[med-svn] [Git][med-team/wise][master] 3 commits: d/patches: Mark patch Forwarded fields as not-needed, since no upstream bug...
Lance Lin (@linqigang)
gitlab at salsa.debian.org
Fri Mar 15 13:10:49 GMT 2024
Lance Lin pushed to branch master at Debian Med / wise
Commits:
7c900cef by Lance Lin at 2024-03-15T19:44:01+07:00
d/patches: Mark patch Forwarded fields as not-needed, since no upstream bug tracking, and update spelling.patch
- - - - -
95d4a892 by Lance Lin at 2024-03-15T20:03:57+07:00
d/patches: Fix executable-not-elf-or-script lintian warning
- - - - -
ec471630 by Lance Lin at 2024-03-15T20:04:59+07:00
d/watch: Remove debian uupdate and access secure uri
- - - - -
17 changed files:
- debian/changelog
- debian/patches/01_welcome-csh.patch
- debian/patches/02_isnumber.patch
- debian/patches/03_doc-nodycache.patch
- debian/patches/04_wise2-pdflatex-update.patch
- debian/patches/06_getline.patch
- debian/patches/07_ld--as-needed.patch
- debian/patches/08_mayhem.patch
- debian/patches/09_dnal-add-return-statement.patch
- debian/patches/10_fix_path_to_data_files.patch
- debian/patches/11_consistent_manual_dates.patch
- debian/patches/cross.patch
- + debian/patches/executable-is-script.patch
- debian/patches/implicit-function-declaration.patch
- debian/patches/series
- debian/patches/spelling.patch
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -5,6 +5,10 @@ wise (2.4.1-24) UNRELEASED; urgency=medium
* debhelper-compat 13 (routine-update)
* watch file standard 4 (routine-update)
* d/patches: Fix implicit-function-declaration errors (Closes: #1066705)
+ * d/patches: Mark patch Forwarded fields as not-needed, since no upstream
+ bug tracking, and update spelling.patch
+ * d/patches: Fix executable-not-elf-or-script lintian warning
+ * d/watch: Remove debian uupdate and access secure uri
-- Lance Lin <lq27267 at gmail.com> Thu, 14 Mar 2024 21:41:46 +0700
=====================================
debian/patches/01_welcome-csh.patch
=====================================
@@ -1,5 +1,6 @@
Author: Philipp Benner <mail at philipp-benner.de>
Description: Avoid dependency from csh
+Forwarded: not-needed
--- wise-2.4.1.orig/src/makefile
+++ wise-2.4.1/src/makefile
=====================================
debian/patches/02_isnumber.patch
=====================================
@@ -1,5 +1,6 @@
Author: Philipp Benner <mail at philipp-benner.de>
Description: Replace isnumber() (which does not exist on linux) by isdigit().
+Forwarded: not-needed
--- wise-2.4.1.orig/src/models/phasemodel.c
+++ wise-2.4.1/src/models/phasemodel.c
=====================================
debian/patches/03_doc-nodycache.patch
=====================================
@@ -1,5 +1,6 @@
Author Philipp Benner <mail at philipp-benner.de>
Description: Documentation bugfix.
+Forwarded: not-needed
--- wise-2.4.1.orig/docs/wise2.tex
+++ wise-2.4.1/docs/wise2.tex
=====================================
debian/patches/04_wise2-pdflatex-update.patch
=====================================
@@ -1,5 +1,6 @@
Author Philipp Benner <mail at philipp-benner.de>
Description: Make wise2.tex pdflatex compatible.
+Forwarded: not-needed
--- wise-2.4.1.orig/docs/wise2.tex
+++ wise-2.4.1/docs/wise2.tex
=====================================
debian/patches/06_getline.patch
=====================================
@@ -2,6 +2,7 @@ Author: Philipp Benner <philipp at debian.org>
Last-Update: Sat, 31 Oct 2009 21:25:52 +0000
Bug-Debian: http://bugs.debian.org/552821
Description: Fixed conflicting definitions of getline().
+Forwarded: not-needed
--- wise-2.4.1.orig/src/HMMer2/sqio.c
+++ wise-2.4.1/src/HMMer2/sqio.c
=====================================
debian/patches/07_ld--as-needed.patch
=====================================
@@ -1,5 +1,6 @@
Description: Fix FTBFS with ld --as-needed.
Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935
+Forwarded: not-needed
--- wise-2.4.1.orig/src/models/makefile
+++ wise-2.4.1/src/models/makefile
=====================================
debian/patches/08_mayhem.patch
=====================================
@@ -1,6 +1,7 @@
Author: Philipp Benner <philipp at debian.org>
Last-Update: Sun, 07 Jul 2013 13:33:01 +0200
Description: Fix run time errors detected by Mayhem
+Forwarded: not-needed
--- wise-2.4.1.orig/src/models/dbac.c
+++ wise-2.4.1/src/models/dbac.c
=====================================
debian/patches/09_dnal-add-return-statement.patch
=====================================
@@ -3,6 +3,7 @@ Last-Update: Mon, 4 Aug 2014 17:10:38 +0000
Bug-Debian: http://bugs.debian.org/751277
Description: Make sure dnal has a valid return value
This affects a bug reported against python-biopython.
+Forwarded: not-needed
--- wise-2.4.1.orig/src/models/dnal.c
+++ wise-2.4.1/src/models/dnal.c
=====================================
debian/patches/10_fix_path_to_data_files.patch
=====================================
@@ -1,5 +1,6 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Mon, 04 Aug 2014 19:25:58 +0200
+Forwarded: not-needed
Description: Brute force patch to fix the PATH to the data files to make the
tools finding the needed data for the test suite
.
=====================================
debian/patches/11_consistent_manual_dates.patch
=====================================
@@ -2,6 +2,8 @@ Description: Use fixed dates for manuals.
These make the build reproducible. I have picked the file modificatin dates of
the corresponding source .tex files.
Author: Sascha Steinbiss <sascha at steinbiss.name>
+Forwarded: not-needed
+
--- a/docs/dynamite.tex
+++ b/docs/dynamite.tex
@@ -1,4 +1,5 @@
=====================================
debian/patches/cross.patch
=====================================
@@ -1,6 +1,7 @@
Date: Sat, 18 Apr 2020 11:59:09 +0200
From: Helmut Grohne <helmut at subdivi.de>
Bug-Debian: https://bugs.debian.org/958094
+Forwarded: not-needed
Description: Do not hard code the build architecture pkg-config
--- a/src/corba/makefile
=====================================
debian/patches/executable-is-script.patch
=====================================
@@ -0,0 +1,14 @@
+Description: Fix perl binary location for
+ executable-not-elf-or-script lintian warning
+Author: Lance Lin <lq27267 at gmail.com>
+Last-Update: 15 Mar 2024
+Forwarded: not-needed
+
+--- a/src/test/testman.pl
++++ b/src/test/testman.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ if( $opt eq 'cf' ) {
+ $conf = shift;
=====================================
debian/patches/implicit-function-declaration.patch
=====================================
@@ -1,6 +1,7 @@
Description: Fix implicit-function-declaration build errors
Author: Lance Lin <lq27267 at gmail.com>
Last-Update: 14 Mar 2024
+Forwarded: not-needed
--- a/src/HMMer2/prior.c
+++ b/src/HMMer2/prior.c
=====================================
debian/patches/series
=====================================
@@ -12,3 +12,4 @@
spelling.patch
cross.patch
implicit-function-declaration.patch
+executable-is-script.patch
=====================================
debian/patches/spelling.patch
=====================================
@@ -1,10 +1,11 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Fri, 22 Sep 2017 09:18:47 +0200
Description: Fix spelling issues
+Forwarded: not-needed
--- a/src/dynlibsrc/hscore.c
+++ b/src/dynlibsrc/hscore.c
-@@ -413,7 +413,7 @@ DataScore * new_DataScore_from_storage(H
+@@ -413,7 +413,7 @@
if( hs->st_len == 0 ) {
new = new_DataScoreStorage();
if( new == NULL ) {
@@ -15,7 +16,7 @@ Description: Fix spelling issues
add_st_Hscore(hs,new);
--- a/src/dynlibsrc/hscore.dy
+++ b/src/dynlibsrc/hscore.dy
-@@ -422,7 +422,7 @@ DataScore * new_DataScore_from_storage(H
+@@ -422,7 +422,7 @@
if( hs->st_len == 0 ) {
new = new_DataScoreStorage();
if( new == NULL ) {
@@ -26,7 +27,16 @@ Description: Fix spelling issues
add_st_Hscore(hs,new);
--- a/docs/dynamite.tex
+++ b/docs/dynamite.tex
-@@ -2839,7 +2839,7 @@ needs at least one offset to be non zero
+@@ -240,7 +240,7 @@
+ communication is on a biologically 'logical' level so theoretically
+ one can drop out the dynamite run-time library, replace it with one's
+ own specific biological typed library (the ncbi toolkit for example)
+-and recompile with a new 'methods' file. This has to assumme that
++and recompile with a new 'methods' file. This has to assume that
+ certain biological concepts are represented in a particular way (for
+ example, Base A is represented by 0, Base C 1 etc), but does allow the
+ underlying data structures complete freedom.
+@@ -2839,7 +2839,7 @@
Once all the semantics of the Dynamite blueprint is ok, the compiler then turns its
attention to the calc lines. This is like a mini-parser operating inside the dynamite
parser, but unlike the dynamite parser, this once was written in yacc/lex and is
@@ -37,7 +47,7 @@ Description: Fix spelling issues
--- a/docs/wise2.tex
+++ b/docs/wise2.tex
-@@ -121,7 +121,7 @@ Warning Error
+@@ -121,7 +121,7 @@
Could not read a GeneFrequency file in human.gf
...
\end{verbatim}
@@ -46,7 +56,7 @@ Description: Fix spelling issues
set up correctly. You need to find where the distribution was downloaded
to (a directory called something like wise2.1.16b) and inside that
directory should be the configuration directory wisecfg. You need to
-@@ -427,7 +427,7 @@ sequence flag) as well. An example run w
+@@ -427,14 +427,14 @@
\begin{verbatim}
genewisedb -pfam Pfam -dnas myseq.fa
\end{verbatim}
@@ -55,7 +65,33 @@ Description: Fix spelling issues
variable HMMERDB, Wise2 will also pick that up as well.
-@@ -675,7 +675,7 @@ mathematically it is almost that easy: t
+
+ \subsubsection{Optimising alignment speed}
+
+-Wise2 assummes you have a rather small amount of memory (20 MBytes).
++Wise2 assumes you have a rather small amount of memory (20 MBytes).
+ When it is making an alignment, if it cannot make the explicit matrix
+ in that size (being length of query $\times$ length of target $\times$
+ state number) it has to move to linear memory (length of query
+@@ -444,7 +444,7 @@
+ If you have more memory than 20 Mbytes, then it is really sensible to
+ up the number, using the -kbyte option. For a machine with say
+ 64Mbytes physical memory I would suggest putting an upper limit of
+-50Mbytes with -kbyte. This does assumme you are not using it for
++50Mbytes with -kbyte. This does assume you are not using it for
+ anything else.
+
+ You can change the compile time default in basematrix.h if you can't
+@@ -576,7 +576,7 @@
+ (of course, your version of Wise2 might be different).
+
+ Once you have made the tar file, it should build completely cleanly as
+-long as you have an ANSI C compiler. If in doubt, just assumme that it
++long as you have an ANSI C compiler. If in doubt, just assume that it
+ is, but in particular sun users might want to use gcc (gnu cc) as the
+ sun cc compiler installed by default is often non-ANSI. To change the
+ cc compiler you only need to edit the line in the top level makefile
+@@ -675,7 +675,7 @@
of the probability.
Perhaps a better known example is the relationship between the old
@@ -64,7 +100,73 @@ Description: Fix spelling issues
others, and its probabilistic partner, profile Hidden Markov Models
(profile HMMs). In terms of the actual algorithm these two methods
are very similar: it is simply that the profile HMM has a strong
-@@ -1639,7 +1639,7 @@ Of course there are many options to chan
+@@ -804,7 +804,7 @@
+ given in half bits, in other words using a 2*log2 mapping from
+ probability space to the give scores in the matrix. By reversing this
+ process one can get pretty good emission probability for the amino
+-acids. I now assumme that the gap penalities are \emph{as if} they were
++acids. I now assume that the gap penalities are \emph{as if} they were
+ written in half bits. A certain amount of normalisation is required to
+ make sure things add to one, and eh voila - one profile HMM from a
+ single sequence.
+@@ -870,7 +870,7 @@
+ splice sites overlap between their consensi and the coding sequence
+ region. These overlaps need to be treated correctly: the problem is
+ that probabilistically we have two processes wanting to account for
+-the same DNA bases. This was solved by assumming conditional
++the same DNA bases. This was solved by assuming conditional
+ independence between the two processes. A more formal mathematicall
+ approach can be found in the documented called 'probappendix'.
+
+@@ -1075,7 +1075,7 @@
+ searches.
+
+ I have been thinking about using a classical statistic method on top
+-of the bit score, assumming the distribution is an extreme value
++of the bit score, assuming the distribution is an extreme value
+ distribution (EVD), but for DNA it becomes difficult to know what to
+ do with the problem of different lengths of DNA. As these can be
+ wildly different, it is hard to know precisely how to handle
+@@ -1222,12 +1222,12 @@
+ \item[-gene] [human.gf] Gene parameter file. Provide statistics for
+ different gene models. Current human.gf and worm.gf are provided. The
+ statistics are basically too complicated to explain here.
+-\item[-subs] [1e-05] Substitution error rate, ie the assummed
++\item[-subs] [1e-05] Substitution error rate, ie the assumed
+ probability of base substitutions in the sequencing reaction/assembly
+ that provided the DNA sequence. The substituion error is what
+ dominates the penalty for stop codons - a higher error rate implies a
+ smaller penalty for stop codons
+-\item[-indel] [1e-05] Insertion/deletion error rate, ie the assummed
++\item[-indel] [1e-05] Insertion/deletion error rate, ie the assumed
+ probability of indel events in the sequencing reaction/assembly that
+ provided the DNA sequence. The indel rate is what provides the penalty
+ for frameshift errors. A higher error rate implies a smaller penalty
+@@ -1475,10 +1475,10 @@
+
+ \item[-codon] [codon.table] Codon file. The default is for the universal code, but
+ you can supply your own
+-\item[-subs] [0.01] Substitution error rate, ie the assummed probability of base substitutions
++\item[-subs] [0.01] Substitution error rate, ie the assumed probability of base substitutions
+ in the sequencing reaction/assembly that provided the DNA sequence. The substituion error is what dominates
+ the penalty for stop codons - a higher error rate implies a smaller penalty for stop codons
+-\item[-indel] [0.01] Insertion/deletion error rate, ie the assummed probability of indel events
++\item[-indel] [0.01] Insertion/deletion error rate, ie the assumed probability of indel events
+ in the sequencing reaction/assembly that provided the DNA sequence. The indel rate is what provides
+ the penalty for frameshift errors. A higher error rate implies a smaller penalty for indels.
