From 5b05749cab04092671551fbbcdc80406b53da7d0 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 22 Sep 2010 21:48:14 +0000 Subject: [PATCH] 2.6 highlights --- help/html/index.html | 4 ++-- help/html/jalviewjnlp.html | 17 +++++++++-------- help/html/whatsNew.html | 41 +++++++++++++++++++++++++---------------- 3 files changed, 36 insertions(+), 26 deletions(-) diff --git a/help/html/index.html b/help/html/index.html index 293790e..9b1191d 100755 --- a/help/html/index.html +++ b/help/html/index.html @@ -16,7 +16,7 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . --> -Home Page +Jalview Documentation @@ -26,7 +26,7 @@ Jalview (2009) is a fast Java multiple alignment editor and analysis tool. It features many of the functions of AMAS, for the analysis of sub-families and the prediction of functional sites, but is -fully interactive. (View the Jalview homepage). +fully interactive. (View the Jalview homepage at www.jalview.org).

If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics:

Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009),
diff --git a/help/html/jalviewjnlp.html b/help/html/jalviewjnlp.html index 0c68bfb..2732a92 100755 --- a/help/html/jalviewjnlp.html +++ b/help/html/jalviewjnlp.html @@ -38,6 +38,7 @@ <association extensions="pfam" mime-type="application-x/ext-file"/> <association extensions="aln" mime-type="application-x/ext-file"/> <association extensions="pir" mime-type="application-x/ext-file"/> + <association extensions="stk" mime-type="application-x/ext-file"/> <offline-allowed/> </information> <security> @@ -45,10 +46,10 @@ </security> <resources> <!-- the additional memory parameters are here --> - <j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/> - <jar href="jalview.jar"/> + <j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/> + <jar href="jalview.jar"/> <jar href="JGoogleAnalytics-0.2.1-SNAPSHOT.jar"/> - <jar href="Jmol-11.0.2.jar"/> + <jar href="Jmol-12.1.13.jar"/> <jar href="activation.jar"/> <jar href="axis.jar"/> <jar href="castor-1.1-cycle-xml.jar"/> @@ -58,20 +59,20 @@ <jar href="jhall.jar"/> <jar href="log4j-1.2.8.jar"/> <jar href="mail.jar"/> + &jt;jar href="min-jaba-client.jar"/> <jar href="regex.jar"/> <jar href="saaj.jar"/> <jar href="vamsas-client.jar"/> <jar href="wsdl4j.jar"/> <jar href="xercesImpl.jar"/> <jar href="xml-apis.jar"/> - <property name="jalview.version" value="2.5"/> + <property name="jalview.version" value="2.6"/> </resources> <application-desc main-class="jalview.bin.Jalview"/> </jnlp> -

-If you have problems, send an email to jalview-discuss -
+
If +you have problems, send an email to jalview-discuss
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 359238a..d908cda 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -21,27 +21,36 @@

What's new ?

-

Jalview 2.6 introduces new web services, and includes an updated version of the Jmol molecular graphics visualization system. See the release -history for the full details.

-

Highlights in Jalview Version 2.5

-
    -
-Jalview Desktop: -
    -
-JalviewLite: -
    -
-

Issues Resolved (a select list)

+

Jalview 2.6 introduces new web services, and includes an updated +version of the Jmol molecular graphics visualization system. See the release history for the full +details.

+

Highlights in Jalview Version 2.6

    +
  • JABA Web Services for + multiple alignment using:
      +
    • ClustalW
      • +
    • MAFFT
      • +
    • Muscle
      • +
    • ProbCons
      • +
    • T-COFFEE
    - Desktop Issues -
      -
    +
    • +
  • User modifiable alignment service parameters
    • +
  • Visualization of superposed structures associated with protein + or nucleotide sequence alignments.
    • +
  • Export coordinates and projection as CSV from PCA viewer
-

 

+

Issues Resolved (a select list - see release history for details)

+
    +
  • clustalx colourscheme colours Ds preferentially when both D+E + are present in over 50% of the column
    • +
  • Prevent sequence fetcher from replacing ',' for ';' when querying DAS sequence sources
    • +
  • InstallAnywhere builds fail to launch on OS X java 10.5 update + 4 (due to apple Java 1.6 update)
    • +

See the Release History page for details of all new features and resolved issues.

-- 1.7.10.2