rampScanInfo** scanInfo)
331 
+{
332 
+    while (++m_currentScan <= m_cramp.getLastScan() && m_cramp.getScanOffset(m_currentScan) <= 0);
333 
+    if (m_currentScan > m_cramp.getLastScan())
334 
+    {
335 
+        return (false);
336 
+    }
337 
+
338 
+    *scanInfo = (rampScanInfo*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_HEADER);
339 
+    return (true);
308 340 
 }
309 341 
 // END HENRY
310 342
311 343 
 // HENRY - sequential access parser that skips over missing scans. This version reads both scan header and peak list.
312 
-bool cRampIterator::nextScan(rampScanInfo** scanInfo, rampPeakList** peakList) {
313 
-  while (++m_currentScan <= m_cramp.getLastScan() && m_cramp.getScanOffset(m_currentScan) <= 0);
314 
-  if (m_currentScan > m_cramp.getLastScan()) {
315 
-    return (false);
316 
-  }
317 
-
318 
-  *scanInfo = (rampScanInfo*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_HEADER);
319 
-  *peakList = (rampPeakList*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_PEAKS);
344 
+bool cRampIterator::nextScan(rampScanInfo** scanInfo, rampPeakList** peakList)
345 
+{
346 
+    while (++m_currentScan <= m_cramp.getLastScan() && m_cramp.getScanOffset(m_currentScan) <= 0);
347 
+    if (m_currentScan > m_cramp.getLastScan())
348 
+    {
349 
+        return (false);
350 
+    }
351 
+
352 
+    *scanInfo = (rampScanInfo*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_HEADER);
353 
+    *peakList = (rampPeakList*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_PEAKS);
320 354
321 
-  return (true);
355 
+    return (true);
322 356
323 357 
 }
324 358 
 // END HENRY
325 359
326 360 
 // HENRY - resets the sequential access parser to the first scan.
327 
-void cRampIterator::reset() {
328 
-  m_currentScan = 1;
361 
+void cRampIterator::reset()
362 
+{
363 
+    m_currentScan = 1;
329 364 
 }
330 365 
 // END HENRY
331 366
332 367 
 /**
333 368 
  * populate from a file handle
334 369 
  **/
335 
-rampPeakList::rampPeakList(RAMPFILE *handle, ramp_fileoffset_t index) {
336 
-   init();
337 
-   m_peaksCount = readPeaksCount(handle,index);
338 
-   m_pPeaks = (rampPeakInfoStruct *)readPeaks(handle,index);
370 
+rampPeakList::rampPeakList(RAMPFILE *handle, ramp_fileoffset_t index)
371 
+{
372 
+    init();
373 
+    m_peaksCount = readPeaksCount(handle,index);
374 
+    m_pPeaks = (rampPeakInfoStruct *)readPeaks(handle,index);
339 375 
 }
340 376
341 377 
 /**
342 378 
  * populate from a file handle
343 379 
  **/
344 
-rampScanInfo::rampScanInfo(RAMPFILE *handle, ramp_fileoffset_t index, int seqNum) {
345 
-   init();
346 
-   readHeader(handle,index,&m_data);
347 
-   m_data.seqNum = seqNum;
380 
+rampScanInfo::rampScanInfo(RAMPFILE *handle, ramp_fileoffset_t index, int seqNum)
381 
+{
382 
+    init();
383 
+    readHeader(handle,index,&m_data);
384 
+    m_data.seqNum = seqNum;
348 385 
 }
349 386
350 387 
 /**
351 388 
  * populate from a file handle
352 389 
  **/
353 
-rampRunInfo::rampRunInfo(RAMPFILE *handle) {
354 
-   init();
355 
-   readMSRun(handle,&m_data);
390 
+rampRunInfo::rampRunInfo(RAMPFILE *handle)
391 
+{
392 
+    init();
393 
+    readMSRun(handle,&m_data);
356 394 
 }
357 395
358 396 
 // HENRY - provides instrument info reading functionality
359 
-rampInstrumentInfo::rampInstrumentInfo(RAMPFILE *handle) {
360 
-  init();
361 
-  m_instrumentStructPtr = getInstrumentStruct(handle);
397 
+rampInstrumentInfo::rampInstrumentInfo(RAMPFILE *handle)
398 
+{
399 
+    init();
400 
+    m_instrumentStructPtr = getInstrumentStruct(handle);
362 401 
 }
363 402 
 // END HENRY
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 967ff13a84539345f77c75211d0c204a3f3d0edc
Commit message: good job everybody
Committed by: Laurent
Author Name: Laurent
Commit date: 2014-06-22 06:54:49 +0100
Author date: 2014-06-22 06:54:49 +0100



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@91685 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 22/06/2014 05:56:07
Showing1 changed files
src/cramp.cpp
History View file @252028c226
... ... 
@@ -1,7 +1,7 @@
1 1 
 /***************************************************************************
2 2 
 cramp.cpp
3 3
4 
-/***************************************************************************
4 
+***************************************************************************
5 5 
 cramp.hpp -- renamed cramp.h to avoid R checker warning
6 6
7 7 
   A C++ wrapper for the RAMP code.
... ... 
@@ -28,7 +28,16 @@ cramp.hpp -- renamed cramp.h to avoid R checker warning
28 28 
 *																								  *
29 29 
 ***************************************************************************/
30 30
31 
+#include<Rcpp.h>
31 32
33 
+// Taken from http://tolstoy.newcastle.edu.au/R/e2/devel/06/11/1242.html
34 
+// and http://stackoverflow.com/questions/11588765/using-rcpp-with-windows-specific-includes
35 
+// Undefine the Realloc macro, which is defined by both R and by Windows stuff
36 
+// Also need to undefine the Free macro
37 
+#if defined(__MINGW32__)
38 
+#undef Realloc
39 
+#undef Free
40 
+#endif
32 41
33 42 
 #include <stdlib.h>
34 43 
 #include <iostream>
... ... 
@@ -40,6 +49,10 @@ cramp.hpp -- renamed cramp.h to avoid R checker warning
40 49 
 #include "cramp.h"
41 50 
 #include<R.h>
42 51
52 
+#if defined(__MINGW32__)
53 
+#include <windows.h>
54 
+#endif
55 
+
43 56 
 /**
44 57 
  * This function performs a non-sequential parsing operation on an indexed
45 58 
  * msxml file.
Browse code

First batch of src printf/cout/cerr cleanup

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@71124 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 12/11/2012 07:29:06
Showing1 changed files
src/cramp.cpp
History View file @4fc5d31294
... ... 
@@ -38,7 +38,7 @@ cramp.hpp -- renamed cramp.h to avoid R checker warning
38 38 
 #include "sys/errno.h"
39 39 
 #endif
40 40 
 #include "cramp.h"
41 
-
41 
+#include<R.h>
42 42
43 43 
 /**
44 44 
  * This function performs a non-sequential parsing operation on an indexed
... ... 
@@ -107,7 +107,7 @@ rampInfo* cRamp::do_ramp( ramp_fileoffset_t arg , eWhatToRead	what )
107 107 
    case RAMP_INSTRUMENT:
108 108 
       break; // OK
109 109 
    default:
110 
-	  std::cerr << "unknown read type!\n";
110 
+     Rf_error("unknown read type!\n");
111 111 
       return NULL;
112 112 
       break;
113 113 
    }
Browse code

Added changelog entry

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@63259 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 28/02/2012 21:53:20
Showing1 changed files
src/cramp.cpp
History View file @19be0c64f0
... ... 
