Further development of the Sequence Checker. Added the RNA Folder and…

… Device Editor. I'm disabling access to the Device Editor for now.
yinxx · Jun 4, 2011 · 2fb088b · 2fb088b
1 parent 6ddc7af
commit 2fb088b
Show file tree

Hide file tree

Showing 30 changed files with 446 additions and 169 deletions.
diff --git a/web/checker/SeqCheckMappingStore.js → deprecated/SeqCheckMappingStore.js b/web/checker/SeqCheckMappingStore.js → deprecated/SeqCheckMappingStore.js
diff --git a/web/checker/SeqCheckResultStore.js → deprecated/SeqCheckResultStore.js b/web/checker/SeqCheckResultStore.js → deprecated/SeqCheckResultStore.js
diff --git a/web/checker/SeqCheckerPanel.old.js → deprecated/SeqCheckerPanel.old.js b/web/checker/SeqCheckerPanel.old.js → deprecated/SeqCheckerPanel.old.js
diff --git a/web/checker/SeqCheckerPanel.old.ui.js → deprecated/SeqCheckerPanel.old.ui.js b/web/checker/SeqCheckerPanel.old.ui.js → deprecated/SeqCheckerPanel.old.ui.js
diff --git a/web/checker/StartStopStore.js → deprecated/StartStopStore.js b/web/checker/StartStopStore.js → deprecated/StartStopStore.js
diff --git a/nbproject/build-impl.xml b/nbproject/build-impl.xml
@@ -173,8 +173,20 @@
         <property name="runmain.jvmargs" value=""/>
         <path id="endorsed.classpath.path" path="${endorsed.classpath}"/>
         <condition else="" property="endorsed.classpath.cmd.line.arg" value="-Xbootclasspath/p:'${toString:endorsed.classpath.path}'">
-            <length length="0" string="${endorsed.classpath}" when="greater"/>
+            <and>
+                <isset property="endorsed.classpath"/>
+                <length length="0" string="${endorsed.classpath}" when="greater"/>
+            </and>
+        </condition>
+        <condition else="false" property="jdkBug6558476">
+            <and>
+                <matches pattern="1\.[56]" string="${java.specification.version}"/>
+                <not>
+                    <os family="unix"/>
+                </not>
+            </and>
         </condition>
+        <property name="javac.fork" value="${jdkBug6558476}"/>
     </target>
     <target depends="init" name="-init-cos" unless="deploy.on.save">
         <condition property="deploy.on.save" value="true">
@@ -245,7 +257,7 @@ or ant -Dj2ee.platform.classpath=&lt;server_classpath&gt; (where no properties f
                 <property location="${build.dir}/empty" name="empty.dir"/>
                 <mkdir dir="${empty.dir}"/>
                 <mkdir dir="@{apgeneratedsrcdir}"/>
-                <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" includeantruntime="false" includes="@{includes}" source="${javac.source}" srcdir="@{srcdir}" target="${javac.target}">
+                <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" srcdir="@{srcdir}" target="${javac.target}">
                     <src>
                         <dirset dir="@{gensrcdir}" erroronmissingdir="false">
                             <include name="*"/>
@@ -315,15 +327,18 @@ or ant -Dj2ee.platform.classpath=&lt;server_classpath&gt; (where no properties f
             <attribute default="${build.classes.dir}" name="destdir"/>
             <sequential>
                 <fail unless="javac.includes">Must set javac.includes</fail>
-                <pathconvert pathsep="," property="javac.includes.binary">
+                <pathconvert pathsep="${line.separator}" property="javac.includes.binary">
                     <path>
                         <filelist dir="@{destdir}" files="${javac.includes}"/>
                     </path>
                     <globmapper from="*.java" to="*.class"/>
                 </pathconvert>
+                <tempfile deleteonexit="true" property="javac.includesfile.binary"/>
+                <echo file="${javac.includesfile.binary}" message="${javac.includes.binary}"/>
                 <delete>
-                    <files includes="${javac.includes.binary}"/>
+                    <files includesfile="${javac.includesfile.binary}"/>
                 </delete>
+                <delete file="${javac.includesfile.binary}"/>
             </sequential>
         </macrodef>
     </target>
@@ -349,6 +364,7 @@ or ant -Dj2ee.platform.classpath=&lt;server_classpath&gt; (where no properties f
                     <formatter type="brief" usefile="false"/>
                     <formatter type="xml"/>
                     <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
+                    <jvmarg value="-ea"/>
                     <jvmarg line="${runmain.jvmargs}"/>
                 </junit>
             </sequential>
@@ -492,6 +508,19 @@ exists or setup the property manually. For example like this:
     <target depends="-init-ap-cmdline-properties,-init-ap-cmdline-supported" name="-init-ap-cmdline">
         <property name="ap.cmd.line.internal" value=""/>
     </target>
+    <target depends="-profile-pre-init, init, -profile-post-init, -profile-init-check" name="profile-init"/>
+    <target name="-profile-pre-init">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target name="-profile-post-init">
+        <!-- Empty placeholder for easier customization. -->
+        <!-- You can override this target in the ../build.xml file. -->
+    </target>
+    <target depends="-profile-pre-init, init, -profile-post-init" name="-profile-init-check">
+        <fail unless="profiler.info.jvm">Must set JVM to use for profiling in profiler.info.jvm</fail>
+        <fail unless="profiler.info.jvmargs.agent">Must set profiler agent JVM arguments in profiler.info.jvmargs.agent</fail>
+    </target>
     <target depends="-pre-init,-init-private,-init-user,-init-project,-do-init,-post-init,-init-check,-init-macrodef-property,-init-macrodef-javac,-init-macrodef-junit,-init-macrodef-java,-init-macrodef-nbjpda,-init-macrodef-nbjsdebug,-init-macrodef-debug,-init-taskdefs,-init-ap-cmdline" name="init"/>
     <!--
                 COMPILATION SECTION
@@ -553,6 +582,8 @@ exists or setup the property manually. For example like this:
         <!-- You can override this target in the ../build.xml file. -->
     </target>
     <target depends="init,deps-jar,-pre-pre-compile,-pre-compile-single,-do-compile-single,-post-compile-single" name="compile-single"/>
+    <property name="jspc.schemas" value="/resources/schemas/"/>
+    <property name="jspc.dtds" value="/resources/dtds/"/>
     <target depends="compile" description="Test compile JSP pages to expose compilation errors." if="do.compile.jsps" name="compile-jsps">
         <mkdir dir="${build.generated.dir}/src"/>
         <java classname="org.netbeans.modules.web.project.ant.JspC" failonerror="true" fork="true">
@@ -561,9 +592,12 @@ exists or setup the property manually. For example like this:
             <arg value="-d"/>
             <arg file="${basedir}/${build.generated.dir}/src"/>
             <arg value="-die1"/>
+            <arg value="-schemas ${jspc.schemas}"/>
+            <arg value="-dtds ${jspc.dtds}"/>
             <arg value="-compilerSourceVM ${javac.source}"/>
             <arg value="-compilerTargetVM ${javac.target}"/>
             <arg value="-javaEncoding ${source.encoding}"/>
+            <arg value="-sysClasspath ${libs.jsp-compilation-syscp.classpath}"/>
             <classpath path="${java.home}/../lib/tools.jar:${libs.jsp-compiler.classpath}:${libs.jsp-compilation.classpath}"/>
         </java>
         <mkdir dir="${build.generated.dir}/classes"/>
@@ -578,6 +612,9 @@ exists or setup the property manually. For example like this:
             <arg value="-d"/>
             <arg file="${basedir}/${build.generated.dir}/src"/>
             <arg value="-die1"/>
