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Searched refs:ExecuteCommands (Results 1 – 25 of 256) sorted by relevance

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/dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/UnitTests/HBLCommands/
H A DExecuteCommands.bf6 return "ExecuteCommands";
21 ExecuteCommands("y = 'testString';");
22 assert(x==y, "failed to set a variable inside ExecuteCommands");
25 …ExecuteCommands("tempStringOne = 'testString'; tempStringTwo = 'Two'; b = tempStringOne+tempString…
26 assert(a==b, "failed to execute three commands in series inside ExecuteCommands");
32 …s ("ExecuteCommands(list1);", "did not evaluate to a String in call to ExecuteCommands"), "Failed …
33 …ExecuteCommands('');", "Empty/missing source code string in call to ExecuteCommands"), "Failed err…
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/
H A DGateaux.bf54 ExecuteCommands ("totalCodonCount = totalCodonCount + filteredData_"+fileID+".sites;");
70 ExecuteCommands ("global " + _cladeRate + "= 1;");
77 ExecuteCommands ("treeString = \"\"+ tree_"+ fileID+ "_0;");
78 ExecuteCommands ("Tree tree_" + fileID + "_" + (rateCount-1) + "= treeString;");
95 ExecuteCommands ("ps["+mi+"]="+"P_"+(mi+1)+";");
136 …ExecuteCommands ("P_"+mi2+"=freqValueMatrix[mi2-1]/runningTerm;runningTerm=runningTerm*(1-P_"+mi2+…
141 ExecuteCommands ("P_"+(rateCount-1)+"=1-freqValueMatrix[rateCount-1]/runningTerm;");
195 ExecuteCommands ("c_scale:="+c_scalerS+";");
196 ExecuteCommands (lfParts);
301 ExecuteCommands ("S_"+(rateCount-1)+"=bestAlpha;NS_"+(rateCount-1)+"=bestBeta;");
[all …]
H A DGateauxMR.bf62 ExecuteCommands ("global " + _cladeRate + " = 1");
69 ExecuteCommands ("treeString = \"\"+tree_"+ fileID+ "_0;");
74 ExecuteCommands ("Tree tree_" + fileID + "_" + (rateCount-1) + "= treeString;");
75 …ExecuteCommands ("ReplicateConstraint (\"this1.?.synRate:=this2.?.synRate\",tree_"+fileID+"_"+(rat…
91 ExecuteCommands ("ps["+mi+"]="+"P_"+(mi+1)+";");
132 …ExecuteCommands ("P_"+mi2+"=freqValueMatrix[mi2-1]/runningTerm;runningTerm=runningTerm*(1-P_"+mi2+…
137 ExecuteCommands ("P_"+(rateCount-1)+"=1-freqValueMatrix[rateCount-1]/runningTerm;");
191 ExecuteCommands ("c_scale:="+c_scalerS+";");
192 ExecuteCommands (lfParts);
297 ExecuteCommands ("S_"+(rateCount-1)+"=bestAlpha;NS_"+(rateCount-1)+"=bestBeta;");
[all …]
H A Dbayesgraph.ibf56 ExecuteCommands (felMXString);
154 ExecuteCommands(cache_name+" = "+cacheStr+";");
243 ExecuteCommands("setOrder ("+_bgm+", with_order);");
256 ExecuteCommands("Optimize(res, "+_bgm+");");
273 ExecuteCommands("Optimize(res, "+_bgm+");");
445 ExecuteCommands("GetString (res, "+_bgm+", 1);");
446 ExecuteCommands(res);
448 ExecuteCommands("params="+_bgm+"_export;");
455 ExecuteCommands("GetString (res, "+_bgm+", 0);");
662 ExecuteCommands(newname+"={};");
[all …]
H A DdSdNTreeTools.ibf62 ExecuteCommands("scaledTreeStrings[\"Syn\"] = Format ("+treeID+", 1, 1);");