+ \item[-null] [syn/flat] Random Model as synchronous or flat [default syn]
+@@ -1580,8 +1580,8 @@
+ for that matter, but in theory it should work better for orthologous
+ regulatory regions, depending on how much active change you expect
+ paralogous regulatory regions to have). Promoterwise reports alignments
+-between these two sequences assumming that alignments cannot overlap in
+-both sequences, but *not* assumming that the alignments have to be co
++between these two sequences assuming that alignments cannot overlap in
++both sequences, but *not* assuming that the alignments have to be co
+ linear or on the same strand.
+
+
+@@ -1639,7 +1639,7 @@
\subsection{dba - Dna Block Aligner}
\label{sec:dba}
@@ -75,7 +177,16 @@ Description: Fix spelling issues
--- a/src/base/wisefile.c
+++ b/src/base/wisefile.c
-@@ -329,7 +329,7 @@ FILE * openfile(const char * filename,co
+@@ -295,7 +295,7 @@
+ return ifp;
+
+ else if ( shouldreporterror )
+- log_full_error(INFO,0,"Expanded personal direcotry open for[%s,%s], expanded to %s failed: Error message is %s",filename,prot,buffer,ERRORSTR);
++ log_full_error(INFO,0,"Expanded personal directory open for[%s,%s], expanded to %s failed: Error message is %s",filename,prot,buffer,ERRORSTR);
+
+
+ /* next line ABSOLUTELY relies on order of evaluation */
+@@ -329,7 +329,7 @@
*
*
*
@@ -84,7 +195,7 @@ Description: Fix spelling issues
* Arg: filename [UNKN ] Undocumented argument [char *]
* Arg: name [READ ] filename to open [NullString]
* Arg: env [UNKN ] Undocumented argument [char *]
-@@ -344,17 +344,17 @@ FILE * envopenfile(char * filename,char
+@@ -344,17 +344,17 @@
char path [512];
if( filename == NULL || env == NULL ) {
@@ -107,7 +218,16 @@ Description: Fix spelling issues
sprintf(path,"%s/%s",filename,envp);
--- a/src/base/wisefile.dy
+++ b/src/base/wisefile.dy
-@@ -302,7 +302,7 @@ in HMMer2. You call it as
+@@ -269,7 +269,7 @@
+ return ifp;
+
+ else if ( shouldreporterror )
+- log_full_error(INFO,0,"Expanded personal direcotry open for[%s,%s], expanded to %s failed: Error message is %s",filename,prot,buffer,ERRORSTR);
++ log_full_error(INFO,0,"Expanded personal directory open for[%s,%s], expanded to %s failed: Error message is %s",filename,prot,buffer,ERRORSTR);
+
+
+ /* next line ABSOLUTELY relies on order of evaluation */
+@@ -302,7 +302,7 @@
%arg
name r filename to open
@@ -116,7 +236,7 @@ Description: Fix spelling issues
return a valid file pointer or NULL
%%
FILE * envopenfile(char * filename,char * env)
-@@ -311,17 +311,17 @@ FILE * envopenfile(char * filename,char
+@@ -311,17 +311,17 @@
char path [512];
if( filename == NULL || env == NULL ) {
@@ -139,7 +259,7 @@ Description: Fix spelling issues
sprintf(path,"%s/%s",filename,envp);
--- a/src/base/wisefile.h
+++ b/src/base/wisefile.h
-@@ -143,7 +143,7 @@ FILE * Wise2_openfile(const char * filen
+@@ -143,7 +143,7 @@
*
*
*
@@ -150,7 +270,7 @@ Description: Fix spelling issues
* Arg: env [UNKN ] Undocumented argument [char *]
--- a/LICENSE
+++ b/LICENSE
-@@ -19,7 +19,7 @@ an acknowledgement of the authorship nee
+@@ -19,7 +19,7 @@
The HMMer2 libaries (Sean Eddy's HMM package) and the models directory
(The algorithms for the Wise2 package, and final executable programs)
@@ -161,7 +281,7 @@ Description: Fix spelling issues
GPL.
--- a/docs/wise3arch.tex
+++ b/docs/wise3arch.tex
-@@ -49,7 +49,7 @@ clear up a considerable amount of confus
+@@ -49,7 +49,7 @@
\subsection{Committment to open source, freely available code}
@@ -172,7 +292,7 @@ Description: Fix spelling issues
freely available, open source package. The aim of the open
--- a/src/corba/scanwise_protein_index.c
+++ b/src/corba/scanwise_protein_index.c
-@@ -19,7 +19,7 @@ char * program_name = "scanwise_protein_
+@@ -19,7 +19,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -183,7 +303,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/assembly/badkmer.c
+++ b/src/dnaindex/assembly/badkmer.c
-@@ -25,7 +25,7 @@ void show_help(FILE * ofp)
+@@ -25,7 +25,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -194,7 +314,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/assembly/pathwise.c
+++ b/src/dnaindex/assembly/pathwise.c
-@@ -40,7 +40,7 @@ void show_help(FILE * ofp)
+@@ -40,7 +40,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -205,7 +325,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/bigseqwise.c
+++ b/src/dnaindex/bigseqwise.c
-@@ -10,7 +10,7 @@ char * program_name = "bigseqwise";
+@@ -10,7 +10,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -216,7 +336,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/findbad_kmer.c
+++ b/src/dnaindex/findbad_kmer.c
-@@ -13,7 +13,7 @@ char * program_name = "findbad_kmer";
+@@ -13,7 +13,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -227,7 +347,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/dnaindex/kwise.c
+++ b/src/dnaindex/kwise.c
-@@ -15,7 +15,7 @@ char * program_name = "kwise";
+@@ -15,7 +15,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -238,7 +358,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/alignwise.c
+++ b/src/models/alignwise.c
-@@ -61,7 +61,7 @@ void show_Gene_debug(AlnBlock * alb,Sequ
+@@ -61,7 +61,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -249,7 +369,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/amplimer_resolver.c
+++ b/src/models/amplimer_resolver.c
-@@ -10,7 +10,7 @@ char * program_name = "amplimer_resolver
+@@ -10,7 +10,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -260,7 +380,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/cdnawise.c
+++ b/src/models/cdnawise.c
-@@ -15,7 +15,7 @@ void show_version(FILE * ofp)
+@@ -15,7 +15,7 @@
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -271,7 +391,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/clonewise.c
+++ b/src/models/clonewise.c
-@@ -25,7 +25,7 @@ int mismatch_score = -1;
+@@ -25,7 +25,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -282,7 +402,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/dbac.c
+++ b/src/models/dbac.c
-@@ -363,7 +363,7 @@ void show_version(FILE * ofp)
+@@ -363,7 +363,7 @@
fprintf(ofp," Released %s\n",RELEASE_DAY);
fprintf(ofp," Compiled %s\n",COMPILE_DATE);
fprintf(ofp,"dba was written by Niclas Jareborg, Ewan Birney and Richard Durbin\n");
@@ -293,7 +413,7 @@ Description: Fix spelling issues
--- a/src/models/dnal.c
+++ b/src/models/dnal.c
-@@ -104,7 +104,7 @@ void show_short_help(FILE * ofp)
+@@ -104,7 +104,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -304,7 +424,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/dnawise.c
+++ b/src/models/dnawise.c
-@@ -8,7 +8,7 @@ char * program_name = "dnawise";
+@@ -8,7 +8,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -315,7 +435,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/editdist.c
+++ b/src/models/editdist.c
-@@ -8,7 +8,7 @@ char * program_name = "editdist";
+@@ -8,7 +8,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -326,7 +446,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/estwise.c
+++ b/src/models/estwise.c
-@@ -557,7 +557,7 @@ void show_help(FILE * ofp)
+@@ -557,7 +557,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -337,7 +457,16 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/estwisedb.c
+++ b/src/models/estwisedb.c
-@@ -807,7 +807,7 @@ boolean show_header(FILE * ofp)
+@@ -206,7 +206,7 @@
+
+ if( make_anchored_aln == TRUE ) {
+ if( tsm == NULL ) {
+- warn("Attempting to make an achored alignment without a HMM. impossible!");
++ warn("Attempting to make an anchored alignment without a HMM. impossible!");
+ make_anchored_aln = FALSE;
+ } else {
+ anchored = single_unit_AlnBlock(tsm->len,"MATCH_STATE");
+@@ -807,7 +807,7 @@
fprintf(ofp,"-------------------------------------------------------------\n");
fprintf(ofp,"Wise2 - database searching mode\n");
fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY);
@@ -346,7 +475,7 @@ Description: Fix spelling issues
fprintf(ofp," See -version for more info on copyright\n");
fprintf(ofp,"Bugs and credits to Ewan Birney <birney at sanger.ac.uk>\n");
fprintf(ofp,"-------------------------------------------------------------\n\n");
-@@ -836,7 +836,7 @@ boolean show_header(FILE * ofp)
+@@ -836,7 +836,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -357,7 +486,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/evopairwise.c
+++ b/src/models/evopairwise.c
-@@ -15,7 +15,7 @@ char * program_name = "evopairwise";
+@@ -15,7 +15,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -368,7 +497,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/fivestar.c
+++ b/src/models/fivestar.c
-@@ -14,7 +14,7 @@ char * program_name = "fivestar";
+@@ -14,7 +14,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -379,7 +508,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/fivestarscan.c
+++ b/src/models/fivestarscan.c
-@@ -14,7 +14,7 @@ char * program_name = "fivestarscan";
+@@ -14,7 +14,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -390,7 +519,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/fivestarsearch.c
+++ b/src/models/fivestarsearch.c
-@@ -12,7 +12,7 @@ char * program_name = "fivestarsearch";
+@@ -12,7 +12,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -401,7 +530,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/genewise.c
+++ b/src/models/genewise.c
-@@ -858,7 +858,7 @@ void show_help(FILE * ofp)
+@@ -858,7 +858,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -412,7 +541,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/genewisedb.c
+++ b/src/models/genewisedb.c
-@@ -505,7 +505,7 @@ boolean show_header(FILE * ofp)
+@@ -505,7 +505,7 @@
{
fprintf(ofp,"Wise2 - database searching mode\n");
fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY);
@@ -421,7 +550,7 @@ Description: Fix spelling issues
fprintf(ofp," See -version for more info on copyright\n");
fprintf(ofp,"Bugs and credits to Ewan Birney <birney at sanger.ac.uk>\n");
fprintf(ofp,"-----------------------------------------------------\n\n");
-@@ -1003,7 +1003,7 @@ void show_help(FILE * ofp)
+@@ -1003,7 +1003,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -432,7 +561,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/genomewise.c
+++ b/src/models/genomewise.c
-@@ -16,7 +16,7 @@ void show_utr_exon_genomewise(AlnBlock *
+@@ -16,7 +16,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -443,7 +572,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/lba.c
+++ b/src/models/lba.c
-@@ -8,7 +8,7 @@ char * program_name = "lba";
+@@ -8,7 +8,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -454,7 +583,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/motifcluster.c
+++ b/src/models/motifcluster.c
-@@ -8,7 +8,7 @@ char * program_name = "motifcluster";
+@@ -8,7 +8,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -465,7 +594,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/motifdiff.c
+++ b/src/models/motifdiff.c
-@@ -8,7 +8,7 @@ char * program_name = "motifdiff";
+@@ -8,7 +8,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -476,7 +605,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/motifwise.c
+++ b/src/models/motifwise.c
-@@ -8,7 +8,7 @@ char * program_name = "motifwise";
+@@ -8,7 +8,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -487,7 +616,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/oldpostwise.c
+++ b/src/models/oldpostwise.c
-@@ -375,7 +375,7 @@ void show_help(char * help_arg)
+@@ -375,7 +375,7 @@
void show_version(void)
{
fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -498,7 +627,7 @@ Description: Fix spelling issues
fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/promotercluster.c
+++ b/src/models/promotercluster.c
-@@ -7,7 +7,7 @@ char * program_name = "promotercluster";
+@@ -7,7 +7,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -509,7 +638,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/promoterwise.c
+++ b/src/models/promoterwise.c
-@@ -15,7 +15,7 @@ char * program_name = "promoterwise";
+@@ -15,7 +15,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -520,7 +649,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/pseudowise.c
+++ b/src/models/pseudowise.c
-@@ -13,7 +13,7 @@ char * program_name = "pseudowise";
+@@ -13,7 +13,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -531,7 +660,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/psw.c
+++ b/src/models/psw.c
-@@ -259,7 +259,7 @@ int main(int argc,char ** argv)
+@@ -259,7 +259,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -542,7 +671,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/pswdb.c
+++ b/src/models/pswdb.c
-@@ -95,7 +95,7 @@ void show_help(FILE * ofp)
+@@ -95,7 +95,7 @@
void show_version(void)
{
fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -551,7 +680,7 @@ Description: Fix spelling issues
fprintf(stdout,"The source code is copyright (c) EMBL 1998 and others\n");
fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n");
fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n");
-@@ -347,7 +347,7 @@ boolean show_header(FILE * ofp)
+@@ -347,7 +347,7 @@
fprintf(ofp,"-------------------------------------------------------------\n");
fprintf(ofp,"Wise2 - Protein vs. Protein\n");
fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY);
@@ -562,7 +691,7 @@ Description: Fix spelling issues
fprintf(ofp," Ewan Birney <birney at sanger.ac.uk>\n");
--- a/src/models/scanwisep.c
+++ b/src/models/scanwisep.c
-@@ -421,7 +421,7 @@ HitList * HitList_from_HSP_HSP2HitListIm
+@@ -421,7 +421,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -573,7 +702,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/statwise.c
+++ b/src/models/statwise.c
-@@ -11,7 +11,7 @@ char * codon_table = "codon.table";
+@@ -11,7 +11,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -584,7 +713,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/models/sywise.c
+++ b/src/models/sywise.c
-@@ -12,7 +12,7 @@ char * codon_table = "codon.table";
+@@ -12,7 +12,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -595,7 +724,7 @@ Description: Fix spelling issues
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
--- a/src/network/wise_proteinindex_server.c
+++ b/src/network/wise_proteinindex_server.c
-@@ -26,7 +26,7 @@ char * program_name = "scanwise_server";
+@@ -26,7 +26,7 @@
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
@@ -658,7 +787,16 @@ Description: Fix spelling issues
Ewan Birney <birney at sanger.ac.uk>
--- a/src/models/genefrequency.c
+++ b/src/models/genefrequency.c
-@@ -636,7 +636,7 @@ double double_from_line(char * buffer)
+@@ -459,7 +459,7 @@
+
+ if( strwhitestartcmp(buffer,"type",spacestr) == 0 ) {
+
+- phase = 3; /** if no phase, assumme it is for all phases **/
++ phase = 3; /** if no phase, assume it is for all phases **/
+
+ type = check_type_GeneFrequency(buffer,ifp,¢er,&phase);
+
+@@ -636,7 +636,7 @@
ret = strtod(runner,&end);
if( end == runner || isalnum((int)*end) ) {
@@ -667,9 +805,36 @@ Description: Fix spelling issues
}
return ret;
+@@ -810,7 +810,7 @@
+
+ /* Function: read_base_GeneConsensus(base_array,line,ifp)
+ *
+- * Descrip: assummes base_array is 4 positions long
++ * Descrip: assumes base_array is 4 positions long
+ *
+ * line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
+ *
+@@ -877,7 +877,7 @@
+
+ /* Function: read_codon_GeneConsensus(codon_array,line,ifp)
+ *
+- * Descrip: assummes codon_array is 64 positions long
++ * Descrip: assumes codon_array is 64 positions long
+ *
+ * line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
+ *
--- a/src/models/genefrequency.dy
+++ b/src/models/genefrequency.dy
-@@ -597,7 +597,7 @@ double double_from_line(char * buffer)
+@@ -428,7 +428,7 @@
+
+ if( strwhitestartcmp(buffer,"type",spacestr) == 0 ) {
+
+- phase = 3; /** if no phase, assumme it is for all phases **/
++ phase = 3; /** if no phase, assume it is for all phases **/
+
+ type = check_type_GeneFrequency(buffer,ifp,¢er,&phase);
+
+@@ -597,7 +597,7 @@
ret = strtod(runner,&end);
if( end == runner || isalnum((int)*end) ) {
@@ -678,9 +843,27 @@ Description: Fix spelling issues
}
return ret;
+@@ -745,7 +745,7 @@
+ }
+
+ %func
+-assummes base_array is 4 positions long
++assumes base_array is 4 positions long
+
+ line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
+
+@@ -802,7 +802,7 @@
+
+
+ %func
+-assummes codon_array is 64 positions long
++assumes codon_array is 64 positions long
+
+ line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
+
--- a/src/models/seqerror.dy
+++ b/src/models/seqerror.dy
-@@ -42,7 +42,7 @@ Sequence * seq
+@@ -42,7 +42,7 @@
SequenceErrorSet * ses
%info
This holds a sequence and what
@@ -691,7 +874,7 @@ Description: Fix spelling issues
--- a/src/models/seqerror.h
+++ b/src/models/seqerror.h
-@@ -72,7 +72,7 @@ typedef struct Wise2_SequenceErrorSet Wi
+@@ -72,7 +72,7 @@
/* Object ErrorSequence
*
* Descrip: This holds a sequence and what
@@ -700,3 +883,2476 @@ Description: Fix spelling issues
*
*
*/
+--- a/src/dynlibsrc/hspscaninterface.c
++++ b/src/dynlibsrc/hspscaninterface.c
+@@ -158,7 +158,7 @@
+ void show_help_HSPScanInterfacePara(FILE * ofp)
+ {
+ fprintf(ofp,"Parameters for word scan\n");
+- fprintf(ofp," -hspscan_impl [vanilla/threaded/twohit] implementation to use if compliled for runtime\n");
++ fprintf(ofp," -hspscan_impl [vanilla/threaded/twohit] implementation to use if compiled for runtime\n");
+ fprintf(ofp," -hspscan_maxres [100] maximum results returned by scan\n");
+ fprintf(ofp," -hspscan_numb [1000] word count to numb word (for low complexity)\n");
+ fprintf(ofp," -hspscan_worddepth [2] maximum offset from word - [0,1,2]\n");
+--- a/src/dynlibsrc/hspscaninterface.dy
++++ b/src/dynlibsrc/hspscaninterface.dy
+@@ -157,7 +157,7 @@
+ void show_help_HSPScanInterfacePara(FILE * ofp)
+ {
+ fprintf(ofp,"Parameters for word scan\n");
+- fprintf(ofp," -hspscan_impl [vanilla/threaded/twohit] implementation to use if compliled for runtime\n");
++ fprintf(ofp," -hspscan_impl [vanilla/threaded/twohit] implementation to use if compiled for runtime\n");
+ fprintf(ofp," -hspscan_maxres [100] maximum results returned by scan\n");
+ fprintf(ofp," -hspscan_numb [1000] word count to numb word (for low complexity)\n");
+ fprintf(ofp," -hspscan_worddepth [2] maximum offset from word - [0,1,2]\n");
+--- a/src/dyc/dbthread.c
++++ b/src/dyc/dbthread.c
+@@ -311,7 +311,7 @@
+ expr(dfp,"holder->%s = %s(holder->querydb,&db_status);",gm->query->name,gm->qtype->init_func);
+ expr(dfp,"holder->query_init = TRUE;");
+ expr(dfp,"if( db_status == DB_RETURN_ERROR )");
+- hang_expr(dfp,"fatal(\"Unable to initalise query database in %s search\");",gm->name);
++ hang_expr(dfp,"fatal(\"Unable to initialise query database in %s search\");",gm->name);
+ closebrace(dfp);
+ expr(dfp,"%s = %s(holder->%s);",gm->query->name,gm->qtype->hard_link_func,gm->query->name);
+ add_block_comment(dfp,"get query information into datascore");
+--- a/src/dyc/dbthread.dy
++++ b/src/dyc/dbthread.dy
+@@ -300,7 +300,7 @@
+ expr(dfp,"holder->%s = %s(holder->querydb,&db_status);",gm->query->name,gm->qtype->init_func);
+ expr(dfp,"holder->query_init = TRUE;");
+ expr(dfp,"if( db_status == DB_RETURN_ERROR )");
+- hang_expr(dfp,"fatal(\"Unable to initalise query database in %s search\");",gm->name);
++ hang_expr(dfp,"fatal(\"Unable to initialise query database in %s search\");",gm->name);
+ closebrace(dfp);
+ expr(dfp,"%s = %s(holder->%s);",gm->query->name,gm->qtype->hard_link_func,gm->query->name);
+ add_block_comment(dfp,"get query information into datascore");
+--- a/src/models/abc.c
++++ b/src/models/abc.c
+@@ -442,7 +442,7 @@
+ holder->query = init_ProteinDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in abc search");
++ fatal("Unable to initialise query database in abc search");
+ }
+ query = hard_link_ComplexSequence(holder->query);
+ /* get query information into datascore */
+@@ -989,7 +989,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/cdnawise10.c
++++ b/src/models/cdnawise10.c
+@@ -694,7 +694,7 @@
+ holder->query = init_cDNADB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in CdnaWise10 search");
++ fatal("Unable to initialise query database in CdnaWise10 search");
+ }
+ query = hard_link_ComplexSequence(holder->query);
+ /* get query information into datascore */
+@@ -1477,7 +1477,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/estloop3.c
++++ b/src/models/estloop3.c
+@@ -697,7 +697,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in EstLoop3 search");
++ fatal("Unable to initialise query database in EstLoop3 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -1470,7 +1470,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/estquick3.c
++++ b/src/models/estquick3.c
+@@ -467,7 +467,7 @@
+ holder->query = init_GeneWiseQuickDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in EstQuick3 search");
++ fatal("Unable to initialise query database in EstQuick3 search");
+ }
+ query = hard_link_GeneWiseScoreFlat(holder->query);
+ /* get query information into datascore */
+@@ -1018,7 +1018,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/estslim3.c
++++ b/src/models/estslim3.c
+@@ -505,7 +505,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in EstSlim3 search");
++ fatal("Unable to initialise query database in EstSlim3 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -1094,7 +1094,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/estslimloop.c
++++ b/src/models/estslimloop.c
+@@ -594,7 +594,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in EstSlimLoop3 search");
++ fatal("Unable to initialise query database in EstSlimLoop3 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -1272,7 +1272,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/estwise3.c
++++ b/src/models/estwise3.c
+@@ -613,7 +613,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in EstWise3 search");
++ fatal("Unable to initialise query database in EstWise3 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -1302,7 +1302,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/geneloop21.c
++++ b/src/models/geneloop21.c
+@@ -1190,7 +1190,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in GeneLoop21 search");
++ fatal("Unable to initialise query database in GeneLoop21 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -2444,7 +2444,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/geneloop6.c
++++ b/src/models/geneloop6.c
+@@ -682,7 +682,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in GeneLoop6 search");
++ fatal("Unable to initialise query database in GeneLoop6 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -1426,7 +1426,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/genestretch6.c
++++ b/src/models/genestretch6.c
+@@ -717,7 +717,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in GeneStretch6 search");
++ fatal("Unable to initialise query database in GeneStretch6 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -1500,7 +1500,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/genewise21.c
++++ b/src/models/genewise21.c
+@@ -1354,7 +1354,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in GeneWise21 search");
++ fatal("Unable to initialise query database in GeneWise21 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -2770,7 +2770,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/genewise4.c
++++ b/src/models/genewise4.c
+@@ -580,7 +580,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in GeneWise4 search");
++ fatal("Unable to initialise query database in GeneWise4 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -1226,7 +1226,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/genewise6.c
++++ b/src/models/genewise6.c
+@@ -638,7 +638,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in GeneWise6 search");
++ fatal("Unable to initialise query database in GeneWise6 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -1338,7 +1338,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/gwlite.c
++++ b/src/models/gwlite.c
+@@ -597,7 +597,7 @@
+ holder->query = init_GwLite_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in GeneLiteModel search");
++ fatal("Unable to initialise query database in GeneLiteModel search");
+ }
+ query = hard_link_GwLiteScore(holder->query);
+ /* get query information into datascore */
+@@ -1275,7 +1275,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/pba.c
++++ b/src/models/pba.c
+@@ -496,7 +496,7 @@
+ holder->q = init_ProteinDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in ProteinBlockAligner search");
++ fatal("Unable to initialise query database in ProteinBlockAligner search");
+ }
+ q = hard_link_ComplexSequence(holder->q);
+ /* get query information into datascore */
+@@ -1102,7 +1102,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/proteinsw.c
++++ b/src/models/proteinsw.c
+@@ -444,7 +444,7 @@
+ holder->query = init_ProteinDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in ProteinSW search");
++ fatal("Unable to initialise query database in ProteinSW search");
+ }
+ query = hard_link_ComplexSequence(holder->query);
+ /* get query information into datascore */
+@@ -988,7 +988,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/pseudowise7.c
++++ b/src/models/pseudowise7.c
+@@ -649,7 +649,7 @@
+ holder->query = init_GeneWiseDB(holder->querydb,&db_status);
+ holder->query_init = TRUE;
+ if( db_status == DB_RETURN_ERROR )
+- fatal("Unable to initalise query database in PseudoWise7 search");
++ fatal("Unable to initialise query database in PseudoWise7 search");
+ }
+ query = hard_link_GeneWiseScore(holder->query);
+ /* get query information into datascore */
+@@ -1368,7 +1368,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/sw_wrap.dy
++++ b/src/models/sw_wrap.dy
+@@ -311,7 +311,7 @@
+
+ %func
+ This is the most correct way of aligning two Proteins,
+-using Protein objects, which can be assummed to be
++using Protein objects, which can be assumed to be
+ proteins with no objections
+
+ To display the alignment use write_pretty_Protein_align
+@@ -359,7 +359,7 @@
+ out = std_score_Hscore(bits_cutoff,report_level);
+
+ if( dbsi == NULL ) {
+- warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
++ warn("Passed a NULL dbsi search implementation object. Exiting without searching");
+ goto exit;
+ }
+
+@@ -411,7 +411,7 @@
+ out = std_score_Hscore(bits_cutoff,report_level);
+
+ if( dbsi == NULL ) {
+- warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
++ warn("Passed a NULL dbsi search implementation object. Exiting without searching");
+ goto exit;
+ }
+
+@@ -464,7 +464,7 @@
+ out = std_score_Hscore(bits_cutoff,report_level);
+
+ if( dbsi == NULL ) {
+- warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
++ warn("Passed a NULL dbsi search implementation object. Exiting without searching");
+ goto exit;
+ }
+
+--- a/src/dynlibsrc/translation.c
++++ b/src/dynlibsrc/translation.c
+@@ -90,7 +90,7 @@
+ if( i+3 >= cd->baseseq->len )
+ break;
+ else {
+- warn("Got a stop codon in the middle of a translation at postion [%d]. Yuk!",i);
++ warn("Got a stop codon in the middle of a translation at position [%d]. Yuk!",i);
+ seq->seq[j] = '*';
+ }
+ } else {
+--- a/src/dynlibsrc/translation.dy
++++ b/src/dynlibsrc/translation.dy
+@@ -118,7 +118,7 @@
+ if( i+3 >= cd->baseseq->len )
+ break;
+ else {
+- warn("Got a stop codon in the middle of a translation at postion [%d]. Yuk!",i);
++ warn("Got a stop codon in the middle of a translation at position [%d]. Yuk!",i);
+ seq->seq[j] = '*';
+ }
+ } else {
+--- a/src/models/phasemodel.c
++++ b/src/models/phasemodel.c
+@@ -102,7 +102,7 @@
+ fprintf(stdout,"for the definition of the intron. For phase 0 introns, it should be labeled as\n");
+ fprintf(stdout,"the amino acid before the intron. For phase 1 and 2 introns, this is on the intron\n\n");
+ fprintf(stdout,"We suggest using a small spread of positions to cope with intron positioning errors\n");
+- fprintf(stdout," eg, defining an intron at position 4, phase 0, make postions 3,4 and 5 with position 0\n\n");
++ fprintf(stdout," eg, defining an intron at position 4, phase 0, make positions 3,4 and 5 with position 0\n\n");
+ fprintf(stdout,"The phase file format is\n");
+ fprintf(stdout,"# lines starting with hash are comments\n");
+ fprintf(stdout,"# three tab delimited columns\n");
+--- a/src/models/phasemodel.dy
++++ b/src/models/phasemodel.dy
+@@ -152,7 +152,7 @@
+ fprintf(stdout,"for the definition of the intron. For phase 0 introns, it should be labeled as\n");
+ fprintf(stdout,"the amino acid before the intron. For phase 1 and 2 introns, this is on the intron\n\n");
+ fprintf(stdout,"We suggest using a small spread of positions to cope with intron positioning errors\n");
+- fprintf(stdout," eg, defining an intron at position 4, phase 0, make postions 3,4 and 5 with position 0\n\n");
++ fprintf(stdout," eg, defining an intron at position 4, phase 0, make positions 3,4 and 5 with position 0\n\n");
+ fprintf(stdout,"The phase file format is\n");
+ fprintf(stdout,"# lines starting with hash are comments\n");
+ fprintf(stdout,"# three tab delimited columns\n");
+--- a/src/models/standardout.c
++++ b/src/models/standardout.c
+@@ -13,7 +13,7 @@
+ fprintf(ofp," -alb show align block format\n");
+ fprintf(ofp," -pal show raw alignment\n");
+ fprintf(ofp," -calb show cumlative align block\n");
+- fprintf(ofp," -cpal show cumlative raw alignemnt\n");
++ fprintf(ofp," -cpal show cumlative raw alignment\n");
+
+ }
+
+--- a/src/models/standardout.dy
++++ b/src/models/standardout.dy
+@@ -27,7 +27,7 @@
+ fprintf(ofp," -alb show align block format\n");
+ fprintf(ofp," -pal show raw alignment\n");
+ fprintf(ofp," -calb show cumlative align block\n");
+- fprintf(ofp," -cpal show cumlative raw alignemnt\n");
++ fprintf(ofp," -cpal show cumlative raw alignment\n");
+
+ }
+
+--- a/src/dyc/method.c
++++ b/src/dyc/method.c
+@@ -149,7 +149,7 @@
+ *
+ * Descrip: function which handles the logical->real mapping
+ *
+- * At the moment "unmappable" types get assummed to be C types,
++ * At the moment "unmappable" types get assumed to be C types,
+ * trigger a warning and return the correct thing.
+ *
+ *
+@@ -166,7 +166,7 @@
+ Type * ty;
+
+ if( (ty = Type_from_name(mts,type)) == NULL ) {
+- warn("Type [%s] is not recognised as a logical Dynamite type. Assumming it is a real C type",type);
++ warn("Type [%s] is not recognised as a logical Dynamite type. Assuming it is a real C type",type);
+ return StructElement_from_nameandtype(name,type);
+ }
+
+--- a/src/dyc/method.dy
++++ b/src/dyc/method.dy
+@@ -168,7 +168,7 @@
+ %func
+ function which handles the logical->real mapping
+
+-At the moment "unmappable" types get assummed to be C types,
++At the moment "unmappable" types get assumed to be C types,
+ trigger a warning and return the correct thing.
+ %%
+ StructElement * StructElement_from_MethodTypeSet(char * name,char * type,MethodTypeSet * mts)
+@@ -176,7 +176,7 @@
+ Type * ty;
+
+ if( (ty = Type_from_name(mts,type)) == NULL ) {
+- warn("Type [%s] is not recognised as a logical Dynamite type. Assumming it is a real C type",type);
++ warn("Type [%s] is not recognised as a logical Dynamite type. Assuming it is a real C type",type);
+ return StructElement_from_nameandtype(name,type);
+ }
+
+--- a/src/models/genewisemodel.c
++++ b/src/models/genewisemodel.c
+@@ -305,7 +305,7 @@
+ /* Function: GeneWise_fold_in_synchronised_RandomModel(gw,rm,cm,*ct,stop_codon_background)
+ *
+ * Descrip: This function places 'log-odd' scores of the
+- * genewise model assumming that the random model
++ * genewise model assuming that the random model
+ * is a protein model with the codon mapper system
+ * added in, *and* that the path of the random model
+ * is synchronous with the query model.
+@@ -526,7 +526,7 @@
+ } else if ( strstr(col->alu[position_in_aln]->text_label,"INSERT") != NULL ) {
+ continue;
+ } else {
+- warn("In processing alignment to peptide, got label %s which cannot handle. Assumming X in protein translation",col->alu[position_in_aln]->text_label);
++ warn("In processing alignment to peptide, got label %s which cannot handle. Assuming X in protein translation",col->alu[position_in_aln]->text_label);
+ buffer[i++] = 'X';
+ }
+ }
+--- a/src/models/genewisemodel.dy
++++ b/src/models/genewisemodel.dy
+@@ -335,7 +335,7 @@
+
+ %func
+ This function places 'log-odd' scores of the
+-genewise model assumming that the random model
++genewise model assuming that the random model
+ is a protein model with the codon mapper system
+ added in, *and* that the path of the random model
+ is synchronous with the query model.
+@@ -516,7 +516,7 @@
+ } else if ( strstr(col->alu[position_in_aln]->text_label,"INSERT") != NULL ) {
+ continue;
+ } else {
+- warn("In processing alignment to peptide, got label %s which cannot handle. Assumming X in protein translation",col->alu[position_in_aln]->text_label);
++ warn("In processing alignment to peptide, got label %s which cannot handle. Assuming X in protein translation",col->alu[position_in_aln]->text_label);
+ buffer[i++] = 'X';
+ }
+ }
+--- a/src/models/motifmatrix.c
++++ b/src/models/motifmatrix.c
+@@ -84,7 +84,7 @@
+ # line 121 "motifmatrix.dy"
+ void show_help_MotifMatrixPara(FILE * ofp)
+ {
+- fprintf(ofp,"Motif Matrix matching paramters\n");
++ fprintf(ofp,"Motif Matrix matching parameters\n");
+ fprintf(ofp," -mm_motif [0.9] Probability of a match in a motif\n");
+ fprintf(ofp," -mm_cons [0.75] Probability of a match in a non-motif conserved\n");
+ fprintf(ofp," -mm_spacer[0.35] Probability of a match in a spacer\n");
+--- a/src/models/motifmatrix.dy
++++ b/src/models/motifmatrix.dy
+@@ -120,7 +120,7 @@
+
+ void show_help_MotifMatrixPara(FILE * ofp)
+ {
+- fprintf(ofp,"Motif Matrix matching paramters\n");
++ fprintf(ofp,"Motif Matrix matching parameters\n");
+ fprintf(ofp," -mm_motif [0.9] Probability of a match in a motif\n");
+ fprintf(ofp," -mm_cons [0.75] Probability of a match in a non-motif conserved\n");
+ fprintf(ofp," -mm_spacer[0.35] Probability of a match in a spacer\n");
+--- a/src/dyc/dynafunc.c
++++ b/src/dyc/dynafunc.c
+@@ -983,7 +983,7 @@
+
+ expr(dfp,"if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)");
+ startbrace(dfp);
+- warn_expr(dfp,"Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn_expr(dfp,"Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ expr(dfp,"return");
+ closebrace(dfp);
+
+@@ -1263,7 +1263,7 @@
+ }
+
+ /****
+- This function requires alot of stuff assummed.
++ This function requires alot of stuff assumed.
+
+ int * reti, int *retj and *retstate *retspecial as parameters which will be set
+ by this block.
+@@ -2020,7 +2020,7 @@
+ *
+ * Descrip: This writes the special to special block movements, if needed.
+ *
+- * If bestscore is not NULL, it assummes that this is the name of
++ * If bestscore is not NULL, it assumes that this is the name of
+ * an int variable which should hold the bestscore by updating
+ * from the end state
+ *
+--- a/src/dyc/dynafunc.dy
++++ b/src/dyc/dynafunc.dy
+@@ -952,7 +952,7 @@
+
+ expr(dfp,"if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT)");
+ startbrace(dfp);
+- warn_expr(dfp,"Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn_expr(dfp,"Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ expr(dfp,"return");
+ closebrace(dfp);
+
+@@ -1228,7 +1228,7 @@
+ }
+
+ /****
+- This function requires alot of stuff assummed.
++ This function requires alot of stuff assumed.
+
+ int * reti, int *retj and *retstate *retspecial as parameters which will be set
+ by this block.
+@@ -1957,7 +1957,7 @@
+ %func
+ This writes the special to special block movements, if needed.
+
+-If bestscore is not NULL, it assummes that this is the name of
++If bestscore is not NULL, it assumes that this is the name of
+ an int variable which should hold the bestscore by updating
+ from the end state
+ %type internal
+--- a/src/dyc/method.h
++++ b/src/dyc/method.h
+@@ -113,7 +113,7 @@
+ *
+ * Descrip: function which handles the logical->real mapping
+ *
+- * At the moment "unmappable" types get assummed to be C types,
++ * At the moment "unmappable" types get assumed to be C types,
+ * trigger a warning and return the correct thing.
+ *
+ *
+--- a/src/dynlibsrc/basematrix.h
++++ b/src/dynlibsrc/basematrix.h
+@@ -84,7 +84,7 @@
+ BASEMATRIX_TYPE_VERYSMALL
+ };
+
+-/* 20 MB assummed. Could break something? */
++/* 20 MB assumed. Could break something? */
+ #define COMPILE_BASEMATRIX_MAX_KB 20000
+
+
+--- a/src/dynlibsrc/proteinindexcons.c
++++ b/src/dynlibsrc/proteinindexcons.c
+@@ -52,8 +52,8 @@
+ fprintf(ofp," -piwaypost [number] - waypost for streamed cases, default 3\n");
+ fprintf(ofp," -pishadow [number] - shadow length for shadow cases, default 15\n");
+ fprintf(ofp," -pishadow_err [number] - errors per 100 identities tolerated, 3\n");
+- fprintf(ofp," -piseqmax - indexes can assumme maximum length of seq\n");
+- fprintf(ofp," -piseqmax_len [number] - assummed max sequnce length, default 1000\n");
++ fprintf(ofp," -piseqmax - indexes can assume maximum length of seq\n");
++ fprintf(ofp," -piseqmax_len [number] - assumed max sequnce length, default 1000\n");
+
+ return;
+ }
+--- a/src/dynlibsrc/proteinindexcons.dy
++++ b/src/dynlibsrc/proteinindexcons.dy
+@@ -63,8 +63,8 @@
+ fprintf(ofp," -piwaypost [number] - waypost for streamed cases, default 3\n");
+ fprintf(ofp," -pishadow [number] - shadow length for shadow cases, default 15\n");
+ fprintf(ofp," -pishadow_err [number] - errors per 100 identities tolerated, 3\n");
+- fprintf(ofp," -piseqmax - indexes can assumme maximum length of seq\n");
+- fprintf(ofp," -piseqmax_len [number] - assummed max sequnce length, default 1000\n");
++ fprintf(ofp," -piseqmax - indexes can assume maximum length of seq\n");
++ fprintf(ofp," -piseqmax_len [number] - assumed max sequnce length, default 1000\n");
+
+ return;
+ }
+--- a/src/models/alignwisedp.c
++++ b/src/models/alignwisedp.c
+@@ -1214,7 +1214,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/bigdba.c
++++ b/src/models/bigdba.c
+@@ -1071,7 +1071,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/clonewisedp.c
++++ b/src/models/clonewisedp.c
+@@ -1040,7 +1040,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/dba.c
++++ b/src/models/dba.c
+@@ -983,7 +983,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/dnaalign.c
++++ b/src/models/dnaalign.c
+@@ -1077,7 +1077,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/dnaprofiledp.c
++++ b/src/models/dnaprofiledp.c
+@@ -1156,7 +1156,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/editdistdp.c
++++ b/src/models/editdistdp.c
+@@ -869,7 +869,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/estfrag3.c
++++ b/src/models/estfrag3.c
+@@ -1129,7 +1129,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/fivestate.c
++++ b/src/models/fivestate.c
+@@ -1044,7 +1044,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/genephase6.c
++++ b/src/models/genephase6.c
+@@ -1653,7 +1653,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/genomewise9.c
++++ b/src/models/genomewise9.c
+@@ -1501,7 +1501,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/largeblockdp.c
++++ b/src/models/largeblockdp.c
+@@ -844,7 +844,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/localclonewisedp.c
++++ b/src/models/localclonewisedp.c
+@@ -960,7 +960,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/localdba.c
++++ b/src/models/localdba.c
+@@ -999,7 +999,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/motifmatrixdp.c
++++ b/src/models/motifmatrixdp.c
+@@ -772,7 +772,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/slimdba.c
++++ b/src/models/slimdba.c
+@@ -761,7 +761,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/statwise10.c
++++ b/src/models/statwise10.c
+@@ -580,7 +580,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/sw_wrap.c
++++ b/src/models/sw_wrap.c
+@@ -333,7 +333,7 @@
+ /* Function: Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
+ *
+ * Descrip: This is the most correct way of aligning two Proteins,
+- * using Protein objects, which can be assummed to be
++ * using Protein objects, which can be assumed to be
+ * proteins with no objections
+ *
+ * To display the alignment use write_pretty_Protein_align
+@@ -394,7 +394,7 @@
+ out = std_score_Hscore(bits_cutoff,report_level);
+
+ if( dbsi == NULL ) {
+- warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
++ warn("Passed a NULL dbsi search implementation object. Exiting without searching");
+ goto exit;
+ }
+
+@@ -452,7 +452,7 @@
+ out = std_score_Hscore(bits_cutoff,report_level);
+
+ if( dbsi == NULL ) {
+- warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
++ warn("Passed a NULL dbsi search implementation object. Exiting without searching");
+ goto exit;
+ }
+
+@@ -511,7 +511,7 @@
+ out = std_score_Hscore(bits_cutoff,report_level);
+
+ if( dbsi == NULL ) {
+- warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
++ warn("Passed a NULL dbsi search implementation object. Exiting without searching");
+ goto exit;
+ }
+
+--- a/src/models/sw_wrap.h
++++ b/src/models/sw_wrap.h
+@@ -144,7 +144,7 @@
+ /* Function: Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
+ *
+ * Descrip: This is the most correct way of aligning two Proteins,
+- * using Protein objects, which can be assummed to be
++ * using Protein objects, which can be assumed to be
+ * proteins with no objections
+ *
+ * To display the alignment use write_pretty_Protein_align
+--- a/src/models/sw_wrap.pod
++++ b/src/models/sw_wrap.pod
+@@ -67,7 +67,7 @@
+ &Wise2::Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
+
+ This is the most correct way of aligning two Proteins,
+- using Protein objects, which can be assummed to be
++ using Protein objects, which can be assumed to be
+ proteins with no objections
+
+ To display the alignment use write_pretty_Protein_align
+--- a/src/models/sw_wrap.tex
++++ b/src/models/sw_wrap.tex
+@@ -80,7 +80,7 @@
+ \item[returns] [UNKN ] Undocumented return value [AlnBlock *]
+ \end{description}
+ This is the most correct way of aligning two Proteins,
+-using Protein objects, which can be assummed to be
++using Protein objects, which can be assumed to be
+ proteins with no objections
+
+
+--- a/src/models/sw_wrap_api.h
++++ b/src/models/sw_wrap_api.h
+@@ -70,7 +70,7 @@
+ /* Function: Wise2_Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
+ *
+ * Descrip: This is the most correct way of aligning two Proteins,
+- * using Protein objects, which can be assummed to be
++ * using Protein objects, which can be assumed to be
+ * proteins with no objections
+ *
+ * To display the alignment use write_pretty_Protein_align
+--- a/src/models/sywise20.c
++++ b/src/models/sywise20.c
+@@ -1531,7 +1531,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/threestatedp.c
++++ b/src/models/threestatedp.c
+@@ -864,7 +864,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/threestateloop.c
++++ b/src/models/threestateloop.c
+@@ -950,7 +950,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/models/transregiondp.c
++++ b/src/models/transregiondp.c
+@@ -1008,7 +1008,7 @@
+ register int i;
+ register int j;
+ if( mat->basematrix->type != BASEMATRIX_TYPE_EXPLICIT) {
+- warn("Cannot iniate matrix, is not an explicit memory type and you have assummed that");
++ warn("Cannot iniate matrix, is not an explicit memory type and you have assumed that");
+ return;
+ }
+
+--- a/src/dyc/dynashadow.c
++++ b/src/dyc/dynashadow.c
+@@ -2438,7 +2438,7 @@
+ register int j;
+ register int k;
+
+- /*** this function assummes the following local variables
++ /*** this function assumes the following local variables
+
+ int score
+ int temp
+--- a/src/dyc/dynashadow.dy
++++ b/src/dyc/dynashadow.dy
+@@ -2358,7 +2358,7 @@
+ register int j;
+ register int k;
+
+- /*** this function assummes the following local variables
++ /*** this function assumes the following local variables
+
+ int score
+ int temp
+--- a/src/dynlibsrc/aln.c
++++ b/src/dynlibsrc/aln.c
+@@ -67,7 +67,7 @@
+
+ /* Function: add_to_anchored_AlnBlock(growing,add)
+ *
+- * Descrip: This function assummes that the first AlnSequence
++ * Descrip: This function assumes that the first AlnSequence
+ * in the current and the adding AlnBlock are the same,
+ * and that you want to add the second AlnSequence of the
+ * second alnblock to the first, anchored on the first
+--- a/src/dynlibsrc/aln.dy
++++ b/src/dynlibsrc/aln.dy
+@@ -157,7 +157,7 @@
+ }
+
+ %func
+-This function assummes that the first AlnSequence
++This function assumes that the first AlnSequence
+ in the current and the adding AlnBlock are the same,
+ and that you want to add the second AlnSequence of the
+ second alnblock to the first, anchored on the first
+--- a/src/dynlibsrc/aln.h
++++ b/src/dynlibsrc/aln.h
+@@ -198,7 +198,7 @@
+
+ /* Function: add_to_anchored_AlnBlock(growing,add)
+ *
+- * Descrip: This function assummes that the first AlnSequence
++ * Descrip: This function assumes that the first AlnSequence
+ * in the current and the adding AlnBlock are the same,
+ * and that you want to add the second AlnSequence of the
+ * second alnblock to the first, anchored on the first
+--- a/src/dynlibsrc/codon.c
++++ b/src/dynlibsrc/codon.c
+@@ -486,7 +486,7 @@
+ *
+ * Descrip: takes an ASCII coded pointer to a 3 base pair
+ * sequence (it could be the part of a sequence: it only
+- * assummes that the seq points with 3 chars at pos 0,1,2
++ * assumes that the seq points with 3 chars at pos 0,1,2
+ * in C coordinates from seq. No NULL is required). It
+ * ives back the codon as made from standard mapping, ie,
+ * 25*base_1+5*base_2 + base3 being a number from 0-124 inc.
