Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 20 May 2014 17:20:10 +0200
Description: Fix spelling

--- a/ChangeLog
+++ b/ChangeLog
@@ -1531,7 +1531,7 @@ Tue, 03 Jun 2003
 
       Nodes can be relabeled by specifying a map file.  This makes it
       easy and fast e.g. to do a one-pass Blast file parse, write the
-      cooccurrence data and a prefered node labeling, and then construct
+      cooccurrence data and a preferred node labeling, and then construct
       the final matrix.  The setup for transforming application-specific
       data into raw data is this:
 
--- a/doc/clmformat.azm
+++ b/doc/clmformat.azm
@@ -393,13 +393,13 @@
    in that cluster (corresponding to neighbours of the node in the
    cluster) relative to the overall amount of edge weights for that node
    (corresponding to all its neighbours).
-   The coverage measure (refered to as \bf{cov})
+   The coverage measure (referred to as \bf{cov})
    is also used. This is similar to the projection
    value, except that a) the coverage measure rewards the inclusion
    of large edge weights (and penalizes the inclusion of insignificant
    edge weights) and b) rewards node/cluster pairs for which the neighbour set
    of the node is very similar to the cluster.
-   The maximum coverage measure (refered to as \bf{maxcov}) is similar
+   The maximum coverage measure (referred to as \bf{maxcov}) is similar
    to the normal coverage measure except that it rewards inclusion
    of large edge weights even more.
    The cov and maxcov performance measures have several nice continuity and
--- a/doc/clmmate.azm
+++ b/doc/clmmate.azm
@@ -70,7 +70,7 @@
    the total number of nodes in clusters\~\v{i} and\~\v{j}
    for example can be obtained as the sum of entries in row\~\v{i}
    and column\~\v{j} respectively, and the difference counts
-   can then be obtained by substracting the intersection count.
+   can then be obtained by subtracting the intersection count.
    The contingency matrix can easily be computed using \mcx;
    e.g.}
 
--- a/doc/clmprotocols.5
+++ b/doc/clmprotocols.5
@@ -287,7 +287,7 @@ undirected, as recommended when using \f
 result in a directed network as BLAST E-values generally differ between two
 sequences\&. The default course of action for \fBmcxload(1)\fP is to use the
 best value found between a pair of labels\&. The next option,
-\fC--abc-neg-log10\fP tranforms the numerical values in the input (the BLAST
+\fC--abc-neg-log10\fP transforms the numerical values in the input (the BLAST
 E-values) by taking the logarithm in base\ \&10 and subsequently negating the
 sign\&. Finally, the transformed values are capped so that any E-value below
 1e-200 is set to a maximum allowed edge weight of\ \&200\&.
--- a/doc/clmprotocols.azm
+++ b/doc/clmprotocols.azm
@@ -237,7 +237,7 @@
    result in a directed network as BLAST E-values generally differ between two
    sequences. The default course of action for \mysib{mcxload} is to use the
    best value found between a pair of labels.  The next option,
-   \v{--abc-neg-log10} tranforms the numerical values in the input (the BLAST
+   \v{--abc-neg-log10} transforms the numerical values in the input (the BLAST
    E-values) by taking the logarithm in base\~10 and subsequently negating the
    sign. Finally, the transformed values are capped so that any E-value below
    1e-200 is set to a maximum allowed edge weight of\~200.
--- a/doc/clmprotocols2.5
+++ b/doc/clmprotocols2.5
@@ -306,7 +306,7 @@ undirected, as recommended when using \f
 result in a directed network as BLAST E-values generally differ between two
 sequences\&. The default course of action for \fBmcxload(1)\fP is to use the
 best value found between a pair of labels\&. The next option,
-\fC--abc-neg-log10\fP tranforms the numerical values in the input (the BLAST
+\fC--abc-neg-log10\fP transforms the numerical values in the input (the BLAST
 E-values) by taking the logarithm in base\ \&10 and subsequently negating the
 sign\&. Finally, the transformed values are capped so that any E-value below
 1e-200 is set to a maximum allowed edge weight of\ \&200\&.
--- a/doc/clmprotocols2.azm
+++ b/doc/clmprotocols2.azm
@@ -222,7 +222,7 @@
    result in a directed network as BLAST E-values generally differ between two
    sequences. The default course of action for \mysib{mcxload} is to use the
    best value found between a pair of labels.  The next option,
-   \v{--abc-neg-log10} tranforms the numerical values in the input (the BLAST
+   \v{--abc-neg-log10} transforms the numerical values in the input (the BLAST
    E-values) by taking the logarithm in base\~10 and subsequently negating the
    sign. Finally, the transformed values are capped so that any E-value below
    1e-200 is set to a maximum allowed edge weight of\~200.
--- a/doc/index.in.azm
+++ b/doc/index.in.azm
@@ -133,7 +133,7 @@
 \utsection{Dealing with matrices}
 \mkentry{mcxio}{5}{the mcl matrix format specification}
 \mkentry{mcx}{1}{interface to basic matrix operations}
-\mkentry{mcxsubs}{1}{extract submatrices by specifiying sets of nodes and clusters}
+\mkentry{mcxsubs}{1}{extract submatrices by specifying sets of nodes and clusters}
 \mkentry{mcxmap}{1}{remap matrix indices / relabel graph nodes}
 \mkentry{mcxassemble}{1}{prepare input matrix from cooccurrence scores}
 \utend
--- a/doc/mcl.azm
+++ b/doc/mcl.azm
@@ -91,7 +91,7 @@ by white space.  The most basic example
    The reason for this is that native mode is understood
    by all programs in the mcl suite. It is a more stringent
    and unambiguous format, and hence more suitable for data exchange.
-   The reader is refered to \mysib{clmprotocols} for more information.
+   The reader is referred to \mysib{clmprotocols} for more information.
    }
 
