From 36435d7f3333d94bd4afaeb68f033ba9dfcc5250 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 8 Aug 2016 14:20:56 +0100 Subject: [PATCH] JAL-2119 updates to invalid / obsolete help links --- help/html/features/dasfeatures.html | 7 +++++-- help/html/features/varna.html | 2 +- help/html/io/index.html | 4 ---- help/html/na/index.html | 2 +- help/html/webServices/index.html | 2 +- utils/HelpLinksChecker.java | 2 +- 6 files changed, 9 insertions(+), 10 deletions(-) diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html index c0c888a..90958ae 100644 --- a/help/html/features/dasfeatures.html +++ b/help/html/features/dasfeatures.html @@ -29,8 +29,7 @@

Jalview includes a client for retrieving sequences and their - features via the Distributed - Annotation System. + features via the Distributed Annotation System.

  1. Open the Feature Settings panel by selecting "View @@ -69,6 +68,10 @@

    DAS support was introduced in Jalview Version 2.1.

    +
    +

    + The DAS registry at http://www.dasregistry.org was decommissioned early in 2015. An unmaintained mirror is currently hosted at http://www.ebi.ac.uk/das-srv/registry/. +

      diff --git a/help/html/features/varna.html b/help/html/features/varna.html index 029edce..ce446f3 100644 --- a/help/html/features/varna.html +++ b/help/html/features/varna.html @@ -27,7 +27,7 @@ The VARNA RNA Viewer

    - VARNA was integrated + VARNA was integrated into Jalview 2.8 to allow interactive viewing of RNA secondary structure annotation. It is opened by selecting the "Structure→View Structure:" option in the sequence diff --git a/help/html/io/index.html b/help/html/io/index.html index c0a89cf2..d2196c1 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -33,10 +33,6 @@ NBRF/PIR (including MODELLER variant), Pfam/Stockholm

    - The EBI has examples - of these file formats. -

    -

    Additionally, whole sets of coloured and annotated alignments and trees can be read from a Jalview (jar) format file using Desktop→Load diff --git a/help/html/na/index.html b/help/html/na/index.html index ae4c1c6..de2741b 100644 --- a/help/html/na/index.html +++ b/help/html/na/index.html @@ -65,7 +65,7 @@ td { annotation.

  2. Clustal files - certain RNA alignment programs, such as LocaRNA output consensus RNA secondary structure lines in the line normally reserved for the Clustal consensus line in a clustal file.
    3. diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index b03bb9d..1463554 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -90,7 +90,7 @@ services were maintained by the Barton group at the University of Dundee, and ran programs on the Life Sciences High-performance Computing Cluster. With the advent of JABAWS, however, it is possible for anyone to host Jalview web services.

    diff --git a/utils/HelpLinksChecker.java b/utils/HelpLinksChecker.java index 1f666a4..1ad5322 100644 --- a/utils/HelpLinksChecker.java +++ b/utils/HelpLinksChecker.java @@ -90,7 +90,7 @@ public class HelpLinksChecker return; } - internetAvailable &= connectToUrl("http://www.example.com"); + internetAvailable &= connectToUrl("http://www.example.org"); Map tocTargets = checkHelpMappings(helpFolder); -- 1.7.10.2