From: Sasha Sherstnev Date: Mon, 28 Apr 2014 21:53:34 +0000 (+0100) Subject: Replace links to Download and last edit date X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=faac303bf9ad8c17b71a55d23b7a2c0a9e6e2efa;hp=68b0d4a40dd4f0730fd28ee4bcf1104aa49ddbe0;p=jabaws.git Replace links to Download and last edit date --- diff --git a/website/contacts.html b/website/contacts.html index 8dcf5f8..7cf944a 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -29,7 +29,7 @@ Home Getting Started Manual - Download + Download Usage Statistics Services Status Contact Us @@ -55,7 +55,7 @@

- + diff --git a/website/index.html b/website/index.html index 5acf856..86d5f94 100644 --- a/website/index.html +++ b/website/index.html @@ -28,7 +28,7 @@ Home Getting Started Manual - Download + Download Usage Statistics Services Status Contact Us @@ -79,7 +79,7 @@ computing resources.

For Users

- The Server: JABAWS Virtual Appliance: (440M) + The Server: JABAWS Virtual Appliance: (440M) or JABAWS on Amazon Webservices Cloud
The Main Client: Jalview (18M)

To use JABAWS web services on most operating systems, just download and install @@ -94,7 +94,7 @@ computing resources.

For System Administrators

- The Server: JABAWS Web + The Server: JABAWS Web Application aRchive (55M)

JABAWS requires a Servlet 2.4 compatible servlet container like Apache Tomcat @@ -107,11 +107,11 @@ computing resources.

For Bioinformaticians/Developers

-The Server: JABAWS Web Application aRchive (55M) +The Server: JABAWS Web Application aRchive (55M)
The Client: - Command Line Client binary | source + Command Line Client binary | source

You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. @@ -126,7 +126,7 @@ Check out the quick start guide for furt

Public JABAWS Server

-

You can access our public JABAWS web services with our command line client, +

You can access our public JABAWS web services with our command line client, Jalview, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2.1. The latest versions of Jalview are configured to use public JABAWS server by default.

    @@ -137,7 +137,7 @@ title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=

These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can - download and run the JABAWS Server on your own hardware.

+ download and run the JABAWS Server on your own hardware.

@@ -161,7 +161,7 @@ Multiple Sequence Alignment - JABAWS:MSA" Bioinformatics doi: 10.1093/bioinformatics/btr304.

- +
diff --git a/website/jabaws_funding.html b/website/jabaws_funding.html index f01d75b..dd850b9 100644 --- a/website/jabaws_funding.html +++ b/website/jabaws_funding.html @@ -28,7 +28,7 @@ Home Getting Started Manual - Download + Download Usage Statistics Services Status Contact Us @@ -63,7 +63,7 @@ Further support comes from Wellcome Trust Strategic Grant: 100476.



- + diff --git a/website/man_about.html b/website/man_about.html index 084288d..4965ffb 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -132,7 +132,7 @@
  • RNAalifold from ViennaRNA (2.0)
    • -All these codes including Jronn and AAcon are available at the Download +All these codes including Jronn and AAcon are available at the Download section (registration is required). @@ -214,13 +214,13 @@ section (registration is required). JABAWS web services are WS-I basic profile compliant, which means they can be accessed using any programming language or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home page, and you can use this to automatically generate service bindings for your program. If you use Java - you may wish to use our client package to access JABAWS. + you may wish to use our client package to access JABAWS. This package is based on the autogenerated source code produced by wsimport, which is the Java tool for creating web service bindings. In addition, this offers some additional methods that simplify working with JABAWS. For more information please refer to the data model javadoc.

    - + diff --git a/website/man_awscloud.html b/website/man_awscloud.html index c2e7d1d..5f8bacd 100644 --- a/website/man_awscloud.html +++ b/website/man_awscloud.html @@ -68,7 +68,7 @@









    - + diff --git a/website/man_awscloud_bs.html b/website/man_awscloud_bs.html index b58b419..8f0143b 100644 --- a/website/man_awscloud_bs.html +++ b/website/man_awscloud_bs.html @@ -78,7 +78,7 @@

     

    - + diff --git a/website/man_awscloud_ec2.html b/website/man_awscloud_ec2.html index a53cb98..384278e 100644 --- a/website/man_awscloud_ec2.html +++ b/website/man_awscloud_ec2.html @@ -96,7 +96,7 @@

     

    - + diff --git a/website/man_client.html b/website/man_client.html index cf6b766..585cb17 100644 --- a/website/man_client.html +++ b/website/man_client.html @@ -53,7 +53,7 @@

    JABAWS Command Line Client Usage

    -The command line client comes as a part of client package which you are welcome to download. +The command line client comes as a part of client package which you are welcome to download. The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via JABAWS API. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client. @@ -94,7 +94,7 @@ Please note that -r and -f options cannot be used together. Alignment is done wi java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters

    The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key. For example you used -h=http://myhost.compbio.ac.uk:8080/jabaws server, now you want to use another server to -h=http://mylabserver.myuni.edu. This comes handy if your favorite server is off and you need to do the job yesterday.

    - + diff --git a/website/man_configuration.html b/website/man_configuration.html index 8e0bb14..6070e76 100644 --- a/website/man_configuration.html +++ b/website/man_configuration.html @@ -455,7 +455,7 @@ class="hightlight">log4j.properties and uncomment section of

    Google Analytics can be disabled or adjusted by removing/editing conf/GA.properties Google Analytics (GA) settings file. We would appreciate it greatly if you could leave it on!

    All calls to GA are very lightweight, completed asynchronously, create very little overhead and do not influence the server response time or performance.

