[med-svn] [iqtree] 05/06: Update spelling patch

[Andreas Tille]

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tille pushed a commit to branch master
in repository iqtree.

commit b61c6aa2899f2ffcef8046a51d83d058d8f1d832
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 29 14:00:00 2016 +0200

    Update spelling patch
---
 debian/patches/spelling.patch | 87 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 87 insertions(+)

diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index f7df2ae..274b3b0 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -13,3 +13,90 @@ Description: Fix spelling
  		throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
  		
  	}
+--- a/mtreeset.cpp
++++ b/mtreeset.cpp
+@@ -677,11 +677,11 @@ void MTreeSet::computeRFDist(int *rfdist
+ 
+ 	if (info_file) {
+ 		oinfo.close();
+-		cout << "Detailed split occurences printed to " << info_file << endl;
++		cout << "Detailed split occurrences printed to " << info_file << endl;
+ 	}
+ 	if (tree_file) {
+ 		otree.close();
+-		cout << "Detailed split occurences on tree printed to " << tree_file << endl;
++		cout << "Detailed split occurrences on tree printed to " << tree_file << endl;
+ 	}
+ }
+ 
+--- a/model/modelfactory.cpp
++++ b/model/modelfactory.cpp
+@@ -872,7 +872,7 @@ double ModelFactory::optimizeParametersG
+     if (write_info)
+         cout << "testInterval: " << testInterval << endl;
+ 
+-	// Now perform testing different inital p_inv values
++	// Now perform testing different initial p_inv values
+ 	while (initPInv <= frac_const) {
+         if (write_info) {
+             cout << endl;
+--- a/tools.h
++++ b/tools.h
+@@ -1854,7 +1854,7 @@ const char ERR_WRITE_OUTPUT[] = "Cannot
+ const char ERR_NO_K[] = "You must specify the number of taxa in the PD set.";
+ const char ERR_TOO_SMALL_K[] = "Size of PD-set must be at least the size of initial set.";
+ const char ERR_NO_BUDGET[] = "Total budget is not specified or less than zero.";
+-const char ERR_TOO_SMALL_BUDGET[] = "Not enough budget to conserve the inital set of taxa.";
++const char ERR_TOO_SMALL_BUDGET[] = "Not enough budget to conserve the initial set of taxa.";
+ 
+ const char ERR_INTERNAL[] = "Internal error, pls contact authors!";
+ 
+--- a/pruning.h
++++ b/pruning.h
+@@ -87,7 +87,7 @@ public:
+ 	LeafSet::iterator nearestLeaf();
+ 
+ 	/**
+-		mark the node in the inital set to be not PRUNABLE
++		mark the node in the initial set to be not PRUNABLE
+ 	*/
+ 	void doInitialSet();
+ 
+--- a/phyloanalysis.cpp
++++ b/phyloanalysis.cpp
+@@ -457,7 +457,7 @@ void reportTree(ofstream &out, Params &p
+             }
+     }
+     if (is_codon)
+-        out << endl << "NOTE: Branch lengths are intepreted as number of nucleotide substitutions per codon site!" 
++        out << endl << "NOTE: Branch lengths are interpreted as number of nucleotide substitutions per codon site!" 
+             << endl << "      Rescale them by 1/3 if you want to have #nt substitutions per nt site" << endl;
+     if (main_tree) 
+     if (params.aLRT_replicates > 0 || params.gbo_replicates || (params.num_bootstrap_samples && params.compute_ml_tree)) {
+@@ -550,7 +550,7 @@ void reportPhyloAnalysis(Params &params,
+ 		}
+ 		for (IntVector::iterator i2 = counts.begin(); i2 != counts.end(); i2++) {
+ 		    if (*i2 != 0) {
+-	            cout << "#Trees occuring " << (i2-counts.begin()) << " times: " << *i2 << endl;
++	            cout << "#Trees occurring " << (i2-counts.begin()) << " times: " << *i2 << endl;
+ 		    }
+ 		}
+ 	}
+--- a/iqtree.h
++++ b/iqtree.h
+@@ -684,13 +684,13 @@ public:
+     /** corresponding log-likelihood on original alignment */
+     DoubleVector boot_orig_logl;
+ 
+-    /** Set of splits occuring in bootstrap trees */
++    /** Set of splits occurring in bootstrap trees */
+     vector<SplitGraph*> boot_splits;
+ 
+     /** log-likelihood of bootstrap consensus tree */
+     double boot_consense_logl;
+ 
+-    /** Corresponding map for set of splits occuring in bootstrap trees */
++    /** Corresponding map for set of splits occurring in bootstrap trees */
+     //SplitIntMap boot_splits_map;
+ 
+     /** summarize all bootstrap trees */

-- 
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