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[Sashimi-commit] SF.net SVN: sashimi:[5107] trunk/trans_proteomic_pipeline/src/Validation
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From: <rb...@us...> - 2010-08-11 18:16:21
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Revision: 5107
http://sashimi.svn.sourceforge.net/sashimi/?rev=5107&view=rev
Author: rbs66
Date: 2010-08-11 18:16:13 +0000 (Wed, 11 Aug 2010)
Log Message:
-----------
iModelParser tool for displaying iProphet models by Richie Stauffer
Added Paths:
-----------
trunk/trans_proteomic_pipeline/src/Validation/iModelParser/
trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.cxx
trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.h
trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParserMain.cxx
Added: trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.cxx (rev 0)
+++ trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.cxx 2010-08-11 18:16:13 UTC (rev 5107)
@@ -0,0 +1,1017 @@
+/*
+Program: iModelParser
+Author: Richard Stauffer, modified from ModelParser: J.Eng and Andrew Keller <ak...@sy...>, Robert Hubley, and open source code
+Date: Summer 2010
+
+Primary data object holding all mixture distributions for each precursor ion charge
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+Andrew Keller
+Insitute for Systems Biology
+1441 North 34th St.
+Seattle, WA 98103 USA
+ak...@sy...
+*/
+
+#include <string.h>
+#include <stdio.h>
+#include <fstream>
+#include "common/TPPVersion.h" //contains version number, name, revision
+#include "common/sysdepend.h"
+#include "common/util.h"
+
+#include "IModelParser.h"
+
+//constructor
+iModelParser::iModelParser(const char* xmlfile, const char* timestamp, const char* spectrum, const char* scores, char* prob) : Parser(NULL)
+{
+ timestamp_ = NULL;
+
+ inputfiles_ = new Array<char*>;
+
+ adjusted_ = False;
+
+ if(timestamp != NULL)
+ {
+ timestamp_ = new char[strlen(timestamp) + 1];
+ strcpy(timestamp_, timestamp);
+ }
+
+ //set text below images (spectrum_)
+ spectrum_ = new char[strlen(spectrum) + 1];
+ strcpy(spectrum_, spectrum);
+
+ //set text below images (scores_)
+ scores_ = new char[strlen(scores) + 1];
+ strcpy(scores_, scores);
+
+ //change : to =
+ for(int k = 0; scores_[k]; k++)
+ if(scores_[k] == ':')
+ scores_[k] = '=';
+
+ if(strlen(prob) > 0 && prob[strlen(prob) - 1] == 'a') //if last character in prob is 'a'
+ {
+ adjusted_ = True;
+ prob[strlen(prob) - 1] = 0;
+ }
+
+ //set text below images (prob_)
+ prob_ = new char[strlen(prob) + 1];
+ strcpy(prob_, prob);
+
+ est_tot_num_correct_ = 0.0;
+
+ //set initial error table values
+ for (char i = 0; i != ERROR_NUM; i++)
+ {
+ errors_[i] = 0.025 * i;
+ min_prob_threshes_[i] = 0.0;
+ est_num_corrects_[i] = 0;
+ }
+
+ prophet_name_ = "interprophet";
+
+ char *xf = strdup(xmlfile);
+
+ fixPath(xf, 1); //tidy up path seperators etc - expect existence
+
+ init(xf);
+
+ free(xf);
+}
+
+//destructor
+iModelParser::~iModelParser()
+{
+ delete[] prophet_name_;
+ delete[] timestamp_;
+ delete[] spectrum_;
+ delete[] scores_;
+
+ //delete all png paths
+ delete[] pngsensgraph_;
+
+ int i;
+ for (i = 0; i != MODEL_IMGS; i++)
+ delete[] pngmodels_[i];
+ for (i = 0; i != PERFORM_IMGS; i++)
+ delete[] pngperforms_[i];
+
+ delete[] prob_;
+
+ if(inputfiles_ != NULL)
+ {
+ for(i = 0; i != inputfiles_->length(); i++)
+ if((*inputfiles_)[i] != NULL)
+ delete[] (*inputfiles_)[i];
+ delete inputfiles_;
+ }
+}
+
+void iModelParser::parse(const char* xmlfile)
+{
+ Tag* tag = NULL;
+ char* data = NULL;
+
+ Boolean analyze = False;
+
+ Array<sensTableDataPoint*>* sensitivity = new Array<sensTableDataPoint*>; //collects sensitivity graph data from xml file
+
+ sensTableDataPoint* next_sens = NULL; //single data set, used to help transfer data
+
+ //collects n-score graph data from xml file
+ nScoreDataSet* nScoreData[MODEL_IMGS];
+
+ for (char i = 0; i != MODEL_IMGS; i++)
+ nScoreData[i] = new nScoreDataSet();
+
+ nScoreDataPoint* next_score = NULL; //single data set, used to help transfer data
+
+ pwiz::util::random_access_compressed_ifstream fin(xmlfile); //can read gzipped files
+
+ if(!fin)
+ {
+ cerr << "iModelParser: error opening" << xmlfile << endl;
+ exit(1);
+ }
+
+ Boolean done = False, collect = False;
+
+ int error_index = 0;
+
+ char options[SIZE_FILE];
+ *options = 0;
+
+ char* nextline = new char[line_width_];
+
+ N_Score curNScore = NONE;
+
+ while(!done && fin.getline(nextline, line_width_))
+ {
+ data = strstr(nextline, "<");
+
+ while(data != NULL)
+ {
+ tag = new Tag(data);
+
+ if(tag != NULL)
+ {
+ if(filter_)
+ analyze = True;
+
+ //assume there won't be an "interprophet_summary" tag, work around by using analysis_summary
+ //set filter function content copied up here since it also uses analysis_summary tag
+ if(filter_memory_) //filter_ and filter_memory_ come from parent parser class
+ {
+ filter_memory_ = False;
+ filter_ = False;
+ }
+
+ if(tag->isStart() && !strcmp(tag->getName(), "analysis_summary"))
+ {
+ //set estimated total correct assignments
+ //est_tot_num_correct_ = atof(tag->getAttributeValue("est_tot_num_correct"));
+ //set run options (part of run parameters)
+ //strcpy(options, tag->getAttributeValue("options"));
+
+ //est_tot_num_correct_ and options not part of xml file yet !!!
