JAL-1641 applet build fix

diff --git a/.classpath b/.classpath
index b7c26a4..0abfdb3 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -58,7 +58,6 @@
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
        <classpathentry kind="lib" path="lib/jersey-client-1.19.jar"/>
        <classpathentry kind="lib" path="lib/jersey-core-1.19.jar"/>
-       <classpathentry kind="lib" path="lib/jersey-json-1.19.jar"/>
        <classpathentry kind="lib" path="lib/jsr311-api-1.1.1.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
        <classpathentry kind="lib" path="lib/jetty-server-9.2.10.v20150310.jar"/>
@@ -66,5 +65,6 @@
        <classpathentry kind="lib" path="lib/jetty-util-9.2.10.v20150310.jar"/>
        <classpathentry kind="lib" path="lib/jetty-http-9.2.10.v20150310.jar"/>
        <classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
+       <classpathentry kind="lib" path="lib/java-json.jar"/>
        <classpathentry kind="output" path="classes"/>
 </classpath>

diff --git a/build.xml b/build.xml
index 49fd37e..273c9e0 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -111,6 +111,9 @@
     <!-- Jalview Applet JMol Jar Dependency -->
     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
     <property name="varnaJar" value="VARNAv3-91.jar" />
+    <property name="jsoup" value="jsoup-1.8.1.jar" />
+    <property name="jsonSimple" value="json_simple-1.1.jar" />
+    <property name="javaJson" value="java-json.jar" />
     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
     <!-- switch to indicate if we should obfuscate jalviewLite -->
     <!-- <property name="donotobfuscate" value="true"/> -->
@@ -165,6 +168,10 @@
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
       <pathelement location="lib/${varnaJar}" />
+      <pathelement location="lib/${jsoup}" />
+      <pathelement location="lib/${jsonSimple}" />
+      <pathelement location="lib/${javaJson}" />
+      
     </path>
     <!-- default location for outputting javadoc -->
     <property name="javadocDir" value="${packageDir}/javadoc"/>

diff --git a/lib/java-json.jar b/lib/java-json.jar
new file mode 100755 (executable)
index 0000000..2f211e3
Binary files /dev/null and b/lib/java-json.jar differ

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index d507362..75e99a6 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,6 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
 package jalview.io;
 
-import jalview.gui.AlignFrame;
+import jalview.api.AlignViewControllerGuiI;
 import jalview.schemes.ColourSchemeI;
 
 import java.io.IOException;
@@ -51,9 +72,9 @@ public class HtmlFile extends AlignFile
       String alignmentJsonString = content.val();
 
       JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
-      seqs = jsonFile.seqs;
-      seqGroups = jsonFile.seqGroups;
-      annotations = jsonFile.annotations;
+      seqs = jsonFile.getSeqs();
+      seqGroups = jsonFile.getSeqGroups();
+      annotations = jsonFile.getAnnotations();
       showSeqFeatures = jsonFile.isShowSeqFeatures();
       colourScheme = jsonFile.getColourScheme();
     } catch (Exception e)
@@ -62,7 +83,7 @@ public class HtmlFile extends AlignFile
     }
   }
 
-  public void applySettingsToAlignFrame(AlignFrame af)
+  public void applySettingsToAlignFrame(AlignViewControllerGuiI af)
   {
     af.setShowSeqFeatures(isShowSeqFeatures());
     af.changeColour(getColourScheme());

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index ff7deaf..30383f3 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -1,3 +1,24 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
 package jalview.io;
 
 import jalview.api.AlignViewControllerGuiI;
@@ -129,10 +150,8 @@ public class JSONFile extends AlignFile
 
       if (jsonExportSettings.isExportJalviewSettings())
       {
-        jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
-        webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
-                "www.jalview.org", "http://www.jalview.org")
-                + "/services/launchApp";
+        jalviewVersion = "";
+        webStartLaunchServletUrl = "www.jalview.org/services/launchApp";
 
         JalviewSettingsPojo jvSettings = new JalviewSettingsPojo();
         jvSettings.setGlobalColorScheme(globalColorScheme);
@@ -178,7 +197,7 @@ public class JSONFile extends AlignFile
           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
         }
       }
-      com.json.JSONObject generatedJSon = new com.json.JSONObject(
+      org.json.JSONObject generatedJSon = new org.json.JSONObject(
               jsonAlignmentPojo);
       jsonOutput = generatedJSon.toString();
       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
@@ -380,7 +399,7 @@ public class JSONFile extends AlignFile
             String desc = annot.get("description") == null ? null : annot
                     .get("description").toString();
 
-            char ss = annot.get("secondaryStructure") == null ? null
+            char ss = annot.get("secondaryStructure") == null ? ' '
                     : annot.get("secondaryStructure").toString().charAt(0);
             String displayChar = annot.get("displayCharacter").toString();
 
@@ -548,6 +567,11 @@ public class JSONFile extends AlignFile
     this.showSeqFeatures = showSeqFeatures;
   }
 
+  public Vector<AlignmentAnnotation> getAnnotations()
+  {
+    return annotations;
+  }
+
   public class JSONExportSettings
   {
     private boolean exportSequence;

diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index f40b302..67ab3f2 100644 (file)
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -21,7 +21,7 @@ import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;
 import com.sun.jersey.api.client.config.ClientConfig;
 import com.sun.jersey.api.client.config.DefaultClientConfig;
-import com.sun.jersey.api.json.JSONConfiguration;
+
 
 /**
  * A rest client for querying the Search endpoing of the PDB REST API
@@ -49,8 +49,6 @@ public class PDBRestClient
     try
     {
       ClientConfig clientConfig = new DefaultClientConfig();
-      clientConfig.getFeatures().put(
-              JSONConfiguration.FEATURE_POJO_MAPPING, Boolean.TRUE);
       Client client = Client.create(clientConfig);
 
       String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest