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Started work on 'swat' module: implemented _Score DP function, and a
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stats driver.

Rearranged documentation into more chapters. Added minimizer,
msacluster, msaweight, normal, paml, ratematrix, rootfinder,
scorematrix, swat modules (some as placeholders). Did some typo fixing
to get the user guide to latex.

Added esl_normal, esl_swat modules to Makefile.in
Added esl_composition_* functions to easel.c
Deleted the ESL_FWD, ESL_XFWD error macros.
Cleaned up easel.h a bit.
Added easel, normal, ratematrix, rootfinder, scorematrix to sqc test.




git-svn-id: https://svn.janelia.org/eddylab/eddys/easel/trunk@168 db3e70e4-12e1-0310-b23f-81a6e3d09ba7
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cryptogenomicon committed Apr 13, 2007
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4 changes: 4 additions & 0 deletions Makefile.in
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ HEADERS = \
esl_msa.h\
esl_msacluster.h\
esl_msaweight.h\
esl_normal.h\
esl_paml.h\
esl_random.h\
esl_ratematrix.h\
Expand All @@ -43,6 +44,7 @@ HEADERS = \
esl_stats.h\
esl_stopwatch.h\
esl_stretchexp.h\
esl_swat.h\
esl_tree.h\
esl_vectorops.h\
esl_weibull.h\
Expand All @@ -68,6 +70,7 @@ OBJS = \
esl_msa.o\
esl_msacluster.o\
esl_msaweight.o\
esl_normal.o\
esl_paml.o\
esl_random.o\
esl_ratematrix.o\
Expand All @@ -80,6 +83,7 @@ OBJS = \
esl_stats.o\
esl_stopwatch.o\
esl_stretchexp.o\
esl_swat.o\
esl_tree.o\
esl_vectorops.o\
esl_weibull.o\
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9 changes: 9 additions & 0 deletions documentation/Makefile
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Expand Up @@ -30,15 +30,24 @@ MODULES = easel\
esl_histogram\
esl_hyperexp\
esl_keyhash\
esl_minimizer\
esl_mixgev\
esl_msa\
esl_msacluster\
esl_msaweight\
esl_normal\
esl_paml\
esl_random\
esl_ratematrix\
esl_regexp\
esl_rootfinder\
esl_scorematrix\
esl_sqio\
esl_ssi\
esl_stack\
esl_stopwatch\
esl_stretchexp\
esl_swat\
esl_tree\
esl_vectorops\
esl_weibull\
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159 changes: 119 additions & 40 deletions documentation/main.tex
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Expand Up @@ -54,24 +54,9 @@ \section{Functions in the easel module}


\newpage
\chapter{Core modules}

\section{\eslmod{alphabet}: digitized biosequences}
\input{../esl_alphabet}
\subsection{Functions in the alphabet module}
\input{autotext/esl_alphabet_functions}

\newpage
\section{\eslmod{dirichlet}: Beta, Gamma, Dirichlet densities and priors}
\input{../esl_dirichlet}
\subsection{Functions in the dirichlet module}
\input{autotext/esl_dirichlet_functions}

\newpage
\section{\eslmod{dmatrix}: 2D matrices and linear algebra}
\input{../esl_dmatrix}
\subsection{Functions in the dmatrix module}
\input{autotext/esl_dmatrix_functions}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Utility modules}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\chapter{Core modules}

\newpage
\section{\eslmod{fileparser}: token-based data file input}
Expand All @@ -91,12 +76,6 @@ \section{\eslmod{keyhash}: keyword hashing, associative array emulation}
\subsection{Functions in the keyhash module}
\input{autotext/esl_keyhash_functions}

\newpage
\section{\eslmod{msa}: multiple sequence alignment i/o}
\input{../esl_msa}
\subsection{Functions in the msa module}
\input{autotext/esl_msa_functions}

\newpage
\section{\eslmod{random}: pseudorandom numbers and basic sampling}
\input{../esl_random}
Expand All @@ -116,10 +95,27 @@ \subsection{Functions in the regexp module}
\input{autotext/esl_regexp_functions}

\newpage
\section{\eslmod{rootfinder}: finding roots of equations}
\input{../esl_rootfinder}
\subsection{Functions in the rootfinder module}
\input{autotext/esl_rootfinder_functions}
\section{\eslmod{stack}: pushdown stacks for integers, chars, and pointers}
\input{../esl_stack}
\subsection{Functions in the stack module}
\input{autotext/esl_stack_functions}

\newpage
\section{\eslmod{stopwatch}: timing parts of programs}
\input{../esl_stopwatch}
\subsection{Functions in the stopwatch module}
\input{autotext/esl_stopwatch_functions}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Biosequence data i/o modules}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newpage
\section{\eslmod{alphabet}: digitized biosequences}
\input{../esl_alphabet}
\subsection{Functions in the alphabet module}
\input{autotext/esl_alphabet_functions}