    - + diff --git a/website/man_dev.html b/website/man_dev.html index a602a7b..de5c544 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -111,8 +111,13 @@

    Connecting to JABAWS

    For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client -source code is available from the download page. Please note that for now all +<<<<<<< HEAD +source code is available from the download page. Please note that for now all +the examples are in Java other languages will follow given a sufficient demand.

    +======= +source code is available from the download page. Please note that for now all the examples are in Java, other languages will follow if there is sufficient demand.

    +>>>>>>> 42a3637e24a7a65b5a1e6048e581df998b4a4f95

    Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee.

    @@ -267,7 +272,7 @@ one of the Clustal web service presets. There is also a JABAWS binary client. +JABAWS binary client. Please make sure that the client is in the Java class path before running this example.

     import java.io.ByteArrayInputStream;
@@ -409,7 +414,7 @@ generate portable artifacts to work with JABAWS from Java. However if programmin
 it provides a handful of useful methods in addition to plain data types. 
    
 
    wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl
    
 
-
+
 
 
 
diff --git a/website/man_server_dev.html b/website/man_server_dev.html
index 791709e..17e2cbb 100644
--- a/website/man_server_dev.html
+++ b/website/man_server_dev.html
@@ -250,7 +250,7 @@ those that depends on the cluster.
    
 
 
     
    
 
-
+
 
  
 
diff --git a/website/man_servervm.html b/website/man_servervm.html
index 0563d99..4b35ca4 100644
--- a/website/man_servervm.html
+++ b/website/man_servervm.html
@@ -154,7 +154,7 @@ in such case. If you want to be able to connect to your VM and let VM connect to
 a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP 
 server to do that)
    
 
-
+
 
 
 
diff --git a/website/man_serverwar.html b/website/man_serverwar.html
index c4bcf80..c0168cb 100644
--- a/website/man_serverwar.html
+++ b/website/man_serverwar.html
@@ -233,7 +233,7 @@ modify the paths in If Tomcat still refuses to unpack the war file, unpack it manually into web application folder (the war file is just a zip archive). Restart the Tomcat.
 
 
-
+
 
 
 
diff --git a/website/man_stats.html b/website/man_stats.html
index 1f322d8..c12b591 100644
--- a/website/man_stats.html
+++ b/website/man_stats.html
@@ -147,7 +147,7 @@ Each table contains the following information for each web service:
 

    
 
    
 
-
+
 
 
 
diff --git a/website/manual_qs_amazon.html b/website/manual_qs_amazon.html
index 2b40520..ea250a7 100644
--- a/website/manual_qs_amazon.html
+++ b/website/manual_qs_amazon.html
@@ -28,7 +28,7 @@
 	Home 
 	Getting Started 
 	Manual 
-	Download 
+	Download 
 	Usage Statistics
 	Services Status
 	Contact Us
@@ -72,7 +72,7 @@
   
  • Configure JABAWS either on the Amazon EC2 cloud or on Amazon Elastic Beanstalk
    • 
 
  
-
+
 
  
 
diff --git a/website/manual_qs_client.html b/website/manual_qs_client.html
index b67437c..8f496ed 100644
--- a/website/manual_qs_client.html
+++ b/website/manual_qs_client.html
@@ -28,7 +28,7 @@
 	Home 
 	Getting Started 
 	Manual 
-	Download 
+	Download 
 	Usage Statistics
 	Services Status
 	Contact Us
@@ -66,7 +66,7 @@
 
 
 
    The JABAWS command line client
    
-
    • Download the Client Jar file
      • 
+
 
      
   This is a single java archive which contains the JABAWS command line client. It requires Java 
@@ -83,7 +83,7 @@
   
 
      
  
-
+
 
  
 
diff --git a/website/manual_qs_va.html b/website/manual_qs_va.html
index 3ca55d6..83021b3 100644
--- a/website/manual_qs_va.html
+++ b/website/manual_qs_va.html
@@ -28,7 +28,7 @@
 	Home 
 	Getting Started 
 	Manual 
-	Download 
+	Download 
 	Usage Statistics
 	Services Status
 	Contact Us
@@ -65,7 +65,7 @@
 
 
 
      Running JABAWS on your local machine
      
-
      • Download JABAWS Virtual Appliance
        • 
+
 
        
 The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a 
@@ -88,7 +88,7 @@ to the JABAWS VA is given in the manual, but for the impatient, a brief inst
 
 
  
-
        
+
 
  
 
diff --git a/website/manual_qs_war.html b/website/manual_qs_war.html
index a9beeed..2ac267b 100644
--- a/website/manual_qs_war.html
+++ b/website/manual_qs_war.html
@@ -28,7 +28,7 @@
 	Home 
 	Getting Started 
 	Manual 
-	Download 
+	Download 
 	Usage Statistics
 	Services Status
 	Contact Us
@@ -73,7 +73,7 @@
 
        
 
 
          
-	
        1. Download the JABAWS WAR file
          2. 
+	
        2. Download the JABAWS WAR file
          3. 
 	
        3. Download and install Apache-Tomcat.
          
 		You will need at least Tomcat version 5.5 of  (we would recommend version 7.0) and at least Java 1.6 (i.e. JAVA 6).
 	
          4. 
@@ -105,7 +105,7 @@
 
 
  
-
+
 
 
 
diff --git a/website/quick_start.html b/website/quick_start.html
index 58258ad..13cfe79 100644
--- a/website/quick_start.html
+++ b/website/quick_start.html
@@ -28,7 +28,7 @@
 	Home 
 	Getting Started 
 	Manual 
-	Download 
+	Download 
 	Usage Statistics
 	Services Status
 	Contact Us
@@ -63,7 +63,7 @@
 
 
  
-
+