65 ExecuteCommands("scaledTreeStrings[\"NonSyn\"] = Format ("+treeID+", 1, 1);");
77 ExecuteCommands("scaledVectors[\"Syn\"] = BranchLength ("+treeID+", -1);");
80 ExecuteCommands("scaledVectors[\"NonSyn\"] = BranchLength ("+treeID+", -1);");
83 ExecuteCommands("scaledVectors[\"Total\"] = BranchLength ("+treeID+", -1);");
93 ExecuteCommands("GetString(_synFormula,`modelID`,-1);");
96 ExecuteCommands("GetString(_nonSynFormula,`modelID`,-1);");
H A DBranchSiteRELMultiModel.bf145 ExecuteCommands ("FindRoot (z,`blG`-"+bl+",t,0,10000);");
146 ExecuteCommands ("mixtureTreeG." + bNames[k] + ".t :< " + 10*z);
157 ExecuteCommands ("mixtureTreeG." + bNames[k] + ".t :< 10000");
168 ExecuteCommands ("FindRoot (z,`blG`-"+bl+",t,0,10000);");
331 ExecuteCommands (resStr);
356 ExecuteCommands ("fprintf (lfOut, CLEAR_FILE, `lfID`);");
365 ExecuteCommands ("mixtureTree." + branch_name + ".t :< " + z);
369 ExecuteCommands ("mixtureTree." + branch_name + ".t :< 10000");
509 ExecuteCommands ("GetString(_lfInfo,"+ID+",-1)");
526 ExecuteCommands (key + " = " + value);
[all …]
H A DdNdSBivariateRateAnalysis.bf93 ExecuteCommands (
164 ExecuteCommands (modelConstraintString);
433 ExecuteCommands (categDef1);
510 ExecuteCommands (nlfDef + ");");
558 ExecuteCommands ("UseModel (MG94MODEL_"+part+");");
562 ExecuteCommands ("Tree "+treeID+"=treeString_" + fileID +";");
578 ExecuteCommands (nlfDef);
593 ExecuteCommands (lfParts + "," + lfDef1 + ");");
653 ExecuteCommands("S_"+k+":=1;");
654 ExecuteCommands("NS_"+k+"=R_"+k+"*S_"+k+";");
[all …]
H A DFitnessAAModels.bf57 ExecuteCommands (commandString);
67 ExecuteCommands (commandString);
84 ExecuteCommands (commandString);
93 ExecuteCommands (commandString+";");
95 ExecuteCommands (commandString);
99 ExecuteCommands (commandString);
225 ExecuteCommands (lfString+",templateString);");
252 ExecuteCommands ("#include\""+LAST_FILE_PATH+"\";");
262 ExecuteCommands ("estimatedFitnessParameters[mi][fC]=F_"+aaCodes[mi]+"_"+fC+";");
266 ExecuteCommands ("estimatedEFVs[mi][fC]=fitnessEFV_"+fC+"[mi];");
[all …]
H A D_MFReader_.ibf84 ExecuteCommands (lfDefCommand);
109 ExecuteCommands (lfDefCommand);
143 ExecuteCommands (
171 ExecuteCommands (
177 ExecuteCommands ("treeString_" + fileID + " = treeString;");
193 …ExecuteCommands ("fprintf (stdout,\"\\n\",ds_" + fileID + ");DataSetFilter nucData_" + fileID + " …
195 ExecuteCommands ("treeString_" + fileID + " = treeString;");
213 …ExecuteCommands ("HarvestFrequencies (ts, nucData_"+fileID+",1,1,1);cfs = nucData_"+fileID+".…
217 …ExecuteCommands ("HarvestFrequencies (tp, filteredData_"+fileID+",3,1,1);HarvestFrequencies (…
H A DdNdSDistributionComparison.bf108 ExecuteCommands (modelConstraintString);
376 ExecuteCommands (categDef_1);
377 ExecuteCommands (categDef_2);
448 ExecuteCommands (nlfDef);
726 ExecuteCommands (modelConstraintString_1);
730 ExecuteCommands (modelConstraintString_2);