 
@@ -605,7 +605,7 @@ option.}
    {\defopt{--write-limit}{write mcl process limit}}
 }
 \car{
-   The first two options are somewhat outdated, in that the prefered way of
+   The first two options are somewhat outdated, in that the preferred way of
    loading networks is by using \mysib{mcxload}. The option
    \genopt{-write-expanded} can be useful for exploring more complicated input
    transformations that incorporate an expansion step, but is not really
@@ -974,7 +974,7 @@ option.}
    although this almost never happens in practice, as it requires some
    particular type of symmetry to be present in the input graph (not just any
    symmetry will do).  Mathematically speaking, this is a conjecture and not a
-   theorem, but the present author wil eat his shoe if it fails to be true (for
+   theorem, but the present author will eat his shoe if it fails to be true (for
    marzipan values of shoe).  It is easy though to construct an input graph for
    which certain mcl settings result in overlap - for example a line graph on
    an odd number of nodes.  The default is to excise overlapping parts and
@@ -1421,7 +1421,7 @@ with value 0.8.}
    Euclidean data. So mcl in its canonical form is certainly not fit for
    boundary detection or image segmentation. I experimented with a modified
    mcl and boundary detection in the thesis pointed to below (see
-   \secref{references}).  This was fun and not entirely unsuccesful, but not
+   \secref{references}).  This was fun and not entirely unsuccessful, but not
    something to be pursued further.
 }
 \par{
--- a/doc/mcl.txt
+++ b/doc/mcl.txt
@@ -59,7 +59,7 @@ mcl(1)                          USER COM
       to  use  native  mode rather than ABC mode.  The reason for this is that
       native mode is understood by all programs in the mcl suite. It is a more
       stringent  and  unambiguous  format,  and  hence  more suitable for data
-      exchange.  The reader is refered to clmprotocols(5)  for  more  informa-
+      exchange.  The reader is referred to clmprotocols(5)  for  more  informa-
       tion.
 
   SYNOPSIS
@@ -378,7 +378,7 @@ mcl(1)                          USER COM
       -write-graphx <fname> (write transformed graph)
       -write-expanded <fname> (write expanded graph)
       --write-limit (write mcl process limit)
-        The  first two options are somewhat outdated, in that the prefered way
+        The  first two options are somewhat outdated, in that the preferred way
         of loading networks is by using mcxload(1). The option -write-expanded
         can  be  useful  for  exploring more complicated input transformations
         that incorporate an expansion step, but is  not  really  relevant  for
@@ -889,7 +889,7 @@ mcl(1)                          USER COM
       from Euclidean data. So mcl in its canonical form is certainly  not  fit
       for boundary detection or image segmentation. I experimented with a mod-
       ified mcl and boundary detection in the thesis  pointed  to  below  (see
-      REFERENCES).  This  was  fun and not entirely unsuccesful, but not some-
+      REFERENCES).  This  was  fun and not entirely unsuccessful, but not some-
       thing to be pursued further.
 
       mcl likes undirected input graphs best, and it  really  dislikes  graphs
--- a/doc/mclfaq.7
+++ b/doc/mclfaq.7
@@ -63,7 +63,7 @@ and mathematics behind the MCL algorithm
 explained\&. A broad view is given in faq\ \&1\&.2,
 and see also faq\ \&1\&.5 and section \fBREFERENCES\fP\&.
 