+--- a/src/dynlibsrc/codon.dy
++++ b/src/dynlibsrc/codon.dy
+@@ -451,7 +451,7 @@
+ %func
+ takes an ASCII coded pointer to a 3 base pair
+ sequence (it could be the part of a sequence: it only
+-assummes that the seq points with 3 chars at pos 0,1,2
++assumes that the seq points with 3 chars at pos 0,1,2
+ in C coordinates from seq. No NULL is required). It
+ ives back the codon as made from standard mapping, ie,
+ 25*base_1+5*base_2 + base3 being a number from 0-124 inc.
+--- a/src/dynlibsrc/codon.h
++++ b/src/dynlibsrc/codon.h
+@@ -324,7 +324,7 @@
+ *
+ * Descrip: takes an ASCII coded pointer to a 3 base pair
+ * sequence (it could be the part of a sequence: it only
+- * assummes that the seq points with 3 chars at pos 0,1,2
++ * assumes that the seq points with 3 chars at pos 0,1,2
+ * in C coordinates from seq. No NULL is required). It
+ * ives back the codon as made from standard mapping, ie,
+ * 25*base_1+5*base_2 + base3 being a number from 0-124 inc.
+--- a/src/dynlibsrc/codon.pod
++++ b/src/dynlibsrc/codon.pod
+@@ -282,7 +282,7 @@
+
+ takes an ASCII coded pointer to a 3 base pair
+ sequence (it could be the part of a sequence: it only
+- assummes that the seq points with 3 chars at pos 0,1,2
++ assumes that the seq points with 3 chars at pos 0,1,2
+ in C coordinates from seq. No NULL is required). It
+ ives back the codon as made from standard mapping, ie,
+ 25*base_1+5*base_2 + base3 being a number from 0-124 inc.
+--- a/src/dynlibsrc/codon.tex
++++ b/src/dynlibsrc/codon.tex
+@@ -121,7 +121,7 @@
+ \end{description}
+ takes an ASCII coded pointer to a 3 base pair
+ sequence (it could be the part of a sequence: it only
+-assummes that the seq points with 3 chars at pos 0,1,2
++assumes that the seq points with 3 chars at pos 0,1,2
+ in C coordinates from seq. No NULL is required). It
+ ives back the codon as made from standard mapping, ie,
+ 25*base_1+5*base_2 + base3 being a number from 0-124 inc.
+--- a/src/dynlibsrc/codon_api.h
++++ b/src/dynlibsrc/codon_api.h
+@@ -279,7 +279,7 @@
+ *
+ * Descrip: takes an ASCII coded pointer to a 3 base pair
+ * sequence (it could be the part of a sequence: it only
+- * assummes that the seq points with 3 chars at pos 0,1,2
++ * assumes that the seq points with 3 chars at pos 0,1,2
+ * in C coordinates from seq. No NULL is required). It
+ * ives back the codon as made from standard mapping, ie,
+ * 25*base_1+5*base_2 + base3 being a number from 0-124 inc.
+--- a/src/dynlibsrc/codonmapper.c
++++ b/src/dynlibsrc/codonmapper.c
+@@ -285,7 +285,7 @@
+
+ /* Function: sprinkle_errors_over_CodonMapper(cm,error)
+ *
+- * Descrip: Takes a codon mapper and assummes that the majority of errors
++ * Descrip: Takes a codon mapper and assumes that the majority of errors
+ * are due to a single base change in the codon at probability error.
+ * Therefore, for each codon it adds error * prob(codon) * 0.25 to each
+ * other codon one base away, taking away therefore the result.
+--- a/src/dynlibsrc/codonmapper.dy
++++ b/src/dynlibsrc/codonmapper.dy
+@@ -271,7 +271,7 @@
+ }
+
+ %func
+-Takes a codon mapper and assummes that the majority of errors
++Takes a codon mapper and assumes that the majority of errors
+ are due to a single base change in the codon at probability error.
+ Therefore, for each codon it adds error * prob(codon) * 0.25 to each
+ other codon one base away, taking away therefore the result.
+--- a/src/dynlibsrc/codonmapper.h
++++ b/src/dynlibsrc/codonmapper.h
+@@ -165,7 +165,7 @@
+
+ /* Function: sprinkle_errors_over_CodonMapper(cm,error)
+ *
+- * Descrip: Takes a codon mapper and assummes that the majority of errors
++ * Descrip: Takes a codon mapper and assumes that the majority of errors
+ * are due to a single base change in the codon at probability error.
+ * Therefore, for each codon it adds error * prob(codon) * 0.25 to each
+ * other codon one base away, taking away therefore the result.
+--- a/src/dynlibsrc/codonmapper.pod
++++ b/src/dynlibsrc/codonmapper.pod
+@@ -50,7 +50,7 @@
+
+ &Wise2::CodonMapper::sprinkle_errors_over_CodonMapper(cm,error)
+
+- Takes a codon mapper and assummes that the majority of errors
++ Takes a codon mapper and assumes that the majority of errors
+ are due to a single base change in the codon at probability error.
+ Therefore, for each codon it adds error * prob(codon) * 0.25 to each
+ other codon one base away, taking away therefore the result.
+--- a/src/dynlibsrc/codonmapper.tex
++++ b/src/dynlibsrc/codonmapper.tex
+@@ -69,7 +69,7 @@
+ \item[error] [UNKN ] substitution error rate [double]
+ \item[returns] Nothing - no return value
+ \end{description}
+-Takes a codon mapper and assummes that the majority of errors
++Takes a codon mapper and assumes that the majority of errors
+ are due to a single base change in the codon at probability error.
+ Therefore, for each codon it adds error * prob(codon) * 0.25 to each
+ other codon one base away, taking away therefore the result.
+--- a/src/dynlibsrc/codonmapper_api.h
++++ b/src/dynlibsrc/codonmapper_api.h
+@@ -21,7 +21,7 @@
+ /* API for object CodonMapper */
+ /* Function: Wise2_sprinkle_errors_over_CodonMapper(cm,error)
+ *
+- * Descrip: Takes a codon mapper and assummes that the majority of errors
++ * Descrip: Takes a codon mapper and assumes that the majority of errors
+ * are due to a single base change in the codon at probability error.
+ * Therefore, for each codon it adds error * prob(codon) * 0.25 to each
+ * other codon one base away, taking away therefore the result.
+--- a/src/dynlibsrc/codonmatrix.c
++++ b/src/dynlibsrc/codonmatrix.c
+@@ -100,7 +100,7 @@
+
+ /* Function: naive_CodonMatrixScore(ct,comp)
+ *
+- * Descrip: Builds a codon matrix from CompMat which assummes:
++ * Descrip: Builds a codon matrix from CompMat which assumes:
+ * No codon Bias
+ * No errors
+ * N codons score 0, stop codons score ??
+--- a/src/dynlibsrc/codonmatrix.dy
++++ b/src/dynlibsrc/codonmatrix.dy
+@@ -85,7 +85,7 @@
+
+
+ %func
+-Builds a codon matrix from CompMat which assummes:
++Builds a codon matrix from CompMat which assumes:
+ No codon Bias
+ No errors
+ N codons score 0, stop codons score ??
+--- a/src/dynlibsrc/codonmatrix.h
++++ b/src/dynlibsrc/codonmatrix.h
+@@ -94,7 +94,7 @@
+
+ /* Function: naive_CodonMatrixScore(ct,comp)
+ *
+- * Descrip: Builds a codon matrix from CompMat which assummes:
++ * Descrip: Builds a codon matrix from CompMat which assumes:
+ * No codon Bias
+ * No errors
+ * N codons score 0, stop codons score ??
+--- a/src/dynlibsrc/genomic.c
++++ b/src/dynlibsrc/genomic.c
+@@ -103,7 +103,7 @@
+
+ /* Function: read_fasta_file_Genomic(filename,length_of_N)
+ *
+- * Descrip: Reads a fasta file assumming that it is Genomic.
++ * Descrip: Reads a fasta file assuming that it is Genomic.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -135,7 +135,7 @@
+
+ /* Function: read_fasta_Genomic(ifp,length_of_N)
+ *
+- * Descrip: Reads a fasta file assumming that it is Genomic.
++ * Descrip: Reads a fasta file assuming that it is Genomic.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -216,7 +216,7 @@
+ /* Function: Genomic_from_Sequence_Nheuristic(seq,length_of_N)
+ *
+ * Descrip: makes a new genomic from a Sequence, but
+- * assummes that all the N runs greater than
++ * assumes that all the N runs greater than
+ * a certain level are actually repeats.
+ *
+ *
+--- a/src/dynlibsrc/genomic.dy
++++ b/src/dynlibsrc/genomic.dy
+@@ -129,7 +129,7 @@
+
+
+ %func
+-Reads a fasta file assumming that it is Genomic.
++Reads a fasta file assuming that it is Genomic.
+ Will complain if it is not, and return NULL.
+ %arg
+ filename filename to be opened and read
+@@ -155,7 +155,7 @@
+
+
+ %func
+-Reads a fasta file assumming that it is Genomic.
++Reads a fasta file assuming that it is Genomic.
+ Will complain if it is not, and return NULL.
+ %arg
+ ifp file point to be read from
+@@ -210,7 +210,7 @@
+
+ %func
+ makes a new genomic from a Sequence, but
+-assummes that all the N runs greater than
++assumes that all the N runs greater than
+ a certain level are actually repeats.
+ %%
+ Genomic * Genomic_from_Sequence_Nheuristic(Sequence * seq,int length_of_N)
+--- a/src/dynlibsrc/genomic.h
++++ b/src/dynlibsrc/genomic.h
+@@ -91,7 +91,7 @@
+
+ /* Function: read_fasta_file_Genomic(filename,length_of_N)
+ *
+- * Descrip: Reads a fasta file assumming that it is Genomic.
++ * Descrip: Reads a fasta file assuming that it is Genomic.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -107,7 +107,7 @@
+
+ /* Function: read_fasta_Genomic(ifp,length_of_N)
+ *
+- * Descrip: Reads a fasta file assumming that it is Genomic.
++ * Descrip: Reads a fasta file assuming that it is Genomic.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -167,7 +167,7 @@
+ /* Function: Genomic_from_Sequence_Nheuristic(seq,length_of_N)
+ *
+ * Descrip: makes a new genomic from a Sequence, but
+- * assummes that all the N runs greater than
++ * assumes that all the N runs greater than
+ * a certain level are actually repeats.
