Merge pull request #331 from SysBioChalmers/devel

RAVEN 2.4.3

.gitattributes

@@ -1,5 +1,8 @@
+# Ensure that EOL characters are properly converted for all files
 *	text=auto
+# Use MATLAB style diff
 *.m	text diff=matlab
+# Files/folders that should not be included when downloading repo as ZIP
 .gitattributes	export-ignore
 .gitignore	export-ignore
-.github	export-ignore
+.github	export-ignore

README.md

@@ -1,6 +1,6 @@
 # ![The RAVEN Toolbox 2](RAVEN2.png)
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3689519.svg)](https://doi.org/10.5281/zenodo.3689519) [![GitHub release](https://img.shields.io/github/release/SysBioChalmers/RAVEN/all.svg)](https://GitHub.com/SysBioChalmers/RAVEN/releases/) [![Join the chat at https://gitter.im/SysBioChalmers/RAVEN](https://badges.gitter.im/SysBioChalmers/RAVEN.svg)](https://gitter.im/SysBioChalmers/RAVEN?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3689518.svg)](https://doi.org/10.5281/zenodo.3689519) [![GitHub release](https://img.shields.io/github/release/SysBioChalmers/RAVEN/all.svg)](https://GitHub.com/SysBioChalmers/RAVEN/releases/) [![Join the chat at https://gitter.im/SysBioChalmers/RAVEN](https://badges.gitter.im/SysBioChalmers/RAVEN.svg)](https://gitter.im/SysBioChalmers/RAVEN?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.
 

doc/INIT/getINITModel.html

@@ -609,6 +609,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0457 fprintf([<span class="string">'\tMean gene score: '</span> num2str(geneS) <span class="string">'\n'</span>]);
 0458 fprintf([<span class="string">'\tReactions with positive scores: '</span> num2str(100*sum(a&gt;0)/numel(a)) <span class="string">'%%\n\n'</span>]);
 0459 <span class="keyword">end</span></pre></div>
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doc/INIT/index.html

@@ -24,6 +24,6 @@ <h2>Matlab files in this directory:</h2>
 
 
 
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doc/INIT/runINIT.html

@@ -447,6 +447,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0343 deletedRxns=model.rxns(I);
 0344 outModel=removeReactions(model,I,true,true);
 0345 <span class="keyword">end</span></pre></div>
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doc/core/FSEOF.html

@@ -190,6 +190,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0132     targets.slope=abs(fseof.results(:,iterations)-fseof.results(:,1))/abs(targetMax-targetMax/iterations); <span class="comment">%Slope calculation</span>
 0133 <span class="keyword">end</span>
 0134 <span class="keyword">end</span></pre></div>
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doc/core/addExchangeRxns.html

@@ -151,6 +151,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0087     model.rxnConfidenceScores=[model.rxnConfidenceScores;NaN(numel(J),1)];
 0088 <span class="keyword">end</span>
 0089 <span class="keyword">end</span></pre></div>
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doc/core/addGenesRaven.html

@@ -187,6 +187,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0122     newModel.rxnGeneMat=[newModel.rxnGeneMat,zeros(length(newModel.rxns),nGenes)];
 0123 <span class="keyword">end</span>
 0124 <span class="keyword">end</span></pre></div>
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doc/core/addMets.html

@@ -412,6 +412,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0316     <span class="keyword">end</span>
 0317 <span class="keyword">end</span>
 0318 <span class="keyword">end</span></pre></div>
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doc/core/addRxns.html

@@ -799,6 +799,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0655 newModel.rxnGeneMat = [newModel.rxnGeneMat; rxnGeneMat];
 0656 newModel.grRules = [newModel.grRules(1:nOldRxns); grRules];
 0657 <span class="keyword">end</span></pre></div>
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doc/core/addRxnsGenesMets.html

@@ -254,6 +254,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0169 fprintf(<span class="string">'\nNumber of reactions added to the model:\n'</span>)
 0170 fprintf([num2str(numel(rxnIdx)),<span class="string">'\n'</span>])
 0171 <span class="keyword">end</span></pre></div>
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doc/core/addTransport.html

@@ -244,6 +244,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0176     addedRxns = [addedRxns; addedRxnsID];
 0177 <span class="keyword">end</span>
 0178 <span class="keyword">end</span></pre></div>
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doc/core/analyzeSampling.html

