Adding current licensing information

Author: Steve Benz

README.mediawiki

@@ -0,0 +1,15 @@
+= PARADIGM =
+== PAthway Representation and Analysis by Direct Reference on Graphical Models ==
+
+Developed by Charles Vaske & Steve Benz
+
+A factor graph framework for pathway inference on high-throughput genomic data
+
+
+=== LICENSE & COPYRIGHT ===
+
+Copyright 2009-2011 -- The Regents of the University of California
+
+
+This code is provided for research purposes to scientists at non-profit organizations.  All other use is strictly prohibited.
+For further details please contact University of California, Santa Cruz or Five3 Genomics, LLC (http://five3genomics.com).

common.h

@@ -1,3 +1,11 @@
+/********************************************************************************/
+/* Copyright 2009-2011 -- The Regents of the University of California           */
+/* This code is provided for research purposes to scientists at non-profit		*/
+/*  organizations.  All other use is strictly prohibited.  For further			*/
+/*  details please contact University of California, Santa Cruz or				*/
+/*	Five3 Genomics, LLC (http://five3genomics.com).								*/
+/********************************************************************************/
+
 #ifndef HEADER_DIGMA_COMMON_H
 #define HEADER_DIGMA_COMMON_H
 

configuration.cpp

@@ -1,3 +1,11 @@
+/********************************************************************************/
+/* Copyright 2009-2011 -- The Regents of the University of California           */
+/* This code is provided for research purposes to scientists at non-profit		*/
+/*  organizations.  All other use is strictly prohibited.  For further			*/
+/*  details please contact University of California, Santa Cruz or				*/
+/*	Five3 Genomics, LLC (http://five3genomics.com).								*/
+/********************************************************************************/
+
 #include "configuration.h"
 
 const std::string RunConfiguration::INFERENCE_CONF_TOKEN("inference");
@@ -16,8 +24,8 @@ RunConfiguration::RunConfiguration(const std::string& configure_filename)
   addConfigurations(is);
 }
 
-PropertySet& 
-RunConfiguration::getInferenceProperties(const std::string& pathway_filename) 
+PropertySet&
+RunConfiguration::getInferenceProperties(const std::string& pathway_filename)
 {
   for (size_t i = 0; i < _inferences.size(); i++)
     {

configuration.h

@@ -1,3 +1,11 @@
+/********************************************************************************/
+/* Copyright 2009-2011 -- The Regents of the University of California           */
+/* This code is provided for research purposes to scientists at non-profit		*/
+/*  organizations.  All other use is strictly prohibited.  For further			*/
+/*  details please contact University of California, Santa Cruz or				*/
+/*	Five3 Genomics, LLC (http://five3genomics.com).								*/
+/********************************************************************************/
+
 #ifndef HEADER_CONFIGURATION_H
 #define HEADER_CONFIGURATION_H
 
@@ -11,7 +19,7 @@
 
 using namespace dai;
 
-class RunConfiguration 
+class RunConfiguration
 {
 public:
   static const std::string INFERENCE_CONF_TOKEN;
@@ -31,7 +39,7 @@ class RunConfiguration
   EMSteps _emsteps;
   PropertySet _em;
   PropertySet _path;
-  
+
 public:
 
   /// Default constructor
@@ -40,8 +48,8 @@ class RunConfiguration
   }
 
   /// Copy constructor
-  RunConfiguration(const RunConfiguration &x) : 
-    _inferences(x._inferences), 
+  RunConfiguration(const RunConfiguration &x) :
+    _inferences(x._inferences),
     _evidences(x._evidences),
     _emsteps(x._emsteps),
     _em(x._em),
@@ -59,7 +67,7 @@ class RunConfiguration
     }
     return *this;
   }
-  
+
   /// Useful constructor
   RunConfiguration(const std::string& configure_filename);
 
@@ -70,11 +78,11 @@ class RunConfiguration
   PropertySet& evidence(size_t i);
 
   PropertySet& pathwayProps() {return _path;}
-  
+
   size_t evidenceSize();
-  
+
   const PropertySet& emProps() { return _em; }
-  
+
   const EMSteps emSteps() const {return _emsteps;}
 };
 

evidencesource.cpp

@@ -1,11 +1,19 @@
+/********************************************************************************/
+/* Copyright 2009-2011 -- The Regents of the University of California           */
+/* This code is provided for research purposes to scientists at non-profit		*/
+/*  organizations.  All other use is strictly prohibited.  For further			*/
+/*  details please contact University of California, Santa Cruz or				*/
+/*	Five3 Genomics, LLC (http://five3genomics.com).								*/
+/********************************************************************************/
+
 #include <fstream>
 
 #include "common.h"
 #include "evidencesource.h"
 
 #define THROW(msg) throw std::runtime_error(msg)
 
-EvidenceFactorGen::EvidenceFactorGen(const PropertySet& p) : _params() 
+EvidenceFactorGen::EvidenceFactorGen(const PropertySet& p) : _params()
 {
   _params.reserve(9);
   if (p.hasKey("factorParams")) {
@@ -33,7 +41,7 @@ EvidenceFactorGen::EvidenceFactorGen(const PropertySet& p) : _params()
   Real minor = epsilon / 2;
   Real major0 = 1 - epsilon0;
   Real minor0 = epsilon0 / 2;
-  
+
   bool flip = false;
   if (p.hasKey("reverse")) {
     if (p.getStringAs<string>("reverse") == "true") {
@@ -49,7 +57,7 @@ EvidenceFactorGen::EvidenceFactorGen(const PropertySet& p) : _params()
     _params.push_back(minor);
     _params.push_back(minor0);
     _params.push_back(major);
- 
+
     _params.push_back(minor);
     _params.push_back(major0);
     _params.push_back(minor);
@@ -61,18 +69,18 @@ EvidenceFactorGen::EvidenceFactorGen(const PropertySet& p) : _params()
     _params.push_back(major);
     _params.push_back(minor0);
     _params.push_back(minor);
-    
+
     _params.push_back(minor);
     _params.push_back(major0);
     _params.push_back(minor);
-    
+
     _params.push_back(minor);
     _params.push_back(minor0);
     _params.push_back(major);
   }
 }
 
-void EvidenceFactorGen::generateValues(const vector< string >& edge_types, 
+void EvidenceFactorGen::generateValues(const vector< string >& edge_types,
 		      vector< Real >& outVals) const
 {
   assert(edge_types.size() == 1);
@@ -81,10 +89,10 @@ void EvidenceFactorGen::generateValues(const vector< string >& edge_types,
   }
 }
 
-EvidenceSource::EvidenceSource(PropertySet &p, string base) : 
+EvidenceSource::EvidenceSource(PropertySet &p, string base) :
   cutoffs(),
   options(p),
-  attachPoint(), 
+  attachPoint(),
   _evidenceFile()
 {
   if (p.hasKey("disc"))
@@ -142,9 +150,9 @@ double stringToDouble(const string& s) {
   return result;
 }
 
-void EvidenceSource::loadFromFile(PathwayTab& p, 
-				  map<string, size_t>& sampleMap, 
-				  vector<Evidence::Observation>& sampleData) 
+void EvidenceSource::loadFromFile(PathwayTab& p,
+				  map<string, size_t>& sampleMap,
+				  vector<Evidence::Observation>& sampleData)
 {
   ifstream infile;
   infile.open( _evidenceFile.c_str() );
@@ -169,7 +177,7 @@ void EvidenceSource::loadFromFile(PathwayTab& p,
 