-Some additional sections preceed the actual faq entries\&.
+Some additional sections precede the actual faq entries\&.
 The TOC section contains a listing of all questions\&.
 .SH RESOURCES
 
@@ -532,7 +532,7 @@ Somehow, directionality thwarts the noti
 .ZB 1m \fB3\&.11\fP
 \s+1\fBHow do I check that my graph/matrix is symmetric/undirected?\fP\s-1
 
-Whether your graph is created by third-party software or by custom sofware
+Whether your graph is created by third-party software or by custom software
 written by someone you know (e\&.g\&. yourself), it is advisable to test whether
 the software generates symmetric matrices\&. This can be done as follows
 using the \fBmcxi utility\fP, assuming that you want to test the
@@ -807,7 +807,7 @@ The latter two are listed when using the
 .ZB 1m \fB6\&.2\fP
 \s+1\fBHow do I compute the maximum amount of RAM needed by mcl?\fP\s-1
 
-It is rougly equal to
+It is roughly equal to
 
 .di ZV
 .in 0
--- a/doc/mclfaq.azm
+++ b/doc/mclfaq.azm
@@ -36,7 +36,7 @@
    and see also faq\~\fnum{innards} and section \secref{references}.}
 
 \par{
-   Some additional sections preceed the actual faq entries.
+   Some additional sections precede the actual faq entries.
    The TOC section contains a listing of all questions.
 \${html}{
    \bf{Clicking on the number of a question}
@@ -374,7 +374,7 @@ dislike uni-directed graphs so much?}
 
 \faq{checksymmetry}{How do I check that my graph/matrix is symmetric/undirected?}
 \car{
-   Whether your graph is created by third-party software or by custom sofware
+   Whether your graph is created by third-party software or by custom software
    written by someone you know (e.g. yourself), it is advisable to test whether
    the software generates symmetric matrices.  This can be done as follows
    using the \sibref{mcxi}{mcxi utility}, assuming that you want to test the
@@ -665,7 +665,7 @@ begin
 
 \faq{}{How do I compute the maximum amount of RAM needed by mcl?}
 \car{
-   It is rougly equal to}
+   It is roughly equal to}
 
 \verbatim{2 * s * K * N}
 
--- a/doc/mclfaq.txt
+++ b/doc/mclfaq.txt
@@ -17,7 +17,7 @@ MCL FAQ(7)                      MISCELLA
           explained. A broad view is given in faq 1.2, and  see  also  faq 1.5
           and section REFERENCES.
 
-          Some  additional  sections  preceed the actual faq entries.  The TOC
+          Some  additional  sections  precede the actual faq entries.  The TOC
           section contains a listing of all questions.
 
   RESOURCES
@@ -366,7 +366,7 @@ MCL FAQ(7)                      MISCELLA
    3.11   How do I check that my graph/matrix is symmetric/undirected?
 
           Whether  your  graph is created by third-party software or by custom
-          sofware written by someone you know (e.g. yourself), it is advisable
+          software written by someone you know (e.g. yourself), it is advisable
           to  test whether the software generates symmetric matrices. This can
           be done as follows using the mcxi utility, assuming that you want to
           test  the  matrix stored in file matrix.mci. The mcxi utility should
@@ -600,7 +600,7 @@ MCL FAQ(7)                      MISCELLA
 
    6.2    How do I compute the maximum amount of RAM needed by mcl?
 
-          It is rougly equal to
+          It is roughly equal to
 
           2 * s * K * N
 
--- a/doc/mclindex.7
+++ b/doc/mclindex.7
@@ -143,7 +143,7 @@ interface to basic matrix operations
 .ZI 2m "\fBmcxsubs(1)\fP"
 \&
 .br
-extract submatrices by specifiying sets of nodes and clusters
+extract submatrices by specifying sets of nodes and clusters
 .in -2m
 .ZI 2m "\fBmcxmap(1)\fP"
 \&
--- a/doc/mclpipeline.azm
+++ b/doc/mclpipeline.azm
@@ -489,7 +489,7 @@ a clustering consisting of tab-separated
 \car{
    Collect clusters in the same file until the total number
    of nodes has exceeded \genarg{num} (in the formatted output).
-   Only meaninful when \genopt{--fmt-fancy} is given.
+   Only meaningful when \genopt{--fmt-fancy} is given.
    }
 