@@ -183,6 +183,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0111     <span class="keyword">end</span>
 0112 <span class="keyword">end</span>
 0113 <span class="keyword">end</span></pre></div>
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doc/core/buildEquation.html

@@ -122,6 +122,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0066     eqn = [eqn plusString stoich mets{i}];
 0067 <span class="keyword">end</span>
 0068 <span class="keyword">end</span></pre></div>
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doc/core/canConsume.html

@@ -76,6 +76,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0020 [model, rxns]=<a href="addExchangeRxns.html" class="code" title="function [model, addedRxns]=addExchangeRxns(model,reactionType,mets)">addExchangeRxns</a>(model,<span class="string">'in'</span>,mets);
 0021 consumed=<a href="haveFlux.html" class="code" title="function I=haveFlux(model,cutOff,rxns)">haveFlux</a>(model,10^-5,rxns);
 0022 <span class="keyword">end</span></pre></div>
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doc/core/canProduce.html

@@ -78,6 +78,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0021 [model, rxns]=<a href="addExchangeRxns.html" class="code" title="function [model, addedRxns]=addExchangeRxns(model,reactionType,mets)">addExchangeRxns</a>(model,<span class="string">'out'</span>,mets);
 0022 produced=<a href="haveFlux.html" class="code" title="function I=haveFlux(model,cutOff,rxns)">haveFlux</a>(model,10^-5,rxns);
 0023 <span class="keyword">end</span></pre></div>
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doc/core/changeGeneAssoc.html

@@ -110,6 +110,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0051 model.grRules = grRules;
 0052 model.rxnGeneMat = rxnGeneMat;
 0053 <span class="keyword">end</span></pre></div>
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doc/core/changeGrRules.html

@@ -114,6 +114,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0055 model.grRules = grRules;
 0056 model.rxnGeneMat = rxnGeneMat;
 0057 <span class="keyword">end</span></pre></div>
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doc/core/changeRxns.html

@@ -245,6 +245,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0149 model=<a href="addRxns.html" class="code" title="function newModel=addRxns(model,rxnsToAdd,eqnType,compartment,allowNewMets,allowNewGenes)">addRxns</a>(model,rxnsToChange,eqnType,compartment,allowNewMets);
 0150 model=<a href="permuteModel.html" class="code" title="function newModel=permuteModel(model, indexes, type)">permuteModel</a>(model,order,<span class="string">'rxns'</span>);
 0151 <span class="keyword">end</span></pre></div>
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doc/core/checkModelStruct.html

@@ -415,6 +415,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0356     I(L)=true;
 0357 <span class="keyword">end</span>
 0358 <span class="keyword">end</span></pre></div>
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doc/core/checkProduction.html

@@ -235,6 +235,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0150     <span class="keyword">end</span>
 0151 <span class="keyword">end</span>
 0152 <span class="keyword">end</span></pre></div>
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doc/core/checkRxn.html

@@ -154,6 +154,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0089     <span class="keyword">end</span>
 0090 <span class="keyword">end</span>
 0091 <span class="keyword">end</span></pre></div>
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doc/core/checkTasks.html

@@ -338,6 +338,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0252     tModel=model;
 0253 <span class="keyword">end</span>
 0254 <span class="keyword">end</span></pre></div>
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doc/core/compareModels.html

@@ -242,6 +242,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0172     nElements(i)=numel(inCommon);
 0173 <span class="keyword">end</span>
 0174 <span class="keyword">end</span></pre></div>
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doc/core/compareMultipleModels.html

@@ -511,6 +511,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0425 
 0426 c = [r g b];
 0427 <span class="keyword">end</span></pre></div>
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doc/core/constructEquations.html

@@ -162,6 +162,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0090 <span class="keyword">end</span>
 0091 
 0092 <span class="keyword">end</span></pre></div>
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doc/core/constructS.html

@@ -216,6 +216,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0149     <span class="keyword">end</span>
 0150 <span class="keyword">end</span>
 0151 <span class="keyword">end</span></pre></div>
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doc/core/consumeSomething.html

@@ -256,6 +256,6 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0173     <span class="keyword">end</span>
 0174 <span class="keyword">end</span>
 0175 <span class="keyword">end</span></pre></div>
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