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From: Michael R. Crusoe <crusoe@debian.org>
Subject: typo fixes
Forwarded: https://github.com/BioPP/bppsuite/pull/19
--- bppsuite.orig/bppSuite/bppAlnScore.cpp
+++ bppsuite/bppSuite/bppAlnScore.cpp
@@ -152,7 +152,7 @@
try
{
BasicSequence motif("motif", phaseOpt, sitesTest->getAlphabet());
- ApplicationTools::displayResult("Phase based on 1st occurence of", motif.toString());
+ ApplicationTools::displayResult("Phase based on 1st occurrence of", motif.toString());
size_t pos = sitesTest->getNumberOfSites();
for (size_t i = 0; i < sitesTest->getNumberOfSequences(); ++i)
{
--- bppsuite.orig/bppSuite/bppAncestor.cpp
+++ bppsuite/bppSuite/bppAncestor.cpp
@@ -270,7 +270,7 @@
{
(*ApplicationTools::error << "Site " << sites->getSite(i).getPosition() << "\tlog likelihood = " << tl->getLogLikelihoodForASite(i)).endLine();
}
- ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences).");
+ ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularly if datasets are big (>~500 sequences).");
exit(-1);
}
tree = new TreeTemplate<Node>(tl->getTree());
--- bppsuite.orig/bppSuite/bppML.cpp
+++ bppsuite/bppSuite/bppML.cpp
@@ -511,7 +511,7 @@
}
debug.close();
ApplicationTools::displayError("!!! Site-specific likelihood have been written in file DEBUG_likelihoods.txt .");
- ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences).");
+ ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularly if datasets are big (>~500 sequences).");
ApplicationTools::displayError("!!! You may want to try input.sequence.remove_saturated_sites = yes to ignore positions with likelihood 0.");
exit(1);
} else {
--- bppsuite.orig/bppSuite/bppMixedLikelihoods.cpp
+++ bppsuite/bppSuite/bppMixedLikelihoods.cpp
@@ -254,7 +254,7 @@
{
(*ApplicationTools::error << "Site " << sites->getSite(i).getPosition() << "\tlog likelihood = " << tl->getLogLikelihoodForASite(i)).endLine();
}
- ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences).");
+ ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularly if datasets are big (>~500 sequences).");
exit(-1);
}
--- bppsuite.orig/bppSuite/bppSeqGen.cpp
+++ bppsuite/bppSuite/bppSeqGen.cpp
@@ -146,7 +146,7 @@
line += tmp;
index1 = line.find_first_of(" \t");
- if (index1 == string::npos) throw Exception("Error when parsing tree file: no begining position.");
+ if (index1 == string::npos) throw Exception("Error when parsing tree file: no beginning position.");
index2 = line.find_first_of(" \t", index1 + 1);
if (index2 == string::npos) throw Exception("Error when parsing tree file: no ending position.");
begin = TextTools::toDouble(line.substr(0, index1));
--- bppsuite.orig/doc/bppsuite.texi
+++ bppsuite/doc/bppsuite.texi
@@ -1508,7 +1508,7 @@
@subsubsection Conditioned models
The transition probabilities on the branches are conditioned by the
-occurence of given events. The model is then no-markovian, but
+occurrence of given events. The model is then no-markovian, but
semi-markovian. The sets of considered events follow the one (ie
register) defined for substitution mapping (see the testnh manual).
--- bppsuite.orig/bppSuite/bppPopStats.cpp
+++ bppsuite/bppSuite/bppPopStats.cpp
@@ -523,7 +523,7 @@
throw Exception("CodonSiteStatstics can only be used with a codon alignment. Check the input alphabet!");
}
string path = ApplicationTools::getAFilePath("output.file", cmdArgs, true, false);
- if (path == "none") throw Exception("You must specify an ouptut file for CodonSiteStatistics");
+ if (path == "none") throw Exception("You must specify an output file for CodonSiteStatistics");
ApplicationTools::displayResult("Site statistics output to:", path);
ofstream out(path.c_str(), ios::out);
out << "Site\tMissingDataFrequency\tNbAlleles\tMinorAlleleFrequency\tMajorAlleleFrequency\tMinorAllele\tMajorAllele";
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