initialization with a URI

org.protege.editor.core.application/src/main/java/org/protege/editor/core/ProtegeApplication.java

@@ -366,13 +366,15 @@ public class ProtegeApplication implements BundleActivator {
 
 
     private void startApplication() throws Exception {
-        createAndSetupDefaultEditorKit();
         if (commandLineURIs != null && !commandLineURIs.isEmpty()) {
             // Open any command line URIs
             for (URI uri : commandLineURIs) {
-                editURI(uri);
+                createAndSetupDefaultEditorKit(uri);
             }
         }
+        else {
+            createAndSetupDefaultEditorKit();
+        }
         checkForUpdates();
     }
 
@@ -431,6 +433,25 @@ public class ProtegeApplication implements BundleActivator {
         }
     }
 
+
+    private void createAndSetupDefaultEditorKit(URI uri) {
+        try {
+            ProtegeManager pm = ProtegeManager.getInstance();
+            List<EditorKitFactoryPlugin> editorKitFactoryPlugins = pm.getEditorKitFactoryPlugins();
+            if (!editorKitFactoryPlugins.isEmpty()) {
+                EditorKitFactoryPlugin defaultPlugin = editorKitFactoryPlugins.get(0);
+                pm.createAndSetupNewEditorKit(defaultPlugin, uri);
+            }
+            else {
+                throw new RuntimeException("No editor kit factory plugins available");
+            }
+        }
+        catch (Exception e) {
+            ErrorLogPanel.showErrorDialog(e);
+        }
+    }
+
+
     /////////////////////////////////////////////////////////////////////////////////
     //
     //  Visible Application Interfaces

org.protege.editor.core.application/src/main/java/org/protege/editor/core/ProtegeManager.java

@@ -158,6 +158,44 @@ public class ProtegeManager {
     }
 
 
+    /**
+     * Creates and sets up a new <code>EditorKit</code> with an ontology specified by a given <code>URI</code>.
+     *
+     * @param plugin The <code>EditorKitFactoryPlugin</code> that describes the <code>EditorKitFactory</code> which will
+     *               be used to create the <code>EditorKit</code>.
+     * @param uri The ontology <code>URI</code> with which the new <code>EditorKit</code> will be instantiated
+     */
+    public EditorKit createAndSetupNewEditorKit(EditorKitFactory editorKitFactory, URI uri) throws Exception {
+        if (editorKitFactory != null) {
+            boolean success = false;
+            EditorKit editorKit = editorKitFactory.createEditorKit();
+
+            try {
+                if (editorKit.handleLoadFrom(uri)) {
+                    getEditorKitManager().addEditorKit(editorKit);
+                    success = true;
+                    if(getEditorKitManager().getEditorKitCount() == 1) {
+                        firstEditorKit = new WeakReference<EditorKit>(editorKit);
+                    }
+                    return editorKit;
+                }
+            }
+            finally {
+                if (!success) {
+                    editorKit.dispose();
+                }
+            }
+        }
+        return null;
+    }
+
+
+    public boolean createAndSetupNewEditorKit(EditorKitFactoryPlugin plugin, URI uri) throws Exception {
+        EditorKitFactory editorKitFactory = getEditorKitFactory(plugin);
+        return createAndSetupNewEditorKit(editorKitFactory, uri) != null;
+    }
+
+
     /**
      * Opens an <code>EditorKit</code> using the <code>EditorKitFactory</code> specified by the given Id.
      *

protege-distribution/src/main/env/linux/run.sh

@@ -7,7 +7,7 @@ jre/bin/java -Xmx500M -Xms250M \
      -DentityExpansionLimit=100000000 \
      -Dfile.encoding=UTF-8 \
      -classpath bin/org.apache.felix.main.jar:bin/ProtegeLauncher.jar \
-     $CMD_OPTIONS org.protege.osgi.framework.Launcher
+     $CMD_OPTIONS org.protege.osgi.framework.Launcher $1
 
 
 

protege-distribution/src/main/env/os-x/run.command

@@ -7,7 +7,7 @@ jre/bin/java -Xmx500M -Xms250M \
      -DentityExpansionLimit=100000000 \
      -Dfile.encoding=UTF-8 \
      -classpath bin/org.apache.felix.main.jar:bin/ProtegeLauncher.jar \
-     $CMD_OPTIONS org.protege.osgi.framework.Launcher
+     $CMD_OPTIONS org.protege.osgi.framework.Launcher $1
 
 
 

protege-distribution/src/main/env/platform-independent/run.bat

@@ -1,2 +1,2 @@
 
-java -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/org.apache.felix.main.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher
+java -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/org.apache.felix.main.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher %1

protege-distribution/src/main/env/platform-independent/run.command

@@ -1,6 +1,6 @@
 cd "$(dirname "$0")"
 
-CMD_OPTIONS="-Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=Protege -Xdock:name=Protege -Xdock:icon=Protege.icns" sh run.sh
+CMD_OPTIONS="-Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=Protege -Xdock:name=Protege -Xdock:icon=Protege.icns" sh run.sh $1
 
 
 

protege-distribution/src/main/env/platform-independent/run.sh

@@ -7,7 +7,7 @@ java -Xmx500M -Xms250M \
      -DentityExpansionLimit=100000000 \
      -Dfile.encoding=UTF-8 \
      -classpath bin/org.apache.felix.main.jar:bin/ProtegeLauncher.jar \
-     $CMD_OPTIONS org.protege.osgi.framework.Launcher
+     $CMD_OPTIONS org.protege.osgi.framework.Launcher $1
 
 
 

protege-distribution/src/main/env/win/run.bat

@@ -1,2 +1,2 @@
 
-jre\bin\java -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/org.apache.felix.main.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher
+jre\bin\java -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/org.apache.felix.main.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher %1