JWS-109 & JWS-116 Moved the docs (source and html built) to a new location that is...

diff --git a/docs/Makefile b/docs/v_2_2_0/Makefile
similarity index 100%
rename from docs/Makefile
rename to docs/v_2_2_0/Makefile

diff --git a/docs/README.txt b/docs/v_2_2_0/README.txt
similarity index 100%
rename from docs/README.txt
rename to docs/v_2_2_0/README.txt

diff --git a/docs/_themes/sphinx_rtd_theme/__init__.py b/docs/v_2_2_0/_themes/sphinx_rtd_theme/__init__.py
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/__init__.py
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/__init__.py

diff --git a/docs/_themes/sphinx_rtd_theme/breadcrumbs.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/breadcrumbs.html
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/breadcrumbs.html

diff --git a/docs/_themes/sphinx_rtd_theme/footer.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/footer.html
similarity index 98%
rename from docs/_themes/sphinx_rtd_theme/footer.html
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/footer.html
index af71c74..ddba32b 100755 (executable)
--- a/docs/_themes/sphinx_rtd_theme/footer.html
+++ b/docs/v_2_2_0/_themes/sphinx_rtd_theme/footer.html
@@ -13,7 +13,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <p><a href="../../">JABAWS 2.2</a>
     {%- if show_copyright %}
       {%- if hasdoc('copyright') %}
         {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}

diff --git a/docs/_themes/sphinx_rtd_theme/layout.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/layout.html
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/layout.html
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/layout.html

diff --git a/docs/_themes/sphinx_rtd_theme/layout_old.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/layout_old.html
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/layout_old.html
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/layout_old.html

diff --git a/docs/_themes/sphinx_rtd_theme/search.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/search.html
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/search.html
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/search.html

diff --git a/docs/_themes/sphinx_rtd_theme/searchbox.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/searchbox.html
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/searchbox.html
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/searchbox.html

diff --git a/docs/_themes/sphinx_rtd_theme/static/css/badge_only.css b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/css/badge_only.css
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/css/badge_only.css
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/css/badge_only.css

diff --git a/docs/_themes/sphinx_rtd_theme/static/css/badge_only.css.map b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/css/badge_only.css.map
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/css/badge_only.css.map
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/css/badge_only.css.map

diff --git a/docs/_themes/sphinx_rtd_theme/static/css/theme.css b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/css/theme.css
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/css/theme.css
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/css/theme.css

diff --git a/docs/_themes/sphinx_rtd_theme/static/css/theme.css.map b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/css/theme.css.map
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/css/theme.css.map
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/css/theme.css.map

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/FontAwesome.otf b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/FontAwesome.otf
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/FontAwesome.otf
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/FontAwesome.otf

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Bold.ttf b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Bold.ttf
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Bold.ttf
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Bold.ttf

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Regular.ttf b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Regular.ttf
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Regular.ttf
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Regular.ttf

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/Lato-Bold.ttf b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/Lato-Bold.ttf
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/Lato-Bold.ttf
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/Lato-Bold.ttf

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/Lato-Regular.ttf b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/Lato-Regular.ttf
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/Lato-Regular.ttf
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/Lato-Regular.ttf

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.ttf b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.ttf
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.ttf
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.ttf

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.ttf b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.ttf
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.ttf
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.ttf

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff

diff --git a/docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2

diff --git a/docs/_themes/sphinx_rtd_theme/static/js/modernizr.min.js b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/js/modernizr.min.js
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/js/modernizr.min.js
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/js/modernizr.min.js

diff --git a/docs/_themes/sphinx_rtd_theme/static/js/theme.js b/docs/v_2_2_0/_themes/sphinx_rtd_theme/static/js/theme.js
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/static/js/theme.js
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/static/js/theme.js

diff --git a/docs/_themes/sphinx_rtd_theme/theme.conf b/docs/v_2_2_0/_themes/sphinx_rtd_theme/theme.conf
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/theme.conf
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/theme.conf

diff --git a/docs/_themes/sphinx_rtd_theme/versions.html b/docs/v_2_2_0/_themes/sphinx_rtd_theme/versions.html
similarity index 100%
rename from docs/_themes/sphinx_rtd_theme/versions.html
rename to docs/v_2_2_0/_themes/sphinx_rtd_theme/versions.html

diff --git a/docs/advanced.rst b/docs/v_2_2_0/advanced.rst
similarity index 99%
rename from docs/advanced.rst
rename to docs/v_2_2_0/advanced.rst
index 38a4185..e636c8a 100644 (file)
--- a/docs/advanced.rst
+++ b/docs/v_2_2_0/advanced.rst
@@ -463,8 +463,8 @@ JABAWS War File Content
 
 .. links
 .. _war file content table: advanced.html#jabaws_war_file_content
-.. _dm_javadoc: http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html
-.. _full_javadoc: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html
+.. _dm_javadoc: ../dm_javadoc/index.html
+.. _full_javadoc: ../full_javadoc/index.html
 .. _prog_docs: http://www.compbio.dundee.ac.uk/jabaws/prog_docs/
 .. _test JABAWS: advanced.html#testing-the-jabaws-server
 .. _deploying on Tomcat tips: war.html

diff --git a/docs/changelog.rst b/docs/v_2_2_0/changelog.rst
similarity index 96%
rename from docs/changelog.rst
rename to docs/v_2_2_0/changelog.rst
index d4016fc..f5f4d93 100644 (file)
--- a/docs/changelog.rst
+++ b/docs/v_2_2_0/changelog.rst
@@ -59,7 +59,7 @@ JABAWS 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2.0
 * Disembl returned swapped strings for HOTLOOPS and REM465
 * Jronn failed to process jobs with more than 3 sequences
 * JABAWS could not deal with FASTA records with '>' symbols in the record identificator
-* Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores in one call
+* Change of parameter description for AACon: parameters have been replaced with options for calculation methods. This allows a user to get several AACon's conservation scores in one call
 * JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties
 * Default web security has been incompatible with Tomcat 7.0.31 and newer
 * Documentation has been updated

diff --git a/docs/citations.rst b/docs/v_2_2_0/citations.rst
similarity index 100%
rename from docs/citations.rst
rename to docs/v_2_2_0/citations.rst

diff --git a/docs/client.rst b/docs/v_2_2_0/client.rst
similarity index 100%
rename from docs/client.rst
rename to docs/v_2_2_0/client.rst

diff --git a/docs/conf.py b/docs/v_2_2_0/conf.py
similarity index 97%
rename from docs/conf.py
rename to docs/v_2_2_0/conf.py
index 41268cb..678f03a 100644 (file)
--- a/docs/conf.py
+++ b/docs/v_2_2_0/conf.py
@@ -130,7 +130,7 @@ latex_elements = {
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
     (master_doc, 'JABAWS.tex', 'JABAWS Documentation',
-     'Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton', 'manual'),
+     'Peter Troshin, et al.', 'manual'),
 ]
 
