<head><title>Jalview Documentation</title></head>
<body>
-<IMG src="Jalview_Logo.png"><font size="4">
-<br><br>
-<strong>Jalview Documentation</strong></font>
-<br><br>
-Jalview (2009) is a fast Java multiple alignment editor and analysis tool. It
-features many of the functions of <a href="http://www.compbio.dundee.ac.uk/Software/Amas/amas.html">AMAS</a>,
-for the analysis of sub-families and the prediction of functional sites, but is
-fully interactive. (View the <a href="http://www.jalview.org">Jalview homepage</a> at www.jalview.org).
-<p></p>
-<p> If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics: </p>
+<IMG src="Jalview_Logo.png">
+<p><strong>Welcome to Jalview's built in documentation.</strong></p>
+<p>If you don't know what Jalview is, then in addition to the pages here, we also suggest you take a look at www.jalview.org.</p>
+<p>Here are some good places to start:</p><ul>
+<li><a href="whatsNew.html">What's New"</a> summarises the new features in this release of Jalview.</li>
+<li>Learn how to <a href="editing/index.html">edit alignments</a> with Jalview.</li>
+<li><a href="features/seqfeatures.html">Import and display sequence features on your alignment</a></li>
+<li>Use <a href="features/viewingpdbs.html">Jmol to view and superpose 3D structures</a> associated with sequences in the alignment</li>
+</ul>
+ <p>If you are using the Jalview Desktop application and are looking
+ for something specific, then this help system also includes a search
+ box. If you're already viewing this in your web browser, then google
+ the online version of these pages. If you don't find what you are
+ looking for, or want to report a bug or make a feature request, then
+ get in contact over at <a href="http://www.jalview.org/community">http://www.jalview.org/community</a></p>
+
+ <p><strong>Citing Jalview</strong><br/>If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics: </p>
<p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), <br>
"Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"<br>
- <em>Bioinformatics</em> <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
+ <em>Bioinformatics</em> <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033</p>
</body>
</html>
</head>
<body>
<p>
- <strong>What's new ?</strong>
- </p>
- <p>Jalview 2.8 includes a brand new logo, which you'll see in file
- browsers, splash screens, and also on the new look Jalview site.</p>
- <p>
- In addition to our new look, Jalview 2.8 includes a number of new
- features.. some of which have been in development since July 2010. The
- highlights are below, and - as usual, for a comprehensive list, take a
- look at the <a href="releases.html#Jalview2.8">Jalview 2.8 Release
- Notes</a>.
- </p>
- <p>
- <strong>Highlights in Jalview Version 2.8</strong>
+ <strong>What's new ?</strong><br/>
+ Jalview 2.8 includes a number of enhancements and new features that
+ have been in development since July 2010. It is also the first Jalview
+ release to incorporate RNA visualization features developed by Lauren
+ Lui and Jan Engelhart during their Google Summer of Code projects
+ (http://code.google.com/soc/). As usual, you can find some highlights
+ below, but to see the comprehensive list, take a look at the look at
+ the <a href="releases.html#Jalview2.8">Jalview 2.8 Release Notes</a>.
</p>
+ <strong>Highlights in Jalview Version 2.8</strong>
<ul>
- <li><strong>Improved <a href="webServices/JABAWS.html">JABAWS</a> client and new JABAWS 2.0 Services</strong>
+ <li><strong>Improved <a href="webServices/JABAWS.html">JABAWS</a>
+ client and new JABAWS 2.0 Services
+ </strong>
<ul>
- <li><a href="webServices/AACon.html">AACon alignment conservation</a></li>
- <li><a href="webServices/proteinDisorder.html">Protein disorder</a> - DisEMBL, RONN, GlobPlot and IUPred</li>
+ <li><a href="webServices/AACon.html">AACon alignment
+ conservation</a></li>
+ <li><a href="webServices/proteinDisorder.html">Protein
+ disorder</a> - DisEMBL, RONN, GlobPlot and IUPred</li>
<li>Clustal Omega for creating huge protein alignments</li>
- </ul>
- </li>
- <li><strong>Support for <a href="na/index.html">RNA</a></strong>
+ </ul></li>
+ <li><strong><a href="na/index.html">RNA</a></strong>
<ul>
- <li>Import sequence and alignment associated WUSS or VIENNA dot-bracket
- notation from files and the <strong>RFAM</strong> database</li>
+ <li>Import sequence and alignment associated WUSS or VIENNA
+ dot-bracket notation from files and the <strong>RFAM</strong>
+ database
+ </li>
<li>Interactive editing of RNA secondary structure annotation</li>
<li>Colour scheme for purine/pyrimidine and to highlight RNA
helices</li>
- <li>RNA canonical <a href="calculations/structureconsensus.html">base pair consensus score</a> and sequence logo</li>
+ <li>RNA canonical <a
+ href="calculations/structureconsensus.html">base pair consensus
+ score</a> and sequence logo
+ </li>
<li>Embedded <a href="features/varna.html">VARNA</a> RNA
secondary structure viewer in the Desktop
</li>
</ul></li>
- <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE alignment quality scores</a> (thanks to Paolo Tomassi of the Notredame Group)</li>
- <li><a href="colourSchemes/annotationColouring.html">Per sequence alignment annotation shading</a></li>
- <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more export options, and switch between
- different PCA modes and residue score models</li>
- <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database fetcher</a> GUI</li>
- <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to new JDAS Distributed Annotation client library)</li>
- <li>Export sequence database annotation as <a href="io/exportseqreport.html">HTML report</a></li>
- <li>Normalised <a href="calculations/consensus.html">Sequence Logo Display</a></li>
+ <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE
+ alignment quality scores</a> (thanks to Paolo Tomasso of the Notredame
+ Group)
+ </li>
+ <li><a href="colourSchemes/annotationColouring.html">Per
+ sequence alignment annotation shading</a></li>
+ <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more
+ export options, and switch between different PCA modes and residue
+ score models
+ </li>
+ <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database
+ fetcher</a> GUI
+ </li>
