Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
Showing1 changed files
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deleted file mode 100644
... ...
@@ -1,402 +0,0 @@
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-/***************************************************************************
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-cramp.cpp
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-
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-***************************************************************************
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-cramp.hpp -- renamed cramp.h to avoid R checker warning
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-
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-  A C++ wrapper for the RAMP code.
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-
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-  Use this library to parse an mzXML file in a non-sequential way, by
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-  taking advantage of the index element.
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-
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-  (C) 2004 by Brian Pratt, Insilicos LLC
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-
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-  Based on mzXML2Other, which has this copyright:
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-	 -------------------
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-	 begin					 : Wed Apr 2
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-	 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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-
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-/***************************************************************************
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-*																								  *
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-*	 This program is free software; you can redistribute it and/or modify  *
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-*	 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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-***************************************************************************/
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-
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-#include<Rcpp.h>
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-
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-// Taken from http://tolstoy.newcastle.edu.au/R/e2/devel/06/11/1242.html
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-// 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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-
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-#if defined(__MINGW32__)
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-#include <windows.h>
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-#endif
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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.
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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  )
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-{
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-    return (rampScanInfo*) do_ramp((ramp_fileoffset_t)whichScan, RAMP_HEADER);
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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 peak info for a numbered scan.
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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 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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- */
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-
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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);
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-}
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-
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-// HENRY - provides instrument info getting method
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-rampInstrumentInfo* cRamp::getInstrumentInfo ()
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-{
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-    return (rampInstrumentInfo*) do_ramp(0, RAMP_INSTRUMENT);
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-}
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-// END HENRY
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-
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-
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-// HENRY - sequential access parser that skips over missing scans. This version only reads scan header.
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-bool cRampIterator::nextScan(rampScanInfo** scanInfo)
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-{
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-    while (++m_currentScan <= m_cramp.getLastScan() && m_cramp.getScanOffset(m_currentScan) <= 0);
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-    if (m_currentScan > m_cramp.getLastScan())
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-    {
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-        return (false);
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-    }
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-
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-    *scanInfo = (rampScanInfo*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_HEADER);
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-    return (true);
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-}
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-// END HENRY
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-
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-// HENRY - sequential access parser that skips over missing scans. This version reads both scan header and peak list.
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-bool cRampIterator::nextScan(rampScanInfo** scanInfo, rampPeakList** peakList)
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-{
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-    while (++m_currentScan <= m_cramp.getLastScan() && m_cramp.getScanOffset(m_currentScan) <= 0);
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-    if (m_currentScan > m_cramp.getLastScan())
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-    {
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-        return (false);
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-    }
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-
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-    *scanInfo = (rampScanInfo*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_HEADER);
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-    *peakList = (rampPeakList*)m_cramp.do_ramp((ramp_fileoffset_t)(m_currentScan), RAMP_PEAKS);
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-
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-    return (true);
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-
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-}
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-// END HENRY
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-
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-// HENRY - resets the sequential access parser to the first scan.
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-void cRampIterator::reset()
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-{
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-    m_currentScan = 1;
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-}
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-// END HENRY
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-
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-/**
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- * populate from a file handle
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- **/
370
-rampPeakList::rampPeakList(RAMPFILE *handle, ramp_fileoffset_t index)
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-{
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-    init();
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-    m_peaksCount = readPeaksCount(handle,index);
374
-    m_pPeaks = (rampPeakInfoStruct *)readPeaks(handle,index);
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-}
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-
377
-/**
378
- * populate from a file handle
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- **/
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-rampScanInfo::rampScanInfo(RAMPFILE *handle, ramp_fileoffset_t index, int seqNum)
381
-{
382
-    init();
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-    readHeader(handle,index,&m_data);
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-    m_data.seqNum = seqNum;
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-}
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-
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-/**
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- * populate from a file handle
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- **/
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-rampRunInfo::rampRunInfo(RAMPFILE *handle)
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-{
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-    init();
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-    readMSRun(handle,&m_data);
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-}
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-
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-// HENRY - provides instrument info reading functionality
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-rampInstrumentInfo::rampInstrumentInfo(RAMPFILE *handle)
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-{
399
-    init();
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-    m_instrumentStructPtr = getInstrumentStruct(handle);
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-}
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-// 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
... ...
@@ -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
... ...
@@ -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
... ...
@@ -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
... ...
@@ -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
... ...
@@ -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
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
+  }