+ //options a temporary value
+ strcpy(options, "no options in XML file");
+
+ if(tag->isEnd() && filter_)
+ filter_memory_ = True;
+ else if(tag->isStart()
+ && !strcmp(tag->getAttributeValue("analysis"), prophet_name_)
+ && (timestamp_ == NULL || !strcmp(tag->getAttributeValue("time"), timestamp_)))
+ {
+ filter_ = True;
+
+ if(timestamp_ == NULL)
+ {
+ //set analysis date, timestamp_ (part of run parameters)
+ timestamp_ = new char[strlen(tag->getAttributeValue("time")) + 1];
+ strcpy(timestamp_, tag->getAttributeValue("time"));
+ }
+ }
+ }
+
+ if(analyze && tag->isEnd() && !strcmp(tag->getName(), "analysis_summary"))
+ {
+ analyze = False; //done
+ done = True;
+ break; //no more need to read summary
+ }
+
+ if(analyze) //grab desired data
+ {
+ if(tag->isStart() && !strcmp(tag->getName(), "inputfile"))
+ {
+ char* next_file = new char[strlen(tag->getAttributeValue("name")) + 1];
+ strcpy(next_file, tag->getAttributeValue("name"));
+ inputfiles_->insertAtEnd(next_file);
+ }
+ else if(!strcmp(tag->getName(), "roc_data_point"))
+ {
+ next_sens = new sensTableDataPoint;
+ next_sens->minprob = atof(tag->getAttributeValue("min_prob"));
+ next_sens->sens = atof(tag->getAttributeValue("sensitivity"));
+ next_sens->err = atof(tag->getAttributeValue("error"));
+
+ //set large table data (sensitivity table)
+ sensitivity->insertAtEnd(next_sens);
+ }
+ else if(error_index < ERROR_NUM && tag->isStart() && !strcmp(tag->getName(), "error_point"))
+ {
+ double nexterr = atof(tag->getAttributeValue("error"));
+ double maxdiff = 0.005;
+
+ if(nexterr == errors_[error_index] ||
+ (nexterr > errors_[error_index] && nexterr - errors_[error_index] <= maxdiff) ||
+ (nexterr < errors_[error_index] && errors_[error_index] - nexterr <= maxdiff))
+ {
+ //set small table MPT and est # corr columns
+ min_prob_threshes_[error_index] = atof(tag->getAttributeValue("min_prob"));
+ est_num_corrects_[error_index] = atoi(tag->getAttributeValue("num_corr"));
+ error_index++;
+ }
+ }
+
+ if(tag->isStart() && !strcmp(tag->getName(), "mixturemodel"))
+ {
+ collect = True;
+
+ char nScoreName[N_SCORE_SIZE]; //scores should be 4 chars long counting \0
+ strcpy(nScoreName, tag->getAttributeValue("name"));
+
+ if(!strcmp(nScoreName, "NSS"))
+ curNScore = NSS;
+ else if(!strcmp(nScoreName, "NRS"))
+ curNScore = NRS;
+ else if(!strcmp(nScoreName, "NSE"))
+ curNScore = NSE;
+ else if(!strcmp(nScoreName, "NSI"))
+ curNScore = NSI;
+ else if(!strcmp(nScoreName, "NSM"))
+ curNScore = NSM;
+ else
+ {
+ if(!strcmp(nScoreName, "TopCat")) //TopCat score is recognized but nothing is done with it yet
+ printf("<!--TopCat score found.-->");
+ else
+ printf("Warning: \"%s\" score not recognized!", nScoreName);
+
+ curNScore = NONE;
+ }
+
+ //set nScoreData score value
+ if (curNScore != NONE)
+ {
+ //parse score value from scores_
+ char* scoreVal = new char[strlen(scores_) + 1];
+ strcpy(scoreVal, scores_);
+
+ char* tmpScore = strstri(scoreVal, nScoreName);
+ scoreVal = strchr(tmpScore, '=') + 1;
+ tmpScore = strchr(scoreVal, ' ');
+
+ if(tmpScore != NULL)
+ *tmpScore = 0;
+
+ nScoreData[curNScore]->scoreVal = atof(scoreVal);
+ //nScoreData[curNScore]->posBW = atof(tag->getAttributeValue("pos_bandwidth"));
+ //nScoreData[curNScore]->negBW = atof(tag->getAttributeValue("neg_bandwidth"));
+
+ delete[] scoreVal;
+ }
+ }
+ else if(tag->isEnd() && !strcmp(tag->getName(), "mixturemodel"))
+ collect = False;
+
+ if (collect && curNScore != NONE && !strcmp(tag->getName(), "point"))
+ {
+ next_score = new nScoreDataPoint();
+ next_score->nScore = atof(tag->getAttributeValue("value"));
+ next_score->pos = atof(tag->getAttributeValue("pos_dens"));
+ next_score->neg = atof(tag->getAttributeValue("neg_dens"));
+ next_score->ln = log(next_score->pos / next_score->neg);
+
+ //check if the observed values are present
+ const char* nObs = tag->getAttributeValue("neg_obs_dens"); //keep in this order, neg obs first in xml
+ const char* pObs = tag->getAttributeValue("pos_obs_dens");
+
+ drawPobs_ = pObs != NULL;
+ drawNobs_ = nObs != NULL;
+ next_score->posObs = drawPobs_ ? atof(pObs) : 0;
+ next_score->negObs = drawNobs_ ? atof(nObs) : 0;
+
+ nScoreData[curNScore]->dataPoints->insertAtEnd(next_score);
+ }
+ }
+
+ if(!collect)
+ delete tag;
+ }
+
+ data = strstr(data + 1, "<");
+ }
+ }
+
+ fin.close();
+ delete[] nextline;
+
+ data = NULL;
+
+ //done reading xml file, now write graphing data to szTmpDataFile and call plotModel to create png's
+
+ if(timestamp_ != NULL && strcmp(prob_, "-nofigs"))
+ {
+ char* filePath = new char[SIZE_FILE];
+ strcpy(filePath, xmlfile);
+
+ char* performPath = setFilePaths(filePath);
+ removeOldFiles(filePath);
+
+ char* szTmpDataFile = new char[SIZE_FILE];
+ sprintf(szTmpDataFile, "%sdata", filePath);
+
+ //write data files
+ FILE* fpTmp;
+
+ char
+ gnuplotBlack = -1,
+ gnuplotRed = 1,
+ gnuplotGreen = 2,
+ gnuplotBlue = 3;
+ //if needed pink/purple = 4
+
+ time_t tStartTime = time((time_t *)NULL);
+ srandom((int)(strlen(filePath) + tStartTime + filePath[strlen(filePath) - 3]));
+
+ long rndPath = random();
+
+ //create sensitivity graph data file and png
+ if(sensitivity->length())
+ {
+ if((fpTmp = fopen(szTmpDataFile, "w")) == NULL)
+ printf("Error - cannot create sensitivity graph data file: %s.", szTmpDataFile);
+ else
+ {
+ for(int i = 0; i != sensitivity->length(); i++) //open and write file
+ fprintf(fpTmp, "%0.2f\t%0.3f\t%0.3f\n", (*sensitivity)[i]->minprob, (*sensitivity)[i]->sens, (*sensitivity)[i]->err);
+ fclose(fpTmp); //close file
+
+ pngsensgraph_ = plotSensitivity(filePath, rndPath, gnuplotRed, gnuplotGreen);
+ }
+ }
+ else
+ pngsensgraph_ = NULL;
+
+ //create n-score graph data files and png's
+ for(char i = 0; i != MODEL_IMGS; i++)
+ {
+ if(nScoreData[i]->dataPoints->length()) //if number of data points is not 0
+ {
+ if((fpTmp = fopen(szTmpDataFile, "w")) == NULL)
+ printf("Error - cannot create N-Score graph data file: %s.", szTmpDataFile);
+ else
+ {
+ for(int j = 0; j != nScoreData[i]->dataPoints->length(); j++) //open and write file
+ {
+ fprintf(fpTmp, "%0.4f\t%0.4f\t%0.4f\t%0.4f\t%0.4f\t%0.4f\n", //rounding to 4 decimal places
+ (*nScoreData[i]->dataPoints)[j]->nScore,
+ (*nScoreData[i]->dataPoints)[j]->pos,
+ (*nScoreData[i]->dataPoints)[j]->neg,
+ (*nScoreData[i]->dataPoints)[j]->ln,
+ (*nScoreData[i]->dataPoints)[j]->posObs,
+ (*nScoreData[i]->dataPoints)[j]->negObs);
+ }
+ fclose(fpTmp); //close file
+
+ char* scoreName = new char[N_SCORE_SIZE];
+ char* scoreTitle = new char[TEXT_SIZE1];
+
+ switch ((N_Score)i)
+ {
+ case NSS:
+ strcpy(scoreName, "NSS");
+ strcpy(scoreTitle, "NSS (Number of Sibling Searches)");
+ break;
+ case NRS:
+ strcpy(scoreName, "NRS");
+ strcpy(scoreTitle, "NRS (Number of Replicate Spectra)");
+ break;
+ case NSE:
+ strcpy(scoreName, "NSE");
+ strcpy(scoreTitle, "NSE (Number of Sibling Expiriments)");
+ break;
+ case NSI:
+ strcpy(scoreName, "NSI");
+ strcpy(scoreTitle, "NSI (Number of Sibling Ions)");
+ break;
+ case NSM:
+ strcpy(scoreName, "NSM");
+ strcpy(scoreTitle, "NSM (Number of Sibling Modifications)");
+ break;
+ default:
+ strcpy(scoreName, "???"); //unknown score
+ strcpy(scoreTitle, "Unknown Score");
+ break;
+ }
+
+ pngmodels_[i] = plotModel(filePath, scoreName, scoreTitle, nScoreData[i]->scoreVal, rndPath,
+ gnuplotBlue, gnuplotRed, gnuplotBlack, gnuplotGreen); //plot model
+ }
+ }
+ else
+ pngmodels_[i] = NULL;
+ }
+
+ char* tmpPath = new char[SIZE_FILE];
+ char* fileName = new char[TEXT_SIZE1];
+ char* xmlCopy = new char[SIZE_FILE];
+ strcpy(xmlCopy, xmlfile);
+
+ *strstr(xmlCopy, ".xml") = 0;
+ strcat(xmlCopy, "_");
+
+ for (char i = 0; i != PERFORM_IMGS; i++)
+ {
+ strcpy(tmpPath, xmlCopy);
+
+ switch(i)
+ {
+ case 0: strcpy(fileName, "FDR"); break;
+ case 1: strcpy(fileName, "FDR_5pc"); break;
+ case 2: strcpy(fileName, "IPPROB"); break;
+ case 3: strcpy(fileName, "PPPROB"); break;
+ case 4: strcpy(fileName, "CORR"); break;
+ case 5: strcpy(fileName, "ROC"); break;
+ }
+ strcat(fileName, ".png");
+
+ strcat(tmpPath, fileName);
+
+ if ((fpTmp = fopen(tmpPath, "r")) == NULL)
+ pngperforms_[i] = NULL;
+ else
+ {
+ strcpy(tmpPath, performPath);
+ strcat(tmpPath, fileName);
+
+ pngperforms_[i] = new char[SIZE_FILE];
+ strcpy(pngperforms_[i], tmpPath);
+ fclose(fpTmp);
+ }
+ }
+
+ delete[] tmpPath;
+ delete[] fileName;
+ delete[] xmlCopy;
+
+ unlink(szTmpDataFile);
+ }
+
+ writeModelResults(cout, options, sensitivity);
+}
+
+//this correctly sets filePath and returns the path of the performance pngs to be loaded
+char* iModelParser::setFilePaths(char* filePath)
+{
+ const char* tmpRoot;
+ char* pngPath = new char[SIZE_FILE];
+ char webserverRoot[SIZE_FILE];
+
+ tmpRoot = getWebserverRoot();
+
+ if (tmpRoot == NULL)
+ {
+ printf("<PRE> Environment variable WEBSERVER_ROOT does not exist.\n\n");
+#ifdef WINDOWS_CYGWIN
+ printf(" For Windows users, you can set this environment variable\n");
+ printf(" through the Advanced tab under System Properties when you\n");
+ printf(" right-mouse-click on your My Computer icon.\n\n");
+
+ printf(" Set this environment variable to your webserver's document\n");
+ printf(" root directory such as c:\\inetpub\\wwwroot for IIS or\n");
+ printf(" c:\\website\\htdocs or WebSite Pro.\n\n");
+#endif
+ printf(" Exiting.\n");
+ exit(0);
+ }
+ else
+ {
+ //must first pass to cygpath program
+#ifdef WINDOWS_CYGWIN
+ char
+ szCommand[SIZE_FILE],
+ szNewRoot[SIZE_FILE];
