From: Fábio Madeira Date: Thu, 18 May 2017 11:06:28 +0000 (+0100) Subject: JWS-116 New fixes to the documentation pages. Various fixes to the content, as well... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0e6c784ff1185e13c3df107982450e7d5eec27b3;p=jabaws.git JWS-116 New fixes to the documentation pages. Various fixes to the content, as well as bumped versions of aacon and dates. New citation, and pdf with full authors and contact information. --- 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 --- 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 %} {{ _('View page source') }} {% elif show_source and has_source and sourcename %} - {{ _('View page source') }} + + Return to the JABAWS homepage {% endif %} {% endif %} diff --git a/docs/v_2_2_0/changelog.rst b/docs/v_2_2_0/changelog.rst index f5f4d93..cc9944b 100644 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- a/website/docs/v_2_2_0/advanced.html +++ b/website/docs/v_2_2_0/advanced.html @@ -175,7 +175,8 @@
  • - View page source + + Return to the JABAWS homepage
    • @@ -576,7 +577,7 @@ After you have completed the editing your configuration may look like this:

    JABAWS 2.2 - © Copyright 2017, 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.

    diff --git a/website/docs/v_2_2_0/changelog.html b/website/docs/v_2_2_0/changelog.html index 89028b4..ec1262c 100644 --- a/website/docs/v_2_2_0/changelog.html +++ b/website/docs/v_2_2_0/changelog.html @@ -101,7 +101,7 @@
  • Usage Statistics
  • Citations
  • Changelog