     FactorGenerator* fgen = new EvidenceFactorGen(options);
     p.addFactorGenerator("protein", _suffix, fgen);
-    
+
     while(getline(infile,line)) {
       vector<string> vals;
       Tokenize(line,vals,"\t");
@@ -179,7 +187,7 @@ void EvidenceSource::loadFromFile(PathwayTab& p,
       string sample = vals[0];
       _sampleNames.push_back(sample);
       vals.erase(vals.begin());
-      
+
       for(size_t i = 0; i < vals.size(); i++) {
 	if(p.getEntityType(header[i]) != "protein") // skip adding evidence if it's not in the pathway
 	  continue;
@@ -220,4 +228,3 @@ void Tokenize(const string& str,
       pos = str.find_first_of(delimiters, lastPos);
     }
 }
-

evidencesource.h

@@ -1,3 +1,11 @@
+/********************************************************************************/
+/* Copyright 2009-2011 -- The Regents of the University of California           */
+/* This code is provided for research purposes to scientists at non-profit		*/
+/*  organizations.  All other use is strictly prohibited.  For further			*/
+/*  details please contact University of California, Santa Cruz or				*/
+/*	Five3 Genomics, LLC (http://five3genomics.com).								*/
+/********************************************************************************/
+
 #ifndef HEADER_EVIDENCESOURCE_H
 #define HEADER_EVIDENCESOURCE_H
 
@@ -16,14 +24,14 @@ class EvidenceFactorGen : public FactorGenerator {
 
   EvidenceFactorGen(const PropertySet& p);
   ~EvidenceFactorGen() {}
-  
-  void generateValues(const vector< string >& edge_types, 
+
+  void generateValues(const vector< string >& edge_types,
 		      vector< Real >& outVals) const;
 };
 
 typedef map<string, map<string,int> > SampleEvidMap;
 
-class EvidenceSource 
+class EvidenceSource
 {
 private:
   vector<double> cutoffs;
@@ -40,8 +48,8 @@ class EvidenceSource
 
 public:
   /// Default constructor
-  EvidenceSource() : cutoffs(), 
-		     attachPoint(), 
+  EvidenceSource() : cutoffs(),
+		     attachPoint(),
 		     _suffix(),
 		     _evidenceFile(),
 		     _disc(),
@@ -53,16 +61,16 @@ class EvidenceSource
     setCutoffs("-1.3;1.3");
   }
   /// Copy constructor
-  EvidenceSource(const EvidenceSource &x) 
-  : cutoffs(x.cutoffs), 
-    attachPoint(x.attachPoint), 
+  EvidenceSource(const EvidenceSource &x)
+  : cutoffs(x.cutoffs),
+    attachPoint(x.attachPoint),
     _suffix(x._suffix),
     _evidenceFile(x._evidenceFile),
     _disc(x._disc),
     _sampleNames(x._sampleNames),
     _sampleFactors(x._sampleFactors),
     _sampleFactorNum(x._sampleFactorNum) {}
-  
+
   /// Assignment operator
   EvidenceSource& operator=(const EvidenceSource &x) {
     if (this != &x) {
@@ -83,10 +91,10 @@ class EvidenceSource
   EvidenceSource(PropertySet &p, string base);
 
   void setCutoffs(string discLimits);
-  int discCutoffs (float x);  
+  int discCutoffs (float x);
 
-  void loadFromFile(PathwayTab& p, 
-		    map<string, size_t>& sampleMap, 
+  void loadFromFile(PathwayTab& p,
+		    map<string, size_t>& sampleMap,
 		    vector<Evidence::Observation>& sampleData);
 
   const string& evidenceFile() {return _evidenceFile;}

externVars.cpp

@@ -1,3 +1,11 @@
+/********************************************************************************/
+/* Copyright 2009-2011 -- The Regents of the University of California           */
+/* This code is provided for research purposes to scientists at non-profit		*/
+/*  organizations.  All other use is strictly prohibited.  For further			*/
+/*  details please contact University of California, Santa Cruz or				*/
+/*	Five3 Genomics, LLC (http://five3genomics.com).								*/
+/********************************************************************************/
+
 #include "common.h"
 
 // globals