 

diff --git a/docs/develop.rst b/docs/v_2_2_0/develop.rst
similarity index 99%
rename from docs/develop.rst
rename to docs/v_2_2_0/develop.rst
index 538923c..4c7db93 100644 (file)
--- a/docs/develop.rst
+++ b/docs/v_2_2_0/develop.rst
@@ -61,7 +61,7 @@ Structure of the project
 The code structure
 ------------------
 
-.. image:: ../website/static/img/ws-structure.png
+.. image:: ../../website/static/img/ws-structure.png
   :height: 414
   :width: 282
   :scale: 95 %
@@ -615,15 +615,15 @@ If you made any changes to the data model and would like to generate a complete
 
 
 
-.. |folder| image:: ../website/static/img/folder-small.png
+.. |folder| image:: ../../website/static/img/folder-small.png
    :align: middle
    :width: 15
 
 
 .. links
 .. _Git-tracker: https://source.jalview.org/crucible/changelog/jabaws
-.. _Data Model JavaDoc: http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html
-.. _Complete JavaDoc: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html
+.. _Data Model JavaDoc: ../dm_javadoc/index.html
+.. _Complete JavaDoc: ../full_javadoc/index.html
 .. _JavaDoc: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html
 .. _Test Results: http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html
 .. _TestNG: http://testng.org/doc/index.html

diff --git a/docs/generate_manual.sh b/docs/v_2_2_0/generate_manual.sh
similarity index 81%
rename from docs/generate_manual.sh
rename to docs/v_2_2_0/generate_manual.sh
index 2d0297f..1effbb4 100755 (executable)
--- a/docs/generate_manual.sh
+++ b/docs/v_2_2_0/generate_manual.sh
@@ -4,12 +4,12 @@
 rm -rf _build
 # generating the html pages
 make html
-mkdir ../website/docs
-cp -r _build/html/* ../website/docs/
+mkdir ../website/docs/v_2_2_0/
+cp -r _build/html/* ../../website/docs/v_2_2_0/
 # extra for testing
 #mkdir ../../jabaws-2.2-dev/docs
 #cp -r _build/html/* ../../jabaws-2.2-dev/docs/
-# rm -rf _build
+rm -rf _build
 
 # # generating the pdf
 # make latex
@@ -20,7 +20,8 @@ cp -r _build/html/* ../website/docs/
 # # Some of the links might not work properly in the pdf version...
 # # \end{sphinxadmonition}
 # cp _build/latex/JABAWS.pdf ../../jabaws-2.2-dev/docs/jabaws_manual.pdf
-# cp _build/latex/JABAWS.pdf ../website/docs/jabaws_manual.pdf
+# cp _build/latex/JABAWS.pdf ../../website/docs/v_2_2_0/jabaws_manual.pdf
+# rm -rf _build
 
 # for multiple versions of this manual we need to implement some solution
 # like this one https://robpol86.github.io/sphinxcontrib-versioning/index.html

diff --git a/docs/getting_started.rst b/docs/v_2_2_0/getting_started.rst
similarity index 100%
rename from docs/getting_started.rst
rename to docs/v_2_2_0/getting_started.rst

diff --git a/docs/included_tools.rst b/docs/v_2_2_0/included_tools.rst
similarity index 100%
rename from docs/included_tools.rst
rename to docs/v_2_2_0/included_tools.rst

diff --git a/docs/index.rst b/docs/v_2_2_0/index.rst
similarity index 96%
rename from docs/index.rst
rename to docs/v_2_2_0/index.rst
index e0a0729..67dc7b0 100644 (file)
--- a/docs/index.rst
+++ b/docs/v_2_2_0/index.rst
@@ -11,7 +11,7 @@ Read on these documentation pages or go back to the `JABAWS homepage`_!
 JABAWS documentation is also available in *pdf*. `Download it here`_!
 
 
-.. _JABAWS homepage: ../
+.. _JABAWS homepage: ../../
 
 
 .. toctree::

diff --git a/docs/make.bat b/docs/v_2_2_0/make.bat
similarity index 100%
rename from docs/make.bat
rename to docs/v_2_2_0/make.bat

diff --git a/docs/stats.rst b/docs/v_2_2_0/stats.rst
similarity index 97%
rename from docs/stats.rst
rename to docs/v_2_2_0/stats.rst
index 7e5ac8c..412731f 100644 (file)
--- a/docs/stats.rst
+++ b/docs/v_2_2_0/stats.rst
@@ -7,7 +7,7 @@ If you are using JABAWS VA (Virtual Appliance) then the username is *jabaws* and
 
 If you have deployed a JABAWS WAR file, then please see the `configuring privileged access`_ for Tomcat web application server section for further details.
 
-.. image:: ../website/static/img/usage_statistics_main.gif
+.. image:: ../../website/static/img/usage_statistics_main.gif
    :height: 318
    :width: 608
    :scale: 100 %
@@ -34,7 +34,7 @@ Detailed View
 
 Detailed execution statistics for each month is available for authenticated users only.
 
-.. image:: ../website/static/img/usage_statistics_month.gif
+.. image:: ../../website/static/img/usage_statistics_month.gif
    :height: 902
    :width: 670
    :scale: 100 %
@@ -62,7 +62,7 @@ Job List
 
 Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view, the application server may need to be configured. Please see the `Configuring JABAWS execution statistics`_ section for further details.
 
-.. image:: ../website/static/img/usage_statistics_details.gif
+.. image:: ../../website/static/img/usage_statistics_details.gif
    :height: 198
    :width: 917
    :scale: 100 %
@@ -88,7 +88,7 @@ Columns:
 Job Directory Contents
 ----------------------
 
-.. image:: ../website/static/img/usage_statistics_job_details.gif
+.. image:: ../../website/static/img/usage_statistics_job_details.gif
    :height: 420
    :width: 716
    :scale: 90 %

diff --git a/docs/va.rst b/docs/v_2_2_0/va.rst
similarity index 97%
rename from docs/va.rst
rename to docs/v_2_2_0/va.rst
index d9e7de2..b5f3de4 100644 (file)
--- a/docs/va.rst
+++ b/docs/v_2_2_0/va.rst
@@ -36,7 +36,7 @@ Usage
 By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.
 
 
-.. image:: ../website/static/img/VMware_cpu.png
+.. image:: ../../website/static/img/VMware_cpu.png
    :height: 267
    :width: 708
    :scale: 95 %
@@ -103,7 +103,7 @@ After booting the JABAWS VM, you should see similar screen, however, the IP addr
 
 .. _Jalview help pages: http://www.jalview.org/help/html/webServices/JABAWS.html
 
-.. image:: ../website/static/img/vm_welcome_screen.png
+.. image:: ../../website/static/img/vm_welcome_screen.png
    :height: 461
    :width: 734
    :scale: 95 %
@@ -111,7 +111,7 @@ After booting the JABAWS VM, you should see similar screen, however, the IP addr
 
 If you click on Advanced Menu, you will see the configuration console, similar to the one below.
 
