From a135a9b598d84cf166735b0671078123e3df2b78 Mon Sep 17 00:00:00 2001
From: sandipde <1sandipde@gmail.com>
Date: Mon, 22 Aug 2016 17:40:31 +0200
Subject: [PATCH] Made read dissimilarity matrix able to read rectangular
matrices
---
src/analysis/ReadDissimilarityMatrix.cpp | 22 +++++++++++++---------
1 file changed, 13 insertions(+), 9 deletions(-)
diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp
index e52b3f6f0..f886d8beb 100644
--- a/src/analysis/ReadDissimilarityMatrix.cpp
+++ b/src/analysis/ReadDissimilarityMatrix.cpp
@@ -46,7 +46,8 @@ private:
unsigned nnodes;
ReferenceConfiguration* fake_data;
std::string fname, wfile;
- Matrix<double> dissimilarities;
+// Matrix<double> dissimilarities;
+ std::vector<std::vector<double> > dissimilarities;
std::vector<double> weights;
public:
static void registerKeywords( Keywords& keys );
@@ -127,16 +128,19 @@ void ReadDissimilarityMatrix::performAnalysis(){
Tools::getParsedLine( mfile, words );
nnodes=words.size();
}
- dissimilarities.resize( nnodes, nnodes );
- for(unsigned j=0;j<nnodes;++j) Tools::convert( words[j], dissimilarities(0,j) );
+ if( mydata && nnodes!=getNumberOfDataPoints() ) error("mismatch between number of data points in trajectory and the dimensions of the dissimilarity matrix");
+
+ std::vector<double> tmpdis( nnodes );
+ for(unsigned j=0;j<nnodes;++j) Tools::convert( words[j], tmpdis[j] );
+ dissimilarities.push_back( tmpdis );
- for(unsigned i=1;i<nnodes;++i){
- Tools::getParsedLine( mfile, words );
- if( words.size()!=nnodes ) error("bad formatting in matrix file");
- for(unsigned j=0;j<nnodes;++j) Tools::convert( words[j], dissimilarities(i,j) );
+ while( Tools::getParsedLine( mfile, words ) ){
+ if( words.size()!=nnodes ) error("bad formatting in matrix file");
+ for(unsigned j=0;j<nnodes;++j) Tools::convert( words[j], tmpdis[j] );
+ dissimilarities.push_back( tmpdis );
}
mfile.close();
- if( mydata && nnodes!=getNumberOfDataPoints() ) error("mismatch between number of data points in trajectory and the dimensions of the dissimilarity matrix");
+ if( dissimilarities.size()>nnodes ) error("number of rows in input matrix should be less than or equal to the number of columns");
weights.resize( nnodes );
if( wfile.length()>0 ){
@@ -156,7 +160,7 @@ unsigned ReadDissimilarityMatrix::getNumberOfDataPoints() const {
}
double ReadDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const unsigned& jframe ){
- return dissimilarities( iframe, jframe )*dissimilarities( iframe, jframe );
+ return dissimilarities[iframe][jframe]*dissimilarities[iframe][jframe];
}
ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( const unsigned& idata, const bool& calcdist ){
--
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