JWS-116 New fixes to the documentation pages. Various fixes to the content, as well...

diff --git a/docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html
index a988ecd..360f552 100755 (executable)
--- a/docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html
+++ b/docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html
@@ -61,7 +61,8 @@
           {% elif show_source and source_url_prefix %}
             <a href="{{ source_url_prefix }}{{ pagename }}{{ suffix }}">{{ _('View page source') }}</a>
           {% elif show_source and has_source and sourcename %}
-            <a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> {{ _('View page source') }}</a>
+            <!-- <a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> {{ _('View page source') }}</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           {% endif %}
         {% endif %}
       </li>

diff --git a/docs/v_2_2_0/changelog.rst b/docs/v_2_2_0/changelog.rst
index f5f4d93..cc9944b 100644 (file)
--- a/docs/v_2_2_0/changelog.rst
+++ b/docs/v_2_2_0/changelog.rst
@@ -4,7 +4,7 @@ Changelog
 
 .. _v2.2:
 
-Version 2.2 (Released 12 April 2017)
+Version 2.2 (Released 19 May 2017)
 ------------------------------------
 
 The website and documentation were improved:
@@ -20,12 +20,14 @@ The versions of several application programs provided by JABAWS were bumped to t
 * ClustalW was updated to version 2.1
 * Mafft was updated to version 7.3.10
 * T-Coffee was updated to version 11.00.8cbe486
+* `AACon`_ was updated to version 1.1
 * Protein secondary structure prediction with Jpred (version 3.0.3) was dropped from the list of provided services, as the use of the dedicated Jpred REST API (Jpred 4) is encouraged and recommended. This is the version that is currently provided within Jalview 2.9 or later.
 
 .. note:: JABAWS version 2.2 is fully backward compatible with JABAWS v1.0 and v2.0. This means all JABAWS 1.0, 2.0, 2.0.1 and 2.1 clients should also be able to use JABAWS 2.2 services.
 
 
 .. _Sphinx: http://www.sphinx-doc.org/en/stable/
+.. _AACon: http://www.compbio.dundee.ac.uk/aacon/
 
 ------------
 

diff --git a/docs/v_2_2_0/citations.rst b/docs/v_2_2_0/citations.rst
index 2dfcfc3..8c43b66 100644 (file)
--- a/docs/v_2_2_0/citations.rst
+++ b/docs/v_2_2_0/citations.rst
@@ -8,4 +8,6 @@ Citations
 
 Peter V. Troshin, James B. Procter and Geoffrey J. Barton - **Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS** Bioinformatics 2011. 27 (14): 2001-2002. doi: `10.1093/bioinformatics/btr304`_
 
+Peter V. Troshin, Alexander Sherstnev, James B. Procter, Daniel L. Barton, Fábio Madeira and Geoffrey J. Barton (2017) **JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure.** *Paper in preparation.*
+
 .. _10.1093/bioinformatics/btr304: https://doi.org/10.1093/bioinformatics/btr304

diff --git a/docs/v_2_2_0/client.rst b/docs/v_2_2_0/client.rst
index aaa5b9e..91dc36b 100644 (file)
--- a/docs/v_2_2_0/client.rst
+++ b/docs/v_2_2_0/client.rst
@@ -30,7 +30,7 @@ Usage
 
 .. code:: bash
 
-      java -jar jaba-client.jar
+      java -jar jabaws-full-client-2.2.0.jar
 
 ::
 
@@ -68,7 +68,7 @@ Align sequences from input.fasta file using Mafft web service with default setti
 
 .. code:: bash
 
-    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta
+    java -jar jabaws-full-client-2.2.0.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta
 
 Content of input.fasta file is show below (please note sequences has been trimmed for clarity)
 
@@ -85,7 +85,7 @@ Align as in above example, but write output alignment in a file out.clustal, usi
 
 .. code:: bash
 
-    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws  -s=MafftWS -i=d:\input.fasta -o=d:\out.clustal -f=prm.in
+    java -jar jabaws-full-client-2.2.0.jar -h=http://myhost.compbio.ac.uk:8080/jabaws  -s=MafftWS -i=d:\input.fasta -o=d:\out.clustal -f=prm.in
 
 The content of the prm.in file is shown below
 
@@ -101,7 +101,7 @@ The format of the file is the same for all JABAWS web services. Parameters are s
 
 .. code:: bash
 
-    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters
+    java -jar jabaws-full-client-2.2.0.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters
 
 The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key.
 

diff --git a/docs/v_2_2_0/conf.py b/docs/v_2_2_0/conf.py
index 678f03a..1b70963 100644 (file)
--- a/docs/v_2_2_0/conf.py
+++ b/docs/v_2_2_0/conf.py
@@ -47,8 +47,8 @@ master_doc = 'index'
 
 # General information about the project.
 project = 'JABAWS'
-copyright = '2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton'
-author = 'Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton'
+copyright = '2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton'
+author = 'Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

diff --git a/docs/v_2_2_0/develop.rst b/docs/v_2_2_0/develop.rst
index 4c7db93..d29c25d 100644 (file)
--- a/docs/v_2_2_0/develop.rst
+++ b/docs/v_2_2_0/develop.rst
@@ -599,15 +599,8 @@ There are a number of ant tasks aimed for preparing distributives for download.
 