-.. image:: ../website/static/img/VMware_booted.png
+.. image:: ../../website/static/img/VMware_booted.png
   :height: 461
   :width: 735
   :scale: 95 %

diff --git a/docs/war.rst b/docs/v_2_2_0/war.rst
similarity index 100%
rename from docs/war.rst
rename to docs/v_2_2_0/war.rst

diff --git a/website/docs/_images/VMware_booted.png b/website/docs/v_2_2_0/_images/VMware_booted.png
similarity index 100%
rename from website/docs/_images/VMware_booted.png
rename to website/docs/v_2_2_0/_images/VMware_booted.png

diff --git a/website/docs/_images/VMware_cpu.png b/website/docs/v_2_2_0/_images/VMware_cpu.png
similarity index 100%
rename from website/docs/_images/VMware_cpu.png
rename to website/docs/v_2_2_0/_images/VMware_cpu.png

diff --git a/website/docs/_images/folder-small.png b/website/docs/v_2_2_0/_images/folder-small.png
similarity index 100%
rename from website/docs/_images/folder-small.png
rename to website/docs/v_2_2_0/_images/folder-small.png

diff --git a/website/docs/_images/usage_statistics_details.gif b/website/docs/v_2_2_0/_images/usage_statistics_details.gif
similarity index 100%
rename from website/docs/_images/usage_statistics_details.gif
rename to website/docs/v_2_2_0/_images/usage_statistics_details.gif

diff --git a/website/docs/_images/usage_statistics_job_details.gif b/website/docs/v_2_2_0/_images/usage_statistics_job_details.gif
similarity index 100%
rename from website/docs/_images/usage_statistics_job_details.gif
rename to website/docs/v_2_2_0/_images/usage_statistics_job_details.gif

diff --git a/website/docs/_images/usage_statistics_main.gif b/website/docs/v_2_2_0/_images/usage_statistics_main.gif
similarity index 100%
rename from website/docs/_images/usage_statistics_main.gif
rename to website/docs/v_2_2_0/_images/usage_statistics_main.gif

diff --git a/website/docs/_images/usage_statistics_month.gif b/website/docs/v_2_2_0/_images/usage_statistics_month.gif
similarity index 100%
rename from website/docs/_images/usage_statistics_month.gif
rename to website/docs/v_2_2_0/_images/usage_statistics_month.gif

diff --git a/website/docs/_images/vm_welcome_screen.png b/website/docs/v_2_2_0/_images/vm_welcome_screen.png
similarity index 100%
rename from website/docs/_images/vm_welcome_screen.png
rename to website/docs/v_2_2_0/_images/vm_welcome_screen.png

diff --git a/website/docs/_images/ws-structure.png b/website/docs/v_2_2_0/_images/ws-structure.png
similarity index 100%
rename from website/docs/_images/ws-structure.png
rename to website/docs/v_2_2_0/_images/ws-structure.png

diff --git a/website/docs/_sources/advanced.rst.txt b/website/docs/v_2_2_0/_sources/advanced.rst.txt
similarity index 99%
rename from website/docs/_sources/advanced.rst.txt
rename to website/docs/v_2_2_0/_sources/advanced.rst.txt
index 38a4185..e636c8a 100644 (file)
--- a/website/docs/_sources/advanced.rst.txt
+++ b/website/docs/v_2_2_0/_sources/advanced.rst.txt
@@ -463,8 +463,8 @@ JABAWS War File Content
 
 .. links
 .. _war file content table: advanced.html#jabaws_war_file_content
-.. _dm_javadoc: http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html
-.. _full_javadoc: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html
+.. _dm_javadoc: ../dm_javadoc/index.html
+.. _full_javadoc: ../full_javadoc/index.html
 .. _prog_docs: http://www.compbio.dundee.ac.uk/jabaws/prog_docs/
 .. _test JABAWS: advanced.html#testing-the-jabaws-server
 .. _deploying on Tomcat tips: war.html

diff --git a/website/docs/_sources/changelog.rst.txt b/website/docs/v_2_2_0/_sources/changelog.rst.txt
similarity index 96%
rename from website/docs/_sources/changelog.rst.txt
rename to website/docs/v_2_2_0/_sources/changelog.rst.txt
index d4016fc..f5f4d93 100644 (file)
--- a/website/docs/_sources/changelog.rst.txt
+++ b/website/docs/v_2_2_0/_sources/changelog.rst.txt
@@ -59,7 +59,7 @@ JABAWS 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2.0
 * Disembl returned swapped strings for HOTLOOPS and REM465
 * Jronn failed to process jobs with more than 3 sequences
 * JABAWS could not deal with FASTA records with '>' symbols in the record identificator
-* Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores in one call
+* Change of parameter description for AACon: parameters have been replaced with options for calculation methods. This allows a user to get several AACon's conservation scores in one call
 * JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties
 * Default web security has been incompatible with Tomcat 7.0.31 and newer
 * Documentation has been updated

diff --git a/website/docs/_sources/citations.rst.txt b/website/docs/v_2_2_0/_sources/citations.rst.txt
similarity index 100%
rename from website/docs/_sources/citations.rst.txt
rename to website/docs/v_2_2_0/_sources/citations.rst.txt

diff --git a/website/docs/_sources/client.rst.txt b/website/docs/v_2_2_0/_sources/client.rst.txt
similarity index 100%
rename from website/docs/_sources/client.rst.txt
rename to website/docs/v_2_2_0/_sources/client.rst.txt

diff --git a/website/docs/_sources/develop.rst.txt b/website/docs/v_2_2_0/_sources/develop.rst.txt
similarity index 99%
rename from website/docs/_sources/develop.rst.txt
rename to website/docs/v_2_2_0/_sources/develop.rst.txt
index 538923c..4c7db93 100644 (file)
--- a/website/docs/_sources/develop.rst.txt
+++ b/website/docs/v_2_2_0/_sources/develop.rst.txt
@@ -61,7 +61,7 @@ Structure of the project
 The code structure
 ------------------
 
-.. image:: ../website/static/img/ws-structure.png
+.. image:: ../../website/static/img/ws-structure.png
   :height: 414
   :width: 282
   :scale: 95 %
@@ -615,15 +615,15 @@ If you made any changes to the data model and would like to generate a complete
 
 
 
-.. |folder| image:: ../website/static/img/folder-small.png
+.. |folder| image:: ../../website/static/img/folder-small.png
    :align: middle
    :width: 15
 
 
 .. links
 .. _Git-tracker: https://source.jalview.org/crucible/changelog/jabaws
-.. _Data Model JavaDoc: http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html
-.. _Complete JavaDoc: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html
+.. _Data Model JavaDoc: ../dm_javadoc/index.html
+.. _Complete JavaDoc: ../full_javadoc/index.html
 .. _JavaDoc: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html
 .. _Test Results: http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html
 .. _TestNG: http://testng.org/doc/index.html

diff --git a/website/docs/_sources/getting_started.rst.txt b/website/docs/v_2_2_0/_sources/getting_started.rst.txt
similarity index 100%
rename from website/docs/_sources/getting_started.rst.txt
rename to website/docs/v_2_2_0/_sources/getting_started.rst.txt

diff --git a/website/docs/_sources/included_tools.rst.txt b/website/docs/v_2_2_0/_sources/included_tools.rst.txt
similarity index 100%
rename from website/docs/_sources/included_tools.rst.txt
rename to website/docs/v_2_2_0/_sources/included_tools.rst.txt

diff --git a/website/docs/_sources/index.rst.txt b/website/docs/v_2_2_0/_sources/index.rst.txt
similarity index 96%
rename from website/docs/_sources/index.rst.txt
rename to website/docs/v_2_2_0/_sources/index.rst.txt
index e0a0729..67dc7b0 100644 (file)
--- a/website/docs/_sources/index.rst.txt
+++ b/website/docs/v_2_2_0/_sources/index.rst.txt
@@ -11,7 +11,7 @@ Read on these documentation pages or go back to the `JABAWS homepage`_!
 JABAWS documentation is also available in *pdf*. `Download it here`_!
 
 
-.. _JABAWS homepage: ../
+.. _JABAWS homepage: ../../
 
 
 .. toctree::

diff --git a/website/docs/_sources/man/advanced.rst.txt b/website/docs/v_2_2_0/_sources/man/advanced.rst.txt
similarity index 100%
rename from website/docs/_sources/man/advanced.rst.txt
rename to website/docs/v_2_2_0/_sources/man/advanced.rst.txt

diff --git a/website/docs/_sources/man/changelog.rst.txt b/website/docs/v_2_2_0/_sources/man/changelog.rst.txt
similarity index 100%
rename from website/docs/_sources/man/changelog.rst.txt
rename to website/docs/v_2_2_0/_sources/man/changelog.rst.txt

diff --git a/website/docs/_sources/man/citations.rst.txt b/website/docs/v_2_2_0/_sources/man/citations.rst.txt
similarity index 100%
rename from website/docs/_sources/man/citations.rst.txt
rename to website/docs/v_2_2_0/_sources/man/citations.rst.txt

diff --git a/website/docs/_sources/man/client.rst.txt b/website/docs/v_2_2_0/_sources/man/client.rst.txt
similarity index 100%
rename from website/docs/_sources/man/client.rst.txt
rename to website/docs/v_2_2_0/_sources/man/client.rst.txt

diff --git a/website/docs/_sources/man/develop.rst.txt b/website/docs/v_2_2_0/_sources/man/develop.rst.txt
similarity index 100%
rename from website/docs/_sources/man/develop.rst.txt
rename to website/docs/v_2_2_0/_sources/man/develop.rst.txt

diff --git a/website/docs/_sources/man/getting_started.rst.txt b/website/docs/v_2_2_0/_sources/man/getting_started.rst.txt
similarity index 100%
rename from website/docs/_sources/man/getting_started.rst.txt
rename to website/docs/v_2_2_0/_sources/man/getting_started.rst.txt

diff --git a/website/docs/_sources/man/included_tools.rst.txt b/website/docs/v_2_2_0/_sources/man/included_tools.rst.txt
similarity index 100%
rename from website/docs/_sources/man/included_tools.rst.txt
rename to website/docs/v_2_2_0/_sources/man/included_tools.rst.txt

diff --git a/website/docs/_sources/man/va.rst.txt b/website/docs/v_2_2_0/_sources/man/va.rst.txt
similarity index 100%
rename from website/docs/_sources/man/va.rst.txt
rename to website/docs/v_2_2_0/_sources/man/va.rst.txt

diff --git a/website/docs/_sources/man/war.rst.txt b/website/docs/v_2_2_0/_sources/man/war.rst.txt
similarity index 100%
rename from website/docs/_sources/man/war.rst.txt
rename to website/docs/v_2_2_0/_sources/man/war.rst.txt

diff --git a/website/docs/_sources/stats.rst.txt b/website/docs/v_2_2_0/_sources/stats.rst.txt
similarity index 97%
rename from website/docs/_sources/stats.rst.txt
rename to website/docs/v_2_2_0/_sources/stats.rst.txt
index 7e5ac8c..412731f 100644 (file)
--- a/website/docs/_sources/stats.rst.txt
+++ b/website/docs/v_2_2_0/_sources/stats.rst.txt
@@ -7,7 +7,7 @@ If you are using JABAWS VA (Virtual Appliance) then the username is *jabaws* and
 
 If you have deployed a JABAWS WAR file, then please see the `configuring privileged access`_ for Tomcat web application server section for further details.
 
-.. image:: ../website/static/img/usage_statistics_main.gif
+.. image:: ../../website/static/img/usage_statistics_main.gif
    :height: 318
    :width: 608
    :scale: 100 %
@@ -34,7 +34,7 @@ Detailed View
 
 Detailed execution statistics for each month is available for authenticated users only.
 
-.. image:: ../website/static/img/usage_statistics_month.gif
+.. image:: ../../website/static/img/usage_statistics_month.gif
    :height: 902
    :width: 670
    :scale: 100 %
@@ -62,7 +62,7 @@ Job List
 
 Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view, the application server may need to be configured. Please see the `Configuring JABAWS execution statistics`_ section for further details.
 
-.. image:: ../website/static/img/usage_statistics_details.gif
+.. image:: ../../website/static/img/usage_statistics_details.gif
    :height: 198
    :width: 917
    :scale: 100 %
@@ -88,7 +88,7 @@ Columns:
 Job Directory Contents
 ----------------------
 
-.. image:: ../website/static/img/usage_statistics_job_details.gif
+.. image:: ../../website/static/img/usage_statistics_job_details.gif
    :height: 420
    :width: 716
    :scale: 90 %

diff --git a/website/docs/_sources/va.rst.txt b/website/docs/v_2_2_0/_sources/va.rst.txt
similarity index 97%
rename from website/docs/_sources/va.rst.txt
rename to website/docs/v_2_2_0/_sources/va.rst.txt
index d9e7de2..b5f3de4 100644 (file)
--- a/website/docs/_sources/va.rst.txt
+++ b/website/docs/v_2_2_0/_sources/va.rst.txt
@@ -36,7 +36,7 @@ Usage
 By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.
 
 
-.. image:: ../website/static/img/VMware_cpu.png
+.. image:: ../../website/static/img/VMware_cpu.png
    :height: 267
    :width: 708
    :scale: 95 %
@@ -103,7 +103,7 @@ After booting the JABAWS VM, you should see similar screen, however, the IP addr
 
 .. _Jalview help pages: http://www.jalview.org/help/html/webServices/JABAWS.html
 
-.. image:: ../website/static/img/vm_welcome_screen.png
+.. image:: ../../website/static/img/vm_welcome_screen.png
    :height: 461
    :width: 734
    :scale: 95 %
@@ -111,7 +111,7 @@ After booting the JABAWS VM, you should see similar screen, however, the IP addr
 
 If you click on Advanced Menu, you will see the configuration console, similar to the one below.
 
-.. image:: ../website/static/img/VMware_booted.png
+.. image:: ../../website/static/img/VMware_booted.png
   :height: 461
   :width: 735
   :scale: 95 %

diff --git a/website/docs/_sources/war.rst.txt b/website/docs/v_2_2_0/_sources/war.rst.txt
similarity index 100%
rename from website/docs/_sources/war.rst.txt
rename to website/docs/v_2_2_0/_sources/war.rst.txt

diff --git a/website/docs/_static/ajax-loader.gif b/website/docs/v_2_2_0/_static/ajax-loader.gif
similarity index 100%
rename from website/docs/_static/ajax-loader.gif
rename to website/docs/v_2_2_0/_static/ajax-loader.gif

diff --git a/website/docs/_static/basic.css b/website/docs/v_2_2_0/_static/basic.css
similarity index 100%
rename from website/docs/_static/basic.css
rename to website/docs/v_2_2_0/_static/basic.css

diff --git a/website/docs/_static/comment-bright.png b/website/docs/v_2_2_0/_static/comment-bright.png
similarity index 100%
rename from website/docs/_static/comment-bright.png
rename to website/docs/v_2_2_0/_static/comment-bright.png

diff --git a/website/docs/_static/comment-close.png b/website/docs/v_2_2_0/_static/comment-close.png
similarity index 100%
rename from website/docs/_static/comment-close.png
rename to website/docs/v_2_2_0/_static/comment-close.png

diff --git a/website/docs/_static/comment.png b/website/docs/v_2_2_0/_static/comment.png
similarity index 100%
rename from website/docs/_static/comment.png
rename to website/docs/v_2_2_0/_static/comment.png

diff --git a/website/docs/_static/css/badge_only.css b/website/docs/v_2_2_0/_static/css/badge_only.css
similarity index 100%
rename from website/docs/_static/css/badge_only.css
rename to website/docs/v_2_2_0/_static/css/badge_only.css

diff --git a/website/docs/_static/css/badge_only.css.map b/website/docs/v_2_2_0/_static/css/badge_only.css.map
similarity index 100%
rename from website/docs/_static/css/badge_only.css.map
rename to website/docs/v_2_2_0/_static/css/badge_only.css.map

diff --git a/website/docs/_static/css/theme.css b/website/docs/v_2_2_0/_static/css/theme.css
similarity index 100%
rename from website/docs/_static/css/theme.css
rename to website/docs/v_2_2_0/_static/css/theme.css

diff --git a/website/docs/_static/css/theme.css.map b/website/docs/v_2_2_0/_static/css/theme.css.map
similarity index 100%
rename from website/docs/_static/css/theme.css.map
rename to website/docs/v_2_2_0/_static/css/theme.css.map

diff --git a/website/docs/_static/doctools.js b/website/docs/v_2_2_0/_static/doctools.js
similarity index 100%
rename from website/docs/_static/doctools.js
rename to website/docs/v_2_2_0/_static/doctools.js

diff --git a/website/docs/_static/down-pressed.png b/website/docs/v_2_2_0/_static/down-pressed.png
similarity index 100%
rename from website/docs/_static/down-pressed.png
rename to website/docs/v_2_2_0/_static/down-pressed.png

diff --git a/website/docs/_static/down.png b/website/docs/v_2_2_0/_static/down.png
similarity index 100%
rename from website/docs/_static/down.png
rename to website/docs/v_2_2_0/_static/down.png

diff --git a/website/docs/_static/file.png b/website/docs/v_2_2_0/_static/file.png
similarity index 100%
rename from website/docs/_static/file.png
rename to website/docs/v_2_2_0/_static/file.png

diff --git a/website/docs/_static/fonts/FontAwesome.otf b/website/docs/v_2_2_0/_static/fonts/FontAwesome.otf
similarity index 100%
rename from website/docs/_static/fonts/FontAwesome.otf
rename to website/docs/v_2_2_0/_static/fonts/FontAwesome.otf

diff --git a/website/docs/_static/fonts/Inconsolata-Bold.ttf b/website/docs/v_2_2_0/_static/fonts/Inconsolata-Bold.ttf
similarity index 100%
rename from website/docs/_static/fonts/Inconsolata-Bold.ttf
rename to website/docs/v_2_2_0/_static/fonts/Inconsolata-Bold.ttf

diff --git a/website/docs/_static/fonts/Inconsolata-Regular.ttf b/website/docs/v_2_2_0/_static/fonts/Inconsolata-Regular.ttf
similarity index 100%
rename from website/docs/_static/fonts/Inconsolata-Regular.ttf
rename to website/docs/v_2_2_0/_static/fonts/Inconsolata-Regular.ttf

diff --git a/website/docs/_static/fonts/Lato-Bold.ttf b/website/docs/v_2_2_0/_static/fonts/Lato-Bold.ttf
similarity index 100%
rename from website/docs/_static/fonts/Lato-Bold.ttf
rename to website/docs/v_2_2_0/_static/fonts/Lato-Bold.ttf

diff --git a/website/docs/_static/fonts/Lato-Regular.ttf b/website/docs/v_2_2_0/_static/fonts/Lato-Regular.ttf
similarity index 100%
rename from website/docs/_static/fonts/Lato-Regular.ttf
rename to website/docs/v_2_2_0/_static/fonts/Lato-Regular.ttf

diff --git a/website/docs/_static/fonts/RobotoSlab-Bold.ttf b/website/docs/v_2_2_0/_static/fonts/RobotoSlab-Bold.ttf
similarity index 100%
rename from website/docs/_static/fonts/RobotoSlab-Bold.ttf
rename to website/docs/v_2_2_0/_static/fonts/RobotoSlab-Bold.ttf

diff --git a/website/docs/_static/fonts/RobotoSlab-Regular.ttf b/website/docs/v_2_2_0/_static/fonts/RobotoSlab-Regular.ttf
similarity index 100%
rename from website/docs/_static/fonts/RobotoSlab-Regular.ttf
rename to website/docs/v_2_2_0/_static/fonts/RobotoSlab-Regular.ttf

diff --git a/website/docs/_static/fonts/fontawesome-webfont.eot b/website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.eot
similarity index 100%
rename from website/docs/_static/fonts/fontawesome-webfont.eot
rename to website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.eot

diff --git a/website/docs/_static/fonts/fontawesome-webfont.svg b/website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.svg
similarity index 100%
rename from website/docs/_static/fonts/fontawesome-webfont.svg
rename to website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.svg

diff --git a/website/docs/_static/fonts/fontawesome-webfont.ttf b/website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.ttf
similarity index 100%
rename from website/docs/_static/fonts/fontawesome-webfont.ttf
rename to website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.ttf

diff --git a/website/docs/_static/fonts/fontawesome-webfont.woff b/website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.woff
similarity index 100%
rename from website/docs/_static/fonts/fontawesome-webfont.woff
rename to website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.woff

diff --git a/website/docs/_static/fonts/fontawesome-webfont.woff2 b/website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.woff2
similarity index 100%
rename from website/docs/_static/fonts/fontawesome-webfont.woff2
rename to website/docs/v_2_2_0/_static/fonts/fontawesome-webfont.woff2

diff --git a/website/docs/_static/jquery-3.1.0.js b/website/docs/v_2_2_0/_static/jquery-3.1.0.js
similarity index 100%
rename from website/docs/_static/jquery-3.1.0.js
rename to website/docs/v_2_2_0/_static/jquery-3.1.0.js