+
+ sprintf(szCommand, "cygpath '%s'", tmpRoot);
+ FILE* fp;
+
+ if((fp = popen(szCommand, "r")) == NULL)
+ {
+ printf("cygpath error, exiting\n");
+ exit(1);
+ }
+ else
+ {
+ fgets(szNewRoot, TEXT_SIZE3, fp);
+ pclose(fp);
+ szBuf[strlen(szNewRoot) - 1] = 0;
+ strcpy(webServerRoot, szNewRoot);
+ }
+#else
+ strcpy(webserverRoot, tmpRoot);
+#endif
+ }
+
+ //Check if webServerRoot is present
+ if (access(webserverRoot, F_OK))
+ {
+ printf(" Cannot access the webserver's root directory:\n");
+ printf(" %s\n", webserverRoot);
+ printf(" This was set as the environment variable WEBSERVER_ROOT\n\n");
+
+ printf(" For Windows users, you can check this environment variable\n");
+ printf(" through the Advanced tab under System Properties when you\n");
+ printf(" right-mouse-click on your My Computer icon.\n\n");
+ printf(" Exiting.\n");
+ exit(1);
+ }
+
+ //set up correct pngPath
+ char* result = NULL;
+
+ result = strstri(filePath, webserverRoot);
+
+ if(result != NULL)
+ {
+ if(strlen(result) > strlen(webserverRoot) && result[strlen(webserverRoot)] != '/')
+ sprintf(pngPath, "/%s", result + strlen(webserverRoot));
+ else
+ strcpy(pngPath, result + strlen(webserverRoot));
+ }
+ else
+ strcpy(pngPath, filePath);
+
+ *strstr(pngPath, ".xml") = 0;
+
+ strcat(pngPath, "_");
+
+ //set up correct filePath
+ replace_path_with_webserver_tmp(filePath, sizeof(filePath)); //do this in designated tmpdir, if any
+
+ strcat(filePath, ".XXXXXX");
+ safe_fclose(FILE_mkstemp(filePath)); //create then close a uniquely named file
+
+ unlink(filePath); //we only wanted its name, we never actually use it
+
+ strcat(filePath, ".");
+
+ return pngPath;
+}
+
+void iModelParser::removeOldFiles(char* filePath)
+{
+ //remove any aging tmpfiles that may be around for any reason
+ std::string pngMask(filePath);
+ int rslash = findRightmostPathSeperator(pngMask);
+
+ if (rslash > 0)
+ pngMask = pngMask.substr(0, rslash + 1);
+
+ pngMask += "*.ISB.png";
+ remove_files_olderthan(pngMask, 600); //kill any png files more than 10 minutes old (600 seconds)
+}
+
+ char* iModelParser::plotSensitivity(char* filePath, long random, char sensColor, char errColor)
+{
+ FILE* fpPlotCode;
+
+ char* pngFilePath = new char[SIZE_FILE];
+ char* dataFilePath = new char[SIZE_FILE]; //by this point data file exists and is populated, but it's file path is known
+ char* plotFilePath = new char[SIZE_FILE];
+
+ char plotCommand[TEXT_SIZE3];
+
+ sprintf(pngFilePath, "%s%ld.ISB.png", filePath, random);
+
+ sprintf(plotFilePath, "%sgp", filePath);
+ sprintf(dataFilePath, "%sdata", filePath);
+
+ if ((fpPlotCode = fopen(plotFilePath, "w")) == NULL)
+ printf("Error - cannot create gnuplot file %s.", plotFilePath);
+ else
+ {
+ //gnuplot code
+ fprintf(fpPlotCode, "set terminal png size %d, %d\n", SENS_IMG_W, SENS_IMG_H);
+ fprintf(fpPlotCode, "set output \"%s\"\n", pngFilePath);
+ fprintf(fpPlotCode, "set border\n");
+ fprintf(fpPlotCode, "set title \"Sensitivity & Error Rates\"\n");
+ fprintf(fpPlotCode, "set xlabel \"Min Probability Threshhold (MPT) To Accept\"\n");
+ fprintf(fpPlotCode, "set ylabel \"Sensitivity & Error\"\n");
+ fprintf(fpPlotCode, "set grid\n");
+ fprintf(fpPlotCode, "set xrange [0:1]\n");
+ fprintf(fpPlotCode, "set yrange [0:1]\n");
+ fprintf(fpPlotCode, "set key bottom right\n");
+ fprintf(fpPlotCode, "plot \"%s\" using 1:2 title 'sensitivity' with lines lc %d, \\\n", dataFilePath, sensColor);
+ fprintf(fpPlotCode, "\"%s\" using 1:3 title 'error' with lines lc %d\n", dataFilePath, errColor);
+
+ fprintf(fpPlotCode, "unset output\n");
+ fclose(fpPlotCode);
+
+ char* plotFileName = findRightmostPathSeperator(plotFilePath);
+ *plotFileName++ = '\0';
+
+ //write and call plot command
+ sprintf(plotCommand, "cd %s; %s %s; rm -f %s", plotFilePath, GNUPLOT_BINARY, plotFileName, plotFileName);
+ verified_system(plotCommand); //system() with verbose error check
+
+#ifdef USING_RELATIVE_WEBSERVER_PATH //fix up the image path if needed
+ pngFilePath = translate_relative_webserver_root_path_to_absolute_filesystem_path(pngFilePath);
+#endif
+ }
+
+ unlink(plotFilePath);
+
+ return pngFilePath;
+}
+
+//draws an N-score graph
+char* iModelParser::plotModel(char* filePath, char* scoreName, char* scoreTitle, double scoreVal, long random,
+char posColor, char negColor, char lnColor, char scoreColor)
+{
+ FILE* fpPlotCode;
+
+ char* pngFilePath = new char[SIZE_FILE];
+ char* dataFilePath = new char[SIZE_FILE]; //by this point data file exists and is populated, but it's file path is known
+ char* plotFilePath = new char[SIZE_FILE];
+
+ char plotCommand[TEXT_SIZE3];
+
+ //assume filePath = c:Inetpub/wwwroot/ISB/data/class/iProphet/xtandem/interact.iproph.pep.xml.a#####.