\newpage
\section{\eslmod{sqio}: i/o of unaligned sequence files}
Expand All @@ -133,23 +129,69 @@ \section{\eslmod{ssi}: indexing database flatfiles for fast record retrieval}
\subsection{Functions in the ssi module}
\input{autotext/esl_ssi_functions}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Multiple sequence alignment modules}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newpage
\section{\eslmod{stack}: pushdown stacks for integers, chars, and pointers}
\input{../esl_stack}
\subsection{Functions in the stack module}
\input{autotext/esl_stack_functions}
\section{\eslmod{msa}: Multiple sequence alignment i/o}
\input{../esl_msa}
\subsection{Functions in the msa module}
\input{autotext/esl_msa_functions}

\newpage
\section{\eslmod{stopwatch}: timing parts of programs}
\input{../esl_stopwatch}
\subsection{Functions in the stopwatch module}
\input{autotext/esl_stopwatch_functions}
\section{\eslmod{msacluster}: Clustering aligned sequence families}
\input{../esl_msacluster}
\subsection{Functions in the msacluster module}
\input{autotext/esl_msacluster_functions}

\newpage
\section{\eslmod{vectorops}: simple vector operations}
\input{../esl_vectorops}
\subsection{Functions in the vectorops module}
\input{autotext/esl_vectorops_functions}
\section{\eslmod{msaweight}: Ad hoc sequence weighting}
\input{../esl_msaweight}
\subsection{Functions in the msaweight module}
\input{autotext/esl_msaweight_functions}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Pairwise sequence alignment}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newpage
\section{\eslmod{swat}: Smith/Waterman local alignment}
\input{../esl_swat}
\subsection{Functions in the swat module}
\input{autotext/esl_swat_functions}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Probabilistic modeling modules}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newpage
\section{\eslmod{scorematrix}: Pairwise alignment scores}
\input{../esl_scorematrix}
\subsection{Functions in the scorematrix module}
\input{autotext/esl_scorematrix_functions}

\newpage
\section{\eslmod{ratematrix}: Continuous-time Markov models of evolution}
\input{../esl_ratematrix}
\subsection{Functions in the ratematrix module}
\input{autotext/esl_ratematrix_functions}

\newpage
\section{\eslmod{paml}: Reading data files from PAML}
\input{../esl_paml}
\subsection{Functions in the paml module}
\input{autotext/esl_paml_functions}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Sequence annotation}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newpage
\section{\eslmod{wuss}: RNA secondary structure annotation}
Expand All @@ -158,8 +200,33 @@ \subsection{Functions in the wuss module}
\input{autotext/esl_wuss_functions}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Numerical computing}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newpage
\section{\eslmod{vectorops}: Vector operations}
\input{../esl_vectorops}
\subsection{Functions in the vectorops module}
\input{autotext/esl_vectorops_functions}

\newpage
\section{\eslmod{dmatrix}: 2D matrices and linear algebra}
\input{../esl_dmatrix}
\subsection{Functions in the dmatrix module}
\input{autotext/esl_dmatrix_functions}

\newpage
\section{\eslmod{minimizer}: Conjugate gradient descent}
\input{../esl_minimizer}
\subsection{Functions in the minimizer module}
\input{autotext/esl_minimizer_functions}

\newpage
\section{\eslmod{rootfinder}: One-dimensional rootfinding}
\input{../esl_rootfinder}
\subsection{Functions in the rootfinder module}
\input{autotext/esl_rootfinder_functions}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Phylogenetic inference modules}
Expand Down Expand Up @@ -194,6 +261,12 @@ \section{\eslmod{histogram}: Collecting histograms}
\subsection{Functions in the histogram module}
\input{autotext/esl_histogram_functions}

\newpage
\section{\eslmod{dirichlet}: Beta, Gamma, Dirichlet densities and priors}
\input{../esl_dirichlet}
\subsection{Functions in the dirichlet module}
\input{autotext/esl_dirichlet_functions}

\newpage
\section{\eslmod{exponential}: Exponential distributions}
\input{../esl_exponential}
Expand Down Expand Up @@ -236,6 +309,12 @@ \section{\eslmod{mixgev}: Mixture generalized extreme value distributions}
\subsection{Functions in the mixgev module}
\input{autotext/esl_mixgev_functions}

\newpage
\section{\eslmod{normal}: Normal (Gaussian) distributions}
\input{../esl_normal}
\subsection{Functions in the normal module}
\input{autotext/esl_normal_functions}

\newpage
\section{\eslmod{stretchexp}: Stretched exponential distributions}
\input{../esl_stretchexp}
Expand Down
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