-Please see doc/building.md for up to date build and running instructions for the Java desktop application.
+Jalview README
+==============
-JalviewJS.
-See README_GRADLE_JALVIEWJS-2019-10-22.md for build instructions for JalviewJS.
-This is a little sparse but enough to do the transpilation.
+Welcome !
+
+Jalview is free (GPLv3 licensed) software for creation, interactive
+visualisation and analysis of alignments of biological sequences. It
+was developed by Michele Clamp in 1996, and now maintained by the
+Jalview Development team in the Barton group at the University of
+Dundee.
+
+If you'd like to help out please check out the website
+(www.jalview.org) and get in touch. See CITATION for the canonical
+reference if you need to cite Jalview.
+
+To build the Jalview Desktop application and JalviewJS, the JavaScript
+transpiled version (with the help of java2script, courtesy of Bob
+Hanson), you will need a Java 11 JDK and a recent version of
+Gradle. For development we recommend Eclipse - you should be able to
+import Jalview as a Gradle project with the Buildship plugin.
+
+Most likely you'll want to take a look at doc/building.md to find out
+exactly what is needed. If you already have Java 11 and Gradle, then
+the tldr:
+
+gradle test # run functional test suite
+
+gradle shadowJar # build a single executable Jar under build/lib/
+
+gradle jalviewjs # builds JalviewJS under build/jalviewjs
+
+If you want to build JalviewJS then you will also need to download
+Eclipse for your platform, since transpilation requires an Eclipse
+plugin.
Chimera.
</li>
<li>
+ <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
+ to 14.31.53
+ </li>
+ <li>
<!-- JAL-3829 -->Discover 3D structure data for sequences
with Uniprot references via 3D-Beacons
</li>
</li>
<li>
<!-- JAL-3018 -->Updated Ensembl REST Client compatibility
- to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now
- rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster)
+ to 15.2 and revised model organism names (rat, xenopus,
+ dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
+ drosophila_melanogaster)
</li>
<li>
<!-- JAL-3881 -->Sequence IDs split on '_' as well as other
<!-- JAL-3837 -->GPL license info on splash screen and About
text
</li>
- </ul>
- <em>Jalview Native App</em>
+ </ul> <em>Jalview Native App</em>
<ul>
<li>
<!-- JAL- -->New Jalview Develop app - making it even easier
than anonymous 'Java' icons
</li>
<li>
- <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
+ <!-- JAL-3608 -->Options to allow user to choose the (Swing)
+ Look and Feel (LaF) used by Jalview
</li>
<li>
- <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved operation on Linux Ubuntu with
- HiDPI display in Java 11 (still known issues with HiDPI screens in java
- 8 and 11. see <a
- href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
+ <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
+ operation on Linux Ubuntu with HiDPI display in Java 11
+ (still known issues with HiDPI screens in java 8 and 11. see
+ <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
</li>
<li>
- <!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
- macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option
- to add this to PATH, or link to it in your PATH.
+ <!-- JAL-3830 -->New command line launcher scripts (.sh,
+ .ps1, .bat) usable on macOS, Linux/Unix, Windows and
+ documentation in Help. Installer wizard has option to add
+ this to PATH, or link to it in your PATH.<br /> <em>This
+ is the recommended workaround for known issue about
+ working directory preservation when running native
+ application from command line. <!-- JAL-3523 -->
+ </em>
</li>
<li>
<!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
</ul> <em>JalviewJS</em>
<ul>
<li>
- <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
- SIFTS
+ <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
+ with SIFTS
</li>
<li>
- <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
+ <!-- JAL-3208 -->setprop commandline argument reinstated for
+ JalviewJS only
</li>
<li>
<!-- JAL-3163 -->Missing message bundle keys are only
<!-- JAL-3168 -->Feature type is included in the title of
the Feature Settings' Colour Chooser dialog
</li>
- <li></li>
+ <li>
+ <!-- JAL-3279 -->Build details reported in About window
+ </li>
+ <li>
+ <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
+ GUI additions and improvements in sync with Java
+ application.
+ </li>
</ul> <em>Development</em>
<ul>
<li>
<!-- JAL-3907 -->Improved compatibility of Jalview build
with Java 17 (next LTS target)
</li>
-
</ul>
-
</td>
<td>
<ul>
<li>
<!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
the first SEQUENCE_GROUP defined
-
</li>
<li>
<!-- JAL-3949 -->Standard out logging broken: messages only
routing to stderr and appear as a raw template
</li>
- </ul> <em>JalviewJS</em>
- <ul>
- <li>
- <!-- JAL-3202 -->Consensus profile may include zero (rounded
- down) percentage values causing a divide by zero
- </li>
- <li>
- <!-- -->
- </li>
<li>
- <!-- -->
+ <!-- JAL-3739 -->Entering web service parameter values in
+ numerical field doesn't update the value of the parameter
+ until return is pressed.
</li>
<li>
- <!-- -->
+ <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
+ concerning duplicate CDS sequences generated when protein
+ products for certain ENA records are repeatedly shown via
+ Calculate->Show Cross Refs
</li>
+ </ul> <em>JalviewJS</em>
+ <ul>
<li>
- <!-- -->
+ <!-- JAL-3202 -->Consensus profile may include zero (rounded
+ down) percentage values causing a divide by zero
</li>
<li>
<!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
</ul>
</li>
- </ul>
- <em>Known Issues</em>
+ </ul> <em>Known Issues</em>
<ul>
<li>
<!-- JAL-3764 -->Display of RESNUM sequence features are not
suppressed when structures associated with a sequence are
- viewed with an external viewer (Regression from 2.11.1 series)
+ viewed with an external viewer (Regression from 2.11.1
+ series)
</li>
</ul>
</td>
git://source.jalview.org / jalview.git / commitdiff