+
+ sprintf(pngFilePath, "%s%ld.%s.ISB.png", filePath, random, scoreName);
+ sprintf(plotFilePath, "%sgp", filePath);
+ sprintf(dataFilePath, "%sdata", filePath);
+
+ //plot command
+ //cd c:/Inetpub/wwwroot/ISB/data/class/iProphet/xtandem; wgnuplot.exe interact.iproph.pep.xml.a02644.gp; rm -f interact.iproph.pep.xml.a02644.gp
+ //return path
+ //c:/Inetpub/wwwroot//ISB/data/class/iProphet/xtandem/interact.iproph.pep.xml.a02644.31533.ISB.png
+
+ if ((fpPlotCode = fopen(plotFilePath, "w")) == NULL)
+ printf("Error - cannot create gnuplot file %s.", plotFilePath);
+ else
+ {
+ //gnuplot code
+ fprintf(fpPlotCode, "set terminal png truecolor size %d, %d\n", IMG_W, IMG_H);
+ fprintf(fpPlotCode, "set output \"%s\"\n", pngFilePath);
+ fprintf(fpPlotCode, "set border 1\n");
+ fprintf(fpPlotCode, "set xzeroaxis linetype -1 linewidth 1.0\n");
+ fprintf(fpPlotCode, "set x2zeroaxis linetype 0 linewidth 1.0\n");
+ fprintf(fpPlotCode, "set xlabel \"%s\"\n", scoreTitle);
+ fprintf(fpPlotCode, "set ylabel \"Density\"\n");
+ fprintf(fpPlotCode, "set y2label \"ln(P/N)\"\n");
+ fprintf(fpPlotCode, "set xtics border nomirror out\n");
+ fprintf(fpPlotCode, "set ytics border nomirror out\n");
+ fprintf(fpPlotCode, "set y2tics border nomirror out\n");
+ fprintf(fpPlotCode, "set mxtics\n");
+ fprintf(fpPlotCode, "set mytics\n");
+ fprintf(fpPlotCode, "set my2tics\n");
+ fprintf(fpPlotCode, "set key bottom right\n");
+ fprintf(fpPlotCode, "set arrow 1 from %f, 0 to %f, 100 nohead lw 2 lc %d\n", scoreVal, scoreVal, scoreColor);
+ fprintf(fpPlotCode, "plot 0 title \"%s = %g\" lw 2 lc %d, \\\n", scoreName, scoreVal, scoreColor);
+ fprintf(fpPlotCode, "\"%s\" using 1:2 title \"Positive Model (P)\" with line lw 2 lc %d, \\\n", dataFilePath, posColor);
+ fprintf(fpPlotCode, "\"%s\" using 1:3 title \"Negative Model (N)\" with line lw 2 lc %d, \\\n", dataFilePath, negColor);
+ if(drawPobs_)
+ fprintf(fpPlotCode, "\"%s\" using 1:5 title \"Positive Observed\" with boxes lc %d fs transparent solid 0.2 noborder, \\\n", dataFilePath, posColor);
+ if(drawNobs_)
+ fprintf(fpPlotCode, "\"%s\" using 1:6 title \"Negative Observed\" with boxes lc %d fs transparent solid 0.2 noborder, \\\n", dataFilePath, negColor);
+ fprintf(fpPlotCode, "\"%s\" using 1:4 title \"ln(P/N)\" axes x1y2 with line lc %d\n", dataFilePath, lnColor);
+
+ fclose(fpPlotCode);
+
+ char* plotFileName = findRightmostPathSeperator(plotFilePath);
+ *plotFileName++ = '\0';
+
+ //write and call plot command
+ sprintf(plotCommand, "cd %s; %s %s; rm -f %s", plotFilePath, GNUPLOT_BINARY, plotFileName, plotFileName);
+ verified_system(plotCommand); //system() with verbose error check
+
+#ifdef USING_RELATIVE_WEBSERVER_PATH //fix up the image path if needed
+ pngFilePath = translate_relative_webserver_root_path_to_absolute_filesystem_path(pngFilePath);
+#endif
+ }
+
+ unlink(plotFilePath);
+
+ return pngFilePath;
+}
+
+//main html generating function
+void iModelParser::writeModelResults(ostream& os, char* options, Array<sensTableDataPoint*>* sensitivity)
+{
+ char *fp = new char[TEXT_SIZE2];
+
+ sprintf(fp, "<html>\n<head>\n<title>%s (%s), %s</title>\n\n", szVERSION, szTPPVersionInfo, szAUTHOR);
+ os << fp;
+
+ //style-sheet
+ os << "<!--Style-sheet-->\n";
+ os << "<style type = \"text/css\">\n";
+ os << ".hideit\n{\n\tdisplay: none;\n}\n";
+ os << ".showit\n{\n\tdisplay: table-row;\n}\n";
+ os << "body\n{\n\tfont-family: Helvetica, sans-serif;\n}\n";
+ os << "table\n{\n\tborder-collapse: collapse;\n\tborder-color: #000000;\n}\n";
+ os << ".banner_cid\n{\n\tbackground: #0e207f;\n\tborder: 2px solid #0e207f;\n\tcolor: #eeeeee;\n\tfont-weight: bold;\n}\n";
+ os << ".formentry\n{\n\tbackground: #eeeeee;\n\tborder: 2px solid #0e207f;\n\tcolor: black;\n\tpadding: 1em;\n}\n";
+ os << ".model\n{\n\tbackground: #ffffff;\n\tborder: 2px solid #0e207f;\n\tcolor: black;\n\tpadding: 1em;\n}\n";
+ os << ".info\n{\n\tcolor: #333333;\n\tfont-size: 10pt;\n}\n";
+ os << ".infoplus\n{\n\tborder-top: 1px solid black;\n\tcolor: #333333;\n\tfont-size: 10pt;\n}\n";
+ os << "</style>\n\n";
+
+ //javascript
+ os << "<!--Javascript variables and functions-->\n";
+ os << "<script language = \"JavaScript\">\n";
+ os << "var showParams = true;\n";
+ os << "function toggleParams()\n{\n";
+ os << "\tvar new_state = 'hideit';\n\n";
+ os << "\tif (showParams)\n\t{\n";
+ os << "\t\tnew_state = 'showit';\n";
+ os << "\t\tdocument.getElementById('paramshead').innerHTML = ': [ - ]';\n";
+ os << "\t}\n\telse\n";