@@ -117,12 +117,19 @@ rampInfo* cRamp::do_ramp( ramp_fileoffset_t arg , eWhatToRead	what )
117 117 
    if ((RAMP_RUNINFO != what) && (RAMP_INSTRUMENT != what) && !m_scanOffsets) {
118 118 
       int iLastScan = 0;
119 119 
      // we need the index to get anything besides the header
120 
+      //      std::cerr << "in: getIndexOffset(m_handle);!\n";
120 121 
       ramp_fileoffset_t indexOffset = getIndexOffset(m_handle);
122 
+      //      std::cerr << "out: getIndexOffset(m_handle);!\n";
123 
+
124 
+      // std::cerr << "in: readIndex();!\n";
121 125 
       m_scanOffsets = readIndex(m_handle, indexOffset, &iLastScan);
126 
+      //std::cerr << "out: readIndex();!\n";
122 127 
       if (iLastScan >= m_runInfo->m_data.scanCount) {
123 128 
 		 if (!m_declaredScansOnly) {
124 129 
            m_runInfo->m_data.scanCount = iLastScan;
125 130 
 		 } else { // get rid of all the fake entries created
131 
+
132 
+		   //  std::cerr << "get rid of all the fake entries created\n";
126 133 
 			 for (int n=1;n<=iLastScan;n++) { // ramp is 1 based
127 134 
 				 if (m_scanOffsets[n]==-1) {
128 135 
 					// find a run of fakes
... ... 
@@ -167,10 +174,14 @@ rampInfo* cRamp::do_ramp( ramp_fileoffset_t arg , eWhatToRead	what )
167 174 
          switch( what )
168 175 
          {
169 176 
          case RAMP_RUNINFO:
177 
+	   //	   std::cerr << "in: rampRunInfo( m_handle )\n";
170 178 
             returnPtr = new rampRunInfo( m_handle );
179 
+	    //  std::cerr << "out: rampRunInfo( m_handle )\n";
171 180 
             break;
172 181 
          case RAMP_HEADER:
182 
+	   //  std::cerr <<  "in: rampScanInfo( m_handle, scanOffset, (int)arg )\n" ;
173 183 
             returnPtr = new rampScanInfo( m_handle, scanOffset, (int)arg );
184 
+	    //std::cerr <<  "out: rampScanInfo( m_handle, scanOffset, (int)arg )\n" ;
174 185 
             if (returnPtr) {
175 186 
 #ifdef HAVE_PWIZ_MZML_LIB
176 187 
 			   if (!m_handle->mzML) // rampadapter already set this for us
... ... 
@@ -198,7 +209,9 @@ rampInfo* cRamp::do_ramp( ramp_fileoffset_t arg , eWhatToRead	what )
198 209
199 210 
          // HENRY -- add the instrument info reading functionality (present in RAMP, but not provided in cRAMP before)
200 211 
          case RAMP_INSTRUMENT:
212 
+	   //	   std::cerr <<  "in: rampInstrumentInfo(m_handle)\n" ;
201 213 
             returnPtr = new rampInstrumentInfo(m_handle);
214 
+	    //std::cerr <<  "out: rampInstrumentInfo(m_handle)\n" ;
202 215 
             if (((rampInstrumentInfo*)returnPtr)->m_instrumentStructPtr == NULL) {
203 216 
               delete ((rampInstrumentInfo*)returnPtr);
204 217 
               returnPtr = NULL;
Browse code

Added the mzR package to the repository.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@57456 bc3139a8-67e5-0310-9ffc-ced21a209358

c.wong authored on 15/08/2011 19:53:29
Showing1 changed files
src/cramp.cpp
History View file @bcff5d52a8
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,337 @@
1 
+/***************************************************************************
2 
+cramp.cpp
3 
+
4 
+/***************************************************************************
5 
+cramp.hpp -- renamed cramp.h to avoid R checker warning
6 
+
7 
+  A C++ wrapper for the RAMP code.
8 
+
9 
+  Use this library to parse an mzXML file in a non-sequential way, by
10 
+  taking advantage of the index element.