 1. Client only (contains classes required to access JABA Web Services)
 2. Platform specific JABAWS (windows and other)
-3. JABAWS without binaries
-4. JABAWS framework
-
-Corresponding build task names are:
-
-1. min-jaba-client
-2. jaba-windows, jaba-complete
-3. jaba-no-binaries
-4. full-jaba-client
+3. JABAWS with and without binaries
+4. JABAWS framework and complete project
 
 The easiest way to build all distributives is to call ``build-all`` ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory.
 

diff --git a/docs/v_2_2_0/generate_manual.sh b/docs/v_2_2_0/generate_manual.sh
index 1effbb4..e544fea 100755 (executable)
--- a/docs/v_2_2_0/generate_manual.sh
+++ b/docs/v_2_2_0/generate_manual.sh
@@ -15,7 +15,25 @@ rm -rf _build
 # make latex
 # # manual edit to remove unecessary ines in the index page
 # # also edit the author list to
-# # \author{Peter Troshin, et al.}
+## add the following to the latex and change the date to match the release date
+
+# \author{Peter Troshin \and Alexander Sherstnev \and Jim Procter \and Daniel Barton \and Fábio Madeira \and Alexey Drozdetskiy \and Suzanne Duce \and Geoffrey J. Barton}
+# \authoraddress{
+# The Barton Group
+#
+# Division of Computational Biology
+#
+# School of Life Sciences
+#
+# University of Dundee
+#
+# Dow Street
+#
+# Dundee DD1 5EH
+#
+# Scotland, UK
+# }
+
 # # \begin{sphinxadmonition}{note}{Note:}
 # # Some of the links might not work properly in the pdf version...
 # # \end{sphinxadmonition}

diff --git a/docs/v_2_2_0/getting_started.rst b/docs/v_2_2_0/getting_started.rst
index 00d1dd2..3d22148 100644 (file)
--- a/docs/v_2_2_0/getting_started.rst
+++ b/docs/v_2_2_0/getting_started.rst
@@ -1,7 +1,7 @@
 Getting Started
 ===============
 
-JABAWS stands for *JAva Bioinformatics Analysis Web Services*. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of `currently supported programs`_). Future versions of JABAWS will incorporate other tools.
+*JABAWS* is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of `currently supported programs`_). Future versions of JABAWS will incorporate other tools.
 
 JABAWS consists of a server and a client, but unlike most bioinformatics web-service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the `JABAWS Virtual Appliance (VA)`_. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the `JABAWS Web Application aRchive (WAR)`_. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the `JABAWS Command Line Interface (CLI)`_ client is what you need.
 
@@ -63,7 +63,7 @@ This is a single Java archive which contains the JABAWS command line interface (
 
       .. code:: bash
 
-            java -jar jaba-client.jar
+            java -jar jabaws-full-client-2.2.0.jar
 
 
 The JABA Web Services are WS-I compliant. This means that you can access them from any language that has libraries or functions for consuming interoperable SOAP web services. More information on how to develop software that access JABAWS services is provided in the `documentation pages`_.

diff --git a/docs/v_2_2_0/included_tools.rst b/docs/v_2_2_0/included_tools.rst
index 22d6290..018c15c 100644 (file)
--- a/docs/v_2_2_0/included_tools.rst
+++ b/docs/v_2_2_0/included_tools.rst
@@ -31,7 +31,7 @@ Protein Disorder Prediction
 Amino Acid Conservation
 -----------------------
 
-* `AACon`_ (version 1.0)
+* `AACon`_ (version 1.1)
 
 
 .. _rnass:

diff --git a/docs/v_2_2_0/index.rst b/docs/v_2_2_0/index.rst
index 67dc7b0..3807d9a 100644 (file)
--- a/docs/v_2_2_0/index.rst
+++ b/docs/v_2_2_0/index.rst
@@ -6,13 +6,9 @@
 Welcome to JABAWS's documentation!
 ==================================
 
-Read on these documentation pages or go back to the `JABAWS homepage`_!
-
 JABAWS documentation is also available in *pdf*. `Download it here`_!
 