+ os << "\t\tdocument.getElementById('paramshead').innerHTML = '... [ + ]';\n\n";
+ os << "\tshowParams = !showParams;\n\n";
+ os << "\tfor(var i = 1; i != 4; i++)\n";
+ os << "\t\tdocument.getElementById(\"parameters\"+i).className = new_state;\n";
+ os << "}\n";
+ os << "</script>\n";
+
+ os << "</head>\n\n";
+
+ //main body code
+ os << "<body bgcolor = \"#c0c0c0\" onload = \"self.focus();\" link = \"#0000FF\" vlink = \"#0000FF\" alink = \"#FF0000\">\n\n";
+
+ os << "<table cellspacing = \"0\"><tr>\n<td class = \"banner_cid\"> iProphet<sup><small>TM</small></sup> Analysis Results </td>\n</tr></table>\n";
+ os << "<div class = \"formentry\">\n\n";
+
+ //analysis results tab
+ os << "<!--Analysis Results Tab-->\n";
+ os << "<table cellpadding = \"2\" border = \"0\"><tbody>\n";
+ os << "<tr>\n";
+
+ //write main graph path to html file
+ if (pngsensgraph_ != NULL)
+ {
+ sprintf(fp, "<td rowspan = \"1\" valign = \"top\"><img border = \"1\" src = \"%s\"></td>\n", makeTmpPNGFileSrcRef(pngsensgraph_).c_str());
+ os << fp;
+ }
+
+ //main graph/table text
+ os << "<td rowspan = \"1\" valign = \"top\">\n";
+
+ //write total correct assignments to html
+ sprintf(fp, "Estimated total number of correct peptide assignments in dataset: <b>%0.1f</b><br/><br/>\n", est_tot_num_correct_);
+ os << fp;
+ //write sensitivity to html
+ sprintf(fp, "<font color = \"red\">Sensitivity:</font> fraction of all correct assignments (<font color = \"DarkBlue\">%0.1f</font>) passing MPT filter<br/><br/>\n", est_tot_num_correct_);
+ os << fp;
+ sprintf(fp, "<font color = \"green\">Error</font>: fraction of peptide assignments passing MPT filter that are incorrect<br/><br/>\n");
+ os << fp;
+ os << "MPT = Minimum Probability Threshhold to Accept<br/><br/>\n";
+
+ //write error table (small one) to html
+ os << "<!--Small table-->\n";
+ os << "<center>\n";
+ os << "<table style = \"font-family: 'Courier New', Courier, mono; font-size: 8pt;\" bgcolor = \"white\" cellpadding = \"2\" frame = \"border\" rules = \"all\">\n";
+ os << "<tr><td><b><i>error</i></b></td><td><b><i>MPT</i></b></td><td><b><i>est # corr</i></b></td></tr>\n";
+
+ for(char i = 0; i != ERROR_NUM; i++) //generate small table
+ {
+ sprintf(fp, "<tr><td>%0.3f</td><td>%0.2f</td><td>%d</td></tr>\n", errors_[i], min_prob_threshes_[i], est_num_corrects_[i]);
+ os << fp;
+ }
+
+ os << "</table>\n</center>\n</td>\n\n";
+
+ //main table
+ os << "<!--Main table-->\n";
+ os << "<td rowspan = \"1\">\n";
+
+ //write large table to html
+ writeSensitivityTable(os, sensitivity); //generate main table
+
+ os << "</td>\n</tr>\n<tr>\n\n";
+
+ //information below tables
+ os << "<!--Information below tables-->\n";
+ os << "<td colspan = \"3\">\n";
+
+ sprintf(fp, "<div class = \"infoplus\">iProphetParser (%s), %s<br/>\n",szTPPVersionInfo, szAUTHOR);
+ os << fp;
+ os << "<a onclick = \"toggleParams()\">Input Files and Run Parameters<font color = \"blue\" id = \"paramshead\">... [ + ]</font></a>\n";
+ os << "</div>\n</td>\n</tr>\n\n";
+
+ os << "<tr id = \"parameters1\" class = \"hideit\">\n";
+ //write analysis date to html
+ os << "<td class = \"info\" align = \"right\" valign = \"top\">Analysis Date: </td>\n";
+ sprintf(fp, "<td class = \"info\" colspan = \"1\"><b>%s</b></td>\n", timestamp_);
+ os << fp;
+
+ os << "</tr>\n";
+ os << "<tr id = \"parameters2\" class = \"hideit\">\n";
+
+ os << "<td class = \"info\" align = \"right\" valign = \"top\">Input Files: </td>\n";
+ os << "<td class = \"info\" colspan = \"3\"><tt>\n";
+
+ //write input file paths to html (part of run parameters)
+ for(char i = 0; i != inputfiles_->length(); i++)
+ {
+ os << (*inputfiles_)[i];
+ os << "<br/>\n";
+ }
+
+ os << "</tt></td></tr>\n";
+
+ os << "<tr id = \"parameters3\" class = \"hideit\">\n";
+ //write run options to html
+ os << "<td class = \"info\" align = \"right\" valign = \"top\">Run Options: </td>\n";
+
+ sprintf(fp, "<td class = \"info\" colspan = \"3\">%s</td>\n", options);
+ os << fp;
+
+ os << "</tr>\n</tbody>\n</table>\n\n</div>\n\n<br/>\n\n";
+
+ //iprophet models tab
+ os << "<!--iProphet Models Tab-->\n";
+ os << "<table cellspacing = \"0\"><tr>\n";
+ os << "<td class = \"banner_cid\"> iProphet Models </td>\n";
+ os << "</tr></table>\n\n";
+
+ os << "<div class = \"model\">\n\n";
+
+ //write model png paths to html, check if null
+ for(char i = 0; i != MODEL_IMGS; i++)
+ {
+ if (pngmodels_[i] != NULL)
+ {
+ sprintf(fp, "<td><img src = \"%s\" \"border = 0\"/></td>\n", makeTmpPNGFileSrcRef(pngmodels_[i]).c_str());
