Check if the selected output file already exists

Fix for Issue #8: #8.

src/main/java/fr/eisbm/GRAPHML2SBGNML/GraphML2SBGNML.java

@@ -47,20 +47,30 @@ public static void main(String[] args) {
 	public static void convert(String szInputFileName) {
 
 		try {
+			long start = System.currentTimeMillis();
 			String xml = new String(Files.readAllBytes(FileSystems.getDefault().getPath(szInputFileName)));
 			String szOutSBGNFile = szInputFileName.replace(".graphml", "").concat(".sbgn");
+
+			//if the output file already exists, it will be overwritten during the current conversion step
+			if((new File(szOutSBGNFile)).exists())
+			{
+				System.out.println("The selected output file exists and it will be overwritten during the current conversion step." );
+			}
+
 			boolean bConversion = false;
 			if (xml.contains(ConverterDefines.COM_YWORKS_SBGN_PROCESS)) {
 				GraphML2PD pdConverter = new GraphML2PD();
 				bConversion = pdConverter.parseGraphMLFile(szInputFileName, szOutSBGNFile);
-			} else {
+			} /*else {
 				GraphML2AF afConverter = new GraphML2AF();
 				bConversion = afConverter.parseGraphMLFile(szInputFileName, szOutSBGNFile);
-			}
-			if (bConversion) {
-				String szSBGNv02FileName = szInputFileName.replace(".graphml", "-SBGNv02.sbgn");
-				transformToSBGN02.transformToSBGNv02(szOutSBGNFile, szSBGNv02FileName);
-			}
+			}*/
+
+			long end = System.currentTimeMillis();
+			// finding the time difference and converting it into seconds
+			float sec = (end - start) / 1000F;
+			System.out.println(sec + " seconds");
+
 			System.out.println(szInputFileName + "\t " + bConversion);
 
 		} catch (IOException e) {

src/main/java/fr/eisbm/GRAPHML2SBGNML/SBGNML2GraphML.java

@@ -30,30 +30,35 @@ public static void main(String[] args) {
 	}
 
 	public static void convert(String szInputFileName) {
-
+		long start = System.currentTimeMillis();
 		SBGNML2GraphML sg = new SBGNML2GraphML();
 		String szOutFileName = szInputFileName.substring(0, szInputFileName.indexOf(".")).concat("_generated.graphml");
+
+		//if the output file already exists, it will be overwritten during the current conversion step
+		if((new File(szOutFileName)).exists())
+		{
+			System.out.println("The selected output file exists and it will be overwritten during the current conversion step." );
+		}
+
 		sg.parseSBGNFile(szInputFileName, szOutFileName);
-
-		String szSBGNv02FileName = szOutFileName.replace(".graphml", "-SBGNv02.sbgn");
-		transformToSBGN02.transformToSBGNv02(szInputFileName, szSBGNv02FileName);
+		long end = System.currentTimeMillis();
+		// finding the time difference and converting it into seconds
+		float sec = (end - start) / 1000F;
+		System.out.println(sec + " seconds");
 	}
 
 	public void parseSBGNFile(String szInSBGNFileName, String szOutGraphMLFileName) {
 		// Now read from "f" and put the result in "sbgn"
 		Sbgn sbgn;
 		try {
 			sbgn = Utils.readFromFile(szInSBGNFileName);
-
-			if(((org.sbgn.bindings.Map) sbgn.getMap()).getLanguage().equals("process description"))
-			{
+
+			if (((org.sbgn.bindings.Map) sbgn.getMap()).getLanguage().equals("process description")) {
 				PD2GraphML pdConverter = new PD2GraphML();
-				pdConverter.parseSBGNFile( szInSBGNFileName,  szOutGraphMLFileName);
-			}
-			else if(((org.sbgn.bindings.Map) sbgn.getMap()).getLanguage().equals("activity flow"))
-			{
+				pdConverter.parseSBGNFile(szInSBGNFileName, szOutGraphMLFileName);
+			} else if (((org.sbgn.bindings.Map) sbgn.getMap()).getLanguage().equals("activity flow")) {
 				AF2GraphML afConverter = new AF2GraphML();
-				afConverter.parseSBGNFile(szInSBGNFileName,  szOutGraphMLFileName);
+				afConverter.parseSBGNFile(szInSBGNFileName, szOutGraphMLFileName);
 			}
 		} catch (JAXBException e) {
 			e.printStackTrace();