 
-.. _JABAWS homepage: ../../
-
 
 .. toctree::
    :maxdepth: 3

diff --git a/website/docs/v_2_2_0/_sources/changelog.rst.txt b/website/docs/v_2_2_0/_sources/changelog.rst.txt
index f5f4d93..cc9944b 100644 (file)
--- a/website/docs/v_2_2_0/_sources/changelog.rst.txt
+++ b/website/docs/v_2_2_0/_sources/changelog.rst.txt
@@ -4,7 +4,7 @@ Changelog
 
 .. _v2.2:
 
-Version 2.2 (Released 12 April 2017)
+Version 2.2 (Released 19 May 2017)
 ------------------------------------
 
 The website and documentation were improved:
@@ -20,12 +20,14 @@ The versions of several application programs provided by JABAWS were bumped to t
 * ClustalW was updated to version 2.1
 * Mafft was updated to version 7.3.10
 * T-Coffee was updated to version 11.00.8cbe486
+* `AACon`_ was updated to version 1.1
 * Protein secondary structure prediction with Jpred (version 3.0.3) was dropped from the list of provided services, as the use of the dedicated Jpred REST API (Jpred 4) is encouraged and recommended. This is the version that is currently provided within Jalview 2.9 or later.
 
 .. note:: JABAWS version 2.2 is fully backward compatible with JABAWS v1.0 and v2.0. This means all JABAWS 1.0, 2.0, 2.0.1 and 2.1 clients should also be able to use JABAWS 2.2 services.
 
 
 .. _Sphinx: http://www.sphinx-doc.org/en/stable/
+.. _AACon: http://www.compbio.dundee.ac.uk/aacon/
 
 ------------
 

diff --git a/website/docs/v_2_2_0/_sources/citations.rst.txt b/website/docs/v_2_2_0/_sources/citations.rst.txt
index 2dfcfc3..8c43b66 100644 (file)
--- a/website/docs/v_2_2_0/_sources/citations.rst.txt
+++ b/website/docs/v_2_2_0/_sources/citations.rst.txt
@@ -8,4 +8,6 @@ Citations
 
 Peter V. Troshin, James B. Procter and Geoffrey J. Barton - **Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS** Bioinformatics 2011. 27 (14): 2001-2002. doi: `10.1093/bioinformatics/btr304`_
 
+Peter V. Troshin, Alexander Sherstnev, James B. Procter, Daniel L. Barton, Fábio Madeira and Geoffrey J. Barton (2017) **JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure.** *Paper in preparation.*
+
 .. _10.1093/bioinformatics/btr304: https://doi.org/10.1093/bioinformatics/btr304

diff --git a/website/docs/v_2_2_0/_sources/client.rst.txt b/website/docs/v_2_2_0/_sources/client.rst.txt
index aaa5b9e..91dc36b 100644 (file)
--- a/website/docs/v_2_2_0/_sources/client.rst.txt
+++ b/website/docs/v_2_2_0/_sources/client.rst.txt
@@ -30,7 +30,7 @@ Usage
 
 .. code:: bash
 
-      java -jar jaba-client.jar
+      java -jar jabaws-full-client-2.2.0.jar
 
 ::
 
@@ -68,7 +68,7 @@ Align sequences from input.fasta file using Mafft web service with default setti
 
 .. code:: bash
 
-    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta
+    java -jar jabaws-full-client-2.2.0.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta
 
 Content of input.fasta file is show below (please note sequences has been trimmed for clarity)
 
@@ -85,7 +85,7 @@ Align as in above example, but write output alignment in a file out.clustal, usi
 
 .. code:: bash
 
-    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws  -s=MafftWS -i=d:\input.fasta -o=d:\out.clustal -f=prm.in
+    java -jar jabaws-full-client-2.2.0.jar -h=http://myhost.compbio.ac.uk:8080/jabaws  -s=MafftWS -i=d:\input.fasta -o=d:\out.clustal -f=prm.in
 
 The content of the prm.in file is shown below
 
@@ -101,7 +101,7 @@ The format of the file is the same for all JABAWS web services. Parameters are s
 
 .. code:: bash
 
-    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters
+    java -jar jabaws-full-client-2.2.0.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters
 
 The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key.
 

diff --git a/website/docs/v_2_2_0/_sources/develop.rst.txt b/website/docs/v_2_2_0/_sources/develop.rst.txt
index 4c7db93..d29c25d 100644 (file)
--- a/website/docs/v_2_2_0/_sources/develop.rst.txt
+++ b/website/docs/v_2_2_0/_sources/develop.rst.txt
@@ -599,15 +599,8 @@ There are a number of ant tasks aimed for preparing distributives for download.
 