11 
+
12 
+  (C) 2004 by Brian Pratt, Insilicos LLC
13 
+
14 
+  Based on mzXML2Other, which has this copyright:
15 
+	 -------------------
16 
+	 begin					 : Wed Apr 2
17 
+	 copyright				 : (C) 2002 by Pedrioli Patrick, ISB, Proteomics
18 
+	 email					 : ppatrick@student.ethz.ch
19 
+ ***************************************************************************/
20 
+
21 
+/***************************************************************************
22 
+*																								  *
23 
+*	 This program is free software; you can redistribute it and/or modify  *
24 
+*	 it under the terms of the GNU Library or "Lesser" General Public 	  *
25 
+*	 License (LGPL) as published by the Free Software Foundation;			  *
26 
+*	 either version 2 of the License, or (at your option) any later		  *
27 
+*	 version.																				  *
28 
+*																								  *
29 
+***************************************************************************/
30 
+
31 
+
32 
+
33 
+#include <stdlib.h>
34 
+#include <iostream>
35 
+#include <fstream>
36 
+#include "stdio.h"
37 
+#if !defined(_MSC_VER) && !defined(__MINGW32__)
38 
+#include "sys/errno.h"
39 
+#endif
40 
+#include "cramp.h"
41 
+
42 
+
43 
+/**
44 
+ * This function performs a non-sequential parsing operation on an indexed
45 
+ * msxml file.
46 
+ *
47 
+ * @param fileName: Name of the msxml file
48 
+ * @param startSCan: Number of the scan we want to read from
49 
+ * @param what: -HEADER will return num, msLevel and retentionTime
50 
+ *              -SCAN will return only the peaks
51 
+ *              -ALL will return everything found in scan, precursorMz and peaks
52 
+ *
53 
+ * @return pData is dynamically allocate and becomes property of the caller, who
54 
+ *         is responsible for its deallocation!!
55 
+ */
56 
+
57 
+
58 
+
59 
+cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
60 
+  m_filename(fileName), m_declaredScansOnly(declaredScansOnly), m_runInfo()
61 
+{
62 
+   m_handle = rampOpenFile(fileName);
63 
+   m_scanOffsets = NULL;
64 
+   m_runInfo = NULL;
65 
+   m_lastScan = 0;
66 
+   if (!OK()) {
67 
+     // HENRY -- I would prefer this to be silent, and let the caller deals with it
68 
+     // cout << "Error: Could not open file " << fileName << ": " << strerror(errno) << endl;
69 
+     // END HENRY
70 
+   } else {
71 
+
72 
+      m_runInfo = getRunInfo();
73 
+
74 
+      // HENRY -- always read index to set scan count, since scan count
75 
+      // declared at the top of the mzXML file is unreliable now that
76 
+      // there are missing scans.
77 
+      // This will also set the structs m_scanOffsets, and the value m_lastScan
78 
+
79 
+      //      if (m_runInfo->m_data.scanCount < 0) { // undeclared scan count
80 
+         // this will provoke reading of index, which sets scan count
81 
+         rampScanInfo* tmp = getScanHeaderInfo ( 1 );
82 
+         free(tmp);
83 
+	 // }
84 
+      // END HENRY
85 
+   }
86 
+}
87 
+
88 
+cRamp::~cRamp() {
89 
+   rampCloseFile(m_handle);
90 
+
91 
+   // NB: these pointers may be null on file open failure,
92 
+   // but free/delete of NULL is OK per C++ standard
93 
+   free(m_scanOffsets);
94 
+   delete m_runInfo; // was free() - but allocated with new
95 
+}
96 
+
97 
+//
98 
+// here are the private guts
99 
+//
100 
+rampInfo* cRamp::do_ramp( ramp_fileoffset_t arg , eWhatToRead	what )
101 
+{
102 
+
103 
+   switch( what ) {
104 
+   case RAMP_RUNINFO:
105 
+   case RAMP_HEADER:
106 
+   case RAMP_PEAKS:
107 
+   case RAMP_INSTRUMENT:
108 
+      break; // OK
109 
+   default:
110 
+	  std::cerr << "unknown read type!\n";
111 
+      return NULL;
112 
+      break;
113 
+   }
114 
+
115 
+   rampInfo* returnPtr=NULL;
116 
+
117 
+   if ((RAMP_RUNINFO != what) && (RAMP_INSTRUMENT != what) && !m_scanOffsets) {
118 
+      int iLastScan = 0;
119 
+     // we need the index to get anything besides the header
120 
+      ramp_fileoffset_t indexOffset = getIndexOffset(m_handle);
121 
