From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 3 Oct 2011 14:23:19 +0000 (+0100)
Subject: Merge branch 'Release_2_7_Branch'
X-Git-Tag: Release_2_8~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a831db70f876aaeeb5b36624c9d10816fd8bb7c7;hp=f335ea905223c014fb305051b45960ec7e28cfc4;p=jalview.git

Merge branch 'Release_2_7_Branch'
---

diff --git a/build.xml b/build.xml
index 6cfaf4e..736b5e6 100755
--- a/build.xml
+++ b/build.xml
@@ -236,45 +236,6 @@
 
 		<!--    codebase="http://www.jalview.org/jalview/webstart" -->
 		<!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
-		<jnlp toFile="${packageDir}/jalview_noa.jnlp" codebase="${WebStartLocation}">
-			<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="logo_big.gif" />
-				<offline_allowed />
-				<!--
-				<association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>-->
-			</information>
-			<resources>
-				<j2se version="${j2sev}" initial_heap_size="10M"  />
-				<fileset dir="${packageDir}">
-					<include name="jalview.jar" />
-				</fileset>
-				<fileset dir="${packageDir}">
-					<include name="*.jar" />
-					<include name="*_*.jar" />
-					<exclude name="jalview.jar" />
-				</fileset>
-				<property name="jalview.version" value="${JALVIEW_VERSION}" />
-			</resources>
-			<application_desc main_class="jalview.bin.Jalview">
-			</application_desc>
-			<security>
-				<all_permissions />
-			</security>
-		</jnlp>
 		<jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 			<information>
 				<title>Jalview</title>
@@ -284,59 +245,9 @@
 				<description kind="short">Jalview</description>
 				<icon href="logo_big.gif" />
 				<offline_allowed />
-				<association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
 			</information>
 			<resources>
-				<j2se version="${j2sev}" initial_heap_size="10M"/>
-				<fileset dir="${packageDir}">
-					<include name="jalview.jar" />
-				</fileset>
-				<fileset dir="${packageDir}">
-					<include name="*.jar" />
-					<include name="*_*.jar" />
-					<exclude name="jalview.jar" />
-				</fileset>
-				<property name="jalview.version" value="${JALVIEW_VERSION}" />
-			</resources>
-			<application_desc main_class="jalview.bin.Jalview">
-			</application_desc>
-			<security>
-				<all_permissions />
-			</security>
-		</jnlp>
-		
-		<jnlp toFile="${packageDir}/jalview_noa_1G.jnlp" codebase="${WebStartLocation}">
-			<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="logo_big.gif" />
-				<offline_allowed />
-				<!--
-				<association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>-->
-			</information>
-			<resources>
-				<j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
+				<j2se version="${j2sev}" initial_heap_size="10M"  />
 				<fileset dir="${packageDir}">
 					<include name="jalview.jar" />
 				</fileset>
@@ -352,7 +263,7 @@
 			<security>
 				<all_permissions />
 			</security>
-		</jnlp>
+		</jnlp>		
 		<jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 			<information>
 				<title>Jalview</title>
@@ -362,16 +273,6 @@
 				<description kind="short">Jalview</description>
 				<icon href="logo_big.gif" />
 				<offline_allowed />
-				<association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
 			</information>
 			<resources>
 				<j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
@@ -391,7 +292,7 @@
 				<all_permissions />
 			</security>
 		</jnlp>
-		<jnlp toFile="${packageDir}/jalview_noac_2G.jnlp" codebase="${WebStartLocation}">
+		<jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 			<information>
 				<title>Jalview</title>
 				<vendor>The Barton Group</vendor>
@@ -400,18 +301,6 @@
 				<description kind="short">Jalview</description>
 				<icon href="logo_big.gif" />
 				<offline_allowed />
-				<!--
-				<association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
-			-->
 			</information>
 			<resources>
 				<j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
@@ -431,15 +320,15 @@
 				<all_permissions />
 			</security>
 		</jnlp>
-		<jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
-			<information>
-				<title>Jalview</title>
-				<vendor>The Barton Group</vendor>
-				<homepage href="http://www.jalview.org" />
-				<description>Jalview Multiple Alignment Editor</description>
-				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif" />
-				<offline_allowed />
+			<!-- finally, need to postprocess to add in associations at end of 'information' element 
+			
+			<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
+		
+		</xslt>
+			
+			
+			-->
+					<!--
 				<association mime-type="application-x/ext-file" extensions="fa"/>
         <association mime-type="application-x/ext-file" extensions="fasta"/>
         <association mime-type="application-x/ext-file" extensions="fastq"/>
@@ -449,27 +338,8 @@
         <association mime-type="application-x/ext-file" extensions="aln"/>
         <association mime-type="application-x/ext-file" extensions="pir"/>
         <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
-			</information>
-			<resources>
-				<j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
-				<fileset dir="${packageDir}">
-					<include name="jalview.jar" />
-				</fileset>
-				<fileset dir="${packageDir}">
-					<include name="*.jar" />
-					<include name="*_*.jar" />
-					<exclude name="jalview.jar" />
-				</fileset>
-				<property name="jalview.version" value="${JALVIEW_VERSION}" />
-			</resources>
-			<application_desc main_class="jalview.bin.Jalview">
-			</application_desc>
-			<security>
-				<all_permissions />
-			</security>
-		</jnlp>
-
+        <association mime-type="application-x/ext-file" extensions="stk"/>-->
+	
 	</target>
 
 	<target name="runenv" depends="init">
diff --git a/lib/jswingreader-0.3.jar b/lib/jswingreader-0.3.jar
index c8a4fff..c632130 100644
Binary files a/lib/jswingreader-0.3.jar and b/lib/jswingreader-0.3.jar differ
diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index f42c0c4..95de391 100644
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -309,18 +309,19 @@ public class RestClient extends WSClient implements WSClientI,
     jalview.ws.rest.params.JobConstant toolp;
     //toolp = new jalview.ws.rest.JobConstant("tool","jalview");
     //iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
-    iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
-    iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
-    iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("blast","0");
-    iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
+    //iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
+    //iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
+    //iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("blast","0");
+    //iparams.put(toolp.token, toolp);
     
     jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
-    aliinput.token = "ali";//_file";
-    aliinput.writeAsFile=false;//true;
+    // SHMR server has a 65K limit for content pasted into the 'ali' parameter, so we always upload our files.
+    aliinput.token = "ali_file";//_file";
+    aliinput.writeAsFile=true;//true;
     //aliinput.token = "ali_file";
     //aliinput.writeAsFile=true;
     iparams.put(aliinput.token, aliinput);