Skip to content

GitLab

Commit c9050154 authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

Merge branch 'version/1.9' into version/2.0 

* version/1.9:
  Added the Doxygen documentation
  Added scripts documentation
  Added docs/index.html and use rawgit in README.md
  typo
  Include the CSS for the eHive HTML doc
  Doc update to please Doxygen
  bugfix: in each branch README.md will have to refer to its own version of docs
  adding reformatted install.html and README.md links to HTML documents (relying on htmlpreview functionality)
parents 7c15f499 41c8920f
Hide whitespace changes
Inline Side-by-side
Showing with 2701 additions and 9 deletions

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.
Plain diff Email patch
README.md
View file @ c9050154
EnsEMBL Hive
============
eHive
=====
EnsEMBL Hive is a system for running computation pipelines on distributed computing resources - clusters, farms or grids.
eHive is a system for running computation pipelines on distributed computing resources - clusters, farms or grids.
The name "Hive" comes from the way pipelines are processed by a swarm of autonomous agents.
The name comes from the way pipelines are processed by a swarm of autonomous agents.
Blackboard, Jobs and Workers
----------------------------
......@@ -28,7 +28,7 @@ However in some sense an Analysis also acts as a "container" for them.
PipeConfig file defines Analyses and dependency rules of the pipeline
---------------------------------------------------------------------
Hive pipeline databases are molded according to PipeConfig files which are Perl modules conforming to a special interface.
eHive pipeline databases are molded according to PipeConfig files which are Perl modules conforming to a special interface.
A PipeConfig file defines the stucture of the pipeline, which is a graph whose nodes are Analyses
(with their code, parameters and resource requirements) and edges are various dependency rules:
* Dataflow rules define how data that flows out of an Analysis can be used to trigger creation of Jobs in other Analyses
......@@ -44,13 +44,17 @@ There are also other parameters of Analyses that control, for example:
* what should be autimatically done with a Job if it needs more memory/time,
etc.
Available documentation
-----------------------
The main entry point is in docs/index.html (available locally, offline).
The online version is hosted [here](https://rawgit.com/Ensembl/ensembl-hive/version/2.0/docs/index.html).
Contact us (mailing list)
-------------------------
EnsEMBL Hive was originally conceived and used within EnsEMBL Compara group
eHive was originally conceived and used within EnsEMBL Compara group
for running Comparative Genomics pipelines, but since then it has been separated
into a separate software tool and is used in many projects both in Genome Campus, Cambridge and outside.
There is a Hive users' mailing list for questions, suggestions, discussions and announcements.
There is eHive users' mailing list for questions, suggestions, discussions and announcements.
To subscribe to it please visit:
http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users
To subscribe to it please visit (http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users)
docs/doxygen/_accumulator_8pm.html 0 → 100644
View file @ c9050154
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.6"/>
<title>ensembl-hive: modules/Bio/EnsEMBL/Hive/Accumulator.pm File Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<script type="text/javascript">
$(document).ready(initResizable);
$(window).load(resizeHeight);
</script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
$(document).ready(function() { searchBox.OnSelectItem(0); });
</script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.6 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<div id="navrow1" class="tabs">
<ul class="tablist">
<li><a href="index.html"><span>Main&#160;Page</span></a></li>
<li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
<li><a href="namespaces.html"><span>Namespaces</span></a></li>
<li><a href="annotated.html"><span>Classes</span></a></li>
<li class="current"><a href="files.html"><span>Files</span></a></li>
<li>
<div id="MSearchBox" class="MSearchBoxInactive">
<span class="left">
<img id="MSearchSelect" src="search/mag_sel.png"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
alt=""/>
<input type="text" id="MSearchField" value="Search" accesskey="S"
onfocus="searchBox.OnSearchFieldFocus(true)"
onblur="searchBox.OnSearchFieldFocus(false)"
onkeyup="searchBox.OnSearchFieldChange(event)"/>
</span><span class="right">
<a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
</span>
</div>
</li>
</ul>
</div>
<div id="navrow2" class="tabs2">
<ul class="tablist">
<li><a href="files.html"><span>File&#160;List</span></a></li>
<li><a href="globals.html"><span>File&#160;Members</span></a></li>
</ul>
</div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
$(document).ready(function(){initNavTree('_accumulator_8pm.html','');});
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Pages</a></div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div class="header">
<div class="summary">
<a href="#nested-classes">Classes</a> &#124;
<a href="#namespaces">Namespaces</a> </div>
<div class="headertitle">
<div class="title">Accumulator.pm File Reference</div> </div>
</div><!--header-->
<div class="contents">
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Bio::EnsEMBL::Hive::Accumulator</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
Namespaces</h2></td></tr>
<tr class="memitem:namespace_bio"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio.html">Bio</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:namespace_bio_1_1_ens_e_m_b_l"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">Bio::EnsEMBL</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:namespace_bio_1_1_ens_e_m_b_l_1_1_hive"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
</div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_67a94abf6e99d454046c3675e3bd1175.html">modules</a></li><li class="navelem"><a class="el" href="dir_2fb356b2600b67fb4ecdf615049082a3.html">Bio</a></li><li class="navelem"><a class="el" href="dir_f09fa94c377b37d40ac85c9124ee4df7.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="dir_6043810977801faf48a2b9bf5611c94b.html">Hive</a></li><li class="navelem"><a class="el" href="_accumulator_8pm.html">Accumulator.pm</a></li>
<li class="footer">Generated by
<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
</ul>
</div>
</body>
</html>
docs/doxygen/_accumulator_adaptor_8pm.html 0 → 100644
View file @ c9050154
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.6"/>
<title>ensembl-hive: modules/Bio/EnsEMBL/Hive/DBSQL/AccumulatorAdaptor.pm File Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<script type="text/javascript">
$(document).ready(initResizable);
$(window).load(resizeHeight);
</script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
$(document).ready(function() { searchBox.OnSelectItem(0); });
</script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.6 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<div id="navrow1" class="tabs">
<ul class="tablist">
<li><a href="index.html"><span>Main&#160;Page</span></a></li>
<li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
<li><a href="namespaces.html"><span>Namespaces</span></a></li>
<li><a href="annotated.html"><span>Classes</span></a></li>
<li class="current"><a href="files.html"><span>Files</span></a></li>
<li>
<div id="MSearchBox" class="MSearchBoxInactive">
<span class="left">
<img id="MSearchSelect" src="search/mag_sel.png"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
alt=""/>
<input type="text" id="MSearchField" value="Search" accesskey="S"
onfocus="searchBox.OnSearchFieldFocus(true)"
onblur="searchBox.OnSearchFieldFocus(false)"
onkeyup="searchBox.OnSearchFieldChange(event)"/>
</span><span class="right">
<a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
</span>
</div>
</li>
</ul>
</div>
<div id="navrow2" class="tabs2">
<ul class="tablist">
<li><a href="files.html"><span>File&#160;List</span></a></li>
<li><a href="globals.html"><span>File&#160;Members</span></a></li>
</ul>
</div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
$(document).ready(function(){initNavTree('_accumulator_adaptor_8pm.html','');});
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Pages</a></div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div class="header">
<div class="summary">
<a href="#nested-classes">Classes</a> &#124;
<a href="#namespaces">Namespaces</a> </div>
<div class="headertitle">
<div class="title">AccumulatorAdaptor.pm File Reference</div> </div>
</div><!--header-->
<div class="contents">
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
Namespaces</h2></td></tr>
<tr class="memitem:namespace_bio"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio.html">Bio</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:namespace_bio_1_1_ens_e_m_b_l"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">Bio::EnsEMBL</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:namespace_bio_1_1_ens_e_m_b_l_1_1_hive"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
</div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_67a94abf6e99d454046c3675e3bd1175.html">modules</a></li><li class="navelem"><a class="el" href="dir_2fb356b2600b67fb4ecdf615049082a3.html">Bio</a></li><li class="navelem"><a class="el" href="dir_f09fa94c377b37d40ac85c9124ee4df7.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="dir_6043810977801faf48a2b9bf5611c94b.html">Hive</a></li><li class="navelem"><a class="el" href="dir_93a0ac18085eba2e5e031450dec1e814.html">DBSQL</a></li><li class="navelem"><a class="el" href="_accumulator_adaptor_8pm.html">AccumulatorAdaptor.pm</a></li>
<li class="footer">Generated by
<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
</ul>
</div>
</body>
</html>
docs/doxygen/_add_together_8pm.html 0 → 100644
View file @ c9050154
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.6"/>
<title>ensembl-hive: modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm File Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<script type="text/javascript">
