Fix for broken ant file when using no IDE like Netbeans, minor adjust…

…ment for cell type stuff in Backend and some help text for SimpleCLI added.

NeuGen/build.xml

@@ -18,6 +18,7 @@
 
     <!-- variables -->
     <property name="lib.dir" value="libs/" />
+    <property name="build.dir" value="build/" />
     <property name="dist.lib.dir" value="dist/"/>
     <property name="mainclass" value="org.neugen.gui.NeuGenApp"/>
     <property name="release.version" value="2.0"/>
@@ -64,7 +65,14 @@
 	  test-report:              JUnit report generation
 	-->
 
-	<!-- copy all dependencies in one jar (TODO add release target=win, mac or linux) -->
+	<!-- ensure that the dist/lib, dist and build dirs are available when not using an IDE -->
+    	<target name="-pre-compile">
+		<mkdir dir="${dist.lib.dir}" />
+		<mkdir dir="${dist.lib.dir}/lib" />
+		<mkdir dir="${build.dir}" />
+    	</target>
+
+	<!-- copy all dependencies in one jar (@todo: add release target=win, mac or linux) -->
 	<target name="copy-dependencies">
 		<mkdir dir="${dist.lib.dir}" />
 		<jar jarfile="${dist.lib.dir}/dependencies-all.jar">
@@ -105,7 +113,7 @@
 		 classname="com.oracle.appbundler.AppBundlerTask"   
 		 classpath="libs/appbundler-1.0.jar" />
 
-	<!-- TODO: probably we should use $JAVA_HOME below, not hardcoded path! -->
+	<!-- @todo: probably we should use $JAVA_HOME below, not hardcoded path! -->
 	<property environment="env" />
 
 	<target name="bundle-NeuGen">

NeuGen/src/org/neugen/backend/NGBackend.java

@@ -454,8 +454,9 @@ public void save_and_close_project(Map<String, XMLObject> paramTrees, String pro
 	 *
 	 * @param type
 	 * @param file
+	 * @param withCellType
 	 */
-	public void export_network(String type, String file) {
+	public void export_network(String type, String file, boolean withCellType) {
 		Net net = ngLib.getNet();
 		if ("NGX".equalsIgnoreCase(type)) {
 			logger.info("Exporting NGX data to... " + file);
@@ -466,7 +467,7 @@ public void export_network(String type, String file) {
         		TXTWriter txtWriter = new TXTWriter(net, new File(file));
 			txtWriter.setCompressed(false);
 			txtWriter.setUncompressed(true);
-			txtWriter.setWithCellType(true);
+			txtWriter.setWithCellType(withCellType);
 			txtWriter.exportNetToTXT();
 		} else {
 			logger.info("Unsupported exporter chosen.");
@@ -778,7 +779,7 @@ public static void main(String... args) {
 			Map<String, XMLObject> params = back.create_and_open_project("foo24", NeuGenConstants.NEOCORTEX_PROJECT, true, false);
 			back.modifyNPartsDensity(params, "foo24/Neocortex", 0.1);
 			back.generate_network(NeuGenConstants.NEOCORTEX_PROJECT);
-			back.export_network("NGX", "foo24.ngx");
+			back.export_network("NGX", "foo24.ngx", false);
 			back.save_and_close_project(params, "foo26");
 		} catch (Exception e) {
 			logger.fatal("Make sure you selected a valid project directory: " + e);

NeuGen/src/org/neugen/backend/main/SimpleCLI.java

@@ -75,6 +75,7 @@ public static void main(String... args) {
 			/// flags
 			boolean open_only = false;
 			boolean force = false;
+			boolean with_cell_type = false;
 			if (args.length == 5) {
 				if ("OPEN".equalsIgnoreCase(args[4])) { open_only = true; }
 			}
@@ -83,6 +84,12 @@ public static void main(String... args) {
 				if ("FORCE".equalsIgnoreCase(args[5]) || ! args[5].isEmpty()) { force = true; }
 			}
 
+			if (args.length == 7) {
+				if ("TRUE".equalsIgnoreCase(args[6])) {
+					with_cell_type = true;
+				}
+			}
+
 			try {
 				final NGBackend backend = new NGBackend();
 				backend.create_and_open_project(project_base_dir, NeuGenConstants.NEOCORTEX_PROJECT, force, open_only);
@@ -93,7 +100,7 @@ public static void main(String... args) {
 				}
 
 				backend.generate_network(project_type);
-				backend.export_network(export_format, output_name);
+				backend.export_network(export_format, output_name, with_cell_type);
 			} catch (Exception e) {
 				logger.fatal(e);
 				e.printStackTrace();
@@ -105,9 +112,15 @@ public static void main(String... args) {
 	 * @brief prints usage for the simple CLI
 	 */
 	private static void usage() {
-		System.out.println("Usage: SimpleCLI PROJECT_BASE_DIR PROJECT_TYPE EXPORT_FORMAT OUTPUT_NAME [OPEN_OR_CREATE] [FORCE]");
-		System.out.println("Project type either Neocortex or Hippocampus");
-		System.out.println("Export format: TXT, HOC or NGX");
-		System.out.println("Note: Only the first four parameters are mandatory.");
+		System.out.println("Usage: SimpleCLI PROJECT_BASE_DIR PROJECT_TYPE EXPORT_FORMAT OUTPUT_NAME [OPEN_OR_CREATE] [FORCE] [WITH_CELL_TYPE]");
+		System.out.println("\tProject base dir on your FS where the project is located");
+		System.out.println("\tProject type either Neocortex or Hippocampus");
+		System.out.println("\tExport format: TXT, HOC or NGX");
+		System.out.println("\tOutput name on your FS for the exported network given your format");
+		System.out.println("\tOpen or create: Depending on your choise you can start with a new project or a existing project (specifeid by project base dir). Default OPEN.");
+		System.out.println("\tForce: If CREATE was chosen previously, specify also FORCE to override if you specify an existing project location. Default. FALSE");
+		System.out.println("\tWith cell type: True or False, depending if we want the cell type to be encoded");
+		System.out.println("\tNote: Only the first four parameters are mandatory.");
+		System.out.println("In case of any questions contact: [email protected]");
 	}
 }