+ *
+ *
+--- a/src/dynlibsrc/genomic.pod
++++ b/src/dynlibsrc/genomic.pod
+@@ -355,7 +355,7 @@
+
+ &Wise2::read_fasta_file_Genomic(filename,length_of_N)
+
+- Reads a fasta file assumming that it is Genomic.
++ Reads a fasta file assuming that it is Genomic.
+ Will complain if it is not, and return NULL.
+
+
+@@ -369,7 +369,7 @@
+
+ &Wise2::read_fasta_Genomic(ifp,length_of_N)
+
+- Reads a fasta file assumming that it is Genomic.
++ Reads a fasta file assuming that it is Genomic.
+ Will complain if it is not, and return NULL.
+
+
+@@ -384,7 +384,7 @@
+ &Wise2::Genomic_from_Sequence_Nheuristic(seq,length_of_N)
+
+ makes a new genomic from a Sequence, but
+- assummes that all the N runs greater than
++ assumes that all the N runs greater than
+ a certain level are actually repeats.
+
+
+--- a/src/dynlibsrc/genomic.tex
++++ b/src/dynlibsrc/genomic.tex
+@@ -22,7 +22,7 @@
+ \item[length_of_N] [UNKN ] length of N to be considered repeat. -1 means none [int]
+ \item[returns] [UNKN ] Undocumented return value [Genomic *]
+ \end{description}
+-Reads a fasta file assumming that it is Genomic.
++Reads a fasta file assuming that it is Genomic.
+ Will complain if it is not, and return NULL.
+
+
+@@ -38,7 +38,7 @@
+ \item[length_of_N] [UNKN ] length of N to be considered repeat. -1 means none [int]
+ \item[returns] [UNKN ] Undocumented return value [Genomic *]
+ \end{description}
+-Reads a fasta file assumming that it is Genomic.
++Reads a fasta file assuming that it is Genomic.
+ Will complain if it is not, and return NULL.
+
+
+@@ -55,7 +55,7 @@
+ \item[returns] [UNKN ] Undocumented return value [Genomic *]
+ \end{description}
+ makes a new genomic from a Sequence, but
+-assummes that all the N runs greater than
++assumes that all the N runs greater than
+ a certain level are actually repeats.
+
+
+--- a/src/dynlibsrc/genomic_api.h
++++ b/src/dynlibsrc/genomic_api.h
+@@ -360,7 +360,7 @@
+ /* These functions are not associated with an object */
+ /* Function: Wise2_read_fasta_file_Genomic(filename,length_of_N)
+ *
+- * Descrip: Reads a fasta file assumming that it is Genomic.
++ * Descrip: Reads a fasta file assuming that it is Genomic.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -374,7 +374,7 @@
+
+ /* Function: Wise2_read_fasta_Genomic(ifp,length_of_N)
+ *
+- * Descrip: Reads a fasta file assumming that it is Genomic.
++ * Descrip: Reads a fasta file assuming that it is Genomic.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -389,7 +389,7 @@
+ /* Function: Wise2_Genomic_from_Sequence_Nheuristic(seq,length_of_N)
+ *
+ * Descrip: makes a new genomic from a Sequence, but
+- * assummes that all the N runs greater than
++ * assumes that all the N runs greater than
+ * a certain level are actually repeats.
+ *
+ *
+--- a/src/dynlibsrc/hspstream.c
++++ b/src/dynlibsrc/hspstream.c
+@@ -38,7 +38,7 @@
+ SequenceSet * out;
+ char buffer[512];
+
+- /* assumme that each HSPset has only one target sequence */
++ /* assume that each HSPset has only one target sequence */
+
+ out = SequenceSet_alloc_len(lm->len+1);
+
+@@ -109,7 +109,7 @@
+ *
+ * Descrip: typed linear hsp manager from stream
+ *
+- * assummes sequences coming in first, with query as first sequence
++ * assumes sequences coming in first, with query as first sequence
+ * and then hsps one after the other
+ *
+ *
+--- a/src/dynlibsrc/hspstream.dy
++++ b/src/dynlibsrc/hspstream.dy
+@@ -31,7 +31,7 @@
+ SequenceSet * out;
+ char buffer[512];
+
+- /* assumme that each HSPset has only one target sequence */
++ /* assume that each HSPset has only one target sequence */
+
+ out = SequenceSet_alloc_len(lm->len+1);
+
+@@ -93,7 +93,7 @@
+ %func
+ typed linear hsp manager from stream
+
+-assummes sequences coming in first, with query as first sequence
++assumes sequences coming in first, with query as first sequence
+ and then hsps one after the other
+ %%
+ LinearHSPmanager * typed_LinearHSPmanager_from_Stream(Wise2ReadStreamInterface * rs)
+--- a/src/dynlibsrc/hspstream.h
++++ b/src/dynlibsrc/hspstream.h
+@@ -64,7 +64,7 @@
+ *
+ * Descrip: typed linear hsp manager from stream
+ *
+- * assummes sequences coming in first, with query as first sequence
++ * assumes sequences coming in first, with query as first sequence
+ * and then hsps one after the other
+ *
+ *
+--- a/src/dynlibsrc/sequence.c
++++ b/src/dynlibsrc/sequence.c
+@@ -296,7 +296,7 @@
+ /* Function: translate_Sequence(dna,ct)
+ *
+ * Descrip: This translates a DNA sequence to a protein.
+- * It assummes that it starts at first residue
++ * It assumes that it starts at first residue
+ * (use trunc_Sequence to chop a sequence up).
+ *
+ *
+@@ -600,7 +600,7 @@
+ * Descrip: reads efetch specificed sequence. calls popen to
+ * efetch. A hack around accession numbers so that if the
+ * thing looks like WP:acc number, calls it with -a...
+- * otherwise assummes you have both database and name in the
++ * otherwise assumes you have both database and name in the
+ * efetchstring
+ *
+ *
+@@ -746,7 +746,7 @@
+
+ /* Function: read_fasta_Sequence(ifp)
+ *
+- * Descrip: reads a fasta file assumming pretty
++ * Descrip: reads a fasta file assuming pretty
+ * standard sanity for the file layout
+ *
+ *
+@@ -806,7 +806,7 @@
+ }
+
+ if( buffer[0] != '>' ) {
+- warn("First character read not >, assumming is not fasta");
++ warn("First character read not >, assuming is not fasta");
+ return NULL;
+ }
+
+@@ -933,7 +933,7 @@
+ return NULL;
+
+ if( c != '>' ) {
+- warn("First letter read is not '>' - assumming it is not a fasta stream");
++ warn("First letter read is not '>' - assuming it is not a fasta stream");
+ return NULL;
+ }
+
+--- a/src/dynlibsrc/sequence.h
++++ b/src/dynlibsrc/sequence.h
+@@ -260,7 +260,7 @@
+ /* Function: translate_Sequence(dna,ct)
+ *
+ * Descrip: This translates a DNA sequence to a protein.
+- * It assummes that it starts at first residue
++ * It assumes that it starts at first residue
+ * (use trunc_Sequence to chop a sequence up).
+ *
+ *
+@@ -407,7 +407,7 @@
+ * Descrip: reads efetch specificed sequence. calls popen to
+ * efetch. A hack around accession numbers so that if the
+ * thing looks like WP:acc number, calls it with -a...
+- * otherwise assummes you have both database and name in the
++ * otherwise assumes you have both database and name in the
+ * efetchstring
+ *
+ *
+@@ -459,7 +459,7 @@
+
+ /* Function: read_fasta_Sequence(ifp)
+ *
+- * Descrip: reads a fasta file assumming pretty
++ * Descrip: reads a fasta file assuming pretty
+ * standard sanity for the file layout
+ *
+ *
+--- a/src/dynlibsrc/sequence.pod
++++ b/src/dynlibsrc/sequence.pod
+@@ -136,7 +136,7 @@
+ &Wise2::Sequence::translate(dna,ct)
+
+ This translates a DNA sequence to a protein.
+- It assummes that it starts at first residue
++ It assumes that it starts at first residue
+ (use trunc_Sequence to chop a sequence up).
+
+
+@@ -267,7 +267,7 @@
+
+ &Wise2::Sequence::read_fasta_Sequence(ifp)
+
+- reads a fasta file assumming pretty
++ reads a fasta file assuming pretty
+ standard sanity for the file layout
+
+
+--- a/src/dynlibsrc/sequence.tex
++++ b/src/dynlibsrc/sequence.tex
+@@ -196,7 +196,7 @@
+ \item[returns] [OWNER] new protein sequence [Sequence *]
+ \end{description}
+ This translates a DNA sequence to a protein.
+-It assummes that it starts at first residue
++It assumes that it starts at first residue
+ (use trunc_Sequence to chop a sequence up).
+
+
+@@ -384,7 +384,7 @@
+ \item[ifp] [UNKN ] Undocumented argument [FILE *]
+ \item[returns] [UNKN ] Undocumented return value [Sequence *]
+ \end{description}
+-reads a fasta file assumming pretty
++reads a fasta file assuming pretty
+ standard sanity for the file layout
+
+
+--- a/src/dynlibsrc/sequence_api.h
++++ b/src/dynlibsrc/sequence_api.h
+@@ -118,7 +118,7 @@
+ /* Function: Wise2_translate_Sequence(dna,ct)
+ *
+ * Descrip: This translates a DNA sequence to a protein.
+- * It assummes that it starts at first residue
++ * It assumes that it starts at first residue
+ * (use trunc_Sequence to chop a sequence up).
+ *
+ *
+@@ -249,7 +249,7 @@
+
+ /* Function: Wise2_read_fasta_Sequence(ifp)
+ *
+- * Descrip: reads a fasta file assumming pretty
++ * Descrip: reads a fasta file assuming pretty
+ * standard sanity for the file layout
+ *
+ *
+--- a/src/dynlibsrc/sequence_codon.c
++++ b/src/dynlibsrc/sequence_codon.c
+@@ -106,7 +106,7 @@
+ /* Function: translate_Sequence(dna,ct)
+ *
+ * Descrip: This translates a DNA sequence to a protein.
+- * It assummes that it starts at first residue
++ * It assumes that it starts at first residue
+ * (use trunc_Sequence to chop a sequence up).
+ *
+ *
+--- a/src/dynlibsrc/sequence_codon.dy
++++ b/src/dynlibsrc/sequence_codon.dy
+@@ -108,7 +108,7 @@
+
+ %func
+ This translates a DNA sequence to a protein.
+-It assummes that it starts at first residue
++It assumes that it starts at first residue
+ (use trunc_Sequence to chop a sequence up).
+ %simple translate
+ %arg
+--- a/src/dynlibsrc/sequence_codon.h
++++ b/src/dynlibsrc/sequence_codon.h
+@@ -62,7 +62,7 @@
+ /* Function: translate_Sequence(dna,ct)
+ *
+ * Descrip: This translates a DNA sequence to a protein.
+- * It assummes that it starts at first residue
++ * It assumes that it starts at first residue
+ * (use trunc_Sequence to chop a sequence up).
+ *
+ *
+--- a/src/dynlibsrc/sequence_codon.pod
++++ b/src/dynlibsrc/sequence_codon.pod
+@@ -54,7 +54,7 @@
+ &Wise2::translate(dna,ct)
+
+ This translates a DNA sequence to a protein.
+- It assummes that it starts at first residue
++ It assumes that it starts at first residue
+ (use trunc_Sequence to chop a sequence up).
+
+
+--- a/src/dynlibsrc/sequence_codon.tex
++++ b/src/dynlibsrc/sequence_codon.tex
+@@ -63,7 +63,7 @@
+ \item[returns] [OWNER] new protein sequence [Sequence *]
+ \end{description}
+ This translates a DNA sequence to a protein.
+-It assummes that it starts at first residue
++It assumes that it starts at first residue
+ (use trunc_Sequence to chop a sequence up).
+
+
+--- a/src/dynlibsrc/sequence_codon_api.h
++++ b/src/dynlibsrc/sequence_codon_api.h
+@@ -52,7 +52,7 @@
+ /* Function: Wise2_translate_Sequence(dna,ct)
+ *
+ * Descrip: This translates a DNA sequence to a protein.
+- * It assummes that it starts at first residue
++ * It assumes that it starts at first residue
+ * (use trunc_Sequence to chop a sequence up).
+ *
+ *
+--- a/src/models/genefrequency.h
++++ b/src/models/genefrequency.h
+@@ -260,7 +260,7 @@
+
+ /* Function: read_base_GeneConsensus(base_array,line,ifp)
+ *
+- * Descrip: assummes base_array is 4 positions long
++ * Descrip: assumes base_array is 4 positions long
+ *
+ * line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
+ *
+@@ -280,7 +280,7 @@
+
+ /* Function: read_codon_GeneConsensus(codon_array,line,ifp)
+ *
+- * Descrip: assummes codon_array is 64 positions long
++ * Descrip: assumes codon_array is 64 positions long
+ *
+ * line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
+ *
+--- a/src/models/genestats.c
++++ b/src/models/genestats.c
+@@ -899,7 +899,7 @@
+
+ /* Function: read_codon_GeneStats(codon_array,line,ifp)
+ *
+- * Descrip: assummes codon_array is 64 positions long
++ * Descrip: assumes codon_array is 64 positions long
+ *
+ * line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
+ *
+--- a/src/models/genestats.dy
++++ b/src/models/genestats.dy
+@@ -810,7 +810,7 @@
+
+
+ %func
+-assummes codon_array is 64 positions long
++assumes codon_array is 64 positions long
+
+ line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
+
+--- a/src/models/genestats.h
++++ b/src/models/genestats.h
+@@ -380,7 +380,7 @@
+
+ /* Function: read_codon_GeneStats(codon_array,line,ifp)
+ *
+- * Descrip: assummes codon_array is 64 positions long
++ * Descrip: assumes codon_array is 64 positions long
+ *
+ * line should have begin consensus on it and be of MAXLINE length as it will be used as the buffer.
+ *
+--- a/src/perl/scripts/blastwise.pl
++++ b/src/perl/scripts/blastwise.pl
+@@ -20,7 +20,7 @@
+ site: I cant second guess all the things you want to do with the
+ output, so you give it a go.
+
+-This assummes that the database you are searching *is* swissprot and
++This assumes that the database you are searching *is* swissprot and
+ you have SRS indexed it into the database called swissprot. If you
+ are running it on different database with a different indexer you will
+ need to change the executable used to retrieve the sequence
+--- a/src/dyc/api.c
++++ b/src/dyc/api.c
+@@ -957,7 +957,7 @@
+ if( fu->fi->ret->argtype == ARGTYPE_STATIC && is_basic_type_API(fu->fi->ret->type) == FALSE) {
+ /* we need to put in the memory handler... */
+ /*
+- * Horrible hack. We assumme the the C type MyType * means dynamite type MyType.
