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Steve Benz
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Adding current licensing information
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‎README.mediawiki‎

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= PARADIGM =
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== PAthway Representation and Analysis by Direct Reference on Graphical Models ==
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Developed by Charles Vaske & Steve Benz
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A factor graph framework for pathway inference on high-throughput genomic data
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=== LICENSE & COPYRIGHT ===
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Copyright 2009-2011 -- The Regents of the University of California
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This code is provided for research purposes to scientists at non-profit organizations. All other use is strictly prohibited.
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For further details please contact University of California, Santa Cruz or Five3 Genomics, LLC (http://five3genomics.com).

‎common.h‎

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/********************************************************************************/
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/* Copyright 2009-2011 -- The Regents of the University of California */
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/* This code is provided for research purposes to scientists at non-profit */
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/* organizations. All other use is strictly prohibited. For further */
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/* details please contact University of California, Santa Cruz or */
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/* Five3 Genomics, LLC (http://five3genomics.com). */
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/********************************************************************************/
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#ifndef HEADER_DIGMA_COMMON_H
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#define HEADER_DIGMA_COMMON_H
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‎configuration.cpp‎

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/********************************************************************************/
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/* Copyright 2009-2011 -- The Regents of the University of California */
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/* This code is provided for research purposes to scientists at non-profit */
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/* organizations. All other use is strictly prohibited. For further */
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/* details please contact University of California, Santa Cruz or */
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/* Five3 Genomics, LLC (http://five3genomics.com). */
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/********************************************************************************/
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#include "configuration.h"
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const std::string RunConfiguration::INFERENCE_CONF_TOKEN("inference");
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addConfigurations(is);
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}
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PropertySet&
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RunConfiguration::getInferenceProperties(const std::string& pathway_filename)
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PropertySet&
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RunConfiguration::getInferenceProperties(const std::string& pathway_filename)
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{
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for (size_t i = 0; i < _inferences.size(); i++)
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{

‎configuration.h‎

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/********************************************************************************/
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/* Copyright 2009-2011 -- The Regents of the University of California */
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/* This code is provided for research purposes to scientists at non-profit */
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/* organizations. All other use is strictly prohibited. For further */
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/* details please contact University of California, Santa Cruz or */
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/* Five3 Genomics, LLC (http://five3genomics.com). */
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/********************************************************************************/
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#ifndef HEADER_CONFIGURATION_H
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#define HEADER_CONFIGURATION_H
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using namespace dai;
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class RunConfiguration
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class RunConfiguration
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{
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public:
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static const std::string INFERENCE_CONF_TOKEN;
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EMSteps _emsteps;
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PropertySet _em;
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PropertySet _path;
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public:
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/// Default constructor
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}
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/// Copy constructor
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RunConfiguration(const RunConfiguration &x) :
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_inferences(x._inferences),
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RunConfiguration(const RunConfiguration &x) :
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_inferences(x._inferences),
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_evidences(x._evidences),
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_emsteps(x._emsteps),
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_em(x._em),
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}
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return *this;
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}
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/// Useful constructor
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RunConfiguration(const std::string& configure_filename);
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PropertySet& evidence(size_t i);
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PropertySet& pathwayProps() {return _path;}
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size_t evidenceSize();
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const PropertySet& emProps() { return _em; }
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const EMSteps emSteps() const {return _emsteps;}
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};
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‎evidencesource.cpp‎

