bug fixes

src/juicebox/MainWindow.java

@@ -52,6 +52,7 @@
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
+import java.io.File;
 
 public class MainWindow extends JFrame {
 
@@ -420,11 +421,11 @@ public void exitActionPerformed() {
         if (option == 0) {
             setVisible(false);
             dispose();
-            String autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" +
+            String autoSaveFileName = DirectoryManager.getHiCDirectory() + File.separator +
                     System.nanoTime() + ".review.autosave.assembly";
             try {
-                autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" +
-                        (SuperAdapter.getDatasetTitle().split(".+?/(?=[^/]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] +
+                autoSaveFileName = DirectoryManager.getHiCDirectory() + File.separator +
+                        (SuperAdapter.getDatasetTitle().split(".+?(/|\\\\)(?=[^(/|\\\\)]+$)")[1]).split("\\.(?=[^\\.]+$)")[0]  +
                         ".review.autosave.assembly";
             } catch (Exception e) {
                 System.err.println("Unable to get desired file name");

src/juicebox/assembly/AssemblyStateTracker.java

@@ -28,6 +28,7 @@
 import juicebox.HiCGlobals;
 import juicebox.gui.SuperAdapter;
 
+import java.io.File;
 import java.util.Stack;
 
 /**
@@ -48,7 +49,7 @@ public AssemblyStateTracker(AssemblyScaffoldHandler assemblyScaffoldHandler, Sup
         redoStack = new Stack<>();
         this.initialAssemblyScaffoldHandler = assemblyScaffoldHandler;
         this.superAdapter = superAdapter;
-        this.autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" + (SuperAdapter.getDatasetTitle().split(".+?/(?=[^/]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] + ".review.autosave";
+        this.autoSaveFileName = DirectoryManager.getHiCDirectory() + File.separator + (SuperAdapter.getDatasetTitle().split(".+?(/|\\\\)(?=[^(/|\\\\)]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] + ".review.autosave";
     }
 
     public AssemblyScaffoldHandler getAssemblyHandler() {

src/juicebox/data/AbstractDatasetReader.java

@@ -35,6 +35,7 @@
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.io.File;
 
 /**
  * Abstract base class for methods that can be shared by V1 and V2 readers.
@@ -63,9 +64,9 @@ public double[] readEigenvector(String chrName, HiCZoom zoom, int number, String
 
         // If there's an eigenvector file load it
         String rootPath = FileUtils.getParent(path);
-        String folder = rootPath + "/" + chrName;
+        String folder = rootPath + File.separator + chrName;
         String eigenFile = "eigen" + "_" + chrName + "_" + chrName + "_" + zoom.getBinSize() + "_" + type + ".wig";
-        String fullPath = folder + "/" + eigenFile;
+        String fullPath = folder + File.separator + eigenFile;
 
         if (FileUtils.resourceExists(fullPath)) {
             System.out.println("Reading " + fullPath);

src/juicebox/data/Dataset.java

@@ -45,6 +45,7 @@
 import java.text.NumberFormat;
 import java.text.ParseException;
 import java.util.*;
+import java.io.File;
 
 /**
  * @author jrobinso
@@ -384,7 +385,7 @@ private String convertStats(String oldStats) {
                 "        <tr> <td> Experiment #:</td> <td>";
         String filename = reader.getPath();
         boolean mapq30 = filename.lastIndexOf("_30") > 0;
-        String[] parts = filename.split("/");
+        String[] parts = filename.split("(/|\\\\\\\\)");
         newStats += parts[parts.length - 2];
         newStats += "</td></tr>";
         newStats += "<tr> <td> Restriction Enzyme:</td><td>";

src/juicebox/gui/SuperAdapter.java

@@ -61,6 +61,7 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Properties;
+import java.io.File;
 
 /**
  * Created by muhammadsaadshamim on 8/4/15.
@@ -391,8 +392,8 @@ private static boolean genomesAreCompatible(Dataset dataset1, Dataset dataset2)
             return true;
         }
 
-        String[] g1 = dataset1.getGenomeId().split("/");
-        String[] g2 = dataset2.getGenomeId().split("/");
+        String[] g1 = dataset1.getGenomeId().split(File.separator);
+        String[] g2 = dataset2.getGenomeId().split(File.separator);
         if (g1[g1.length - 1].equalsIgnoreCase(g2[g2.length - 1])) {
             return true;
         }
@@ -725,7 +726,7 @@ private void updateTitle() {
         if (controlTitle != null && controlTitle.length() > 0) {
             newTitle += "  (control=" + controlTitle + ")";
             try {
-                fileVersions += "/" + hic.getControlDataset().getVersion();
+                fileVersions += File.separator + hic.getControlDataset().getVersion();
             } catch (Exception ignored) {
             }
         }

src/juicebox/tools/clt/juicer/MotifFinder.java

@@ -37,6 +37,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.io.File;
 
 /**
  * Created by muhammadsaadshamim on 9/4/15.
@@ -272,7 +273,7 @@ private void retrieveAllBEDFiles(String path) throws IOException {
             String inferredBEDFilesPath = path + "/inferred";
 
             // if the '/' was already included
-            if (path.endsWith("/")) {
+            if (path.endsWith(File.separator)) {
                 uniqueBEDFilesPath = path + "unique";
                 inferredBEDFilesPath = path + "inferred";
             }

src/juicebox/tools/clt/old/BPToFragment.java

@@ -35,6 +35,7 @@
 import java.util.HashMap;
 import java.util.Map;
 import java.util.regex.Pattern;
+import java.io.File;
 
 
 public class BPToFragment extends JuiceboxCLT {
@@ -84,7 +85,7 @@ private static void bpToFrag(String fragmentFile, String inputFile, String outpu
             String nextLine;
             while ((nextLine = reader.readLine()) != null) {
                 String path = nextLine.trim();
-                int lastSlashIdx = path.lastIndexOf("/");
+                int lastSlashIdx = path.lastIndexOf(File.separator);
                 if (lastSlashIdx < 0) lastSlashIdx = path.lastIndexOf("\\");  // Windows convention
                 String fn = lastSlashIdx < 0 ? path : path.substring(lastSlashIdx);
 

src/juicebox/tools/clt/old/LibraryComplexity.java

@@ -37,6 +37,7 @@
 import java.util.Locale;
 import java.util.concurrent.*;
 import java.util.concurrent.atomic.AtomicBoolean;
+import java.io.File;
 
 public class LibraryComplexity extends JuiceboxCLT {
 
@@ -231,9 +232,9 @@ public void run() {
                 Future<Long> futureUniqueReads = executor.submit(taskUniqueReads);
                 Future<Long> futureDupReadPairs = executor.submit(taskDupReadPairs);
 
-                File f = new File(localWorkingDirectory + "/" + fileName);
+                File f = new File(localWorkingDirectory + File.separator + fileName);
                 if (f.exists()) {
-                    BufferedReader reader = new BufferedReader(new FileReader(localWorkingDirectory + "/" + fileName));
+                    BufferedReader reader = new BufferedReader(new FileReader(localWorkingDirectory + File.separator + fileName));
                     String line = reader.readLine();
                     boolean done = false;
                     while (line != null && !done) {

src/juicebox/tools/dev/APAvsDistance.java

@@ -42,6 +42,7 @@
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
+import java.io.File;
 
 
 /**
@@ -219,7 +220,7 @@ public void run()  {
             XYSeries XYresults = new XYSeries("APA Result: " + resolution);
             for (int i = 0; i < numBuckets; i++) {
                 APA apa = new APA();
-                apa.initializeDirectly(hicFilePaths, PeaksFile, SaveFolderPath + "/" + (int) minPeakDist + "-" + (int) maxPeakDist, new int[]{resolution}, minPeakDist, maxPeakDist);
+                apa.initializeDirectly(hicFilePaths, PeaksFile, SaveFolderPath + File.separator + (int) minPeakDist + "-" + (int) maxPeakDist, new int[]{resolution}, minPeakDist, maxPeakDist);
                 windows[i] = minPeakDist + "-" + maxPeakDist;
                 System.out.println("Bucket:" + (i + 1) + " Window: " + windows[i]);
 

src/juicebox/tools/dev/TriplesAPA.java

@@ -36,6 +36,7 @@
 import java.io.BufferedReader;
 import java.io.FileReader;
 import java.util.*;
+import java.io.File;
 
 public class TriplesAPA extends JuicerCLT {
     public TriplesAPA() {
@@ -155,7 +156,7 @@ public void process(String chr, List<IntraChromTriple> tripleList) {
                     int min = Collections.min(plot3D.values());
 
                     int limit = Math.max((2 * max) / 3, min * 2);
-                    System.out.println(chr + " max/min/limit vals: " + max + "/" + min + "/" + limit);
+                    System.out.println(chr + " max/min/limit vals: " + max + File.separator + min + File.separator + limit);
                     for (String key : plot3D.keySet()) {
                         int val = plot3D.get(key);
                         if (val > limit) {

src/juicebox/track/LoadAction.java

@@ -48,6 +48,7 @@
 import java.util.List;
 import java.util.jar.JarEntry;
 import java.util.jar.JarFile;
+import java.io.File;
 
 
 /**
@@ -253,7 +254,7 @@ private ArrayList<String> getAvaliableXmlResourses() throws Exception {
             jar.close();
         } else { // Run with IDE
             System.out.println("Within IDE");
-            URL url = MainWindow.class.getResource("/" + resourses_path);
+            URL url = MainWindow.class.getResource(File.separator + resourses_path);
             if (url != null) {
                 try {
                     final File apps = new File(url.toURI());

src/juicebox/windowui/SaveAssemblyDialog.java

@@ -73,7 +73,7 @@ private void menuOptions() {
                     assemblyFileExporter.exportAssemblyFile();
                 }
 
-                String autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" + (SuperAdapter.getDatasetTitle().split(".+?/(?=[^/]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] + ".review.autosave.assembly";
+                String autoSaveFileName = DirectoryManager.getHiCDirectory() + File.separator + (SuperAdapter.getDatasetTitle().split(".+?(/|\\\\)(?=[^(/|\\\\)]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] + ".review.autosave.assembly";
                 File autoSaveFile = new File(autoSaveFileName);
                 autoSaveFile.delete();
             }