tandem.cpp

/*
 Copyright (C) 2003-2004 Ronald C Beavis, all rights reserved
 X! tandem 
 This software is a component of the X! proteomics software
 development project

Use of this software governed by the Artistic license, as reproduced here:

The Artistic License for all X! software, binaries and documentation

Preamble
The intent of this document is to state the conditions under which a
Package may be copied, such that the Copyright Holder maintains some 
semblance of artistic control over the development of the package, 
while giving the users of the package the right to use and distribute 
the Package in a more-or-less customary fashion, plus the right to 
make reasonable modifications. 

Definitions
"Package" refers to the collection of files distributed by the Copyright 
	Holder, and derivatives of that collection of files created through 
	textual modification. 

"Standard Version" refers to such a Package if it has not been modified, 
	or has been modified in accordance with the wishes of the Copyright 
	Holder as specified below. 

"Copyright Holder" is whoever is named in the copyright or copyrights 
	for the package. 

"You" is you, if you're thinking about copying or distributing this Package. 

"Reasonable copying fee" is whatever you can justify on the basis of 
	media cost, duplication charges, time of people involved, and so on. 
	(You will not be required to justify it to the Copyright Holder, but 
	only to the computing community at large as a market that must bear 
	the fee.) 

"Freely Available" means that no fee is charged for the item itself, 
	though there may be fees involved in handling the item. It also means 
	that recipients of the item may redistribute it under the same
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1. You may make and give away verbatim copies of the source form of the 
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disclaimers. 

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	together with instructions (in the manual page or equivalent) on 
	where to get the Standard Version. 
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	document the differences in manual pages (or equivalent), together 
	with instructions on where to get the Standard Version. 
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5. You may charge a reasonable copying fee for any distribution of 
this Package. You may charge any fee you choose for support of 
this Package. You may not charge a fee for this Package itself. 
However, you may distribute this Package in aggregate with other 
(possibly commercial) programs as part of a larger (possibly 
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this shall be construed as a mere form of aggregation, provided that 
the complete Standard Version of the interpreter is so embedded. 

6. The scripts and library files supplied as input to or produced as 
output from the programs of this Package do not automatically fall 
under the copyright of this Package, but belong to whomever generated 
them, and may be sold commercially, and may be aggregated with this 
Package. If such scripts or library files are aggregated with this 
Package via the so-called "undump" or "unexec" methods of producing 
a binary executable image, then distribution of such an image shall 
neither be construed as a distribution of this Package nor shall it 
fall under the restrictions of Paragraphs 3 and 4, provided that you 
do not represent such an executable image as a Standard Version of 
this Package. 

7. C subroutines (or comparably compiled subroutines in other languages) 
supplied by you and linked into this Package in order to emulate 
subroutines and variables of the language defined by this Package 
shall not be considered part of this Package, but are the equivalent 
of input as in Paragraph 6, provided these subroutines do not change 
the language in any way that would cause it to fail the regression 
tests for the language. 

8. Aggregation of this Package with a commercial distribution is always 
permitted provided that the use of this Package is embedded; that is, 
when no overt attempt is made to make this Package's interfaces visible 
to the end user of the commercial distribution. Such use shall not be 
construed as a distribution of this Package. 

9. The name of the Copyright Holder may not be used to endorse or promote 
products derived from this software without specific prior written permission. 

10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED 
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF 
MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. 

The End 
*/

// File version: 2004-02-01
// File version: 2004-03-01

/*
   Modified 2010 Brian Pratt for X!!Tandem MapReduce+MPI version.
   See mapreducehandler.cpp for details.
*/

/*
	tandem.cpp provides a command line interface to the main processing class, mprocess.
	A single command line parameter is accepted, which is the file name for an XML class
	containing the parameters for performing the protein modelling session. The input file 
	also contains the name of an output file, which will contain the output from the session.
*/



// This file contains main().  It starts one mprocess object, uses it
// to load settings and data, then (optionally) spins up additional
// threads, setting each one to begin at mprocess::process.



