Added folder.exist() checks

Author: cctsou

CrossLinker/nbproject/private/private.xml

@@ -29,8 +29,14 @@
             <file>file:/C:/Umich/MS-Umpire/CrossLinker/src/crosslinker/CrossLinkerHandler.java</file>
         </group>
         <group name="MS_Umpire_Tsou">
-            <file>file:/C:/Umich/MS-Umpire/CrossLinker/src/Exec/CrossLinkerDetection.java</file>
-            <file>file:/C:/Umich/MS-Umpire/CrossLinker/src/crosslinker/CrossLinkerHandler.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PrecursorCrossPepFinder.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/CrosslinkerPepFinder.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/CXL_MALDI.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PeakPairFinder.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/MS2PeakPairFinder.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/Exec/cxl.params</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/SortedFragFinder.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/Exec/CrossLinkerDetection.java</file>
         </group>
         <group name="DIA-Umpire_Release">
             <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PrecursorCrossPepFinder.java</file>

DIA_Umpire_ExtLibSearch/src/dia_umpire_quant/DIA_Umpire_ExtLibSearch.java

@@ -171,6 +171,10 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         ArrayList<DIAPack> FileList = new ArrayList<>();
 
             File folder = new File(WorkFolder);
+            if(!folder.exists()){
+                Logger.getRootLogger().info("The path : "+ WorkFolder + " cannot be found.");
+                System.exit(1);
+            }
             for (final File fileEntry : folder.listFiles()) {
                 if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                         && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")

DIA_Umpire_IntLibSearch/src/dia_umpire_quant/DIA_Umpire_IntLibSearch.java

@@ -172,6 +172,10 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         ArrayList<DIAPack> FileList = new ArrayList<>();
         try {
             File folder = new File(WorkFolder);
+            if(!folder.exists()){
+                Logger.getRootLogger().info("The path : "+ WorkFolder + " cannot be found.");
+                System.exit(1);
+            }
             for (final File fileEntry : folder.listFiles()) {
                 if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                         && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")

DIA_Umpire_LCMSIDGen/src/dia_umpire_quant/DIA_Umpire_LCMSIDGen.java

@@ -132,6 +132,10 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         ArrayList<DIAPack> FileList = new ArrayList<>();
 
         File folder = new File(WorkFolder);
+        if (!folder.exists()) {
+            Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found.");
+            System.exit(1);
+        }
         for (final File fileEntry : folder.listFiles()) {
             if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                     && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")

DIA_Umpire_ProtQuant/nbproject/private/private.xml

@@ -3,6 +3,9 @@
     <editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/2" lastBookmarkId="0"/>
     <open-files xmlns="http://www.netbeans.org/ns/projectui-open-files/2">
         <group name="DIA-Umpire_release"/>
+        <group name="MS_Umpire_Tsou">
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/DIA_Umpire_ProtQuant/src/dia_umpire_quant/DIA_Umpire_ProtQuant.java</file>
+        </group>
         <group name="DIA-Umpire_Release">
             <file>file:/C:/Umich/GitHub/DIA-Umpire/DIA_Umpire_ProtQuant/src/dia_umpire_quant/DIA_Umpire_ProtQuant.java</file>
         </group>

DIA_Umpire_ProtQuant/src/dia_umpire_quant/DIA_Umpire_ProtQuant.java

@@ -283,6 +283,10 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         ArrayList<DIAPack> FileList = new ArrayList<>();
         try {
             File folder = new File(WorkFolder);
+            if(!folder.exists()){
+                Logger.getRootLogger().info("The path : "+ WorkFolder + " cannot be found.");
+                System.exit(1);
+            }
             for (final File fileEntry : folder.listFiles()) {
                 if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                         && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")

DIA_Umpire_Quant/src/dia_umpire_quant/DIA_Umpire_Quant.java

@@ -361,6 +361,10 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         ArrayList<DIAPack> FileList = new ArrayList<>();
         try {
             File folder = new File(WorkFolder);
+            if(!folder.exists()){
+                Logger.getRootLogger().info("The path : "+ WorkFolder + " cannot be found.");
+                System.exit(1);
+            }
             for (final File fileEntry : folder.listFiles()) {
                 if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                         && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")