+ os << fp;
+ }
+ }
+
+ os << "<br/>\n";
+
+ //text below model graphs
+ os << "<!--Text below model graphs-->\n";
+ os << "<div class = \"infoplus\">\n";
+ os << "<table cellpadding = \"10\"><tr>\n";
+
+ //the spectrum, scores, and prob values will probably change eventually
+
+ //spectrum and scores
+ if(strlen(spectrum_) > 0)
+ {
+ sprintf(fp, "<td>");
+ os << fp;
+
+ //write text below images to html
+ sprintf(fp, "<b><i>spectrum:</i></b> %s</td>\n<td><b><i>scores:</i></b> %s</td>\n", format(spectrum_), scores_);
+ os << fp;
+ }
+
+ //prob
+ if(strlen(prob_) > 0)
+ {
+ sprintf(fp, "<td>");
+ os << fp;
+
+ Boolean abbrev = strlen(prob_) == 1 || *prob_ == '-';
+
+ if(abbrev)
+ {
+ sprintf(fp, "<b><i>iprob:</i></b> %s", prob_);
+ os << fp;
+
+ if(strlen(prob_) > 0 && *prob_ == '-')
+ sprintf(fp, " (possibly correct)");
+ else
+ sprintf(fp, " (unlikely correct)"); //fv
+
+ os << fp;
+ }
+ else
+ {
+ if(adjusted_)
+ sprintf(fp, "<b><i>iprob:</i></b> %s (adj)", prob_);
+ else
+ sprintf(fp, "<b><i>iprob:</i></b> %s", prob_);
+
+ os << fp;
+ }
+
+ sprintf(fp, "</td>\n");
+ os << fp;
+ }
+
+ os << "</tr></table></div>\n\n</div>\n\n<br/>\n\n";
+
+ Boolean drawPerformTab = false;
+ for(char i = 0; i != PERFORM_IMGS; i++)
+ {
+ if(pngperforms_[i] != NULL)
+ {
+ drawPerformTab = true;
+ break;
+ }
+ }
+
+ if (drawPerformTab)
+ {
+ //iprophet performance tab
+ os << "<!--iProphet Performance Tab-->\n";
+ os << "<table cellspacing = \"0\"><tr>";
+ os << "<td class = \"banner_cid\"> iProphet Performance </td>";
+ os << "</tr></table>";
+
+ os << "<div class = \"model\">\n";
+
+ //write performance png paths to html, check if null
+ for (char i = 0; i != PERFORM_IMGS; i++)
+ {
+ if (pngperforms_[i] != NULL)
+ {
+ sprintf(fp, "<td><a href = \"%s\"><img src = \"%s\" width = \"%d\" height = \"%d\" border = \"0\"/></a></td>\n",
+ pngperforms_[i], pngperforms_[i], IMG_W, IMG_H);
+ os << fp;
+ }
+ }
+ }
+
+ os << "</body>\n";
+ os << "</html>\n";
+
+ //html code finished
+
+ delete []fp;
+}
+
+void iModelParser::writeSensitivityTable(ostream& os, Array<sensTableDataPoint*>* sensitivity)
+{
+ char text[TEXT_SIZE3];
+
+ sprintf(text, "<table frame = \"border\" rules = \"all\" cellpadding = \"2\" bgcolor = \"white\" style = \"font-family: \'Courier New\', Courier, mono; font-size: 8pt;\">\n");
+ os << text;
+ sprintf(text, "<tr><td><b><i>Min Prob</i></b></td><td><b><i>Sensitivity</i></b></td><td><b><i>Error</i></b></td>\n");
+ os << text;
+
+ for(int k = 0; k < sensitivity->length(); k++)
+ {
+ sprintf(text, "<tr><td>%0.2f</td><td>%0.3f</td><td>%0.3f</td></tr>\n", (*sensitivity)[k]->minprob, (*sensitivity)[k]->sens, (*sensitivity)[k]->err);
+ os << text;
+ }
+
+ sprintf(text, "</table>\n\n");
+ os << text;
+}
+
+char* iModelParser::format(char* spec) //used to format spectrum_
+{
+ char output[SIZE_FILE * 2];
+ *output = 0;
+ char insertion[] = "<br>";
+ int k;
+ int num_insertions = (int)(strlen(spec) - 1) / TEXT_SIZE1;
+
+ if(num_insertions < 1 || strlen(spec) - TEXT_SIZE1 < 8)
+ return spec; //nothing to do
+
+ for(k = 0; k < num_insertions; k++)
+ {
+ strncat(output, spec + (k * TEXT_SIZE1), TEXT_SIZE1);
+ output[(k + 1) * TEXT_SIZE1 + k * strlen(insertion)] = 0;
+ strcat(output, insertion);
+ }
+
+ //last piece
+ strcat(output, spec + num_insertions * TEXT_SIZE1);
+ strcpy(spec, output);
+
+ return spec;
+}
Added: trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.h
===================================================================
--- trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.h (rev 0)
+++ trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.h 2010-08-11 18:16:13 UTC (rev 5107)
@@ -0,0 +1,141 @@
+#ifndef MODEL_PARSER_H
+#define MODEL_PARSER_H
+
+/*
+Program: iModelParser
+Author: Richard Stauffer, modified from ModelParser: J.Eng and Andrew Keller <ak...@sy...>, Robert Hubley, and open source code
+Date: Summer 2010
+
+Primary data object holding all mixture distributions for each precursor ion charge
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+Andrew Keller
+Insitute for Systems Biology
+1441 North 34th St.
+Seattle, WA 98103 USA
+ak...@sy...
+*/
+
+#include "common/constants.h"
+#include "Parsers/Parser/Parser.h"
+#include "Parsers/Parser/TagFilter.h"
+#include "Validation/PeptideProphet/PeptideProphetParser/PeptideProphetParser.h"
+
+//definitions
+#define szVERSION "PLOTMODEL"
+#define szAUTHOR "by J.Eng A.Keller, Institute for Systems Biology, 2002. All rights reserved."