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/********************************************************************************/
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/* Copyright 2009-2011 -- The Regents of the University of California */
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/* This code is provided for research purposes to scientists at non-profit */
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/* organizations. All other use is strictly prohibited. For further */
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/* details please contact University of California, Santa Cruz or */
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/* Five3 Genomics, LLC (http://five3genomics.com). */
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/********************************************************************************/
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#include <fstream>
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#include "common.h"
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#include "evidencesource.h"
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#define THROW(msg) throw std::runtime_error(msg)
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8-
EvidenceFactorGen::EvidenceFactorGen(const PropertySet& p) : _params()
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EvidenceFactorGen::EvidenceFactorGen(const PropertySet& p) : _params()
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{
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_params.reserve(9);
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if (p.hasKey("factorParams")) {
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Real minor = epsilon / 2;
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Real major0 = 1 - epsilon0;
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Real minor0 = epsilon0 / 2;
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bool flip = false;
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if (p.hasKey("reverse")) {
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if (p.getStringAs<string>("reverse") == "true") {
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_params.push_back(minor);
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_params.push_back(minor0);
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_params.push_back(major);
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_params.push_back(minor);
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_params.push_back(major0);
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_params.push_back(minor);
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_params.push_back(major);
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_params.push_back(minor0);
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_params.push_back(minor);
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_params.push_back(minor);
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_params.push_back(major0);
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_params.push_back(minor);
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_params.push_back(minor);
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_params.push_back(minor0);
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_params.push_back(major);
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}
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}
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void EvidenceFactorGen::generateValues(const vector< string >& edge_types,
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void EvidenceFactorGen::generateValues(const vector< string >& edge_types,
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vector< Real >& outVals) const
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{
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assert(edge_types.size() == 1);
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}
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}
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EvidenceSource::EvidenceSource(PropertySet &p, string base) :
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EvidenceSource::EvidenceSource(PropertySet &p, string base) :
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cutoffs(),
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options(p),
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attachPoint(),
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attachPoint(),
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_evidenceFile()
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{
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if (p.hasKey("disc"))
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return result;
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}
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void EvidenceSource::loadFromFile(PathwayTab& p,
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map<string, size_t>& sampleMap,
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vector<Evidence::Observation>& sampleData)
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void EvidenceSource::loadFromFile(PathwayTab& p,
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map<string, size_t>& sampleMap,
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vector<Evidence::Observation>& sampleData)
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{
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ifstream infile;
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infile.open( _evidenceFile.c_str() );
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170178
FactorGenerator* fgen = new EvidenceFactorGen(options);
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p.addFactorGenerator("protein", _suffix, fgen);
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while(getline(infile,line)) {
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vector<string> vals;
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Tokenize(line,vals,"\t");
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string sample = vals[0];
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_sampleNames.push_back(sample);
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vals.erase(vals.begin());
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for(size_t i = 0; i < vals.size(); i++) {
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if(p.getEntityType(header[i]) != "protein") // skip adding evidence if it's not in the pathway
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continue;
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pos = str.find_first_of(delimiters, lastPos);
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}
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}
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‎evidencesource.h‎

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/********************************************************************************/
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/* Copyright 2009-2011 -- The Regents of the University of California */
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/* This code is provided for research purposes to scientists at non-profit */
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/* organizations. All other use is strictly prohibited. For further */
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/* details please contact University of California, Santa Cruz or */
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/* Five3 Genomics, LLC (http://five3genomics.com). */
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/********************************************************************************/
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#ifndef HEADER_EVIDENCESOURCE_H
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#define HEADER_EVIDENCESOURCE_H
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EvidenceFactorGen(const PropertySet& p);
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~EvidenceFactorGen() {}
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20-
void generateValues(const vector< string >& edge_types,
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void generateValues(const vector< string >& edge_types,
2129
vector< Real >& outVals) const;
2230
};
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2432
typedef map<string, map<string,int> > SampleEvidMap;
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26-
class EvidenceSource
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class EvidenceSource
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{
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private:
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vector<double> cutoffs;
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4149
public:
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/// Default constructor
43-
EvidenceSource() : cutoffs(),
44-
attachPoint(),
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EvidenceSource() : cutoffs(),
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attachPoint(),
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_suffix(),
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_evidenceFile(),
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_disc(),
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setCutoffs("-1.3;1.3");
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}
5563
/// Copy constructor
56-
EvidenceSource(const EvidenceSource &x)
57-
: cutoffs(x.cutoffs),
58-
attachPoint(x.attachPoint),
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EvidenceSource(const EvidenceSource &x)
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: cutoffs(x.cutoffs),
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attachPoint(x.attachPoint),
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_suffix(x._suffix),
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_evidenceFile(x._evidenceFile),
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_disc(x._disc),
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_sampleNames(x._sampleNames),
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_sampleFactors(x._sampleFactors),
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_sampleFactorNum(x._sampleFactorNum) {}
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/// Assignment operator
6775
EvidenceSource& operator=(const EvidenceSource &x) {
6876
if (this != &x) {
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8391
EvidenceSource(PropertySet &p, string base);
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8593
void setCutoffs(string discLimits);
86-
int discCutoffs (float x);
94+
int discCutoffs (float x);
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88-
void loadFromFile(PathwayTab& p,
89-
map<string, size_t>& sampleMap,
96+
void loadFromFile(PathwayTab& p,
97+
map<string, size_t>& sampleMap,
9098
vector<Evidence::Observation>& sampleData);
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92100
const string& evidenceFile() {return _evidenceFile;}

‎externVars.cpp‎

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/********************************************************************************/
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/* Copyright 2009-2011 -- The Regents of the University of California */
3+
/* This code is provided for research purposes to scientists at non-profit */
4+
/* organizations. All other use is strictly prohibited. For further */
5+
/* details please contact University of California, Santa Cruz or */
6+
/* Five3 Genomics, LLC (http://five3genomics.com). */
7+
/********************************************************************************/
8+
19
#include "common.h"
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// globals

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