diff --git a/website/docs/_static/jquery.js b/website/docs/v_2_2_0/_static/jquery.js
similarity index 100%
rename from website/docs/_static/jquery.js
rename to website/docs/v_2_2_0/_static/jquery.js

diff --git a/website/docs/_static/js/modernizr.min.js b/website/docs/v_2_2_0/_static/js/modernizr.min.js
similarity index 100%
rename from website/docs/_static/js/modernizr.min.js
rename to website/docs/v_2_2_0/_static/js/modernizr.min.js

diff --git a/website/docs/_static/js/theme.js b/website/docs/v_2_2_0/_static/js/theme.js
similarity index 100%
rename from website/docs/_static/js/theme.js
rename to website/docs/v_2_2_0/_static/js/theme.js

diff --git a/website/docs/_static/minus.png b/website/docs/v_2_2_0/_static/minus.png
similarity index 100%
rename from website/docs/_static/minus.png
rename to website/docs/v_2_2_0/_static/minus.png

diff --git a/website/docs/_static/plus.png b/website/docs/v_2_2_0/_static/plus.png
similarity index 100%
rename from website/docs/_static/plus.png
rename to website/docs/v_2_2_0/_static/plus.png

diff --git a/website/docs/_static/pygments.css b/website/docs/v_2_2_0/_static/pygments.css
similarity index 100%
rename from website/docs/_static/pygments.css
rename to website/docs/v_2_2_0/_static/pygments.css

diff --git a/website/docs/_static/searchtools.js b/website/docs/v_2_2_0/_static/searchtools.js
similarity index 100%
rename from website/docs/_static/searchtools.js
rename to website/docs/v_2_2_0/_static/searchtools.js

diff --git a/website/docs/_static/underscore-1.3.1.js b/website/docs/v_2_2_0/_static/underscore-1.3.1.js
similarity index 100%
rename from website/docs/_static/underscore-1.3.1.js
rename to website/docs/v_2_2_0/_static/underscore-1.3.1.js

diff --git a/website/docs/_static/underscore.js b/website/docs/v_2_2_0/_static/underscore.js
similarity index 100%
rename from website/docs/_static/underscore.js
rename to website/docs/v_2_2_0/_static/underscore.js

diff --git a/website/docs/_static/up-pressed.png b/website/docs/v_2_2_0/_static/up-pressed.png
similarity index 100%
rename from website/docs/_static/up-pressed.png
rename to website/docs/v_2_2_0/_static/up-pressed.png

diff --git a/website/docs/_static/up.png b/website/docs/v_2_2_0/_static/up.png
similarity index 100%
rename from website/docs/_static/up.png
rename to website/docs/v_2_2_0/_static/up.png

diff --git a/website/docs/_static/websupport.js b/website/docs/v_2_2_0/_static/websupport.js
similarity index 100%
rename from website/docs/_static/websupport.js
rename to website/docs/v_2_2_0/_static/websupport.js

diff --git a/website/docs/advanced.html b/website/docs/v_2_2_0/advanced.html
similarity index 99%
rename from website/docs/advanced.html
rename to website/docs/v_2_2_0/advanced.html
index 3cdb12a..c64a862 100644 (file)
--- a/website/docs/advanced.html
+++ b/website/docs/v_2_2_0/advanced.html
@@ -540,10 +540,10 @@ After you have completed the editing your configuration may look like this:</p>
 <tr class="row-even"><td>/</td>
 <td>help pages, index.html is the starting page</td>
 </tr>
-<tr class="row-odd"><td><a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">dm_javadoc</a></td>
+<tr class="row-odd"><td><a class="reference external" href="../dm_javadoc/index.html">dm_javadoc</a></td>
 <td>JavaDoc for the JABAWS Data Model</td>
 </tr>
-<tr class="row-even"><td><a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html">full_javadoc</a></td>
+<tr class="row-even"><td><a class="reference external" href="../full_javadoc/index.html">full_javadoc</a></td>
 <td>JavaDoc for the complete JABAWS</td>
 </tr>
 <tr class="row-odd"><td><a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/prog_docs/">prog_docs</a></td>
@@ -575,7 +575,7 @@ After you have completed the editing your configuration may look like this:</p>
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/changelog.html b/website/docs/v_2_2_0/changelog.html
similarity index 98%
rename from website/docs/changelog.html
rename to website/docs/v_2_2_0/changelog.html
index 277cdad..89028b4 100644 (file)
--- a/website/docs/changelog.html
+++ b/website/docs/v_2_2_0/changelog.html
@@ -219,7 +219,7 @@
 <li>Disembl returned swapped strings for HOTLOOPS and REM465</li>
 <li>Jronn failed to process jobs with more than 3 sequences</li>
 <li>JABAWS could not deal with FASTA records with &#8216;&gt;&#8217; symbols in the record identificator</li>
-<li>Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon&#8217;s conservation scores in one call</li>
+<li>Change of parameter description for AACon: parameters have been replaced with options for calculation methods. This allows a user to get several AACon&#8217;s conservation scores in one call</li>
 <li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties</li>
 <li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>
 <li>Documentation has been updated</li>
@@ -269,7 +269,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/citations.html b/website/docs/v_2_2_0/citations.html
similarity index 99%
rename from website/docs/citations.html
rename to website/docs/v_2_2_0/citations.html
index 0db9016..58b388e 100644 (file)
--- a/website/docs/citations.html
+++ b/website/docs/v_2_2_0/citations.html
@@ -195,7 +195,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/client.html b/website/docs/v_2_2_0/client.html
similarity index 99%
rename from website/docs/client.html
rename to website/docs/v_2_2_0/client.html
index 4858aef..3fdffc3 100644 (file)
--- a/website/docs/client.html
+++ b/website/docs/v_2_2_0/client.html
@@ -271,7 +271,7 @@ Please note that -r and -f options cannot be used together. Alignment is done wi
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/develop.html b/website/docs/v_2_2_0/develop.html
similarity index 98%
rename from website/docs/develop.html
rename to website/docs/v_2_2_0/develop.html
index fb1d0f8..5d32d15 100644 (file)
--- a/website/docs/develop.html
+++ b/website/docs/v_2_2_0/develop.html
@@ -206,8 +206,8 @@
 </div>
 <div class="section" id="the-api">
 <span id="jabaws-api"></span><h2>The API<a class="headerlink" href="#the-api" title="Permalink to this headline">¶</a></h2>
-<p><a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">Data Model JavaDoc</a> - read this if your are coding against JABA Web Services</p>
-<p><a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html">Complete JavaDoc</a> - for developers who want to use JABAWS framework and use Engines and Executables directly</p>
+<p><a class="reference external" href="../dm_javadoc/index.html">Data Model JavaDoc</a> - read this if your are coding against JABA Web Services</p>
+<p><a class="reference external" href="../full_javadoc/index.html">Complete JavaDoc</a> - for developers who want to use JABAWS framework and use Engines and Executables directly</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="structure-of-the-project">
@@ -337,7 +337,7 @@ JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse w
 </tbody>
 </table>
 <p>Additional utility libraries that this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.</p>
-<p>Please refer to a <a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">Data Model JavaDoc</a> for a detailed description of each class and its methods.</p>
+<p>Please refer to a <a class="reference external" href="../dm_javadoc/index.html">Data Model JavaDoc</a> for a detailed description of each class and its methods.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="connecting-to-jabaws">
@@ -587,7 +587,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
 <span class="o">}</span>
 </pre></div>
 </div>
-<p>For a more detailed description of all available types and their functions please refer to the <a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">Data Model JavaDoc</a>.</p>
+<p>For a more detailed description of all available types and their functions please refer to the <a class="reference external" href="../dm_javadoc/index.html">Data Model JavaDoc</a>.</p>
 <hr class="docutils" />
 </div>
 </div>
@@ -695,7 +695,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/genindex.html b/website/docs/v_2_2_0/genindex.html
similarity index 99%
rename from website/docs/genindex.html
rename to website/docs/v_2_2_0/genindex.html
index 0aeab05..d257af0 100644 (file)
--- a/website/docs/genindex.html
+++ b/website/docs/v_2_2_0/genindex.html
@@ -181,7 +181,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/getting_started.html b/website/docs/v_2_2_0/getting_started.html
similarity index 99%
rename from website/docs/getting_started.html
rename to website/docs/v_2_2_0/getting_started.html
index 8dc1cb1..4fbe3c0 100644 (file)
--- a/website/docs/getting_started.html
+++ b/website/docs/v_2_2_0/getting_started.html
@@ -324,7 +324,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/included_tools.html b/website/docs/v_2_2_0/included_tools.html
similarity index 99%
rename from website/docs/included_tools.html
rename to website/docs/v_2_2_0/included_tools.html
index 1de623b..d95061e 100644 (file)
--- a/website/docs/included_tools.html
+++ b/website/docs/v_2_2_0/included_tools.html
@@ -230,7 +230,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/index.html b/website/docs/v_2_2_0/index.html
similarity index 99%
rename from website/docs/index.html
rename to website/docs/v_2_2_0/index.html
index 6fced19..2f76723 100644 (file)
--- a/website/docs/index.html
+++ b/website/docs/v_2_2_0/index.html
@@ -166,7 +166,7 @@
             