+
+//string length maximum constants
+#define TEXT_SIZE1 64
+#define TEXT_SIZE2 512
+#define TEXT_SIZE3 4096
+
+#define N_SCORE_SIZE 4
+
+//definitions for image size constants, gnuplot default image size is 640 by 480
+#define SENS_IMG_W 11 * 640 / 20
+#define SENS_IMG_H 3 * 480 / 5
+
+#define IMG_W 3 * 640 / 4
+#define IMG_H 3 * 480 / 4
+
+#define MODEL_IMGS 5
+#define PERFORM_IMGS 6
+
+#define ERROR_NUM 3
+
+enum N_Score
+{
+ NSS,
+ NSE,
+ NSI,
+ NSM,
+ NRS,
+ NONE
+};
+
+struct sensTableDataPoint
+{
+ double minprob, sens, err;
+};
+
+struct nScoreDataPoint
+{
+ double nScore, pos, neg, ln, posObs, negObs;
+};
+
+struct nScoreDataSet
+{
+ double scoreVal;
+ Array<nScoreDataPoint*>* dataPoints;
+
+ nScoreDataSet()
+ {
+ scoreVal = 0;
+ dataPoints = new Array<nScoreDataPoint*>;
+ }
+};
+
+class iModelParser : public Parser
+{
+public:
+ //functions
+
+ iModelParser(const char* xmlfile, const char* timestamp, const char* spectrum, const char* scores, char* prob);
+ ~iModelParser();
+
+protected:
+ //functions
+
+ void parse(const char* xmlfile);
+ char* iModelParser::setFilePaths(char* filePath);
+ void removeOldFiles(char* filePath);
+
+ void writeModelResults(ostream& os, char* options, Array<sensTableDataPoint*>* sensitivity);
+ void writeSensitivityTable(ostream& os, Array<sensTableDataPoint*>* sensitivity);
+ char* format(char* spec);
+
+ char* iModelParser::plotSensitivity(char* filePath, long random, char sensColor, char errColor);
+
+ char* iModelParser::plotModel(char* filePath, char* scoreName, char* scoreTitle, double scoreVal, long random,
+ char posColor, char negColor, char lnColor, char scoreColor);
+
+ //variables
+
+ Boolean adjusted_, drawPobs_, drawNobs_;
+
+ Array<char*>* inputfiles_;
+
+ char* timestamp_;
+ char* spectrum_;
+ char* scores_;
+ char* prob_;
+ char* prophet_name_;
+
+ //paths of image files
+ char* pngsensgraph_; //sensitivity graph
+ char* pngmodels_[MODEL_IMGS]; //images for models tab
+ char* pngperforms_[PERFORM_IMGS]; //images for performance tab
+
+ double est_tot_num_correct_;
+
+ //error table
+ double errors_[ERROR_NUM];
+ double min_prob_threshes_[ERROR_NUM];
+ int est_num_corrects_[ERROR_NUM];
+};
+
+#endif
Added: trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParserMain.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParserMain.cxx (rev 0)
+++ trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParserMain.cxx 2010-08-11 18:16:13 UTC (rev 5107)
@@ -0,0 +1,153 @@
+/*
+Program: iModelParser
+Author: Richard Stauffer, modified from ModelParser: J.Eng and Andrew Keller <ak...@sy...>, Robert Hubley, and open source code
+Date: Summer 2010
+
+Primary data object holding all mixture distributions for each precursor ion charge
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+Andrew Keller
+Insitute for Systems Biology
+1441 North 34th St.
+Seattle, WA 98103 USA
+ak...@sy...
+*/
+
+#include "stdio.h"
+#include "string.h"
+#include "common/util.h"
+#include "IModelParser.h"
+#include "common/TPPVersion.h" //contains version number, name, revision
+
+void EXTRACT_QUERY_STRING(char* xmlile, char* timestamp, char* spec, char* scores, char* prob);
+void EXTRACT_QUERY_STRING_helper(char* szQuery, char* xmlile, char* timestamp, char* spec, char* scores, char* prob);
+
+//main
+int main(int argc, char** argv)
+{
+ hooks_tpp handler(argc, argv); //set up install paths, etc
+
+ char xmlfile[TEXT_SIZE2];
+ char timestamp[TEXT_SIZE2];
+ char spec[TEXT_SIZE2];
+ char scores[TEXT_SIZE2];
+ char prob[TEXT_SIZE1];
+
+ *xmlfile = 0;
+ *timestamp = 0;
+ *spec = 0;
+ *scores = 0;
+ *prob = 0;
+
+ if(argc == 1) //make sure format is correct, 1 = CGI format
+ {
+ cout << "Content-type: text/html" << endl << endl;
+ EXTRACT_QUERY_STRING(xmlfile, timestamp, spec, scores, prob);
+ }
+ else //this should be changed over to cgi format: extracting arguments from posted information
+ EXTRACT_QUERY_STRING_helper(argv[1], xmlfile, timestamp, spec, scores, prob);
+
+ iModelParser *iModel = new iModelParser(xmlfile, timestamp, spec, scores, prob); //create new iModelParser which does everything on it's own
+ delete iModel; //then delete it
+
+ return 0;
+}
+
+void EXTRACT_QUERY_STRING(char* xmlfile, char* timestamp, char* spec, char* scores, char* prob)
+{
+ char *pStr = getenv("REQUEST_METHOD");
+
+ if (pStr == NULL)
+ {
+ printf(" Error - this is a CGI program that cannot be\nrun from the command line.\n\n");
+ exit(EXIT_FAILURE);
+ }
+ else if (!strcmp(pStr, "GET"))
+ {
+ char *szQuery;
+
+ szQuery = getenv("QUERY_STRING");
+
+ if (szQuery == NULL)
+ {
+ printf("<P>No query information to decode.\n</BODY>\n</HTML>\n");
+ exit(EXIT_FAILURE);
+ }
+
+ EXTRACT_QUERY_STRING_helper(szQuery, xmlfile, timestamp, spec, scores, prob);
+ }
+ else
+ {
+ printf(" Error not called with GET method\n");
+ exit(1);
+ }
+}
+
+void EXTRACT_QUERY_STRING_helper(char *szQuery, char* xmlfile, char* timestamp, char* spec, char* scores, char* prob)
+{
+ char szWord[TEXT_SIZE2];
+
+ for (int i = 0; *szQuery != '\0'; i++)
+ {
+ getword(szWord, szQuery, '=');
+ plustospace(szWord);
+ unescape_url(szWord);
+
+ if (!strcmp(szWord, "Xmlfile"))
+ {
+ getword(szWord, szQuery, '&');
+ plustospace(szWord);
+ unescape_url(szWord);
+ sscanf(szWord, "%s", xmlfile);
+
+ fixPath(xmlfile, 1); //tidy up path seperators etc - expect existence
+ }
+ else if (!strcmp(szWord, "Timestamp")) //odd order
+ {
+ getword(szWord, szQuery, '&');
+ sscanf(szWord, "%s", timestamp);
+ plustospace(timestamp);
+ unescape_url(timestamp);
+ }
+ else if (!strcmp(szWord, "Spectrum"))
+ {
+ getword(szWord, szQuery, '&');
+ plustospace(szWord);
+ unescape_url(szWord);
+ sscanf(szWord, "%s", spec);
+ }
+ else if (!strcmp(szWord, "Scores")) //odd order, but only way it works
+ {
+ getword(szWord, szQuery, '&');
+ sscanf(szWord, "%s", scores);
+ plustospace(scores);
+ unescape_url(scores);
+ }
+ else if (!strcmp(szWord, "Prob"))
+ {
+ getword(szWord, szQuery, '&');
+ plustospace(szWord);
+ unescape_url(szWord);
+ sscanf(szWord, "%s", prob);
+ }
+ else
+ {
+ getword(szWord, szQuery, '&');
+ plustospace(szWord);
+ unescape_url(szWord);
+ }
+ }
+}
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