+            <arg value="-schemas ${jspc.schemas}"/>
+            <arg value="-dtds ${jspc.dtds}"/>
+            <arg value="-sysClasspath ${libs.jsp-compilation-syscp.classpath}"/>
             <arg value="-jspc.files"/>
             <arg path="${jsp.includes}"/>
             <arg value="-compilerSourceVM ${javac.source}"/>
@@ -815,6 +852,35 @@ exists or setup the property manually. For example like this:
         <webproject1:nbjpdareload/>
     </target>
     <target depends="init,-pre-debug-fix,-do-debug-fix" if="netbeans.home" name="debug-fix"/>
+    <!--
+            =================
+            PROFILING SECTION
+            =================
+            -->
+    <target description="Profile a J2EE project in the IDE." name="profile">
+        <condition else="start-profiled-server" property="profiler.startserver.target" value="start-profiled-server-extraargs">
+            <isset property="profiler.info.jvmargs.extra"/>
+        </condition>
+        <antcall target="${profiler.startserver.target}"/>
+        <antcall target="run"/>
+        <antcall target="start-loadgen"/>
+    </target>
+    <target name="start-profiled-server">
+        <nbstartprofiledserver forceRestart="${profiler.j2ee.serverForceRestart}" javaPlatform="${profiler.info.javaPlatform}" startupTimeout="${profiler.j2ee.serverStartupTimeout}">
+            <jvmarg value="${profiler.info.jvmargs.agent}"/>
+            <jvmarg value="${profiler.j2ee.agentID}"/>
+        </nbstartprofiledserver>
+    </target>
+    <target name="start-profiled-server-extraargs">
+        <nbstartprofiledserver forceRestart="${profiler.j2ee.serverForceRestart}" javaPlatform="${profiler.info.javaPlatform}" startupTimeout="${profiler.j2ee.serverStartupTimeout}">
+            <jvmarg value="${profiler.info.jvmargs.extra}"/>
+            <jvmarg value="${profiler.info.jvmargs.agent}"/>
+            <jvmarg value="${profiler.j2ee.agentID}"/>
+        </nbstartprofiledserver>
+    </target>
+    <target if="profiler.loadgen.path" name="start-loadgen">
+        <loadgenstart path="${profiler.loadgen.path}"/>
+    </target>
     <!--
                 JAVADOC SECTION
             -->
@@ -936,6 +1002,35 @@ exists or setup the property manually. For example like this:
         <webproject1:nbjpdareload dir="${build.test.classes.dir}"/>
     </target>
     <target depends="init,-pre-debug-fix,-do-debug-fix-test" if="netbeans.home" name="debug-fix-test"/>
+    <!--
+        =========================
+        TESTS PROFILING  SECTION
+        =========================
+        -->
+    <target depends="profile-init,compile-test-single" if="netbeans.home" name="profile-test-single">
+        <nbprofiledirect>
+            <classpath>
+                <path path="${run.test.classpath}"/>
+                <path path="${j2ee.platform.classpath}"/>
+            </classpath>
+        </nbprofiledirect>
+        <junit dir="${profiler.info.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" jvm="${profiler.info.jvm}" showoutput="true">
+            <env key="${profiler.info.pathvar}" path="${profiler.info.agentpath}:${profiler.current.path}"/>
+            <jvmarg value="${profiler.info.jvmargs.agent}"/>
+            <jvmarg line="${profiler.info.jvmargs}"/>
+            <test name="${profile.class}"/>
+            <classpath>
+                <path path="${run.test.classpath}"/>
+                <path path="${j2ee.platform.classpath}"/>
+            </classpath>
+            <syspropertyset>
+                <propertyref prefix="test-sys-prop."/>
+                <mapper from="test-sys-prop.*" to="*" type="glob"/>
+            </syspropertyset>
+            <formatter type="brief" usefile="false"/>
+            <formatter type="xml"/>
+        </junit>
+    </target>
     <!--
                 
