From 79da59855c8eb16c5afef75d9d5701b7a39fb4c4 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 23 Sep 2010 08:31:44 +0000 Subject: [PATCH] typos and indicate 'legacy' service documentation --- help/helpTOC.xml | 7 +++-- help/html/jalviewjnlp.html | 4 +-- help/html/webServices/JABAWS.html | 23 ++------------- help/html/webServices/clustalw.html | 1 + help/html/webServices/jnet.html | 14 +++++---- help/html/webServices/mafft.html | 1 + help/html/webServices/msaclient.html | 54 ++++++++++++++++++---------------- help/html/webServices/muscle.html | 1 + 8 files changed, 50 insertions(+), 55 deletions(-) diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 95aa62a..d416dfa 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -20,9 +20,10 @@ - - - + + + + diff --git a/help/html/jalviewjnlp.html b/help/html/jalviewjnlp.html index 590401a..f821c23 100755 --- a/help/html/jalviewjnlp.html +++ b/help/html/jalviewjnlp.html @@ -22,7 +22,7 @@

Jalview local Jnlp File

-<jnlp spec="1.0+" codebase="http://www.jalview.org/webstart/" href="http://www.jalview.org/webstart/jalview.jnlp">
+<jnlp spec="1.0+" codebase="http://www.jalview.org/webstart/">
   <information>
     <title>Jalview</title>
     <vendor>The Barton Group</vendor>
@@ -59,7 +59,7 @@
 		<jar href="jhall.jar"/>
 		<jar href="log4j-1.2.8.jar"/>
 		<jar href="mail.jar"/>
-		&jt;jar href="min-jaba-client.jar"/>
+		<jar href="min-jaba-client.jar"/>
 		<jar href="regex.jar"/>
 		<jar href="saaj.jar"/>
 		<jar href="vamsas-client.jar"/>
diff --git a/help/html/webServices/JABAWS.html b/help/html/webServices/JABAWS.html
index 90de537..e54d5dd 100644
--- a/help/html/webServices/JABAWS.html
+++ b/help/html/webServices/JABAWS.html
@@ -1,4 +1,4 @@
-
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see .
--->
-
 
 The JABAWS system
 
@@ -46,7 +29,7 @@ service model, developed at the University of Dundee by Peter Troshin
 and Geoff Barton. This is an open source system that provides a
 framework for wrapping command line bioinformatics analysis programs
 that enables them to be executed locally or on a cluster using data and
-analysis parameters provided by a program linked with JABAWS directly or
+analysis parameters provided by a program linked with the JABA engine directly or
 accessing it remotely via its web services interface.
 The list of JABAWS servers known to the Jalview desktop is shown
 in the Web Services Preferences
@@ -65,7 +48,7 @@ for more information.

 Configuring your own JABAWS services for use by
 Jalview

 Once you have downloaded and installed JABAWS, and verified it is
-working, all that is needed is to add your new JABAWS server's URL to
+working, all that is needed is to add the URL for your JABAWS server(s) to
 the list in the Web Services
 Preferences Panel. After adding your service and saving your preferences
 or hitting the 'refresh web services' button, you should be able to
diff --git a/help/html/webServices/clustalw.html b/help/html/webServices/clustalw.html
index 89032c0..120a186 100755
--- a/help/html/webServices/clustalw.html
+++ b/help/html/webServices/clustalw.html
@@ -41,5 +41,6 @@ on the selected region, if any, or the whole sequence set:
     Submits the sequences with existing gaps to clustalW, which will preserve 
     existing gaps and re-align those regions which are not optimal. 
 
+As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services.
 
 
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 237ca63..3537554 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -27,11 +27,10 @@ composition and similarity to sequences with known secondary structure.
 The JNet method uses several different neural networks and decides on
 the most likely prediction via a jury network. 

 
-	
-	Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3 secondary structure prediction server
-	Nucleic Acids Research 36 W197-W201
-	
-	Cuff J. A and Barton G.J (1999) Application of enhanced
+	
Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3
+	secondary structure prediction server Nucleic Acids Research 36
+	W197-W201
+	Cuff J. A and Barton G.J (1999) Application of enhanced
 	multiple sequence alignment profiles to improve protein secondary
 	structure prediction Proteins 40 502-511
 
@@ -108,5 +107,10 @@ The annotation bars below the alignment are as follows:
 	invoked to rationalise significantly different primary predictions.
 
 
+As of Jalview 2.6, the Jnet service accessed accessed via the
+'Secondary structure prediction' submenu should be considered a legacy
+Jalview SOAP service, and will be replaced in the near future by a
+JABAWS Jnet service.
+
 
 
diff --git a/help/html/webServices/mafft.html b/help/html/webServices/mafft.html
index 94a8ce6..d3dd142 100644
--- a/help/html/webServices/mafft.html
+++ b/help/html/webServices/mafft.html
@@ -31,5 +31,6 @@ homologous regions in a fast-fourier transform representation of each
 sequence. The Jalview web service runs MAFFT using the
 '--auto' option which picks optimal parameters
 for the set of sequences to be aligned.
+As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services.
 
 
diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html
index 889e1f5..a203849 100644
--- a/help/html/webServices/msaclient.html
+++ b/help/html/webServices/msaclient.html
@@ -21,34 +21,38 @@
 
 
 Multiple Sequence Alignment Web Services
-
-Multiple sequence alignment services are accessed from the Web
-Service→Alignment menu. When an entry from this menu is
-selected, either the currently selected residues, or the whole
-sequence set (if there is no selection or only one sequence is
-selected) will be submitted for multiple sequence alignment.
-
+Multiple sequence alignment services can be accessed from either
+the Alignment or the JABAWS Alignment
+submenu of the Alignment Window's Web Service menu.
+When an entry from one of these menus is selected, either the currently
+selected residues, or the whole sequence set (if there is no selection
+or only one sequence is selected) will be submitted for multiple
+sequence alignment.
 There are two kinds of multiple sequence alignment operations
-available:

-alignment - where a new alignment is constructed from the input
-
-realignment -
-where any aligned sequences will be used by the service
-to construct a profile based alignment of the remaining unaligned sequences.
-
+available:
+
+	alignment - where a new alignment is constructed from
+	the input
+	realignment - where any aligned sequences will be
+	used by the service to construct a profile based alignment of the
+	remaining unaligned sequences.
 
-
+The JABAWS Alignment services also offer a
+range of predefined alignment settings and the opportunity for you to
+define your own set of parameters for running the alingment program.
+Multiple Alignments of Sequences with hidden
+columns

+Multiple alignment services are 'column separable' analysis operations.
+If the input contains hidden
+columns then each visible segment of the input sequence set will be
+submitted for alignment separately, and the results concatenated (with
+the hidden regions preserved) once all alignment functions have
+completed. Each sub-job's state is reported in its own tab:
 

-Multiple Alignments of Sequences with hidden columns

-Multiple alignment services are 'column separable' analysis
-operations. If the input contains hidden columns then each
-visible segment of the input sequence set will be submitted for
-alignment separately, and the results concatenated (with the hidden
-regions preserved) once all alignment functions have completed. Each
-sub-job's state is reported in its own tab:
-
Multiple Multiple Sequence Alignment sub jobs running at
-once
+Multiple Multiple Sequence Alignment
+sub jobs running at once
+
+
 
 
 
diff --git a/help/html/webServices/muscle.html b/help/html/webServices/muscle.html
index 606640e..04fe696 100755
--- a/help/html/webServices/muscle.html
+++ b/help/html/webServices/muscle.html
@@ -27,5 +27,6 @@ accuracy and high throughput

  This alignment method is applied to the selected region, if any, or the whole 
   sequence set when the Web Service→Alignment→Muscle 
   Protein Sequence Alignment menu item is selected. 
+As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services.
 
 
-- 
1.7.10.2