#include "stdafx.h"
#include <sys/timeb.h>
#include <ctime>
#include <sstream>
#include "msequence.h"
#include "msequencecollection.h"
#include "msequenceserver.h"
#include "msequtilities.h"
#include "mspectrum.h"
#include "xmlparameter.h"
#include "mscore.h"
#include "mprocess.h"
#ifdef HAVE_MULTINODE_TANDEM // support for Hadoop and/or MPI?
#include "mapreducehelper.h" // for hadoop and MPI, ISB/LabKey/Insilicos
#endif

#ifndef X_P3

/*
 * windows.h and the definition of ProcessThread are necessary for multithreading
 * in the Windows 32 environment. UNIX platforms that use POSIX threads use an
 * alternate version of this file.
 */
#ifdef MSVC
	#include "windows.h"
	DWORD WINAPI ProcessThread(LPVOID);
	DWORD WINAPI RefineThread(LPVOID);
#else
	#include <pthread.h>
	void* ProcessThread(void *pParam);
	void* RefineThread(void *pParam);
#endif

int main(int argc, char* argv[])
{
#ifdef HAVE_MULTINODE_TANDEM // support for Hadoop and/or MPI?
	mapreducehelper mrh(argc, argv); // mapreduce and mpi runs go down this path and don't return
#endif
	/*
	* Check the argv array for at least one parameter.
	* mprocess checks the validity of the file.
	*/
	if(argc < 2 || argc > 1 && strstr(argv[1],"-L") == argv[1] || argc > 1 && strstr(argv[1],"-h") == argv[1])	{
		cout << "\n\nUSAGE: tandem filename\n\nwhere filename is any valid path to an XML input file.\n\n+-+-+-+-+-+-+\n";
 		cout << "\nX! TANDEM " << VERSION << "\n";
		cout << "\nCopyright (C) 2003-2008 Ronald C Beavis, all rights reserved\n";
#ifdef HAVE_MULTINODE_TANDEM // support for Hadoop and/or MPI?
		cout << "\nAdapted for use with Hadoop, these modifications are\n";
		cout << "Copyright (C) 2010 Insilicos LLC, all rights reserved\n\n";
#ifdef XBANGBANG
		cout << "Also adapted for MPI, based on X!!Tandem work which is\n";
		cout << "Copyright (C) 2007 Robert D Bjornson, all rights reserved\n\n";
#endif
#endif
 		cout << "This software is a component of the GPM  project.\n";
		cout << "Use of this software governed by the Artistic license.\n";
		cout << "If you do not have this license, you can get a copy at\n";
		cout << "http://www.perl.com/pub/a/language/misc/Artistic.html\n";
		cout << "\n+-+-+-+-+-+-+\n\npress <Enter> to continue ...";
		char *pValue = new char[128];
		cin.getline(pValue,127);
		delete pValue;
		return -1;
	}
	cout << "\nX! TANDEM " << VERSION << "\n\n";
	/*
	* Create an mprocess object array
	*/
	unsigned long lMaxThreads = 16;
	mprocess **pProcess = new mprocess*[lMaxThreads];
	if(pProcess == NULL)	{
		cout << "An error was detected creating the processing objects.\nPlease contact a GPM administrator.\n";
		return -2;
	}
	unsigned long a = 0;
	while(a < lMaxThreads)	{
		pProcess[a] = NULL;
		a++;
	}
#ifdef MSVC
	DWORD *pId = new DWORD[lMaxThreads];
	HANDLE *pHandle = new HANDLE[lMaxThreads];
#else
	int *pId = new int[lMaxThreads];
	int *pHandle = new int[lMaxThreads];
	pthread_t pThreads[lMaxThreads];

#endif
	pProcess[0] = new mprocess;
	cout << "Loading spectra .";
	cout.flush();
	/*
	* Initialize the first mprocess object with the input file name.
	*/
	if(!pProcess[0]->load(argv[1]))	{
		cout << "\n\nAn error was detected while loading the input parameters.\nPlease follow the advice above or contact a GPM administrator to help you.";
		delete pProcess[0];
		delete pProcess;
		return -4;
	}
	cout << " loaded.\n";
	if(pProcess[0]->m_vSpectra.size() == 0)	{
		cout << "No input spectra met the acceptance criteria.\n";
		cout.flush();
		delete pProcess[0];
		delete pProcess;
		return 1;
	}
	cout << "Spectra matching criteria = " << (unsigned long)pProcess[0]->m_vSpectra.size() << "\n";
	cout.flush();
#ifdef PLUGGABLE_SCORING
 	cout << "Pluggable scoring enabled.\n";
#endif
      /*

        * Start the mprocess object and wait for it to return.

        */
	unsigned long lThread =	pProcess[0]->get_thread();
	unsigned long lThreads = pProcess[0]->get_threads();
	if(lThreads	> lMaxThreads)	{
		lThreads = lMaxThreads;
	}
	if(pProcess[0]->m_vSpectra.size() <	lThreads)	{
		lThreads = (unsigned long)pProcess[0]->m_vSpectra.size();
		if(lThreads	< 1)		{
			lThreads = 1;
		}
		pProcess[0]->set_threads(lThreads);
	}
#ifdef MSVC
	DWORD dCount = lThreads	- 1;
#else
	int	dCount = lThreads -	1;
#endif
	long lSpectra =	lThreads + (long)pProcess[0]->m_vSpectra.size()/lThreads;
	bool bSpectra =	true;
	cout <<	"Starting threads .";
	cout.flush();
	if(lThread != 0xFFFFFFFF)		{
		while(dCount > 0)		{
			pProcess[dCount] = new mprocess;
			pProcess[dCount]->set_thread(dCount);						 
			/*

			* initialize the new mprocess objects with	the	spectra	already	loaded into	the	first mprocess

			*/
			pProcess[dCount]->m_vSpectra.reserve(lSpectra);
			dCount--;
		}
		size_t tCount = pProcess[0]->m_vSpectra.size();
		size_t tProcesses = lThreads;
		size_t tRing = 0;
		vector<mspectrum> vZero;
		vZero.reserve(lSpectra);
		do	{
			if(tRing == 0)	{
				vZero.push_back(pProcess[0]->m_vSpectra.back());
			}
			else	{
				pProcess[tRing]->m_vSpectra.push_back(pProcess[0]->m_vSpectra.back());
			}
			tRing++;
			pProcess[0]->m_vSpectra.pop_back();
			if(tRing == tProcesses)	{
				tRing = 0;

			}
		}	while(pProcess[0]->m_vSpectra.size() != 0);
		pProcess[0]->m_vSpectra.reserve(vZero.size());
		do	{
			pProcess[0]->m_vSpectra.push_back(vZero.back());
			vZero.pop_back();
		}	while(vZero.size() != 0);
		dCount = lThreads - 1;
		while(dCount > 0)		{
			if(!pProcess[dCount]->load(argv[1],pProcess[0]))	{
				cout <<	"error pProcess->LoadParameters	returned error (main)\r\n";
				delete pProcess;
				return -4;
			}
			dCount--;
			cout <<	".";
			cout.flush();
		}
	}
	dCount = 0;
#ifdef MSVC
	pHandle[dCount] = CreateThread(NULL,0,ProcessThread,(void *)pProcess[dCount],0,&pId[dCount]);
#else
	pthread_create(&pThreads[dCount],NULL,ProcessThread,(void*)pProcess[dCount]);
#endif
	dCount++;
	/*
	* Initialize more mprocess objects, if lThread is not 0xFFFFFFFF, which signifies default single
	* threaded operation.
	*/
	if(lThread != 0xFFFFFFFF && bSpectra)	{
		while(dCount < lThreads)	{
#ifdef MSVC
			pHandle[dCount] = CreateThread(NULL,0,ProcessThread,(void *)pProcess[dCount],0,&pId[dCount]);
#else
			pthread_create(&pThreads[dCount],NULL,ProcessThread,(void*)pProcess[dCount]);
#endif
			dCount++;
		}
	}
	cout << " started.\n";
	cout.flush();
	cout << "Computing models:\n";
	cout.flush();
	/*
	* wait until all of the mprocess objects return.
	*/
#ifdef MSVC
//	DWORD wait = WaitForMultipleObjects(dCount,pHandle,true,INFINITE);
	a = 0;
	DWORD dwTime = 200000;
	DWORD wait = WAIT_TIMEOUT;
	int iTics = 0;
	while(a < dCount)	{
		wait = WaitForSingleObject(pHandle[a],100);
		if(a > 0 && wait == WAIT_TIMEOUT)	{
			if(a == 1)	{
				cout << "waiting for " << a+1;
			}
			else	{
				cout << a+1;
			}
			while(wait == WAIT_TIMEOUT)	{
				wait = WaitForSingleObject(pHandle[a],dwTime);
				cout << ".";
				cout.flush();
				iTics++;
				if(iTics > 50)	{
					cout << "|\n\t\t";
					cout.flush();
					iTics = 0;
				}
			}
		}
		else	{
			while(wait == WAIT_TIMEOUT)	{
				wait = WaitForSingleObject(pHandle[a],dwTime);
			}
			if(a == 1)	{
				cout << "waiting for " << a+1;
			}
			else if(a == 0)	{
				cout << "\n\t";
				cout.flush();
			}
			else	{
				cout << a+1;
			}
		}
		a++;
	}
	if(dCount > 1)	{
			cout << " done.\n\n";
			cout.flush();
	}
	else	{
		cout << "\n";
		cout.flush();
	}
#else
	//2003-03-01:note - the declaration below was changed from void **vp;	
	void *vp;
	int x=0;
	int wait;
	for(x=0;x<dCount;x++){
		//2003-03-01:note - the 2nd parameter in the call to pthread_join() was changed from vp
		wait = pthread_join(pThreads[x],&vp);
	}
#endif
	cout << "\tsequences modelled = "<< (long)(pProcess[0]->get_protein_count()/1000.0 + 0.5) << " ks\n";
	cout.flush();
	pProcess[0]->merge_spectra();
	a = 1;
	/*
	* merge the results into the first object
	*/
	while(a < dCount)	{
		pProcess[0]->merge_map(pProcess[a]->m_mapSequences);
		pProcess[0]->merge_spectra(pProcess[a]->m_vSpectra);
		a++;
	}
	a = 1;
	pProcess[0]->load_sequences();
	while(a < dCount)	{
		pProcess[a]->merge_map(pProcess[0]->m_mapSequences);
		pProcess[a]->m_vseqBest = pProcess[0]->m_vseqBest;
		a++;
	}

	/*
	* Report the contents of the mprocess objects into an XML file as described
	* in the input file.
	*/
	cout << "Model refinement:\n";
	cout.flush();
	dCount = 0;
#ifdef MSVC
	pHandle[dCount] = CreateThread(NULL,0,RefineThread,(void *)pProcess[dCount],0,&pId[dCount]);
#else
	pthread_create(&pThreads[dCount],NULL,RefineThread,(void*)pProcess[dCount]);
#endif
	dCount++;
	/*
	* Initialize more mprocess objects, if lThread is not 0xFFFFFFFF, which signifies default single
	* threaded operation.
	*/
	if(lThread != 0xFFFFFFFF)	{
		while(dCount < lThreads)	{
#ifdef MSVC
			pHandle[dCount] = CreateThread(NULL,0,RefineThread,(void *)pProcess[dCount],0,&pId[dCount]);
#else
			pthread_create(&pThreads[dCount],NULL,RefineThread,(void*)pProcess[dCount]);
#endif
			dCount++;
		}
	}
	/*
	* wait until all of the mprocess objects return.
	*/
#ifdef MSVC
//	wait = WaitForMultipleObjects(dCount,pHandle,true,INFINITE);
	a = 0;
	iTics = 0;
	while(a < dCount)	{
		wait = WaitForSingleObject(pHandle[a],10000);
		if(a > 0 && wait == WAIT_TIMEOUT)	{
			if(a == 1)	{
				cout << "waiting for " << a+1;
			}
			else	{
				cout << a+1;
			}
			cout.flush();
			while(wait == WAIT_TIMEOUT)	{
				wait = WaitForSingleObject(pHandle[a],dwTime);
				cout << ".";
				cout.flush();
				iTics++;
				if(iTics > 50)	{
					cout << "|\n\t\t";
					cout.flush();
					iTics = 0;
				}
			}
		}
		else	{
			while(wait == WAIT_TIMEOUT)	{
				cout << ".";
				cout.flush();
				wait = WaitForSingleObject(pHandle[a],dwTime);
			}
			if(a == 1)	{
				cout << "waiting for " << a+1;
			}
			else if(a == 0)	{
				cout << "\n\t";
				cout.flush();
			}
			else	{
				cout << a+1;
			}
		}
		a++;
	}
	if(dCount > 1)	{
		cout << " done.\n\n";
		cout.flush();
	}
	else	{
		cout << "\n";
		cout.flush();
	}
#else
	//2003-03-01:note - the declaration below was changed from void **vp;	
	x=0;
	for(x=0;x<dCount;x++){
		//2003-03-01:note - the 2nd parameter in the call to pthread_join() was changed from vp
		wait = pthread_join(pThreads[x],&vp);
	}
#endif
	a = 1;
	/*
	* merge the results into the first object
	*/
	if(dCount > 1)	{
		cout << "Merging results:\n";
		cout.flush();
	}
	while(a < dCount)	{
		if(a == 1)	{
			cout << "\tfrom " << a+1;
		}
		else	{
			cout << a+1;
		}
		cout.flush();
		if(!pProcess[0]->add_spectra(pProcess[a]->m_vSpectra))	{
			cout << "adding spectra failed.\n";
		}
		pProcess[0]->merge_statistics(pProcess[a]);
		pProcess[a]->clear();
		pProcess[a]->m_mapSequences.clear();
		a++;
	}
	if(dCount > 1)	{
		cout << "\n\n";
		cout.flush();
	}
	cout.flush();
	cout << "Creating report:\n";
	cout.flush();
	pProcess[0]->report();
	size_t tValid = pProcess[0]->get_valid();
	size_t tUnique = pProcess[0]->get_unique();
	double dE = pProcess[0]->get_threshold();
	unsigned long lE = (unsigned long)(0.5+(double)tUnique/(1.0+1.0/dE));
	unsigned long lEe = (unsigned long)(0.5 + sqrt((double)lE));
	if(lEe == 0)	{
		lEe = 1;
	}
	if(dE <= 0.0)	{
		dE = 1.0;
	}
	cout << "\nValid models = " << (unsigned long)tValid << "\n";
	if(tUnique > 0)	{
		cout << "Unique models = " << (unsigned long)tUnique << "\n";
		cout << "Estimated false positives = " << lE << " &#177; ";
		cout << lEe << "\n";
	}
	lE = pProcess[0]->get_reversed();
	if(lE != -1)	{
		cout << "False positive rate (reversed sequences) = " << lE << "\n";
	}
	cout << "\n\n";