   <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>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>
@@ -305,7 +305,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/jabaws_manual.pdf b/website/docs/v_2_2_0/jabaws_manual.pdf
similarity index 92%
rename from website/docs/jabaws_manual.pdf
rename to website/docs/v_2_2_0/jabaws_manual.pdf
index 0e23b76..08d4df9 100644 (file)
Binary files a/website/docs/jabaws_manual.pdf and b/website/docs/v_2_2_0/jabaws_manual.pdf differ

diff --git a/website/docs/objects.inv b/website/docs/v_2_2_0/objects.inv
similarity index 100%
rename from website/docs/objects.inv
rename to website/docs/v_2_2_0/objects.inv

diff --git a/website/docs/search.html b/website/docs/v_2_2_0/search.html
similarity index 99%
rename from website/docs/search.html
rename to website/docs/v_2_2_0/search.html
index c2141ce..2979a34 100644 (file)
--- a/website/docs/search.html
+++ b/website/docs/v_2_2_0/search.html
@@ -186,7 +186,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/searchindex.js b/website/docs/v_2_2_0/searchindex.js
similarity index 100%
rename from website/docs/searchindex.js
rename to website/docs/v_2_2_0/searchindex.js

diff --git a/website/docs/stats.html b/website/docs/v_2_2_0/stats.html
similarity index 99%
rename from website/docs/stats.html
rename to website/docs/v_2_2_0/stats.html
index 96abbb2..0e19253 100644 (file)
--- a/website/docs/stats.html
+++ b/website/docs/v_2_2_0/stats.html
@@ -298,7 +298,7 @@ local.stat.maxruntime<span class="o">=</span><span class="m">6</span>
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/va.html b/website/docs/v_2_2_0/va.html
similarity index 99%
rename from website/docs/va.html
rename to website/docs/v_2_2_0/va.html
index 90b468f..2a2ddee 100644 (file)
--- a/website/docs/va.html
+++ b/website/docs/v_2_2_0/va.html
@@ -273,7 +273,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/docs/war.html b/website/docs/v_2_2_0/war.html
similarity index 99%
rename from website/docs/war.html
rename to website/docs/v_2_2_0/war.html
index 4f8d45e..b8b1e48 100644 (file)
--- a/website/docs/war.html
+++ b/website/docs/v_2_2_0/war.html
@@ -239,7 +239,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p><a href="../">JABAWS 2.2</a>
+    <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.
 
     </p>

diff --git a/website/download.jsp b/website/download.jsp
index e700cc4..40e2d38 100644 (file)
--- a/website/download.jsp
+++ b/website/download.jsp
@@ -21,7 +21,7 @@
                 <p class="justify">
                     Read the <a href="${pageContext.request.contextPath}/getting_started.jsp"><em>Getting Started</em></a>
                     guides to better decide which JABAWS distribution better suits your needs.
-                    Additional information is available in the <a href="${pageContext.request.contextPath}/docs/index.html">
+                    Additional information is available in the <a href="${pageContext.request.contextPath}/docs/v_2_2_0/index.html">
                     documentation pages</a>.
                 </p>
                 <br>
@@ -99,18 +99,18 @@
                 <ul>
                     <li>
                         <a href='${pageContext.request.contextPath}/archive/min-jabaws-client-2.2.0.jar'>
-                            <i class="fa fa-download" aria-hidden="true"></i>CLI jar file with binaries</a> (with log4j)</li>
+                            <i class="fa fa-download" aria-hidden="true"></i> CLI jar file with binaries</a> (with log4j)</li>
                     <li>
                         <a href='${pageContext.request.contextPath}/archive/min-jabaws-client-nolog-2.2.0.jar'>
-                            <i class="fa fa-download" aria-hidden="true"></i>CLI jar file with binaries</a> (without log4j)</li>
+                            <i class="fa fa-download" aria-hidden="true"></i> CLI jar file with binaries</a> (without log4j)</li>
                     <li>
                         <a href='${pageContext.request.contextPath}/archive/jabaws-client-src-2.2.0.jar'>
-                            <i class="fa fa-download" aria-hidden="true"></i>CLI client source</a></li>
+                            <i class="fa fa-download" aria-hidden="true"></i> CLI client source</a></li>
                 </ul>
                 <p class="justify">
                     The command line client displays help when executed without arguments,
                     more details is available from the JABAWS
-                    <a href="${pageContext.request.contextPath}/docs/client.html">document pages</a>.
+                    <a href="${pageContext.request.contextPath}/docs/v_2_2_0/client.html">document pages</a>.
                 </p>
                 <p class="text-right">
                     <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
@@ -143,7 +143,7 @@
                         (includes source and precompiled Linux x86 and Windows binaries)</li>
                 </ul>
                 <p class="justify">
-                    Please check the JABAWS <a href="${pageContext.request.contextPath}/docs/war.html">document pages</a>
+                    Please check the JABAWS <a href="${pageContext.request.contextPath}/docs/v_2_2_0/war.html">document pages</a>
                     for further instructions.
                 </p>
                 <p class="text-right">
@@ -175,7 +175,7 @@
                             <i class="fa fa-download" aria-hidden="true"></i> JABAWS Virtual Appliance</a></li>
                 </ul>
                 <p class="justify">
-                    Please check the JABAWS <a href="${pageContext.request.contextPath}/docs/va.html">document pages</a>
+                    Please check the JABAWS <a href="${pageContext.request.contextPath}/docs/v_2_2_0/va.html">document pages</a>
                     for further instructions.
                 </p>
                 <p class="text-right">