778 ExecuteCommands ("R_2_"+k+":=R_1_"+k+";");
825 ExecuteCommands ("P_2_"+k+":=P_1_"+k+";");
873 ExecuteCommands ("R_2_"+k+":=R_1_"+k+";");
878 ExecuteCommands ("P_2_"+k+":=P_1_"+k+";");
[all …]
H A DTestCladeMeans.bf30 ExecuteCommands ("#include \""+incFileName+"\";");
78 ExecuteCommands ("#include \""+incFileName+"\";");
290 ExecuteCommands ("global SUM_"+smallCladeName+":="+cladeConstraint+";");
296 ExecuteCommands ("global SUM_"+cladeName+":="+cladeConstraint+";");
309 …ExecuteCommands ("ReplicateConstraint (\"this1.?."+funnyString+":= SUM_"+smallCladeName+"*"+(clade…
314 …ExecuteCommands ("ReplicateConstraint (\"this1.?."+funnyString+":= SUM_"+smallCladeName+"*"+(clade…
316 ExecuteCommands ("aTree."+cladeName+"."+funnyString+"=0.1;");
352 ExecuteCommands ("global SUM_"+smallCladeName+":="+cladeConstraint+";");
359 ExecuteCommands ("global SUM_"+cladeName+":="+cladeConstraint+";");
369 …ExecuteCommands ("ReplicateConstraint (\"this1.?."+funnyString+":= SUM_"+smallCladeName+"*"+(clade…
[all …]
H A Dqndhelper2_mf.ibf9 ExecuteCommands ("Tree nucTree_" + fileID + "=" + treeStrings[fileID] + ";");
11 ExecuteCommands (constructLF("nucLF", "nucData", "nucTree", fileCount));
176 ExecuteCommands ("Tree codonTree_" + fileID + "=" + treeStrings[fileID] + ";");
207 ExecuteCommands (constructLF("lf", "filteredData", "codonTree", fileCount));
231 …ExecuteCommands ("ReplicateConstraint(\"this1.?.synRate:=rConstr*this2.?.t__\",codonTree_"+fileID+…
240 …ExecuteCommands ("ReplicateConstraint(\"this1.?.synRate:=this2.?.t__*rConstr\",codonTree_"+fileID+…
289 …ExecuteCommands("ReplicateConstraint(\"this1.?.synRate:=this2.?.t__*rConstr\",codonTree_"+fileID+"…
348 ExecuteCommands ("`_pname`=1");
357 ExecuteCommands ("`_pname`=_mixingP");
419 ExecuteCommands ("`_pname`=1");
[all …]
H A DCodonBivariateRateProcessor.bf96 ExecuteCommands ("ps["+mi+"]="+"P_"+(mi+1)+";");
101 ExecuteCommands ("rateInfo[mi][1]="+"S_"+mi+"/c_scale;");
102 ExecuteCommands ("rateInfo[mi][2]="+"NS_"+mi+"/c_scale;");
203 ExecuteCommands ("codonCount=filteredData_"+fileID+".sites;");
268 ExecuteCommands ("branchNames = BranchName (tree_"+fileID+"_0,-1);");
281 ExecuteCommands("GetInformation (aRateMx, tree_"+fileID+"_"+treeCounter+"."+abn+");");
294 ExecuteCommands ("treeAVL = tree_"+fileID+"_0^0");
309 …ExecuteCommands ("Tree synSubsTree_"+fileID+"= synTreeString;Tree nonsynSubsTree_"+fileID+" = no…
358 ExecuteCommands ("treeAVL2 = "+treeName + " ^ 0;leafCount=TipCount("+treeName+");");
409 ExecuteCommands ("bNames = BranchName ("+treeID+",-1);");
[all …]
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/Samplers/
H A Dsrs.ibf90 ExecuteCommands ("Export(lfExport,"+LF_NAME+");");
99 ExecuteCommands ("LFCompute ("+LF_NAME+",LF_START_COMPUTE);");
103 ExecuteCommands (_ADD_TO_SRS_["INIT"]);
121 ExecuteCommands ("mpiRes="+res);
137 ExecuteCommands ("LFCompute ("+LF_NAME+",LF_START_COMPUTE);");