 1. Client only (contains classes required to access JABA Web Services)
 2. Platform specific JABAWS (windows and other)
-3. JABAWS without binaries
-4. JABAWS framework
-
-Corresponding build task names are:
-
-1. min-jaba-client
-2. jaba-windows, jaba-complete
-3. jaba-no-binaries
-4. full-jaba-client
+3. JABAWS with and without binaries
+4. JABAWS framework and complete project
 
 The easiest way to build all distributives is to call ``build-all`` ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory.
 

diff --git a/website/docs/v_2_2_0/_sources/getting_started.rst.txt b/website/docs/v_2_2_0/_sources/getting_started.rst.txt
index 00d1dd2..3d22148 100644 (file)
--- a/website/docs/v_2_2_0/_sources/getting_started.rst.txt
+++ b/website/docs/v_2_2_0/_sources/getting_started.rst.txt
@@ -1,7 +1,7 @@
 Getting Started
 ===============
 
-JABAWS stands for *JAva Bioinformatics Analysis Web Services*. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of `currently supported programs`_). Future versions of JABAWS will incorporate other tools.
+*JABAWS* is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of `currently supported programs`_). Future versions of JABAWS will incorporate other tools.
 
 JABAWS consists of a server and a client, but unlike most bioinformatics web-service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the `JABAWS Virtual Appliance (VA)`_. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the `JABAWS Web Application aRchive (WAR)`_. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the `JABAWS Command Line Interface (CLI)`_ client is what you need.
 
@@ -63,7 +63,7 @@ This is a single Java archive which contains the JABAWS command line interface (
 
       .. code:: bash
 
-            java -jar jaba-client.jar
+            java -jar jabaws-full-client-2.2.0.jar
 
 
 The JABA Web Services are WS-I compliant. This means that you can access them from any language that has libraries or functions for consuming interoperable SOAP web services. More information on how to develop software that access JABAWS services is provided in the `documentation pages`_.

diff --git a/website/docs/v_2_2_0/_sources/included_tools.rst.txt b/website/docs/v_2_2_0/_sources/included_tools.rst.txt
index 22d6290..018c15c 100644 (file)
--- a/website/docs/v_2_2_0/_sources/included_tools.rst.txt
+++ b/website/docs/v_2_2_0/_sources/included_tools.rst.txt
@@ -31,7 +31,7 @@ Protein Disorder Prediction
 Amino Acid Conservation
 -----------------------
 
-* `AACon`_ (version 1.0)
+* `AACon`_ (version 1.1)
 
 
 .. _rnass:

diff --git a/website/docs/v_2_2_0/_sources/index.rst.txt b/website/docs/v_2_2_0/_sources/index.rst.txt
index 67dc7b0..3807d9a 100644 (file)
--- a/website/docs/v_2_2_0/_sources/index.rst.txt
+++ b/website/docs/v_2_2_0/_sources/index.rst.txt
@@ -6,13 +6,9 @@
 Welcome to JABAWS's documentation!
 ==================================
 
-Read on these documentation pages or go back to the `JABAWS homepage`_!
-
 JABAWS documentation is also available in *pdf*. `Download it here`_!
 
 
-.. _JABAWS homepage: ../../
-
 
 .. toctree::
    :maxdepth: 3

diff --git a/website/docs/v_2_2_0/_static/pygments.css b/website/docs/v_2_2_0/_static/pygments.css
index 20c4814..8213e90 100644 (file)
--- a/website/docs/v_2_2_0/_static/pygments.css
+++ b/website/docs/v_2_2_0/_static/pygments.css
@@ -47,10 +47,8 @@
 .highlight .mh { color: #208050 } /* Literal.Number.Hex */
 .highlight .mi { color: #208050 } /* Literal.Number.Integer */
 .highlight .mo { color: #208050 } /* Literal.Number.Oct */
-.highlight .sa { color: #4070a0 } /* Literal.String.Affix */
 .highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
 .highlight .sc { color: #4070a0 } /* Literal.String.Char */
-.highlight .dl { color: #4070a0 } /* Literal.String.Delimiter */
 .highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
 .highlight .s2 { color: #4070a0 } /* Literal.String.Double */
 .highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
@@ -61,9 +59,7 @@
 .highlight .s1 { color: #4070a0 } /* Literal.String.Single */
 .highlight .ss { color: #517918 } /* Literal.String.Symbol */
 .highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
-.highlight .fm { color: #06287e } /* Name.Function.Magic */
 .highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
 .highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
 .highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
-.highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */
 .highlight .il { color: #208050 } /* Literal.Number.Integer.Long */
\ No newline at end of file

