Merge branch 'Release_2_7_Branch'

diff --git a/build.xml b/build.xml
index 6cfaf4e..736b5e6 100755 (executable)
--- 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 (file)
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 (file)
--- 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);