Changeset 257

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Timestamp:
12/12/07 12:50:26 (1 year ago)
Author:
t
Message:

doc renaming, updating a bit

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  • trunk/motility/doc/Makefile

    r251 r257  
    22        rst2html.py $< $@ 
    33 
    4 all: index.html intro.html python-interface.html c++-interface.html motility-introduction.html 
     4all: index.html intro.html python-interface.html c++-interface.html \ 
     5        python-tutorial.html 

  • trunk/motility/doc/index.html

    r251 r257  
    311311<li><a class="reference" href="c++-interface.html">C++ API</a></li> 
    312312<li><a class="reference" href="python-interface.html">Python interface</a></li> 
    313 <li><a class="reference" href="motility-introduction.html">Doctest-style tutorial on motility</a></li> 
     313<li><a class="reference" href="python-tutorial.html">Tutorial</a></li> 
    314314</ul> 
    315315</blockquote> 
    316316<pre class="literal-block"> 
    317 CTB 12/05 
     317CTB 12/07 
    318318</pre> 
    319319</div> 

  • trunk/motility/doc/index.txt

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    2626  * `Python interface`_ 
    2727 
    28   * `Doctest-style tutorial on motility <motility-introduction.html>`__ 
     28  * `Tutorial <python-tutorial.html>`__ 
    2929 
    3030:: 
    3131 
    32    CTB 12/05 
     32   CTB 12/07 
    3333 
    3434.. _Introduction to motility and motif types: intro.html 

  • trunk/motility/doc/python-interface.html

    r245 r257  
    319319<pre class="literal-block"> 
    320320energy = operator.calc_energy(match) 
     321energy = operator.calc_score(match) 
    321322 
    322323score = pwm.calc_score(match) 
    …… 
    355356<p>'start' is always less than 'end', 'orientation' is 1 or -1, and 'match' is 
    356357the matching string in the appropriate orientation (forward or RC).</p> 
     358<div class="section"> 
     359<h1><a id="building-motifs-and-matrices" name="building-motifs-and-matrices">Building motifs and matrices</a></h1> 
     360<p>See <a class="reference" href="python-tutorial.html">the Python tutorial</a> for more information. 
     361.. &#64;CTB</p> 
     362</div> 
    357363<div class="section"> 
    358364<h1><a id="using-motility-an-example" name="using-motility-an-example">Using <tt class="docutils literal"><span class="pre">motility</span></tt>: An Example</a></h1> 

  • trunk/motility/doc/python-interface.txt

    r252 r257  
    8484---------------------------- 
    8585 
    86 See `the tutorial <motility-introduction.html>`__ for more information. 
     86See `the Python tutorial <python-tutorial.html>`__ for more information. 
    8787.. @CTB 
    8888 

  • trunk/motility/doc/python-tutorial.txt

    r256 r257  
    222222another reason is that their scores represent an information-theoretic 
    223223or statistical-mechanical measure on motif content.  Check out Stormo 
    224 (2007) for a review. 
     224(2000) for a review. 
    225225 
    226226General matrix utility functions