diff --git a/website/docs/v_2_2_0/advanced.html b/website/docs/v_2_2_0/advanced.html
index c64a862..36fbc72 100644 (file)
--- a/website/docs/v_2_2_0/advanced.html
+++ b/website/docs/v_2_2_0/advanced.html
@@ -175,7 +175,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/advanced.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/advanced.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -576,7 +577,7 @@ After you have completed the editing your configuration may look like this:</p>
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/changelog.html b/website/docs/v_2_2_0/changelog.html
index 89028b4..ec1262c 100644 (file)
--- a/website/docs/v_2_2_0/changelog.html
+++ b/website/docs/v_2_2_0/changelog.html
@@ -101,7 +101,7 @@
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="citations.html">Citations</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Changelog</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#version-2-2-released-12-april-2017">Version 2.2 (Released 12 April 2017)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#version-2-2-released-19-may-2017">Version 2.2 (Released 19 May 2017)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#version-2-1-released-1st-oct-2013">Version 2.1 (Released 1st Oct 2013)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#version-2-0-1-released-2nd-jul-2013">Version 2.0.1 (Released 2nd Jul 2013)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#version-2-released-16th-dec-2011">Version 2 (Released 16th Dec 2011)</a></li>
@@ -157,7 +157,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/changelog.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/changelog.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -172,8 +173,8 @@
             
   <div class="section" id="changelog">
 <h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="version-2-2-released-12-april-2017">
-<span id="v2-2"></span><h2>Version 2.2 (Released 12 April 2017)<a class="headerlink" href="#version-2-2-released-12-april-2017" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="version-2-2-released-19-may-2017">
+<span id="v2-2"></span><h2>Version 2.2 (Released 19 May 2017)<a class="headerlink" href="#version-2-2-released-19-may-2017" title="Permalink to this headline">¶</a></h2>
 <p>The website and documentation were improved:</p>
 <ul class="simple">
 <li><a class="reference external" href="http://www.sphinx-doc.org/en/stable/">Sphinx</a> is now used to generate our documentation pages.</li>
@@ -187,6 +188,7 @@
 <li>ClustalW was updated to version 2.1</li>
 <li>Mafft was updated to version 7.3.10</li>
 <li>T-Coffee was updated to version 11.00.8cbe486</li>
+<li><a class="reference external" href="http://www.compbio.dundee.ac.uk/aacon/">AACon</a> was updated to version 1.1</li>
 <li>Protein secondary structure prediction with Jpred (version 3.0.3) was dropped from the list of provided services, as the use of the dedicated Jpred REST API (Jpred 4) is encouraged and recommended. This is the version that is currently provided within Jalview 2.9 or later.</li>
 </ul>
 <div class="admonition note">
@@ -270,7 +272,7 @@
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/citations.html b/website/docs/v_2_2_0/citations.html
index 58b388e..1174473 100644 (file)
--- a/website/docs/v_2_2_0/citations.html
+++ b/website/docs/v_2_2_0/citations.html
@@ -152,7 +152,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/citations.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/citations.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -172,6 +173,7 @@
 <p class="last">It is important that you cite JABAWS when you use it. Citing us helps us funding the work we do and allow us to continue to improve the project further.</p>
 </div>
 <p id="id1">Peter V. Troshin, James B. Procter and Geoffrey J. Barton - <strong>Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS</strong> Bioinformatics 2011. 27 (14): 2001-2002. doi: <a class="reference external" href="https://doi.org/10.1093/bioinformatics/btr304">10.1093/bioinformatics/btr304</a></p>
+<p>Peter V. Troshin, Alexander Sherstnev, James B. Procter, Daniel L. Barton, Fábio Madeira and Geoffrey J. Barton (2017) <strong>JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure.</strong> <em>Paper in preparation.</em></p>
 </div>
 
 
@@ -196,7 +198,7 @@
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/client.html b/website/docs/v_2_2_0/client.html
index 3fdffc3..a2c7b11 100644 (file)
--- a/website/docs/v_2_2_0/client.html
+++ b/website/docs/v_2_2_0/client.html
@@ -157,7 +157,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/client.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/client.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -187,7 +188,7 @@ Please see the <cite>Java</cite> web site for up to date instructions and downlo
 </div>
 <div class="section" id="usage">
 <span id="cli-usage"></span><h2>Usage<a class="headerlink" href="#usage" title="Permalink to this headline">¶</a></h2>
-<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jaba</span><span class="o">-</span><span class="n">client</span><span class="o">.</span><span class="n">jar</span>
+<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="n">full</span><span class="o">-</span><span class="n">client</span><span class="o">-</span><span class="mf">2.2</span><span class="o">.</span><span class="mf">0.</span><span class="n">jar</span>
 </pre></div>
 </div>
 <div class="highlight-default"><div class="highlight"><pre><span></span>Usage:
@@ -217,7 +218,7 @@ Please note that -r and -f options cannot be used together. Alignment is done wi
 <div class="section" id="example-usage">
 <span id="cli-example"></span><h2>Example Usage<a class="headerlink" href="#example-usage" title="Permalink to this headline">¶</a></h2>
 <p>Align sequences from input.fasta file using Mafft web service with default settings, print alignment in Clustal format to console.</p>
-<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="nb">min</span><span class="o">-</span><span class="n">client</span><span class="o">.</span><span class="n">jar</span> <span class="o">-</span><span class="n">h</span><span class="o">=</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">myhost</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="p">:</span><span class="mi">8080</span><span class="o">/</span><span class="n">jabaws</span> <span class="o">-</span><span class="n">s</span><span class="o">=</span><span class="n">MafftWS</span> <span class="o">-</span><span class="n">i</span><span class="o">=</span><span class="n">d</span><span class="p">:</span>\<span class="nb">input</span><span class="o">.</span><span class="n">fasta</span>
+<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="n">full</span><span class="o">-</span><span class="n">client</span><span class="o">-</span><span class="mf">2.2</span><span class="o">.</span><span class="mf">0.</span><span class="n">jar</span> <span class="o">-</span><span class="n">h</span><span class="o">=</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">myhost</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="p">:</span><span class="mi">8080</span><span class="o">/</span><span class="n">jabaws</span> <span class="o">-</span><span class="n">s</span><span class="o">=</span><span class="n">MafftWS</span> <span class="o">-</span><span class="n">i</span><span class="o">=</span><span class="n">d</span><span class="p">:</span>\<span class="nb">input</span><span class="o">.</span><span class="n">fasta</span>
 </pre></div>
 </div>
 <p>Content of input.fasta file is show below (please note sequences has been trimmed for clarity)</p>
@@ -230,7 +231,7 @@ Please note that -r and -f options cannot be used together. Alignment is done wi
 </pre></div>
 </div>
 <p>Align as in above example, but write output alignment in a file out.clustal, using parameters defined in prm.in file</p>
-<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="nb">min</span><span class="o">-</span><span class="n">client</span><span class="o">.</span><span class="n">jar</span> <span class="o">-</span><span class="n">h</span><span class="o">=</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">myhost</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="p">:</span><span class="mi">8080</span><span class="o">/</span><span class="n">jabaws</span>  <span class="o">-</span><span class="n">s</span><span class="o">=</span><span class="n">MafftWS</span> <span class="o">-</span><span class="n">i</span><span class="o">=</span><span class="n">d</span><span class="p">:</span>\<span class="nb">input</span><span class="o">.</span><span class="n">fasta</span> <span class="o">-</span><span class="n">o</span><span class="o">=</span><span class="n">d</span><span class="p">:</span>\<span class="n">out</span><span class="o">.</span><span class="n">clustal</span> <span class="o">-</span><span class="n">f</span><span class="o">=</span><span class="n">prm</span><span class="o">.</span><span class="ow">in</span>
+<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="n">full</span><span class="o">-</span><span class="n">client</span><span class="o">-</span><span class="mf">2.2</span><span class="o">.</span><span class="mf">0.</span><span class="n">jar</span> <span class="o">-</span><span class="n">h</span><span class="o">=</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">myhost</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="p">:</span><span class="mi">8080</span><span class="o">/</span><span class="n">jabaws</span>  <span class="o">-</span><span class="n">s</span><span class="o">=</span><span class="n">MafftWS</span> <span class="o">-</span><span class="n">i</span><span class="o">=</span><span class="n">d</span><span class="p">:</span>\<span class="nb">input</span><span class="o">.</span><span class="n">fasta</span> <span class="o">-</span><span class="n">o</span><span class="o">=</span><span class="n">d</span><span class="p">:</span>\<span class="n">out</span><span class="o">.</span><span class="n">clustal</span> <span class="o">-</span><span class="n">f</span><span class="o">=</span><span class="n">prm</span><span class="o">.</span><span class="ow">in</span>
 </pre></div>
 </div>
 <p>The content of the prm.in file is shown below</p>
@@ -242,7 +243,7 @@ Please note that -r and -f options cannot be used together. Alignment is done wi
 </pre></div>
 </div>
 <p>The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but because any output has to be handled by JABAWS, settings controlling output are not allowed to be changed. For a list of parameters supported by a web service see the next example. In prm.in parameters are separated by the new line, and name of the parameter is separated from its value with an equals sign. This format is constant no matter which JABAWS web service is used.</p>
-<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="nb">min</span><span class="o">-</span><span class="n">client</span><span class="o">.</span><span class="n">jar</span> <span class="o">-</span><span class="n">h</span><span class="o">=</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">myhost</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="p">:</span><span class="mi">8080</span><span class="o">/</span><span class="n">jabaws</span> <span class="o">-</span><span class="n">s</span><span class="o">=</span><span class="n">MafftWS</span> <span class="o">-</span><span class="n">parameters</span>
+<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="n">full</span><span class="o">-</span><span class="n">client</span><span class="o">-</span><span class="mf">2.2</span><span class="o">.</span><span class="mf">0.</span><span class="n">jar</span> <span class="o">-</span><span class="n">h</span><span class="o">=</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">myhost</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="p">:</span><span class="mi">8080</span><span class="o">/</span><span class="n">jabaws</span> <span class="o">-</span><span class="n">s</span><span class="o">=</span><span class="n">MafftWS</span> <span class="o">-</span><span class="n">parameters</span>
 </pre></div>
 </div>
 <p>The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key.</p>
@@ -272,7 +273,7 @@ Please note that -r and -f options cannot be used together. Alignment is done wi
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/develop.html b/website/docs/v_2_2_0/develop.html
index 5d32d15..ec79d44 100644 (file)
--- a/website/docs/v_2_2_0/develop.html
+++ b/website/docs/v_2_2_0/develop.html
@@ -177,7 +177,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/develop.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/develop.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -658,15 +659,8 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
 <ol class="arabic simple">
 <li>Client only (contains classes required to access JABA Web Services)</li>
 <li>Platform specific JABAWS (windows and other)</li>
-<li>JABAWS without binaries</li>
-<li>JABAWS framework</li>
-</ol>
-<p>Corresponding build task names are:</p>
-<ol class="arabic simple">
-<li>min-jaba-client</li>
-<li>jaba-windows, jaba-complete</li>
-<li>jaba-no-binaries</li>
-<li>full-jaba-client</li>
+<li>JABAWS with and without binaries</li>
+<li>JABAWS framework and complete project</li>
 </ol>
 <p>The easiest way to build all distributives is to call <code class="docutils literal"><span class="pre">build-all</span></code> ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory.</p>
 <p>If you made any changes to the data model and would like to generate a complete JABAWS distro make sure you have rebuilt jaxws artifact as described below.</p>
@@ -696,7 +690,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/genindex.html b/website/docs/v_2_2_0/genindex.html
index d257af0..1cd0fe8 100644 (file)
--- a/website/docs/v_2_2_0/genindex.html
+++ b/website/docs/v_2_2_0/genindex.html
@@ -182,7 +182,7 @@
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/getting_started.html b/website/docs/v_2_2_0/getting_started.html
index 4fbe3c0..23b2ff0 100644 (file)
--- a/website/docs/v_2_2_0/getting_started.html
+++ b/website/docs/v_2_2_0/getting_started.html
@@ -162,7 +162,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/getting_started.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/getting_started.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -177,7 +178,7 @@
             
   <div class="section" id="getting-started">
 <h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
-<p>JABAWS stands for <em>JAva Bioinformatics Analysis Web Services</em>. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of <a class="reference external" href="included_tools.html">currently supported programs</a>). Future versions of JABAWS will incorporate other tools.</p>
+<p><em>JABAWS</em> is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of <a class="reference external" href="included_tools.html">currently supported programs</a>). Future versions of JABAWS will incorporate other tools.</p>
 <p>JABAWS consists of a server and a client, but unlike most bioinformatics web-service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the <a class="reference external" href="va.html">JABAWS Virtual Appliance (VA)</a>. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the <a class="reference external" href="war.html">JABAWS Web Application aRchive (WAR)</a>. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the <a class="reference external" href="client.html">JABAWS Command Line Interface (CLI)</a> client is what you need.</p>
 <hr class="docutils" />
 <div class="section" id="jabaws-benefits">
@@ -222,7 +223,7 @@
 </li>
 <li><p class="first">Provided that you have the Java ready to run, you can get command line help by changing to the directory where you downloaded the client jar, and typing:</p>
 <blockquote>
-<div><div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jaba</span><span class="o">-</span><span class="n">client</span><span class="o">.</span><span class="n">jar</span>
+<div><div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">java</span> <span class="o">-</span><span class="n">jar</span> <span class="n">jabaws</span><span class="o">-</span><span class="n">full</span><span class="o">-</span><span class="n">client</span><span class="o">-</span><span class="mf">2.2</span><span class="o">.</span><span class="mf">0.</span><span class="n">jar</span>
 </pre></div>
 </div>
 </div></blockquote>
@@ -325,7 +326,7 @@
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/included_tools.html b/website/docs/v_2_2_0/included_tools.html
index d95061e..a4d7cea 100644 (file)
--- a/website/docs/v_2_2_0/included_tools.html
+++ b/website/docs/v_2_2_0/included_tools.html
@@ -158,7 +158,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/included_tools.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/included_tools.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -198,7 +199,7 @@
 <div class="section" id="amino-acid-conservation">
 <span id="aac"></span><h2>Amino Acid Conservation<a class="headerlink" href="#amino-acid-conservation" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
-<li><a class="reference external" href="http://www.compbio.dundee.ac.uk/aacon">AACon</a> (version 1.0)</li>
+<li><a class="reference external" href="http://www.compbio.dundee.ac.uk/aacon">AACon</a> (version 1.1)</li>
 </ul>
 </div>
 <div class="section" id="rna-secondary-structure">
@@ -231,7 +232,7 @@
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/index.html b/website/docs/v_2_2_0/index.html
index 2f76723..a06267d 100644 (file)
--- a/website/docs/v_2_2_0/index.html
+++ b/website/docs/v_2_2_0/index.html
@@ -151,7 +151,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -166,7 +167,6 @@
             
   <div class="section" id="welcome-to-jabaws-s-documentation">
 <h1>Welcome to JABAWS&#8217;s documentation!<a class="headerlink" href="#welcome-to-jabaws-s-documentation" title="Permalink to this headline">¶</a></h1>
-<p>Read on these documentation pages or go back to the <a class="reference external" href="../../">JABAWS homepage</a>!</p>
 <p>JABAWS documentation is also available in <em>pdf</em>. <a class="reference external" href="./jabaws_manual.pdf">Download it here</a>!</p>
 <div class="toctree-wrapper compound">
 <p class="caption"><span class="caption-text">Contents:</span></p>
@@ -271,7 +271,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="citations.html">Citations</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="changelog.html#version-2-2-released-12-april-2017">Version 2.2 (Released 12 April 2017)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="changelog.html#version-2-2-released-19-may-2017">Version 2.2 (Released 19 May 2017)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-2-1-released-1st-oct-2013">Version 2.1 (Released 1st Oct 2013)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-2-0-1-released-2nd-jul-2013">Version 2.0.1 (Released 2nd Jul 2013)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-2-released-16th-dec-2011">Version 2 (Released 16th Dec 2011)</a></li>
@@ -306,7 +306,7 @@
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/jabaws_manual.pdf b/website/docs/v_2_2_0/jabaws_manual.pdf
index 08d4df9..abed494 100644 (file)
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diff --git a/website/docs/v_2_2_0/objects.inv b/website/docs/v_2_2_0/objects.inv
index c05592d..4ecdefe 100644 (file)
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diff --git a/website/docs/v_2_2_0/search.html b/website/docs/v_2_2_0/search.html
index 2979a34..c7598a5 100644 (file)
--- a/website/docs/v_2_2_0/search.html
+++ b/website/docs/v_2_2_0/search.html
@@ -187,7 +187,7 @@
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/searchindex.js b/website/docs/v_2_2_0/searchindex.js
index 6c4b8fd..1554e06 100644 (file)
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\ No newline at end of file

diff --git a/website/docs/v_2_2_0/stats.html b/website/docs/v_2_2_0/stats.html
index 0e19253..0764fe8 100644 (file)
--- a/website/docs/v_2_2_0/stats.html
+++ b/website/docs/v_2_2_0/stats.html
@@ -159,7 +159,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/stats.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/stats.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -246,13 +247,13 @@
 <div class="highlight-bash"><div class="highlight"><pre><span></span><span class="c1"># Enable/disable cluster statistics collector true = enable, false = disable</span>
 cluster.stat.collector.enable<span class="o">=</span><span class="nb">false</span>
 <span class="c1"># Maximum amount of time the job is considered be running in hours. Optional defaults to 7 days (168h)</span>
-cluster.stat.maxruntime<span class="o">=</span><span class="m">24</span>
+cluster.stat.maxruntime<span class="o">=</span>24
 </pre></div>
 </div>
 <div class="highlight-bash"><div class="highlight"><pre><span></span><span class="c1"># Enable/disable cluster statistics collector true = enable, false = disable</span>
 local.stat.collector.enable<span class="o">=</span><span class="nb">true</span>
 <span class="c1"># Maximum amount of time the job is considered to be running in hours. Optional defaults to 24 hours</span>
-local.stat.maxruntime<span class="o">=</span><span class="m">6</span>
+local.stat.maxruntime<span class="o">=</span>6
 </pre></div>
 </div>
 <p>If the statistics collector is enabled then the crawler starts automatically soon after (10 minutes for local engine, and 60 minutes for cluster engine) the JABAWS web application and will be collecting the execution statistics every 24 hours after the start.</p>
@@ -299,7 +300,7 @@ local.stat.maxruntime<span class="o">=</span><span class="m">6</span>
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/va.html b/website/docs/v_2_2_0/va.html
index 2a2ddee..3763890 100644 (file)
--- a/website/docs/v_2_2_0/va.html
+++ b/website/docs/v_2_2_0/va.html
@@ -161,7 +161,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/va.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/va.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -274,7 +275,7 @@
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>

diff --git a/website/docs/v_2_2_0/war.html b/website/docs/v_2_2_0/war.html
index b8b1e48..a99492b 100644 (file)
--- a/website/docs/v_2_2_0/war.html
+++ b/website/docs/v_2_2_0/war.html
@@ -157,7 +157,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/war.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/war.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -240,7 +241,7 @@
 
   <div role="contentinfo">
     <p><a href="../../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>