From 3076342c6e07eabb8ddfd21829517da31be1d657 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 3 Dec 2014 08:16:02 +0000 Subject: [PATCH] JAL-1517 dropped jnlp file in help documentation in favour of link to Jalview launchApp service --- help/help.jhm | 1 - help/helpTOC.xml | 4 +-- help/html/jalviewjnlp.html | 81 -------------------------------------------- help/html/memory.html | 43 +++++++++++++---------- 4 files changed, 27 insertions(+), 102 deletions(-) delete mode 100755 help/html/jalviewjnlp.html diff --git a/help/help.jhm b/help/help.jhm index 6a7a112..af010a4 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -127,7 +127,6 @@ - diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 4a32606..b67eb6f 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -128,9 +128,7 @@ - - - + diff --git a/help/html/jalviewjnlp.html b/help/html/jalviewjnlp.html deleted file mode 100755 index 8f32a2b..0000000 --- a/help/html/jalviewjnlp.html +++ /dev/null @@ -1,81 +0,0 @@ - - - -Jalview local Jnlp File - - -

Jalview local Jnlp File

-
-<jnlp spec="1.0+" codebase="http://www.jalview.org/webstart/">
-  <information>
-    <title>Jalview</title>
-    <vendor>The Barton Group</vendor>
-    <homepage href="http://www.jalview.org"/>
-    <description>Jalview Multiple Alignment Editor</description>
-    <description kind="short">Jalview</description>
-    <icon href="http://www.jalview.org/webstart/logo_big.gif" kind="default"/>
-    <association extensions="fa" mime-type="application-x/ext-file"/>
-    <association extensions="fasta" mime-type="application-x/ext-file"/>
-    <association extensions="fastq" mime-type="application-x/ext-file"/>
-    <association extensions="blc" mime-type="application-x/ext-file"/>
-    <association extensions="msf" mime-type="application-x/ext-file"/>
-    <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>
-    <all-permissions/>
-  </security>
-  <resources>
-  <!-- the additional memory parameters are here -->
-  <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-12.1.13.jar"/>
-		<jar href="activation.jar"/>
-		<jar href="axis.jar"/>
-		<jar href="castor-1.1-cycle-xml.jar"/>
-		<jar href="commons-discovery.jar"/>
-		<jar href="commons-logging.jar"/>
-		<jar href="jaxrpc.jar"/>
-		<jar href="jhall.jar"/>
-		<jar href="log4j-1.2.8.jar"/>
-		<jar href="mail.jar"/>
-		<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="2.6.1"/>
-  </resources>
-  <application-desc main-class="jalview.bin.Jalview"/>
-</jnlp>
-
-
If -you have problems, send an email to jalview-discuss
- - diff --git a/help/html/memory.html b/help/html/memory.html index 3ef4d77..1cb9596 100755 --- a/help/html/memory.html +++ b/help/html/memory.html @@ -45,24 +45,33 @@ The way you increase the memory settings for the JVM depends on which installation of Jalview you use:

    -
  • Web Start Version -

    JavaWS sets the JVM parameters through special tags in the JNLP file. You'll - need to make your own jnlp file and add the following parameter into the - <resources> element. - 

    -<j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/>
-
    - Save the jnlp file somewhere and then - if you start Jalview through your - web browser, point your browser at the file's url, othewise simply run javaws - with the file location as its argument. The file's url is something like :
    - 
    +		
  • Web Start Version
+			
    
+				JavaWS sets the JVM parameters through special tags in the JNLP
+				file. You can obtain a JNLP file with modified memory settings from
+				our service with the following link (replace 2G with desired memory
+				in G or M):
     http://www.jalview.org/services/launchApp?jvm-max-heap=2G
+			
    
+			
    
+				Alternatively, if you want to create your own JNLP file then please
+				download the latest JNLP file from http://www.jalview.org/webstart/jalview.jnlp
+				and modify the max-heap-size parameter for the j2se tag in the
+				<resources> element. e.g.
+			
    +<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/>
+
     In both cases, you should save your new jnlp file somewhere and
+			then either point your web browser at the file's url, launch it from
+			your file browser, or from a terminal window run javaws (located in
+			your Java installation's bin directory) with the file location as its
+			argument. The file's url is something like :
     
     file://<full path to file>
-
    
-    If jalview doesn't start up, see below. You'll have
-    to edit the above settings in the JNLP file using a text editor, save it,
-    and try starting Jalview with it once more.
-    
    • 
-  
  • Install Anywhere version
+
    • If jalview doesn't start up, see below. + You'll have to edit the above settings in the JNLP file using a text + editor, save it, and try starting Jalview with it once more. +

    • +
  • Install Anywhere version

    You need to change the InstallAnywhere configuration settings for the application. These are found in different places depending upon which operating system you have : -- 1.7.10.2