                 CLEANUP SECTION

diff --git a/nbproject/genfiles.properties b/nbproject/genfiles.properties
@@ -4,5 +4,5 @@ [email protected]
 # This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
 # Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
 nbproject/build-impl.xml.data.CRC32=60fd2e8b
-nbproject/build-impl.xml.script.CRC32=52ab0b3c
-nbproject/build-impl.xml.stylesheet.CRC32=8419264d@1.24.3.1
+nbproject/build-impl.xml.script.CRC32=58f56806
+nbproject/build-impl.xml.stylesheet.CRC32=8ca9f0e6@1.31.1.1
diff --git a/nbproject/private/private.properties b/nbproject/private/private.properties
@@ -1,4 +1,5 @@
 deploy.ant.properties.file=/Users/cesarr/.netbeans/6.9/gfv31680656997.properties
+j2ee.platform.classpath=${j2ee.server.home}/modules/javax.servlet.jar:${j2ee.server.home}/modules/jsf-api.jar:${j2ee.server.home}/modules/jsr311-api.jar:${j2ee.server.home}/modules/endorsed/javax.annotation.jar:${j2ee.server.home}/modules/javax.security.jacc.jar:${j2ee.server.home}/modules/endorsed/webservices-api-osgi.jar:${j2ee.server.home}/modules/javax.transaction.jar:${j2ee.server.home}/modules/javax.servlet.jsp.jstl.jar:${j2ee.server.home}/modules/javax.jms.jar:${j2ee.server.home}/modules/endorsed/jaxb-api-osgi.jar:${j2ee.server.home}/modules/weld-osgi-bundle.jar:${j2ee.server.home}/modules/bean-validator.jar:${j2ee.server.home}/modules/javax.ejb.jar:${j2ee.server.home}/modules/javax.servlet.jsp.jar:${j2ee.server.home}/modules/javax.enterprise.deploy.jar:${j2ee.server.home}/modules/jstl-impl.jar:${j2ee.server.home}/modules/jsf-impl.jar:${j2ee.server.home}/modules/javax.management.j2ee.jar:${j2ee.server.home}/modules/mail.jar:${j2ee.server.home}/modules/javax.resource.jar:${j2ee.server.home}/modules/javax.persistence.jar:${j2ee.server.home}/modules/javax.security.auth.message.jar
 j2ee.platform.is.jsr109=true
 j2ee.server.home=/Applications/NetBeans/glassfish-3.0.1/glassfish
 j2ee.server.instance=[/Applications/NetBeans/glassfish-3.0.1/glassfish]deployer:gfv3ee6:localhost:4848

diff --git a/nbproject/private/private.xml b/nbproject/private/private.xml
@@ -1,2 +1,4 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project-private xmlns="http://www.netbeans.org/ns/project-private/1"/>
+<project-private xmlns="http://www.netbeans.org/ns/project-private/1">
+    <editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/1"/>
+</project-private>
diff --git a/nbproject/project.properties b/nbproject/project.properties
@@ -27,9 +27,10 @@ endorsed.classpath=\
     ${libs.javaee-endorsed-api-6.0.classpath}
 excludes=
 includes=**
+j2ee.compile.on.save=true
 j2ee.deploy.on.save=true
 j2ee.platform=1.6-web
-j2ee.platform.classpath=${j2ee.server.home}/modules/javax.servlet.jar:${j2ee.server.home}/modules/jsf-api.jar:${j2ee.server.home}/modules/jsr311-api.jar:${j2ee.server.home}/modules/endorsed/javax.annotation.jar:${j2ee.server.home}/modules/javax.security.jacc.jar:${j2ee.server.home}/modules/endorsed/webservices-api-osgi.jar:${j2ee.server.home}/modules/javax.transaction.jar:${j2ee.server.home}/modules/javax.servlet.jsp.jstl.jar:${j2ee.server.home}/modules/javax.jms.jar:${j2ee.server.home}/modules/endorsed/jaxb-api-osgi.jar:${j2ee.server.home}/modules/weld-osgi-bundle.jar:${j2ee.server.home}/modules/bean-validator.jar:${j2ee.server.home}/modules/javax.ejb.jar:${j2ee.server.home}/modules/javax.servlet.jsp.jar:${j2ee.server.home}/modules/javax.enterprise.deploy.jar:${j2ee.server.home}/modules/jstl-impl.jar:${j2ee.server.home}/modules/jsf-impl.jar:${j2ee.server.home}/modules/javax.management.j2ee.jar:${j2ee.server.home}/modules/mail.jar:${j2ee.server.home}/modules/javax.resource.jar:${j2ee.server.home}/modules/javax.persistence.jar:${j2ee.server.home}/modules/javax.security.auth.message.jar
+j2ee.platform.classpath=
 j2ee.platform.embeddableejb.classpath=${j2ee.server.home}/lib/embedded/glassfish-embedded-static-shell.jar
 j2ee.platform.wscompile.classpath=${j2ee.server.home}/modules/webservices-osgi.jar
 j2ee.platform.wsgen.classpath=${j2ee.server.home}/modules/webservices-osgi.jar:${j2ee.server.home}/modules/endorsed/webservices-api-osgi.jar:${j2ee.server.home}/modules/jaxb-osgi.jar:${j2ee.server.home}/modules/endorsed/jaxb-api-osgi.jar:${j2ee.server.home}/modules/javax.ejb.jar

diff --git a/web/.DS_Store b/web/.DS_Store
diff --git a/web/StudioViewport.js b/web/StudioViewport.js
@@ -8,12 +8,34 @@ StudioViewport = Ext.extend(StudioViewportUi, {
 
     initComponent: function() 
     {
-    	StudioViewport.superclass.initComponent.call(this);
-        var button = Ext.ComponentManager.get('checkerButton');
+    	var button;
+
+        StudioViewport.superclass.initComponent.call(this);
+        button = Ext.ComponentManager.get('rnaFolderButton');
+        button.setHandler(this.rnaFolderButtonClickHandler, this);
+        button = Ext.ComponentManager.get('checkerButton');
         button.setHandler(this.checkerButtonClickHandler, this);
+        button = Ext.ComponentManager.get('deviceEditorButton');
+        button.setHandler(this.deviceEditorButtonClickHandler, this);
         this.newSequenceChecker();
     },
 
+    rnaFolderButtonClickHandler:function(button, event)
+    {
+        var folder = new RnaFolder();
+        var tabPanel = this.getComponent('centerTabPanel');
+        var tab = tabPanel.add(folder);
+        tabPanel.setActiveTab(tab);
+    },
+
+    deviceEditorButtonClickHandler: function(button, event)
+    {
+        var editor = new DeviceEditor();
+        var tabPanel = this.getComponent('centerTabPanel');
+        var tab = tabPanel.add(editor);
+        tabPanel.setActiveTab(tab);
+    },
+
     checkerButtonClickHandler: function(button, event)
     {
         this.newSequenceChecker();

diff --git a/web/StudioViewport.ui.js b/web/StudioViewport.ui.js
@@ -50,7 +50,24 @@ StudioViewportUi = Ext.extend(Ext.Viewport, {
                         items: [
                             {
                                 xtype: 'button',
-                                text: 'Checker',
+                                text: 'RNA Folder',
+                                id: 'rnaFolderButton'
+                            },
+                            {
+                                xtype: 'tbseparator'
+                            },
+                            {
+                                xtype: 'button',
+                                text: 'Device Editor',
+                                id: 'deviceEditorButton',
+                                disabled: true
+                            },
+                            {
+                                xtype: 'tbseparator'
+                            },
+                            {
+                                xtype: 'button',
+                                text: 'Sequence Checker',
                                 id: 'checkerButton'
                             }
                         ]

diff --git a/web/apps/DeviceEditor.js b/web/apps/DeviceEditor.js
@@ -0,0 +1,23 @@
+/*
+ *
+ *
+ *
+ */
+
+Ext.define('DeviceEditor',
+    {
+        extend: 'Ext.panel.Panel',
+        title: 'Device Editor',
+        layout: 'fit',
+        tpl: '',
+        closable: true,
+        autoScroll: true,
+        html: '<iframe style="overflow:auto;width:100%;height:100%;" frameborder="0"  src="http://j5.jbei.org/bin/deviceeditor.pl"></iframe>',
+
+        constructor: function() {
+
+            this.items = [];
+            this.callParent();
+        }
+    }
+);
diff --git a/web/apps/RnaFolder.js b/web/apps/RnaFolder.js
@@ -0,0 +1,23 @@
+/*
+ *
+ *
+ *
+ */
+
+Ext.define('RnaFolder',
+    {
+        extend: 'Ext.panel.Panel',
+        title: 'RNA Folder',
+        layout: 'fit',
+        tpl: '',
+        closable: true,
+        autoScroll: true,
+        html: '<iframe style="overflow:auto;width:100%;height:100%;" frameborder="0"  src="http://biofab.jbei.org/webtools/rnafold.html"></iframe>',
+
+        constructor: function() {
+
+            this.items = [];
+            this.callParent();
+        }
+    }
+);