140 ExecuteCommands (_ADD_TO_SRS_["INIT"]);
180 ExecuteCommands (aKey + "=" + stashedValues[k][0] + ";");
193 ExecuteCommands ("LFCompute ("+LF_NAME+",LF_DONE_COMPUTE);");
219 ExecuteCommands ("LFCompute ("+LF_NAME+",LF_START_COMPUTE);");
301 ExecuteCommands (aKey + "=" + stashedValues[k][0] + ";");
[all …]
H A Dsrs-ErrorEst.ibf3 ExecuteCommands ("LFCompute ("+LF_NAME+",LF_START_COMPUTE);");
12 ExecuteCommands (assignmentString+"LFCompute ("+LF_NAME+",lfWeight);");
31 ExecuteCommands (aKey + "=" + stashedValues[k][0] + ";");
34 ExecuteCommands ("LFCompute ("+LF_NAME+",LF_DONE_COMPUTE);");
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/tasks/
H A Dbayesgraph.ibf57 ExecuteCommands (felMXString);
152 ExecuteCommands(cache_name+" = "+cacheStr+";");
249 ExecuteCommands("Optimize(res, "+_bgm+");");
435 ExecuteCommands("GetString (res, "+_bgm+", 1);");
436 ExecuteCommands(res);
438 ExecuteCommands("params="+_bgm+"_export;");
445 ExecuteCommands("GetString (res, "+_bgm+", 0);");
453 ExecuteCommands("GetInformation (s, "+_bgm+", 0);");
459 ExecuteCommands("GetInformation (s, "+_bgm+", 1);");
652 ExecuteCommands(newname+"={};");
[all …]
/dports/biology/hyphy/hyphy-2.5.33/res/SubstitutionModels/Aminoacid/
H A DFitness.mdl42 ExecuteCommands (commandString);
52 ExecuteCommands (commandString);
69 ExecuteCommands (commandString);
79 ExecuteCommands (commandString+";");
81 ExecuteCommands (commandString);
85 ExecuteCommands (commandString);
/dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/UnitTests/HBLCommands/res/SCFG/
H A DSCFG.ibf209 ExecuteCommands("GetString (scfgInfo, "+scfg_string+", -1);");
231 ExecuteCommands("LFCompute ("+scfg_string+", logL);");
236 ExecuteCommands ("Optimize(res,"+scfg_string+");");
268 ExecuteCommands("GetString (scfgInfo, "+scfg_string+", -1);");
294 ExecuteCommands(importScfg);
303 ExecuteCommands("LFCompute ("+scfg_string+", LF_START_COMPUTE);");
304 ExecuteCommands("LFCompute ("+scfg_string+", logL);");
314 ExecuteCommands("GetString (scfgInfo, "+scfg_string+", -1);");
435 ExecuteCommands("GetString (scfgInfo, "+scfg_string+", -1);");
480 ExecuteCommands("GetString (scfgInfo, "+scfg_string+", -1);");
[all …]
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/Utility/
H A DReadDelimitedFiles.bf174 ExecuteCommands ("_lineStatus = " + func + "(splitOnRegExp (thisLine, regExp),lineID)");
218 ExecuteCommands (felMXString);
415 ExecuteCommands ("_treeAVL = `treeName`^0");
422 ExecuteCommands ("GetString(_seqNames,`filterName`,-1)");
432 ExecuteCommands ("SetParameter (`filterName`,_k,_seqName2)");
437 ExecuteCommands ("SetParameter (`treeName`, _node_id_by_name [_seqNames[_k]]-1,_seqName2)");
444 ExecuteCommands ("Topology `treeName` = " + PostOrderAVL2String (_treeAVL));
467 ExecuteCommands ("GetString(_seqNames,`filterName`,-1)");
485 ExecuteCommands ("GetDataInfo(_uniquePatterns,`filterName`," + matchMode + ")");
486 ExecuteCommands ("GetString(_seqNames,`filterName`,-1)");