    ////////////////////////////////////// 
    //    CHEEZEBALL REGRESSION TEST!   //
    // pass output through Tandem2XML,  //
    // then InteractParser in test mode //
    //////////////////////////////////////
    if ((argc>2) && ! strncmp(argv[2],"-t",2)) { // match -t or -t!
        if (!strncmp(argv[2],"-t!",3)) {
            cout << "learning new regression test..." << endl;
	}
        else {
            cout << "performing regression test..." << endl;
	}
	string strKey = "output, path";
	string strValue;
	pProcess[0]->m_xmlValues.get(strKey,strValue); // ex. strValue="foo.tandem"
        // run Tandem2XML "foo.tandem" > "foo.tandem.pepXML"

	string builddir = "";
	if (argc>3) { // use a build directory
	  builddir = argv[3];
	  cout << "(finding TPP executables in " << builddir << ")" << endl;
	}
        string cmd("Tandem2XML \"");
	cmd = builddir + cmd; // build directory prefix
        cmd += strValue;
        cmd += "\" > \"";
        string pepxml(strValue);
        pepxml += ".pepXML\"";
        cmd += pepxml;
        cout << cmd << endl;
        int err = system(cmd.c_str());
        // run InteractParser -t[!]"foo.tandem.test" "foo.tandem.interact.pepXML" "foo.tandem.pepXML" 
        cmd = "InteractParser ";
	cmd = builddir + cmd;  // build directory prefix
        cmd += argv[2]; 
        cmd += "\"";
        cmd += strValue;
        cmd += ".test\" \"";
        cmd += strValue;
        cmd += ".interact.pepXML\" \"";
        cmd += pepxml;
        cout << cmd << endl;
        err |= system(cmd.c_str());
        if (err)
            return err;
    }
    ///////////////////////////////// 

	/*
	* Delete the mprocess objects and exit
	*/
	a = 0;
	while(a < 16)	{
		if(pProcess[a] != NULL)	{
			delete pProcess[a];
		}
		a++;
	}
	delete pProcess;
	delete pId;
	delete pHandle;
	return 0;
}
/*
 * Process thread is used to create the worker threads for each mprocess object
 */

#ifdef MSVC
DWORD WINAPI ProcessThread(LPVOID _p)
{
	((mprocess *)_p)->process();
	return 0;
}
DWORD WINAPI RefineThread(LPVOID _p)
{
	((mprocess *)_p)->refine();
	return 0;
}
#else
void* ProcessThread(void *_p){
	((mprocess *)_p)->process();
 	return (void*)0;
}
void* RefineThread(void *_p){
	((mprocess *)_p)->refine();
 	return (void*)0;
}
#endif

#endif