From: Fábio Madeira Date: Fri, 21 Apr 2017 14:51:46 +0000 (+0100) Subject: JWS-109 & JWS-116 Moved the docs (source and html built) to a new location that is... X-Git-Url: http://source.jalview.org/gitweb/?p=jabaws.git;a=commitdiff_plain;h=2da44d18582e4d851e137573346a4916435c220b JWS-109 & JWS-116 Moved the docs (source and html built) to a new location that is based on the version. --- 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 --- a/docs/_themes/sphinx_rtd_theme/footer.html +++ b/docs/v_2_2_0/_themes/sphinx_rtd_theme/footer.html @@ -13,7 +13,7 @@
-

JABAWS 2.2 +

JABAWS 2.2 {%- if show_copyright %} {%- if hasdoc('copyright') %} {% trans path=pathto('copyright'), copyright=copyright|e %}© Copyright {{ 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 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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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 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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 --- 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:

/ help pages, index.html is the starting page -dm_javadoc +dm_javadoc JavaDoc for the JABAWS Data Model -full_javadoc +full_javadoc JavaDoc for the complete JABAWS prog_docs @@ -575,7 +575,7 @@ After you have completed the editing your configuration may look like this:

-

JABAWS 2.2 +

JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

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 --- a/website/docs/changelog.html +++ b/website/docs/v_2_2_0/changelog.html @@ -219,7 +219,7 @@
  • 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
    • @@ -269,7 +269,7 @@
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- a/website/docs/citations.html +++ b/website/docs/v_2_2_0/citations.html @@ -195,7 +195,7 @@
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- 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
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- a/website/docs/develop.html +++ b/website/docs/v_2_2_0/develop.html @@ -206,8 +206,8 @@

    The API¶

    -

    Data Model JavaDoc - read this if your are coding against JABA Web Services

    -

    Complete JavaDoc - for developers who want to use JABAWS framework and use Engines and Executables directly

    +

    Data Model JavaDoc - read this if your are coding against JABA Web Services

    +

    Complete JavaDoc - for developers who want to use JABAWS framework and use Engines and Executables directly

    @@ -337,7 +337,7 @@ JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse w

    Additional utility libraries that this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.

    -

    Please refer to a Data Model JavaDoc for a detailed description of each class and its methods.

    +

    Please refer to a Data Model JavaDoc for a detailed description of each class and its methods.

    @@ -587,7 +587,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien }
    -

    For a more detailed description of all available types and their functions please refer to the Data Model JavaDoc.

    +

    For a more detailed description of all available types and their functions please refer to the Data Model JavaDoc.

    @@ -695,7 +695,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- a/website/docs/genindex.html +++ b/website/docs/v_2_2_0/genindex.html @@ -181,7 +181,7 @@
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- a/website/docs/getting_started.html +++ b/website/docs/v_2_2_0/getting_started.html @@ -324,7 +324,7 @@
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- a/website/docs/included_tools.html +++ b/website/docs/v_2_2_0/included_tools.html @@ -230,7 +230,7 @@
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- a/website/docs/index.html +++ b/website/docs/v_2_2_0/index.html @@ -166,7 +166,7 @@

    Welcome to JABAWS’s documentation!¶

    -

    Read on these documentation pages or go back to the JABAWS homepage!

    +

    Read on these documentation pages or go back to the JABAWS homepage!

    JABAWS documentation is also available in pdf. Download it here!

    Contents:

    @@ -305,7 +305,7 @@
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 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 --- a/website/docs/search.html +++ b/website/docs/v_2_2_0/search.html @@ -186,7 +186,7 @@
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- a/website/docs/stats.html +++ b/website/docs/v_2_2_0/stats.html @@ -298,7 +298,7 @@ local.stat.maxruntime=6
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- a/website/docs/va.html +++ b/website/docs/v_2_2_0/va.html @@ -273,7 +273,7 @@
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    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 --- a/website/docs/war.html +++ b/website/docs/v_2_2_0/war.html @@ -239,7 +239,7 @@
    -

    JABAWS 2.2 +

    JABAWS 2.2 © Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.

    diff --git a/website/download.jsp b/website/download.jsp index e700cc4..40e2d38 100644 --- a/website/download.jsp +++ b/website/download.jsp @@ -21,7 +21,7 @@

    Read the Getting Started guides to better decide which JABAWS distribution better suits your needs. - Additional information is available in the + Additional information is available in the documentation pages.


    @@ -99,18 +99,18 @@

    The command line client displays help when executed without arguments, more details is available from the JABAWS - document pages. + document pages.

    Back to top @@ -143,7 +143,7 @@ (includes source and precompiled Linux x86 and Windows binaries)

    - Please check the JABAWS document pages + Please check the JABAWS document pages for further instructions.

    @@ -175,7 +175,7 @@ JABAWS Virtual Appliance

    - Please check the JABAWS document pages + Please check the JABAWS document pages for further instructions.

    diff --git a/website/getting_started.jsp b/website/getting_started.jsp index 19978f3..df22a01 100644 --- a/website/getting_started.jsp +++ b/website/getting_started.jsp @@ -20,7 +20,7 @@

    Choose the JABAWS distribution that better suits your needs and read the Getting Started guides below. - Detailed information is available in the + Detailed information is available in the documentation pages.


    @@ -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 - documentation pages, + documentation pages, but a brief instructions are given below:

      @@ -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 - documentation pages. + documentation pages.

      @@ -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 - documentation pages, but brief instructions are given below: + documentation pages, but brief instructions are given below:

      1. Download the JABAWS WAR file
        2. @@ -198,7 +198,7 @@

        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 documentation pages, + to the JABAWS VA is given in the documentation pages, but for the impatient, brief instructions are given below:

        diff --git a/website/index.jsp b/website/index.jsp index c80ffb3..9e40bf8 100644 --- a/website/index.jsp +++ b/website/index.jsp @@ -141,7 +141,7 @@

        You can access our public JABAWS web services with Jalview, JABAWS CLI, or - with your own program. + with your own program. 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.

        diff --git a/website/template_footer.jsp b/website/template_footer.jsp index 631460f..e3781ef 100644 --- a/website/template_footer.jsp +++ b/website/template_footer.jsp @@ -55,31 +55,31 @@

        - Site Last updated: 12 April 2017. This site was built using the Bootstrap framework. + Site Last updated: 21 April 2017. This site was built using the Bootstrap framework.

    diff --git a/website/template_header.jsp b/website/template_header.jsp index a447d8f..831284b 100644 --- a/website/template_header.jsp +++ b/website/template_header.jsp @@ -103,34 +103,34 @@