++ * Horrible hack. We assume the the C type MyType * means dynamite type MyType.
+ *
+ * YUK!!!! Also - v.v.v.v.v bad hard coded Wise2
+ *
+--- a/src/dyc/api.dy
++++ b/src/dyc/api.dy
+@@ -973,7 +973,7 @@
+ if( fu->fi->ret->argtype == ARGTYPE_STATIC && is_basic_type_API(fu->fi->ret->type) == FALSE) {
+ /* we need to put in the memory handler... */
+ /*
+- * Horrible hack. We assumme the the C type MyType * means dynamite type MyType.
++ * Horrible hack. We assume the the C type MyType * means dynamite type MyType.
+ *
+ * YUK!!!! Also - v.v.v.v.v bad hard coded Wise2
+ *
+--- a/src/dyc/funcinfo.c
++++ b/src/dyc/funcinfo.c
+@@ -271,7 +271,7 @@
+
+ ***/
+
+- /** assumme type (*name)(type,type,type) ***/
++ /** assume type (*name)(type,type,type) ***/
+
+ held = stringalloc(str);
+
+--- a/src/dyc/funcinfo.dy
++++ b/src/dyc/funcinfo.dy
+@@ -318,7 +318,7 @@
+
+ ***/
+
+- /** assumme type (*name)(type,type,type) ***/
++ /** assume type (*name)(type,type,type) ***/
+
+ held = stringalloc(str);
+
+--- a/src/dynlibsrc/genomicdb.c
++++ b/src/dynlibsrc/genomicdb.c
+@@ -63,7 +63,7 @@
+ warn("Cannot get entry for %s from Genomic db",de->name);
+ }
+
+- /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
++ /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
+ if( seq->type != SEQUENCE_DNA) {
+ warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",de->name);
+ }
+@@ -142,7 +142,7 @@
+ return NULL;
+ }
+
+- /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
++ /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
+ if( seq->type != SEQUENCE_DNA) {
+ warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",seq->name);
+ }
+@@ -247,7 +247,7 @@
+
+ uppercase_Sequence(seq);
+
+- /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
++ /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
+ if( seq->type != SEQUENCE_DNA) {
+ warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",seq->name);
+ }
+--- a/src/dynlibsrc/genomicdb.dy
++++ b/src/dynlibsrc/genomicdb.dy
+@@ -112,7 +112,7 @@
+ warn("Cannot get entry for %s from Genomic db",de->name);
+ }
+
+- /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
++ /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
+ if( seq->type != SEQUENCE_DNA) {
+ warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",de->name);
+ }
+@@ -175,7 +175,7 @@
+ return NULL;
+ }
+
+- /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
++ /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
+ if( seq->type != SEQUENCE_DNA) {
+ warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",seq->name);
+ }
+@@ -273,7 +273,7 @@
+
+ uppercase_Sequence(seq);
+
+- /* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
++ /* check dna status. We assume someone knows what he is doing when he makes a genomic db!*/
+ if( seq->type != SEQUENCE_DNA) {
+ warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",seq->name);
+ }
+--- a/src/dynlibsrc/genomicregion.c
++++ b/src/dynlibsrc/genomicregion.c
+@@ -975,7 +975,7 @@
+
+ /* Function: write_Embl_FT_GenomicRegion(gr,ofp)
+ *
+- * Descrip: Writes Embl feature table. Does assumme that
++ * Descrip: Writes Embl feature table. Does assume that
+ * there is only one transcript per gene and only
+ * cds exons are used
+ *
+@@ -1008,7 +1008,7 @@
+
+ /* Function: write_Diana_FT_GenomicRegion(gr,ofp)
+ *
+- * Descrip: Writes Embl feature table for diana use. Does assumme that
++ * Descrip: Writes Embl feature table for diana use. Does assume that
+ * there is only one transcript per gene and only
+ * cds exons are used
+ *
+--- a/src/dynlibsrc/genomicregion.dy
++++ b/src/dynlibsrc/genomicregion.dy
+@@ -847,7 +847,7 @@
+ }
+
+ %func
+-Writes Embl feature table. Does assumme that
++Writes Embl feature table. Does assume that
+ there is only one transcript per gene and only
+ cds exons are used
+
+@@ -873,7 +873,7 @@
+ }
+
+ %func
+-Writes Embl feature table for diana use. Does assumme that
++Writes Embl feature table for diana use. Does assume that
+ there is only one transcript per gene and only
+ cds exons are used
+
+--- a/src/dynlibsrc/genomicregion.h
++++ b/src/dynlibsrc/genomicregion.h
+@@ -455,7 +455,7 @@
+
+ /* Function: write_Embl_FT_GenomicRegion(gr,ofp)
+ *
+- * Descrip: Writes Embl feature table. Does assumme that
++ * Descrip: Writes Embl feature table. Does assume that
+ * there is only one transcript per gene and only
+ * cds exons are used
+ *
+@@ -474,7 +474,7 @@
+
+ /* Function: write_Diana_FT_GenomicRegion(gr,ofp)
+ *
+- * Descrip: Writes Embl feature table for diana use. Does assumme that
++ * Descrip: Writes Embl feature table for diana use. Does assume that
+ * there is only one transcript per gene and only
+ * cds exons are used
+ *
+--- a/src/dynlibsrc/genomicregion.pod
++++ b/src/dynlibsrc/genomicregion.pod
+@@ -133,7 +133,7 @@
+
+ &Wise2::GenomicRegion::write_Diana_FT_GenomicRegion(gr,ofp)
+
+- Writes Embl feature table for diana use. Does assumme that
++ Writes Embl feature table for diana use. Does assume that
+ there is only one transcript per gene and only
+ cds exons are used
+
+@@ -152,7 +152,7 @@
+
+ &Wise2::GenomicRegion::write_Embl_FT_GenomicRegion(gr,ofp)
+
+- Writes Embl feature table. Does assumme that
++ Writes Embl feature table. Does assume that
+ there is only one transcript per gene and only
+ cds exons are used
+
+--- a/src/dynlibsrc/genomicregion.tex
++++ b/src/dynlibsrc/genomicregion.tex
+@@ -164,7 +164,7 @@
+ \item[ofp] [UNKN ] Undocumented argument [FILE *]
+ \item[returns] Nothing - no return value
+ \end{description}
+-Writes Embl feature table for diana use. Does assumme that
++Writes Embl feature table for diana use. Does assume that
+ there is only one transcript per gene and only
+ cds exons are used
+
+@@ -192,7 +192,7 @@
+ \item[ofp] [UNKN ] Undocumented argument [FILE *]
+ \item[returns] Nothing - no return value
+ \end{description}
+-Writes Embl feature table. Does assumme that
++Writes Embl feature table. Does assume that
+ there is only one transcript per gene and only
+ cds exons are used
+
+--- a/src/dynlibsrc/genomicregion_api.h
++++ b/src/dynlibsrc/genomicregion_api.h
+@@ -106,7 +106,7 @@
+
+ /* Function: Wise2_write_Diana_FT_GenomicRegion(gr,ofp)
+ *
+- * Descrip: Writes Embl feature table for diana use. Does assumme that
++ * Descrip: Writes Embl feature table for diana use. Does assume that
+ * there is only one transcript per gene and only
+ * cds exons are used
+ *
+@@ -125,7 +125,7 @@
+
+ /* Function: Wise2_write_Embl_FT_GenomicRegion(gr,ofp)
+ *
+- * Descrip: Writes Embl feature table. Does assumme that
++ * Descrip: Writes Embl feature table. Does assume that
+ * there is only one transcript per gene and only
+ * cds exons are used
+ *
+--- a/src/dynlibsrc/proteinstreamedindex.c
++++ b/src/dynlibsrc/proteinstreamedindex.c
+@@ -299,7 +299,7 @@
+ }
+ add_lookup_GenericIndexResult_from_Pos(p->prev[i],psir,backtrace,waylength);
+ }
+- /* can assumme this is ok */
++ /* can assume this is ok */
+
+ break;
+ } else {
+--- a/src/dynlibsrc/proteinstreamedindex.dy
++++ b/src/dynlibsrc/proteinstreamedindex.dy
+@@ -256,7 +256,7 @@
+ }
+ add_lookup_GenericIndexResult_from_Pos(p->prev[i],psir,backtrace,waylength);
+ }
+- /* can assumme this is ok */
++ /* can assume this is ok */
+
+ break;
+ } else {
+--- a/src/models/threestatemodel.c
++++ b/src/models/threestatemodel.c
+@@ -470,7 +470,7 @@
+ *
+ * Arg: pro [READ ] protein sequence [Protein *]
+ * Arg: mat [READ ] comparison matrix to use [CompMat *]
+- * Arg: rm [READ ] random model which you assumme the matrix was built with [RandomModel *]
++ * Arg: rm [READ ] random model which you assume the matrix was built with [RandomModel *]
+ * Arg: gap [READ ] gap open penalty [int]
+ * Arg: ext [READ ] gap ext penalty [int]
+ *
+@@ -595,7 +595,7 @@
+ *
+ * Arg: pro [READ ] protein sequence [Protein *]
+ * Arg: mat [READ ] comparison matrix to use [CompMat *]
+- * Arg: rm [READ ] random model which you assumme the matrix was built with [RandomModel *]
++ * Arg: rm [READ ] random model which you assume the matrix was built with [RandomModel *]
+ * Arg: gap [READ ] gap open penalty [int]
+ * Arg: ext [READ ] gap ext penalty [int]
+ *
+--- a/src/models/threestatemodel.dy
++++ b/src/models/threestatemodel.dy
+@@ -480,14 +480,14 @@
+
+ %func
+ Makes a local three-state-model from a sequence. this is scary
+-hackery, assumming that the matrix is half-bits and normalising in a
++hackery, assuming that the matrix is half-bits and normalising in a
+ *very* wrong way to get "probabilities" out.
+
+ Works though
+ %arg
+ pro r protein sequence
+ mat r comparison matrix to use
+-rm r random model which you assumme the matrix was built with
++rm r random model which you assume the matrix was built with
+ gap r gap open penalty
+ ext r gap ext penalty
+ %%
+@@ -587,7 +587,7 @@
+
+ %func
+ Makes a global three-state-model from a sequence.
+-Like the local version, this is scary hackery, assumming
++Like the local version, this is scary hackery, assuming
+ that the matrix is half-bits and normalising in a *very*
+ wrong way to get "probabilities" out.
+
+@@ -595,7 +595,7 @@
+ %arg
+ pro r protein sequence
+ mat r comparison matrix to use
+-rm r random model which you assumme the matrix was built with
++rm r random model which you assume the matrix was built with
+ gap r gap open penalty
+ ext r gap ext penalty
+ %%
+--- a/src/models/threestatemodel.h
++++ b/src/models/threestatemodel.h
+@@ -340,7 +340,7 @@
+ /* Function: ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext)
+ *
+ * Descrip: Makes a local three-state-model from a sequence. this is scary
+- * hackery, assumming that the matrix is half-bits and normalising in a
++ * hackery, assuming that the matrix is half-bits and normalising in a
+ * *very* wrong way to get "probabilities" out.
+ *
+ * Works though
+@@ -348,7 +348,7 @@
+ *
+ * Arg: pro [READ ] protein sequence [Protein *]
+ * Arg: mat [READ ] comparison matrix to use [CompMat *]
+- * Arg: rm [READ ] random model which you assumme the matrix was built with [RandomModel *]
++ * Arg: rm [READ ] random model which you assume the matrix was built with [RandomModel *]
+ * Arg: gap [READ ] gap open penalty [int]
+ * Arg: ext [READ ] gap ext penalty [int]
+ *
+@@ -362,7 +362,7 @@
+ /* Function: global_ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext)
+ *
+ * Descrip: Makes a global three-state-model from a sequence.
+- * Like the local version, this is scary hackery, assumming
++ * Like the local version, this is scary hackery, assuming
+ * that the matrix is half-bits and normalising in a *very*
+ * wrong way to get "probabilities" out.
+ *
+@@ -371,7 +371,7 @@
+ *
+ * Arg: pro [READ ] protein sequence [Protein *]
+ * Arg: mat [READ ] comparison matrix to use [CompMat *]
+- * Arg: rm [READ ] random model which you assumme the matrix was built with [RandomModel *]
++ * Arg: rm [READ ] random model which you assume the matrix was built with [RandomModel *]
+ * Arg: gap [READ ] gap open penalty [int]
+ * Arg: ext [READ ] gap ext penalty [int]
+ *
+--- a/src/models/threestatemodel.pod
++++ b/src/models/threestatemodel.pod
+@@ -95,7 +95,7 @@
+ &Wise2::ThreeStateModel::ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext)
+
+ Makes a local three-state-model from a sequence. this is scary
+- hackery, assumming that the matrix is half-bits and normalising in a
++ hackery, assuming that the matrix is half-bits and normalising in a
+ *very* wrong way to get "probabilities" out.
+
+ Works though
+@@ -104,7 +104,7 @@
+
+ Argument pro [READ ] protein sequence [Protein *]
+ Argument mat [READ ] comparison matrix to use [CompMat *]
+- Argument rm [READ ] random model which you assumme the matrix was built with [RandomModel *]
++ Argument rm [READ ] random model which you assume the matrix was built with [RandomModel *]
+ Argument gap [READ ] gap open penalty [int]
+ Argument ext [READ ] gap ext penalty [int]
+ Return [UNKN ] Undocumented return value [ThreeStateModel *]
+--- a/src/models/threestatemodel.tex
++++ b/src/models/threestatemodel.tex
+@@ -126,13 +126,13 @@
+ \begin{description}
+ \item[pro] [READ ] protein sequence [Protein *]
+ \item[mat] [READ ] comparison matrix to use [CompMat *]
+-\item[rm] [READ ] random model which you assumme the matrix was built with [RandomModel *]
++\item[rm] [READ ] random model which you assume the matrix was built with [RandomModel *]
+ \item[gap] [READ ] gap open penalty [int]
+ \item[ext] [READ ] gap ext penalty [int]
+ \item[returns] [UNKN ] Undocumented return value [ThreeStateModel *]
+ \end{description}
+ Makes a local three-state-model from a sequence. this is scary
+-hackery, assumming that the matrix is half-bits and normalising in a
++hackery, assuming that the matrix is half-bits and normalising in a
+ *very* wrong way to get "probabilities" out.
