[med-svn] [fastml] 02/02: More spelling fixes and upload to new

[Andreas Tille]

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tille pushed a commit to branch master
in repository fastml.

commit f372b9c36b7e9905e17035faa1bb7e0569dc65c1
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 19 09:01:43 2015 +0100

    More spelling fixes and upload to new
---
 debian/changelog              |  6 +++---
 debian/patches/spelling.patch | 24 ++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 57b24e0..9e2b14c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-fastml (3.1-1) UNRELEASED; urgency=low
+fastml (3.1-1) unstable; urgency=low
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #805529)
 
- -- Andreas Tille <tille at debian.org>  Mon, 22 Jun 2015 09:47:25 +0200
+ -- Andreas Tille <tille at debian.org>  Thu, 19 Nov 2015 09:01:33 +0100
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index 17e6ed9..32610f9 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -53,6 +53,15 @@ Description: Fix some spelling issues
  	return -1;
 --- a/programs/fastml/bb_options_list.h
 +++ b/programs/fastml/bb_options_list.h
+@@ -9,7 +9,7 @@ static string usage() {
+ 	tmp +=" |-t tree input file                                                          |\n";
+ 	tmp +=" |   (if tree is not given, a neighbor joining tree is computed).             |\n";
+ 	tmp +=" |-g Assume among site rate variation model (Gamma) [By default the program   |\n";
+-	tmp +=" |   will assume an homogenous model. very fast, but less accurate!]          |\n";
++	tmp +=" |   will assume an homogeneous model. very fast, but less accurate!]         |\n";
+ 	tmp += "|-m     model name                                                           |\n";
+ 	tmp += "|-mj    [JTT]                                                                |\n";
+ 	tmp += "|-ml    LG                                                                   |\n";
 @@ -36,7 +36,7 @@ static string usage() {
  	tmp +=" |     -qm = MOLPHY, -qs = MASE, -qp = PHLIYP, -qn = Nexus                    |\n";
  	tmp +=" +----------------------------------------------------------------------------+\n";         
@@ -84,3 +93,18 @@ Description: Fix some spelling issues
  		else
  		LOGnOUT(4,<<"Root(1) freq is sampled once for the entire replication (sim all positions)"<<endl)
  		if(isComputeEmpiricalCorrection 
+--- a/libs/phylogeny/likeDistfixRoot.cpp
++++ b/libs/phylogeny/likeDistfixRoot.cpp
+@@ -145,10 +145,10 @@ MDOUBLE likeDistfixRoot::evalLogLikeliho
+ //						const sequence& s2,
+ //						const vector<MDOUBLE>  * weights,
+ //						MDOUBLE* score) const {
+-//    // only in the case of homogenous model - work through pairwise EM like
++//    // only in the case of homogeneous model - work through pairwise EM like
+ //    countTableComponentGam ctc;
+ //    if (_sp.categories() != 1) {
+-//	errorMsg::reportError("this function only work for homogenous model.");
++//	errorMsg::reportError("this function only work for homogeneous model.");
+ //    }
+ //    ctc.countTableComponentAllocatePlace(s1.getAlphabet()->size(),1);
+ //    for (int i=0; i<s1.seqLen(); ++i) {

-- 
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