diff --git a/website/getting_started.jsp b/website/getting_started.jsp
index 19978f3..df22a01 100644 (file)
--- a/website/getting_started.jsp
+++ b/website/getting_started.jsp
@@ -20,7 +20,7 @@
             <div class="panel-body">
                 <p class="justify">
                     Choose the JABAWS distribution that better suits your needs and read the <em>Getting Started</em> guides below.
-                    Detailed information is available in the <a href="${pageContext.request.contextPath}/docs/index.html">
+                    Detailed information is available in the <a href="${pageContext.request.contextPath}/docs/v_2_2_0/index.html">
                     documentation pages</a>.
                 </p>
                 <br>
@@ -94,7 +94,7 @@
                     It allows anyone who wants to connect to the JABAWS web-services running at the
                     University of Dundee's Public Server, or to run a local private JABAWS server from their own software.
                     You can read more about how to use JABAWS command line (CLI) client given in the
-                    <a href="docs/client.html">documentation pages</a>,
+                    <a href="docs/v_2_2_0/client.html">documentation pages</a>,
                     but a brief instructions are given below:
                 </p>
                 <ol>
@@ -110,7 +110,7 @@
                     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
-                    <a href="docs/develop.html#accessing-jabaws-from-your-program">documentation pages</a>.
+                    <a href="docs/v_2_2_0/develop.html#accessing-jabaws-from-your-program">documentation pages</a>.
                     <!-- TODO Provide list of libraries for different languages -->
                 </p>
                 <p class="text-right">
@@ -133,7 +133,7 @@
                     The JABAWS Web Application aRchive (WAR) is for anyone who wants to run JABAWS for their group, lab or organization,
                     or wants to enable their local JABAWS server to use the cluster or perform very large tasks.
                     Complete documentation is provided in the
-                    <a href="docs/war.html">documentation pages</a>, but brief instructions are given below:
+                    <a href="docs/v_2_2_0/war.html">documentation pages</a>, but brief instructions are given below:
                 </p>
                 <ol>
                     <li>Download the <a href="${pageContext.request.contextPath}/download.jsp#war">JABAWS WAR file</a></li>
@@ -198,7 +198,7 @@
                 <p class="justify">
                     The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a
                     virtual machine on your laptop or desktop computer. A complete guide
-                    to the JABAWS VA is given in the <a href="${pageContext.request.contextPath}/docs/va.html">documentation pages</a>,
+                    to the JABAWS VA is given in the <a href="${pageContext.request.contextPath}/docs/v_2_2_0/va.html">documentation pages</a>,
                     but for the impatient, brief instructions are given below:
                 </p>
 

diff --git a/website/index.jsp b/website/index.jsp
index c80ffb3..9e40bf8 100644 (file)
--- a/website/index.jsp
+++ b/website/index.jsp
@@ -141,7 +141,7 @@
                 <p class="justify">
                     You can access our public JABAWS web services with <a href="http://www.jalview.org/">Jalview</a>,
                     <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS CLI</a>, or
-                    <a href="${pageContext.request.contextPath}/docs/develop.html#accessing-jabaws-from-your-program">with your own program</a>.
+                    <a href="${pageContext.request.contextPath}/docs/v_2_2_0/develop.html#accessing-jabaws-from-your-program">with your own program</a>.
                     The latest versions of Jalview (version 2.9 or later) are fully compatible
                     with JABAWS 2.2 and are configured to use the public JABAWS server by default.
                 </p>

diff --git a/website/template_footer.jsp b/website/template_footer.jsp
index 631460f..e3781ef 100644 (file)
--- a/website/template_footer.jsp
+++ b/website/template_footer.jsp
@@ -55,31 +55,31 @@
         <div class="col-md-4">
             <ul class="list-unstyled">
                 <li>
-                    <strong><a href="${pageContext.request.contextPath}/docs/index.html">Documentation</a></strong>
+                    <strong><a href="${pageContext.request.contextPath}/docs/v_2_2_0/index.html">Documentation</a></strong>
                     <ul>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/getting_started.html">Getting Started</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/getting_started.html">Getting Started</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/included_tools.html">Included Tools</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/included_tools.html">Included Tools</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/client.html">Command Line Client (CLI)</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/client.html">Command Line Client (CLI)</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/war.html">Web Application Archive (WAR)</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/war.html">Web Application Archive (WAR)</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/va.html">Virtual Appliance (VA)</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/va.html">Virtual Appliance (VA)</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/advanced.html">Advanced Usage</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/advanced.html">Advanced Usage</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/develop.html">For Developers</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/develop.html">For Developers</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/changelog.html">Changelog</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/changelog.html">Changelog</a>
                         </li>
                     </ul>
                 </li>
@@ -93,7 +93,7 @@
     </div>
     <hr>
     <p class="text-right"><small>
-        Site Last updated: 12 April 2017. This site was built using the <a href="http://getbootstrap.com">Bootstrap framework.</a>
+        Site Last updated: 21 April 2017. This site was built using the <a href="http://getbootstrap.com">Bootstrap framework.</a>
     </small></p>
 </div>
 

diff --git a/website/template_header.jsp b/website/template_header.jsp
index a447d8f..831284b 100644 (file)
--- a/website/template_header.jsp
+++ b/website/template_header.jsp
@@ -103,34 +103,34 @@
 
                     <ul class="dropdown-menu">
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/getting_started.html">Getting Started</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/getting_started.html">Getting Started</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/included_tools.html">Included Tools</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/included_tools.html">Included Tools</a>
                         </li>
                         <li class="divider"></li>
                        <li>
-                            <a href="${pageContext.request.contextPath}/docs/client.html">Command Line Client (CLI)</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/client.html">Command Line Client (CLI)</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/war.html">Web Application Archive (WAR)</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/war.html">Web Application Archive (WAR)</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/va.html">Virtual Appliance (VA)</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/va.html">Virtual Appliance (VA)</a>
                         </li>
                         <li class="divider"></li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/advanced.html">Advanced Usage</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/advanced.html">Advanced Usage</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/develop.html">For Developers</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/develop.html">For Developers</a>
                         </li>
                         <li class="divider"></li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/changelog.html">Changelog</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/changelog.html">Changelog</a>
                         </li>
                         <li>
-                            <a href="${pageContext.request.contextPath}/docs/stats.html">Usage Statistics</a>
+                            <a href="${pageContext.request.contextPath}/docs/v_2_2_0/stats.html">Usage Statistics</a>
                         </li>
                         <li class="divider"></li>
                         <li>