[all …]
H A DCoalescentPostProcessor.bf3 ExecuteCommands ("#include \""+incFileName + "\";");
131 ExecuteCommands (ConstraintString);
164 ExecuteCommands ("Tree tree_" + pccounter + " = " + treeStrings[pccounter] + ";");
173 ExecuteCommands (lfDef);
194 ExecuteCommands ("siteCount = part_" + pccounter + ".sites;");
205 …ExecuteCommands ("siteCount = compareTreesForSplits(\"tree_" +pccounter + "\",\"tree_"+pc2+"\");");
298 ExecuteCommands ("treeAVL2="+treeID+"^0;leafCount=TipCount("+treeID+")");
335 ExecuteCommands ("bNames = BranchName ("+treeID+",-1);");
336 ExecuteCommands ("bLen = BranchLength ("+treeID+",-1);");
355 ExecuteCommands ("_astavl_="+tName+"^1;");
[all …]
H A DGrabBag.bf192 ExecuteCommands (_lfInfo[_gb_idx] + "=" + _lfInfo[_gb_idx]);
202 ExecuteCommands ("GetString (_lfInfo," + _lfName + ",-1);");
208 ExecuteCommands (_lfInfo[_gb_idx] + ":=" + _tval + ";");
218 ExecuteCommands ("GetString (_lfInfo," + _lfName + ",-1);");
222 ExecuteCommands ("_tval = "+_lfInfo[_gb_idx]);
234 ExecuteCommands ("GetString (_lfInfo," + _lfName + ",-1);");
252 ExecuteCommands ("global `_parName`="+_parValue+";");
381 ExecuteCommands ("_gb_dim=BranchName("+_treeID2+",-1);");
388 ExecuteCommands ("_gb_idx2="+_gb_idx2);
691 ExecuteCommands ("global "+probPrefix+"_"+mi+":>0;");
[all …]
H A DLocalMGREVMLFreqs.bf24 ExecuteCommands ("global _mlFreqNormalizer := " + normString);
40 ExecuteCommands ("freqMx[h-hshift]:="+result[h-hshift]+"/_mlFreqNormalizer");
148 ExecuteCommands ("global R"+_MG94GlobalSuffix+"=1;");
226 ExecuteCommands (modelDefString);
230 ExecuteCommands (MGCustomModelConstraintString);
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/TemplateModels/
H A Dfitness.mdl36 ExecuteCommands (commandString);
53 ExecuteCommands (commandString);
68 ExecuteCommands (commandString);
78 ExecuteCommands (commandString+";");
84 ExecuteCommands (commandString);
H A DRNA16.mdl120 …ExecuteCommands ("global "+varName+"=obsFreqs[idx];"+varName+":<1;vectorOfFrequencies["+idx+"]:="+…
124 ExecuteCommands ("f_weight:="+v[1][Abs(v)-1]+";");
155 ExecuteCommands ("ModelMatrixName["+h+"]["+v+"]:="+rateEntry +"*rate_Normalizer*t");
156 ExecuteCommands ("ModelMatrixName["+v+"]["+h+"]:="+rateEntry +"*rate_Normalizer*t");
161 ExecuteCommands ("rate_Normalizer:=100./rate_Norm__;");
178 ExecuteCommands ("global "+rateEntry + "=1;");
188 ExecuteCommands ("ModelMatrixName["+h+"]["+v+"]:="+rateEntry +"*rate_Normalizer*t");
189 ExecuteCommands ("ModelMatrixName["+v+"]["+h+"]:="+rateEntry +"*rate_Normalizer*t");
194 ExecuteCommands ("rate_Normalizer:=100./("+rate_Norm[1][Abs(rate_Norm)-1]+");");
H A DmtREV.mdl50 ExecuteCommands("global "+subString +"=1; ModelMatrixName[k][k2]:= c*t*"+subString+
62 ExecuteCommands("global "+subString +"=1; ModelMatrixName[k][k2]:= t*"+subString+
69 ExecuteCommands(subString +":=1;");

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