+      m_scanOffsets = readIndex(m_handle, indexOffset, &iLastScan);
122 
+      if (iLastScan >= m_runInfo->m_data.scanCount) {
123 
+		 if (!m_declaredScansOnly) {
124 
+           m_runInfo->m_data.scanCount = iLastScan;
125 
+		 } else { // get rid of all the fake entries created
126 
+			 for (int n=1;n<=iLastScan;n++) { // ramp is 1 based
127 
+				 if (m_scanOffsets[n]==-1) {
128 
+					// find a run of fakes
129 
+				    int m;
130 
+					for (m=n+1;(m<=iLastScan)&&(m_scanOffsets[m]==-1);m++);
131 
+					if (m<=iLastScan) {
132 
+						memmove(m_scanOffsets+n,m_scanOffsets+m,
133 
+						  sizeof(ramp_fileoffset_t)*((iLastScan-m)+1));
134 
+					}
135 
+					iLastScan-=(m-n);
136 
+				 }
137 
+			 }
138 
+		 }
139 
+      }
140 
+      // HENRY - store last scan explicitly.
141 
+      m_lastScan = iLastScan;
142 
+      // END HENRY
143 
+   }
144 
+
145 
+
146 
+   // HENRY -- arg is out of bounds. instead of creating havoc in RAMP, let's just kill it here.
147 
+   if (RAMP_RUNINFO != what && (RAMP_INSTRUMENT != what) && (arg > m_runInfo->m_data.scanCount || arg < 1)) {
148 
+     return (NULL);
149 
+   }
150 
+
151 
+   if (m_scanOffsets || (RAMP_RUNINFO == what) || (RAMP_INSTRUMENT == what)) {
152 
+      ramp_fileoffset_t scanOffset=-1;
153 
+      if (RAMP_RUNINFO == what || RAMP_INSTRUMENT == what) {
154 
+	scanOffset = 0; // read from head of file
155 
+      } else {
156 
+	scanOffset = m_scanOffsets[arg]; // ramp is one-based
157 
+      }
158 
+
159 
+      if (scanOffset >= 0) {
160 
+
161 
+         // -----------------------------------------------------------------------
162 
+         // And now we can parse the info we were looking for
163 
+         // -----------------------------------------------------------------------
164 
+
165 
+
166 
+         // Ok now we have to copy everything in our structure
167 
+         switch( what )
168 
+         {
169 
+         case RAMP_RUNINFO:
170 
+            returnPtr = new rampRunInfo( m_handle );
171 
+            break;
172 
+         case RAMP_HEADER:
173 
+            returnPtr = new rampScanInfo( m_handle, scanOffset, (int)arg );
174 
+            if (returnPtr) {
175 
+#ifdef HAVE_PWIZ_MZML_LIB
176 
+			   if (!m_handle->mzML) // rampadapter already set this for us
177 
+#endif
178 
+              ((rampScanInfo *)returnPtr)->m_data.filePosition = scanOffset; // for future reference
179 
+
180 
+              // HENRY -- error checking here
181 
+              if (((rampScanInfo*)returnPtr)->m_data.acquisitionNum < 0) {
182 
+                // something failed in RAMP, possibly because it's a missing scan
183 
+                delete ((rampScanInfo*)returnPtr);
184 
+                returnPtr = NULL;
185 
+              }
186 
+            }
187 
+            break;
188 
+         case RAMP_PEAKS:
189 
+            returnPtr = new rampPeakList( m_handle, scanOffset);
190 
+
191 
+            // HENRY -- error checking here
192 
+            if (returnPtr && ((rampPeakList*)returnPtr)->getPeakCount() <= 0) {
193 
+              // something failed in RAMP, possibly because it's a missing scan
194 
+              delete ((rampPeakList*)returnPtr);
195 
+              returnPtr = NULL;
196 
+            }
197 
+            break;
198 
+
199 
+         // HENRY -- add the instrument info reading functionality (present in RAMP, but not provided in cRAMP before)
200 
+         case RAMP_INSTRUMENT:
201 
+            returnPtr = new rampInstrumentInfo(m_handle);
202 
+            if (((rampInstrumentInfo*)returnPtr)->m_instrumentStructPtr == NULL) {
203 
+              delete ((rampInstrumentInfo*)returnPtr);
204 
+              returnPtr = NULL;
205 
+            }
206 
+            break;
207 
+         }
208 
+
209 
+      }
210 
+   }
211 
+
212 
+
213 
+
214 
+   return returnPtr;
215 
+}
216 
+
217 
+
218 
+/**
219 
+ * This function performs a non-sequential parsing operation on an indexed
220 
+ * msxml file to obtain minimal info on the msRun contained in the file.