 \item{\defopt{--fmt-tab}{use this tab file}}
--- a/doc/mcxassemble.azm
+++ b/doc/mcxassemble.azm
@@ -317,7 +317,7 @@ begin
    \useopt{-cmap} and its siblings are used to explicitly specify the 
    map file to be used, rather than combining a base name with a fixed
    suffix.
-   \useopt{-tag} and its siblings work in conjuction with
+   \useopt{-tag} and its siblings work in conjunction with
    the \useopt{-b}\~option, and require that a tag be specified from
    which to construct the map file (by appending it to the base name).
    }
--- a/doc/mcxio.5
+++ b/doc/mcxio.5
@@ -34,7 +34,7 @@ mcxio \- the format specifications for i
 The easiest format to create graphs from is a line-based format where each lines
 represents an edge or arc\&. This format is known as the \fILarge Graph Layout\fP, as
 \fIncol\fP format (in \fIigraph\fP), and as \fIpairwise\fP format in BioLayout\&.
-In \fBmcl-edge\fP it is additionally refered to
+In \fBmcl-edge\fP it is additionally referred to
 as \fIlabel\fP format or \fIabc\fP format\&.
 In this format each line has two or three fields\&. The first two fields
 define the source and destination node of an arc\&. Such an arc may be
@@ -96,7 +96,7 @@ Their relative merits are described furt
 \&
 .br
 This always pertains to matrices in native format concatenated in a single
-file, refered to as a \fIcat file\fP\&. It is used for example to encode
+file, referred to as a \fIcat file\fP\&. It is used for example to encode
 hierarchical clusterings as generated by \fBmclcm\fP\&. A cat file either
 consists of matrices in interchange format or of matrices in binary format\&.
 .in -2m
@@ -160,7 +160,7 @@ utilities may be in order here\&. The pr
 matrix functionality, the prefix \fBclm\fP is used for generic cluster
 functionaliy\&. The \fIutility\fP \fBmcx\fP is a general purpose interpreter for
 manipulating matrices (and grahps, sets, and clusterings)\&. The set of all
-\fBmcl\fP siblings (cf\&. \fBmclfamily(7)\fP) is loosely refered to as the mcl
+\fBmcl\fP siblings (cf\&. \fBmclfamily(7)\fP) is loosely referred to as the mcl
 family, which makes use of the mcl libraries (rather than the mcx
 libraries)\&. The full truth is even more horrible, as the mcl/mcx prefix
 conventions used in the C source code follow still other rules\&.
--- a/doc/mcxio.azm
+++ b/doc/mcxio.azm
@@ -28,7 +28,7 @@
    The easiest format to create graphs from is a line-based format where each lines
    represents an edge or arc. This format is known as the \it{Large Graph Layout}, as
    \it{ncol} format (in \it{igraph}), and as \it{pairwise} format in BioLayout.
-   In \mcle it is additionally refered to
+   In \mcle it is additionally referred to
    as \it{label} format or \it{abc} format.
    In this format each line has two or three fields. The first two fields
    define the source and destination node of an arc. Such an arc may be
@@ -98,7 +98,7 @@
 \item{\it{concatenated native matrix format}}
 \car{
    This always pertains to matrices in native format concatenated in a single
-   file, refered to as a \it{cat file}.  It is used for example to encode
+   file, referred to as a \it{cat file}.  It is used for example to encode
    hierarchical clusterings as generated by \mclcm.  A cat file either
    consists of matrices in interchange format or of matrices in binary format.}
 
@@ -164,7 +164,7 @@
    matrix functionality, the prefix \bf{clm} is used for generic cluster
    functionaliy.  The \it{utility} \mcx is a general purpose interpreter for
    manipulating matrices (and grahps, sets, and clusterings).  The set of all
-   \mcl siblings (cf. \mysib{mclfamily}) is loosely refered to as the mcl
+   \mcl siblings (cf. \mysib{mclfamily}) is loosely referred to as the mcl
    family, which makes use of the mcl libraries (rather than the mcx
    libraries). The full truth is even more horrible, as the mcl/mcx prefix
    conventions used in the C source code follow still other rules.}
--- a/doc/mcxquery.azm
+++ b/doc/mcxquery.azm
@@ -279,7 +279,7 @@
 \item{\defopt{--node-attr}{output node degree and weight attributes}}
 \car{
    Output is in the form of a tab separated file.
-   The option \genopt{-icl} can be used in conjuction.
+   The option \genopt{-icl} can be used in conjunction.
    }
 
 
--- a/doc/tingea.log.7
+++ b/doc/tingea.log.7
@@ -142,7 +142,7 @@ for the other units are given below\&.
 .fi \fR
 
 The leading tag can be used to set levels for all categories at once\&.
-Subsequent units may then alter this intial setting\&.
+Subsequent units may then alter this initial setting\&.
 The lead tag settings and their meaning are these:
 