+ <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to the new
+ JDAS Distributed Annotation client library (see
+ http://code.google.com/p/jdas))</li>
+ <li>Export sequence database annotation as an <a
+ href="io/exportseqreport.html">HTML report</a></li>
+ <li>Normalised <a href="calculations/consensus.html">Sequence
+ Logo Display</a></li>
</ul>
<p>
- <strong>Issues Resolved (a select list - see the <a
- href="releases.html#Jalview2.8">release history</a> for full details)
- </strong>
+ <strong>Issues resolved in the Jalview Desktop</strong>
</p>
- <p>
- <strong>Issues in the Jalview Desktop</strong>
<ul>
<li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service<!--<a href='http://issues.jalview.org/browse/JAL-636'>JAL-636</a>-->
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-368'>JAL-368</a>] - -->
- <!--[<a href='http://issues.jalview.org/browse/JAL-153'>JAL-153</a>] - -->Stop
- windows being moved outside desktop on OSX
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-758'>JAL-758</a>] - -->Filetype
- associations not installed for webstart launch
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-849'>JAL-849</a>] - -->Jalview
- does not always retrieve progress of a JABAWS job execution in full
- once it is complete
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-983'>JAL-983</a>] - -->View
- all structures superposed fails with exception
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-994'>JAL-994</a>] - -->Jnet
- job queues forever if a very short sequence is submitted for
- prediction
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1022'>JAL-1022</a>] - -->Structure
- view highlighting doesn't work on windows 7
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1026'>JAL-1026</a>] - -->Jalview
- desktop fails to launch with exception when using proxy
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1031'>JAL-1031</a>] - -->Tree
- calculation reports 'you must have 2 or more sequences
- selected' when selection is empty
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1062'>JAL-1062</a>] - -->DAS
- Sequence retrieval with range qualification results in sequence xref
- which includes range qualification
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1111'>JAL-1111</a>] - -->Cannot
- close news reader when JABAWS server warning dialog is shown
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1131'>JAL-1131</a>] - -->Edited
- sequence not submitted to web service
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1134'>JAL-1134</a>] - -->Jalview
- 2.7 Webstart and InstallAnywhere installer doesn't unpack and run
+ REST service</li>
+ <li>Stop windows being moved outside desktop on OSX</li>
+ <li>Jnet job queues forever if a very short sequence is submitted
+ for prediction</li>
+ <li>Structure view highlighting doesn't work on windows 7</li>
+ <li>Jalview desktop fails to launch with exception when using
+ proxy</li>
+ <li>DAS Sequence retrieval with range qualification results in
+ sequence xref which includes range qualification</li>
+ <li>Cannot close news reader when JABAWS server warning dialog is
+ shown</li>
+ <li>Edited sequence not submitted to web service</li>
+ <li>Jalview 2.7 InstallAnywhere installer doesn't unpack and run
on OSX Mountain Lion
<ul>
- <li>The workaround for webstart is to go into the Security
- panel (gatekeeper symbol) under System settings, and select the
- 'allow any code to run' setting.</li>
+ <li>If you use webstart then you may need to go into the
+ Security panel (<em>a.k.a</em> the gatekeeper) in your System
+ Settings, and select the 'allow any code to run' option.
+ </li>
</ul>
</li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1144'>JAL-1144</a>] - -->Annotation
- panel not given a scroll bar when sequences with alignment annotation
- are pasted into the alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1148'>JAL-1148</a>] - -->Sequence
- associated annotation rows not associated when loaded from jalview
- project
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1145'>JAL-1145</a>] - -->Exceptions
- when copy/paste sequences with grouped annotation rows to new window
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1149'>JAL-1149</a>] - -->Browser
- launch fails with NPE on java 1.7
- </li>
-
</ul>
-
- <strong>Issues specific to the JalviewLite Applet</strong>
+ <p>
+ <strong>Issues specific to the JalviewLite Applet</strong>
+ </p>
<ul>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-962'>JAL-962</a>] - -->Sequence
- features are momentarily displayed before they are hidden using
- hidefeaturegroups applet parameter
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-965'>JAL-965</a>] - -->loading
- features via javascript API automatically enables feature display
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1170'>JAL-1170</a>] - -->scrollToColumnIn
- javascript API method doesn't work
- </li>
+ <li>Sequence features are momentarily displayed before they are
+ hidden using hidefeaturegroups applet parameter</li>
+ <li>loading features via javascript API automatically enables
+ feature display</li>
+ <li>scrollToColumnIn javascript API method doesn't work</li>
</ul>
- <strong>Issues affecting both applet and application</strong>
+ <p>
+ <strong>Issues affecting both applet and application</strong>
+ </p>
<ul>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1007'>JAL-1007</a>] - -->Redundancy
- removal fails for rna alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1033'>JAL-1033</a>] - -->PCA
- window shows grey box when first opened on OSX
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1086'>JAL-1086</a>] - -->Letters
- coloured pink in sequence logo when alignment coloured with clustalx
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1099'>JAL-1099</a>] - -->Choosing
- fonts without letter symbols defined causes exceptions and redraw
- errors
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1123'>JAL-1123</a>] - -->Initial
- PCA plot view is not same as manually reconfigured view
- </li>
+ <li>Redundancy removal fails for rna alignment</li>
+ <li>PCA window shows grey box when first opened on OSX</li>
+ <li>Letters coloured pink in sequence logo when alignment
+ coloured with clustalx</li>
</ul>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff