91 lines
3.6 KiB
Diff
91 lines
3.6 KiB
Diff
diff -ur spack-src.org/bppSuite/bppAncestor.cpp spack-src/bppSuite/bppAncestor.cpp
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--- spack-src.org/bppSuite/bppAncestor.cpp 2019-11-18 15:59:34.786164416 +0900
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+++ spack-src/bppSuite/bppAncestor.cpp 2019-11-18 16:26:25.385749490 +0900
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@@ -237,7 +237,7 @@
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delete tree;
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double logL = tl->getValue();
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- if (isinf(logL))
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+ if (std::isinf(logL))
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{
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// This may be due to null branch lengths, leading to null likelihood!
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ApplicationTools::displayWarning("!!! Warning!!! Likelihood is zero.");
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@@ -251,7 +251,7 @@
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tl->matchParametersValues(pl);
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logL = tl->getValue();
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}
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- if (isinf(logL))
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+ if (std::isinf(logL))
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{
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ApplicationTools::displayError("!!! Unexpected likelihood == 0.");
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ApplicationTools::displayError("!!! Looking at each site:");
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diff -ur spack-src.org/bppSuite/bppML.cpp spack-src/bppSuite/bppML.cpp
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--- spack-src.org/bppSuite/bppML.cpp 2019-11-18 15:59:34.786164416 +0900
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+++ spack-src/bppSuite/bppML.cpp 2019-11-18 16:29:09.373021202 +0900
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@@ -425,7 +425,7 @@
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//Check initial likelihood:
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double logL = tl->getValue();
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- if (isinf(logL))
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+ if (std::isinf(logL))
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{
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// This may be due to null branch lengths, leading to null likelihood!
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ApplicationTools::displayWarning("!!! Warning!!! Initial likelihood is zero.");
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@@ -440,7 +440,7 @@
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logL = tl->getValue();
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}
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ApplicationTools::displayResult("Initial log likelihood", TextTools::toString(-logL, 15));
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- if (isinf(logL))
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+ if (std::isinf(logL))
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{
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ApplicationTools::displayError("!!! Unexpected initial likelihood == 0.");
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if (codonAlphabet)
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@@ -448,7 +448,7 @@
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bool f = false;
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size_t s;
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for (size_t i = 0; i < sites->getNumberOfSites(); i++) {
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- if (isinf(tl->getLogLikelihoodForASite(i))) {
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+ if (std::isinf(tl->getLogLikelihoodForASite(i))) {
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const Site& site = sites->getSite(i);
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s = site.size();
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for (size_t j = 0; j < s; j++) {
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@@ -477,7 +477,7 @@
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} else {
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ApplicationTools::displayBooleanResult("Saturated site removal enabled", true);
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for (size_t i = sites->getNumberOfSites(); i > 0; --i) {
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- if (isinf(tl->getLogLikelihoodForASite(i - 1))) {
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+ if (std::isinf(tl->getLogLikelihoodForASite(i - 1))) {
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ApplicationTools::displayResult("Ignore saturated site", sites->getSite(i - 1).getPosition());
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sites->deleteSite(i - 1);
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}
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@@ -486,7 +486,7 @@
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tl->setData(*sites);
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tl->initialize();
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logL = tl->getValue();
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- if (isinf(logL)) {
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+ if (std::isinf(logL)) {
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throw Exception("Likelihood is still 0 after saturated sites are removed! Looks like a bug...");
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}
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ApplicationTools::displayResult("Initial log likelihood", TextTools::toString(-logL, 15));
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diff -ur spack-src.org/bppSuite/bppMixedLikelihoods.cpp spack-src/bppSuite/bppMixedLikelihoods.cpp
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--- spack-src.org/bppSuite/bppMixedLikelihoods.cpp 2019-11-18 15:59:34.786164416 +0900
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+++ spack-src/bppSuite/bppMixedLikelihoods.cpp 2019-11-18 16:26:48.338168188 +0900
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@@ -220,7 +220,7 @@
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tl->initialize();
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double logL = tl->getValue();
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- if (isinf(logL))
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+ if (std::isinf(logL))
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{
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// This may be due to null branch lengths, leading to null likelihood!
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ApplicationTools::displayWarning("!!! Warning!!! Likelihood is zero.");
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@@ -235,7 +235,7 @@
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tl->matchParametersValues(pl);
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logL = tl->getValue();
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}
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- if (isinf(logL))
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+ if (std::isinf(logL))
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{
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ApplicationTools::displayError("!!! Unexpected likelihood == 0.");
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ApplicationTools::displayError("!!! Looking at each site:");
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