$(document).ready(initResizable);
$(window).load(resizeHeight);
</script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
$(document).ready(function() { searchBox.OnSelectItem(0); });
</script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.6 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<div id="navrow1" class="tabs">
<ul class="tablist">
<li><a href="index.html"><span>Main&#160;Page</span></a></li>
<li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
<li><a href="namespaces.html"><span>Namespaces</span></a></li>
<li><a href="annotated.html"><span>Classes</span></a></li>
<li class="current"><a href="files.html"><span>Files</span></a></li>
<li>
<div id="MSearchBox" class="MSearchBoxInactive">
<span class="left">
<img id="MSearchSelect" src="search/mag_sel.png"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
alt=""/>
<input type="text" id="MSearchField" value="Search" accesskey="S"
onfocus="searchBox.OnSearchFieldFocus(true)"
onblur="searchBox.OnSearchFieldFocus(false)"
onkeyup="searchBox.OnSearchFieldChange(event)"/>
</span><span class="right">
<a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
</span>
</div>
</li>
</ul>
</div>
<div id="navrow2" class="tabs2">
<ul class="tablist">
<li><a href="files.html"><span>File&#160;List</span></a></li>
<li><a href="globals.html"><span>File&#160;Members</span></a></li>
</ul>
</div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
$(document).ready(function(){initNavTree('_add_together_8pm.html','');});
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Pages</a></div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div class="header">
<div class="summary">
<a href="#nested-classes">Classes</a> &#124;
<a href="#namespaces">Namespaces</a> </div>
<div class="headertitle">
<div class="title">AddTogether.pm File Reference</div> </div>
</div><!--header-->
<div class="contents">
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
Namespaces</h2></td></tr>
<tr class="memitem:namespace_bio"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio.html">Bio</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:namespace_bio_1_1_ens_e_m_b_l"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">Bio::EnsEMBL</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:namespace_bio_1_1_ens_e_m_b_l_1_1_hive"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
</div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_67a94abf6e99d454046c3675e3bd1175.html">modules</a></li><li class="navelem"><a class="el" href="dir_2fb356b2600b67fb4ecdf615049082a3.html">Bio</a></li><li class="navelem"><a class="el" href="dir_f09fa94c377b37d40ac85c9124ee4df7.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="dir_6043810977801faf48a2b9bf5611c94b.html">Hive</a></li><li class="navelem"><a class="el" href="dir_37dace174d02f5d47e04516fd3505bcc.html">RunnableDB</a></li><li class="navelem"><a class="el" href="dir_f28a85ebe1691758bfcdb2bec935205f.html">LongMult</a></li><li class="navelem"><a class="el" href="_add_together_8pm.html">AddTogether.pm</a></li>
<li class="footer">Generated by
<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
</ul>
</div>
</body>
</html>
docs/doxygen/_analysis_8pm.html 0 → 100644
View file @ c9050154
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.6"/>
<title>ensembl-hive: modules/Bio/EnsEMBL/Hive/Analysis.pm File Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<script type="text/javascript">
$(document).ready(initResizable);
$(window).load(resizeHeight);
</script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
$(document).ready(function() { searchBox.OnSelectItem(0); });
</script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.6 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<div id="navrow1" class="tabs">
<ul class="tablist">
<li><a href="index.html"><span>Main&#160;Page</span></a></li>
<li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
<li><a href="namespaces.html"><span>Namespaces</span></a></li>
<li><a href="annotated.html"><span>Classes</span></a></li>
<li class="current"><a href="files.html"><span>Files</span></a></li>
<li>
<div id="MSearchBox" class="MSearchBoxInactive">
<span class="left">
<img id="MSearchSelect" src="search/mag_sel.png"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
alt=""/>
<input type="text" id="MSearchField" value="Search" accesskey="S"
onfocus="searchBox.OnSearchFieldFocus(true)"
onblur="searchBox.OnSearchFieldFocus(false)"
onkeyup="searchBox.OnSearchFieldChange(event)"/>
</span><span class="right">
<a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
</span>
</div>
</li>
</ul>
</div>
<div id="navrow2" class="tabs2">
<ul class="tablist">
<li><a href="files.html"><span>File&#160;List</span></a></li>
<li><a href="globals.html"><span>File&#160;Members</span></a></li>
</ul>
</div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
$(document).ready(function(){initNavTree('_analysis_8pm.html','');});
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Pages</a></div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>