+
+
+--- a/src/models/threestatemodel_api.h
++++ b/src/models/threestatemodel_api.h
+@@ -82,7 +82,7 @@
+ /* Function: Wise2_ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext)
+ *
+ * Descrip: Makes a local three-state-model from a sequence. this is scary
+- * hackery, assumming that the matrix is half-bits and normalising in a
++ * hackery, assuming that the matrix is half-bits and normalising in a
+ * *very* wrong way to get "probabilities" out.
+ *
+ * Works though
+@@ -90,7 +90,7 @@
+ *
+ * Arg: pro protein sequence [Wise2_Protein *]
+ * Arg: mat comparison matrix to use [Wise2_CompMat *]
+- * Arg: rm random model which you assumme the matrix was built with [Wise2_RandomModel *]
++ * Arg: rm random model which you assume the matrix was built with [Wise2_RandomModel *]
+ * Arg: gap gap open penalty [int]
+ * Arg: ext gap ext penalty [int]
+ *
+--- a/src/dyc/type.c
++++ b/src/dyc/type.c
+@@ -259,7 +259,7 @@
+ if( su == NULL ) {
+ pe |= PERR_OUT_OF_SCOPE;
+ if( dycw == NULL || dycw->warn_extern == TRUE )
+- warn("Name [%s] is out of scope: assumming extern",ExprTree->word);
++ warn("Name [%s] is out of scope: assuming extern",ExprTree->word);
+ } else {
+ /* fprintf(stderr,"Ok.[%d] for name %s, going to add %s\n",ExprTree->attrib,ExprTree->word,su->app);*/
+ strcat(buffer,su->app);
+--- a/src/dyc/type.dy
++++ b/src/dyc/type.dy
+@@ -271,7 +271,7 @@
+ if( su == NULL ) {
+ pe |= PERR_OUT_OF_SCOPE;
+ if( dycw == NULL || dycw->warn_extern == TRUE )
+- warn("Name [%s] is out of scope: assumming extern",ExprTree->word);
++ warn("Name [%s] is out of scope: assuming extern",ExprTree->word);
+ } else {
+ /* fprintf(stderr,"Ok.[%d] for name %s, going to add %s\n",ExprTree->attrib,ExprTree->word,su->app);*/
+ strcat(buffer,su->app);
+--- a/src/dynlibsrc/cdna.c
++++ b/src/dynlibsrc/cdna.c
+@@ -29,7 +29,7 @@
+
+ /* Function: read_fasta_file_cDNA(filename)
+ *
+- * Descrip: Reads a fasta file assumming that it is cDNA.
++ * Descrip: Reads a fasta file assuming that it is cDNA.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -54,7 +54,7 @@
+
+ /* Function: read_fasta_cDNA(ifp)
+ *
+- * Descrip: Reads a fasta file assumming that it is cDNA.
++ * Descrip: Reads a fasta file assuming that it is cDNA.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+--- a/src/dynlibsrc/cdna.dy
++++ b/src/dynlibsrc/cdna.dy
+@@ -48,7 +48,7 @@
+ }
+
+ %func
+-Reads a fasta file assumming that it is cDNA.
++Reads a fasta file assuming that it is cDNA.
+ Will complain if it is not, and return NULL.
+ %arg
+ filename filename to be opened and read
+@@ -67,7 +67,7 @@
+
+
+ %func
+-Reads a fasta file assumming that it is cDNA.
++Reads a fasta file assuming that it is cDNA.
+ Will complain if it is not, and return NULL.
+ %arg
+ ifp file point to be read from
+--- a/src/dynlibsrc/cdna.h
++++ b/src/dynlibsrc/cdna.h
+@@ -53,7 +53,7 @@
+
+ /* Function: read_fasta_file_cDNA(filename)
+ *
+- * Descrip: Reads a fasta file assumming that it is cDNA.
++ * Descrip: Reads a fasta file assuming that it is cDNA.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -68,7 +68,7 @@
+
+ /* Function: read_fasta_cDNA(ifp)
+ *
+- * Descrip: Reads a fasta file assumming that it is cDNA.
++ * Descrip: Reads a fasta file assuming that it is cDNA.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+--- a/src/dynlibsrc/cdna.pod
++++ b/src/dynlibsrc/cdna.pod
+@@ -55,7 +55,7 @@
+
+ &Wise2::cDNA::read_fasta_file_cDNA(filename)
+
+- Reads a fasta file assumming that it is cDNA.
++ Reads a fasta file assuming that it is cDNA.
+ Will complain if it is not, and return NULL.
+
+
+--- a/src/dynlibsrc/cdna.tex
++++ b/src/dynlibsrc/cdna.tex
+@@ -57,7 +57,7 @@
+ \item[filename] [UNKN ] filename to be opened and read [char *]
+ \item[returns] [UNKN ] Undocumented return value [cDNA *]
+ \end{description}
+-Reads a fasta file assumming that it is cDNA.
++Reads a fasta file assuming that it is cDNA.
+ Will complain if it is not, and return NULL.
+
+
+--- a/src/dynlibsrc/cdna_api.h
++++ b/src/dynlibsrc/cdna_api.h
+@@ -37,7 +37,7 @@
+
+ /* Function: Wise2_read_fasta_file_cDNA(filename)
+ *
+- * Descrip: Reads a fasta file assumming that it is cDNA.
++ * Descrip: Reads a fasta file assuming that it is cDNA.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+--- a/src/dynlibsrc/dna.c
++++ b/src/dynlibsrc/dna.c
+@@ -29,7 +29,7 @@
+
+ /* Function: read_fasta_file_DNA (filename)
+ *
+- * Descrip: Reads a fasta file assumming that it is DNA.
++ * Descrip: Reads a fasta file assuming that it is DNA.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -54,7 +54,7 @@
+
+ /* Function: read_fasta_DNA (ifp)
+ *
+- * Descrip: Reads a fasta file assumming that it is DNA.
++ * Descrip: Reads a fasta file assuming that it is DNA.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+--- a/src/dynlibsrc/dna.dy
++++ b/src/dynlibsrc/dna.dy
+@@ -33,7 +33,7 @@
+ }
+
+ %func
+-Reads a fasta file assumming that it is DNA.
++Reads a fasta file assuming that it is DNA.
+ Will complain if it is not, and return NULL.
+ %arg
+ filename filename to be opened and read
+@@ -52,7 +52,7 @@
+
+
+ %func
+-Reads a fasta file assumming that it is DNA.
++Reads a fasta file assuming that it is DNA.
+ Will complain if it is not, and return NULL.
+ %arg
+ ifp file point to be read from
+--- a/src/dynlibsrc/dna.h
++++ b/src/dynlibsrc/dna.h
+@@ -53,7 +53,7 @@
+
+ /* Function: read_fasta_file_DNA (filename)
+ *
+- * Descrip: Reads a fasta file assumming that it is DNA.
++ * Descrip: Reads a fasta file assuming that it is DNA.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -68,7 +68,7 @@
+
+ /* Function: read_fasta_DNA (ifp)
+ *
+- * Descrip: Reads a fasta file assumming that it is DNA.
++ * Descrip: Reads a fasta file assuming that it is DNA.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+--- a/src/dynlibsrc/dynlibcross.c
++++ b/src/dynlibsrc/dynlibcross.c
+@@ -31,7 +31,7 @@
+ /* Function: std_bits_Hscore(cut_off_level,report_stagger)
+ *
+ * Descrip: This gives you a standard Hscore
+- * module with a cutoff in bits (assumming
++ * module with a cutoff in bits (assuming
+ * the score is being made from a standard
+ * Probability2Score type function).
+ *
+--- a/src/dynlibsrc/dynlibcross.dy
++++ b/src/dynlibsrc/dynlibcross.dy
+@@ -31,7 +31,7 @@
+
+ %func
+ This gives you a standard Hscore
+-module with a cutoff in bits (assumming
++module with a cutoff in bits (assuming
+ the score is being made from a standard
+ Probability2Score type function).
+ %%
+--- a/src/dynlibsrc/dynlibcross.h
++++ b/src/dynlibsrc/dynlibcross.h
+@@ -32,7 +32,7 @@
+ /* Function: std_bits_Hscore(cut_off_level,report_stagger)
+ *
+ * Descrip: This gives you a standard Hscore
+- * module with a cutoff in bits (assumming
++ * module with a cutoff in bits (assuming
+ * the score is being made from a standard
+ * Probability2Score type function).
+ *
+--- a/src/dynlibsrc/pairbase.c
++++ b/src/dynlibsrc/pairbase.c
+@@ -219,7 +219,7 @@
+
+ /* Function: make_flat_PairBaseCodonModel(cp,nonm,gap,ct)
+ *
+- * Descrip: Makes a PairBaseCodonModel from a protein matrix - assumming a flat
++ * Descrip: Makes a PairBaseCodonModel from a protein matrix - assuming a flat
+ * mapping to CodonMatrix
+ *
+ *
+--- a/src/dynlibsrc/pairbase.dy
++++ b/src/dynlibsrc/pairbase.dy
+@@ -210,7 +210,7 @@
+
+
+ %func
+-Makes a PairBaseCodonModel from a protein matrix - assumming a flat
++Makes a PairBaseCodonModel from a protein matrix - assuming a flat
+ mapping to CodonMatrix
+ %%
+ PairBaseCodonModel * make_flat_PairBaseCodonModel(CompProb * cp,Probability nonm,Probability gap,CodonTable * ct)
+--- a/src/dynlibsrc/pairbase.h
++++ b/src/dynlibsrc/pairbase.h
+@@ -164,7 +164,7 @@
+
+ /* Function: make_flat_PairBaseCodonModel(cp,nonm,gap,ct)
+ *
+- * Descrip: Makes a PairBaseCodonModel from a protein matrix - assumming a flat
++ * Descrip: Makes a PairBaseCodonModel from a protein matrix - assuming a flat
+ * mapping to CodonMatrix
+ *
+ *
+--- a/src/dynlibsrc/protein.c
++++ b/src/dynlibsrc/protein.c
+@@ -29,7 +29,7 @@
+
+ /* Function: read_fasta_file_Protein (filename)
+ *
+- * Descrip: Reads a fasta file assumming that it is protein.
++ * Descrip: Reads a fasta file assuming that it is protein.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -57,7 +57,7 @@
+
+ /* Function: read_fasta_Protein (ifp)
+ *
+- * Descrip: Reads a fasta file assumming that it is protein.
++ * Descrip: Reads a fasta file assuming that it is protein.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+--- a/src/dynlibsrc/protein.dy
++++ b/src/dynlibsrc/protein.dy
+@@ -48,7 +48,7 @@
+ }
+
+ %func
+-Reads a fasta file assumming that it is protein.
++Reads a fasta file assuming that it is protein.
+ Will complain if it is not, and return NULL.
+ %arg
+ filename filename to be opened and read
+@@ -70,7 +70,7 @@
+
+
+ %func
+-Reads a fasta file assumming that it is protein.
++Reads a fasta file assuming that it is protein.
+ Will complain if it is not, and return NULL.
+ %arg
+ ifp file point to be read from
+--- a/src/dynlibsrc/protein.h
++++ b/src/dynlibsrc/protein.h
+@@ -63,7 +63,7 @@
+
+ /* Function: read_fasta_file_Protein (filename)
+ *
+- * Descrip: Reads a fasta file assumming that it is protein.
++ * Descrip: Reads a fasta file assuming that it is protein.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+@@ -78,7 +78,7 @@
+
+ /* Function: read_fasta_Protein (ifp)
+ *
+- * Descrip: Reads a fasta file assumming that it is protein.
++ * Descrip: Reads a fasta file assuming that it is protein.
+ * Will complain if it is not, and return NULL.
+ *
+ *
+--- a/src/models/genewisemodel.h
++++ b/src/models/genewisemodel.h
+@@ -332,7 +332,7 @@
+ /* Function: GeneWise_fold_in_synchronised_RandomModel(gw,rm,cm,*ct,stop_codon_background)
+ *
+ * Descrip: This function places 'log-odd' scores of the
+- * genewise model assumming that the random model
++ * genewise model assuming that the random model
+ * is a protein model with the codon mapper system
+ * added in, *and* that the path of the random model
+ * is synchronous with the query model.
+--- a/src/models/genewisemodeldb.c
++++ b/src/models/genewisemodeldb.c
+@@ -233,7 +233,7 @@
+ /* Function: new_GeneWiseDB_cdna(syn,tdb,cp,cm,rmd,use_syn,flat_insert,allN)
+ *
+ * Descrip: makes a new GeneWiseDB from its component parts,
+- * assumming a cDNA db.
++ * assuming a cDNA db.
+ *
+ * All the objects are hard-linked internally, so you can, if you
+ * wish, free them once passing them into this function
+--- a/src/models/genewisemodeldb.dy
++++ b/src/models/genewisemodeldb.dy
+@@ -220,7 +220,7 @@
+
+ %func
+ makes a new GeneWiseDB from its component parts,
+-assumming a cDNA db.
++assuming a cDNA db.
+
+ All the objects are hard-linked internally, so you can, if you
+ wish, free them once passing them into this function
+--- a/src/models/genewisemodeldb.h
++++ b/src/models/genewisemodeldb.h
+@@ -126,7 +126,7 @@
+ /* Function: new_GeneWiseDB_cdna(syn,tdb,cp,cm,rmd,use_syn,flat_insert,allN)
+ *
+ * Descrip: makes a new GeneWiseDB from its component parts,
+- * assumming a cDNA db.
++ * assuming a cDNA db.
+ *
+ * All the objects are hard-linked internally, so you can, if you
+ * wish, free them once passing them into this function
+--- a/src/perl/scripts/halfwise.pl
++++ b/src/perl/scripts/halfwise.pl
+@@ -141,7 +141,7 @@
+ =item HMMer2.1.1
+
+ type './configure' followed by 'make' in the hmmer-2.1.1 directory and then 'make install'
+-(assumming you want to install in /usr/local/bin)
++(assuming you want to install in /usr/local/bin)
+
+ =item bioperl-0.04.2
+
=====================================
debian/watch
=====================================
@@ -1,4 +1,3 @@
version=4
-http://www.ebi.ac.uk/~birney/wise2/ (?:./)?wise(.*)\.tar\.gz \
- debian uupdate
+https://www.ebi.ac.uk/~birney/wise2/ (?:./)?wise(.*)\.tar\.gz
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/db6df7047ece158a76184da0fc8e12544c314ead...ec47163022bfbcfd27bfaeade97080a4e7d8cd24
--
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/db6df7047ece158a76184da0fc8e12544c314ead...ec47163022bfbcfd27bfaeade97080a4e7d8cd24
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