 .di ZV
--- a/doc/tingea.log.azm
+++ b/doc/tingea.log.azm
@@ -130,7 +130,7 @@
 
 \car{
    The leading tag can be used to set levels for all categories at once.
-   Subsequent units may then alter this intial setting.
+   Subsequent units may then alter this initial setting.
    The lead tag settings and their meaning are these:}
 
 \verbatim{\:/
--- a/src/alien/oxygen/doc/mcxdeblast.azm
+++ b/src/alien/oxygen/doc/mcxdeblast.azm
@@ -61,7 +61,7 @@ output directly into mcl or write mcxass
 
 \sec{stream}{STREAM MODE}
 
-\car{Enter stream mode by specifiying \genkvp{--line-mode}{abc}.
+\car{Enter stream mode by specifying \genkvp{--line-mode}{abc}.
 Use \genopt{--m9} if the input is in columnar output. Pipe the result
 to a file or directly to mcl. Example invocations can be found
 in \sibref{mcl}{the mcl manual}.}
--- a/src/clew/clm.c
+++ b/src/clew/clm.c
@@ -259,7 +259,7 @@ mclx* clmMeet
       }
 
       if (i_clmeet != n_clmeet)
-      mcxErr(mepanic, "internal math does not substract")
+      mcxErr(mepanic, "internal math does not subtract")
 
    ;  mclxFree(&abmeet)
    ;  return clmeet
--- a/src/impala/vector.h
+++ b/src/impala/vector.h
@@ -546,7 +546,7 @@ mclVector* mcldMinus
 mclVector* mcldMerge
 (  const mclVector*  lft
 ,  const mclVector*  rgt
-,  mclVector*        dst      /* values in lft prefered over rgt */
+,  mclVector*        dst      /* values in lft preferred over rgt */
 )  ;
 
 
--- a/util/io.c
+++ b/util/io.c
@@ -452,7 +452,7 @@ fprintf(stderr, "nobuffer\n")
 
 /* fixme todo
  *
- * look at bc; substract it from sz (we might have read a part already).
+ * look at bc; subtract it from sz (we might have read a part already).
  *
  * support growing files. and look at other items in the grep source code.
 */
--- a/scripts/mlm-quilt
+++ b/scripts/mlm-quilt
@@ -12,7 +12,7 @@
 #
 #  !!!
 #     try tree search with depth 2 when testing descend.
-#  !encapsulate PN_keep etc initalization and updating.
+#  !encapsulate PN_keep etc initialization and updating.
 #  write clusters with scores, consensus.
 
 # [bc-9-1-02|fam41/rip26] mlmimpromptu --ignore-size=3 --fnannot=../data/paf41.ipro
--- a/src/mcl/procinit.c
+++ b/src/mcl/procinit.c
@@ -209,7 +209,7 @@ mcxOptAnchor mclProcOptions[] =
    ,  MCX_OPT_HASARG | MCX_OPT_HIDDEN
    ,  PROC_OPT_RPRUNE
    ,  "<int>"
-   ,  "use inital pruning cutoff <MAX>/<int>"
+   ,  "use initial pruning cutoff <MAX>/<int>"
    }
 ,  {  "-skid"
    ,  MCX_OPT_HASARG | MCX_OPT_HIDDEN
--- a/src/shmx/mcxdiameter.c
+++ b/src/shmx/mcxdiameter.c
@@ -916,7 +916,7 @@ void compute_scores_up_vc              /
 )
    {  dim j
    ;  for (j=0;j<N_COLS(up);j++)
-      up->cols[j].val = 1.0            /* accumulator; initalised */
+      up->cols[j].val = 1.0            /* accumulator; initialised */
                                        /* question: initialise everywhere? */
 
    ;  for (j=0;j<n_order;j++)
--- a/doc/clmorder.azm
+++ b/doc/clmorder.azm
@@ -66,7 +66,7 @@
 {\defopt{-o}{<fname>}}
 }
 \car{
-   As decribed above.
+   As described above.
    }
 
 \'end{itemize}
--- a/doc/mcxload.azm
+++ b/doc/mcxload.azm
@@ -467,7 +467,7 @@
    {\defopt{-pack-rnum}{<num>}{set row range}}
 }
 \car{
-   The \genopt{-packed} option allows to read machine-readable data
+   The \genopt{-packed} option allows one to read machine-readable data
    directly. The data has to correspond to the data types for indexes
    and values with with MCL was compiled. The use of \genopt{-pack-cnum}
    and \genopt{-pack-rnum} is required to set the limits of