221 
+
222 
+ *
223 
+ * @return rapRunInfo* is dynamically allocate and becomes property of the caller, who
224 
+ *         is responsible for its deallocation!!
225 
+ */
226 
+
227 
+rampRunInfo* cRamp::getRunInfo (  ) {
228 
+   rampRunInfo* result;
229 
+   if (m_runInfo) { // did we derive this already?
230 
+      result = new rampRunInfo(*m_runInfo);
231 
+   } else {
232 
+      result = (rampRunInfo*) do_ramp(0, RAMP_RUNINFO);
233 
+   }
234 
+   return result;
235 
+}
236 
+
237 
+/**
238 
+ * This function performs a non-sequential parsing operation on an indexed
239 
+ * msxml file to obtain minimal header info for a numbered scan (thus minimizing parse time).
240 
+ *
241 
+ * @param fileName: Name of the msxml file
242 
+ * @param startSCan: Number of the scan we want to read from
243 
+ * @return rapHeaderInfo* is dynamically allocate and becomes property of the caller, who
244 
+ *         is responsible for its deallocation!! returns just the minimal header info num, msLevel and retentionTime
245 
+ */
246 
+
247 
+rampScanInfo* cRamp::getScanHeaderInfo ( int whichScan  ) {
248 
+   return (rampScanInfo*) do_ramp((ramp_fileoffset_t)whichScan, RAMP_HEADER);
249 
+}
250 
+
251 
+
252 
+/**
253 
+ * This function performs a non-sequential parsing operation on an indexed
254 
+ * msxml file to obtain peak info for a numbered scan.
255 
+ *
256 
+ * @param fileName: Name of the msxml file
257 
+ * @param startSCan: Number of the scan we want to read from
258 
+ * @return rapPeakList* is dynamically allocate and becomes property of the caller, who
259 
+ *         is responsible for its deallocation!! returns everything found in scan, precursorMz and peaks
260 
+ */
261 
+
262 
+rampPeakList* cRamp::getPeakList ( int whichScan ) {
263 
+   return (rampPeakList*) do_ramp((ramp_fileoffset_t)whichScan, RAMP_PEAKS);
264 
+}
265 
+
266 
+// HENRY - provides instrument info getting method
267 
+rampInstrumentInfo* cRamp::getInstrumentInfo () {
268 
+  return (rampInstrumentInfo*) do_ramp(0, RAMP_INSTRUMENT);
269 
+}
270 
+// END HENRY
271 
+
272 
+
273 
+// HENRY - sequential access parser that skips over missing scans. This version only reads scan header.
274 
+bool cRampIterator::nextScan(rampScanInfo** scanInfo) {
275 
+	while (++m_currentScan <= m_cramp.getLastScan() && m_cramp.getScanOffset(m_currentScan) <= 0);
276 
+  if (m_currentScan > m_cramp.getLastScan()) {
277 
+    return (false);
278 
+  }