Fixing shift-click JBAT autosave bug

src/juicebox/AnnotatedExample.java

@@ -0,0 +1,172 @@
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ *  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ *  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *  FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
+ *  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ *  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ *  THE SOFTWARE.
+ */
+
+
+package juicebox;
+import  java.io.*;
+
+import com.opencsv.CSVWriter;
+import juicebox.data.*;
+import juicebox.data.basics.Chromosome;
+import juicebox.windowui.HiCZoom;
+import juicebox.windowui.NormalizationHandler;
+import juicebox.windowui.NormalizationType;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+
+public class AnnotatedExample {
+    public static void main(String[] args) throws IOException {
+        // do you want to cache portions of the file?
+        // this uses more RAM, but if you want to repeatedly
+        // query nearby regions, it can improve speed by a lot
+
+        String[] timedata = { "80", "10", "620","100", "230" };
+
+        boolean useCache = false;
+        String filename = "https://www.dropbox.com/s/a6ykz8ajgszv0b6/Trachops_cirrhosus.rawchrom.hic";
+        filename = juicebox.data.HiCFileTools.cleanUpDropboxURL(filename);
+
+        // create a hic dataset object
+
+        long s1 = System.nanoTime();
+
+        List<String> files = new ArrayList<>();
+        files.add(filename);
+        Dataset ds = HiCFileTools.extractDatasetForCLT(files, false);
+        long s2 = System.nanoTime();
+        System.out.println((s2 - s1) * 1e-9);
+        System.out.println("^^^^ line 29 execution line");
+
+        timedata[0]=String.valueOf((s2 - s1) * 1e-9);
+
+        // pick the normalization we would like
+        // this line will check multiple possible norms
+        // and pick whichever is available (in order of preference)
+
+        NormalizationType norm = NormalizationHandler.NONE;
+
+        System.out.println("Norm being used: " + norm.getLabel());
+
+        int resolution = 5000;
+
+
+        juicebox.data.basics.Chromosome[] chromosomes = ds.getChromosomeHandler().getChromosomeArrayWithoutAllByAll();
+
+
+
+        // now let's iterate on every chromosome (only intra-chromosomal regions for now)
+        for (Chromosome chromosome : chromosomes) {
+            if (chromosome.getIndex() > 6) continue;
+            long s7 = System.nanoTime();
+            Matrix matrix = ds.getMatrix(chromosome, chromosome);
+            long s8 = System.nanoTime();
+            System.out.println((s8 - s7) * 1e-9);
+            System.out.println("^^^^ line 49 execution line");
+
+            timedata[1]=String.valueOf((s8 - s7) * 1e-9);
+
+
+
+            if (matrix == null) continue;
+            long s9 = System.nanoTime();
+
+            MatrixZoomData zd = matrix.getZoomData(new HiCZoom(HiC.Unit.BP, resolution));
+            long s10 = System.nanoTime();
+            System.out.println((s10 - s9) * 1e-9);
+            System.out.println("^^^^ line 57 execution line");
+
+            timedata[2]=String.valueOf((s10 - s9) * 1e-9);
+
+
+
+
+            if (zd == null) continue;
+
+            // zd is now a data structure that contains pointers to the data
+            // *** Let's show 2 different ways to access data ***
+
+            // OPTION 2
+            // just grab sparse data for a specific region
+
+            // choose your setting for when the diagonal is in the region
+            boolean getDataUnderTheDiagonal = true;
+
+            // our bounds will be binXStart, binYStart, binXEnd, binYEnd
+            // these are in BIN coordinates, not genome coordinates
+            int binXStart = 500, binYStart = 600, binXEnd = 1000, binYEnd = 1200;
+            long s11 = System.nanoTime();
+            List<Block> blocks = zd.getNormalizedBlocksOverlapping(binXStart, binYStart, binXEnd, binYEnd, norm,false, getDataUnderTheDiagonal);
+            long s12 = System.nanoTime();
+            System.out.println((s12 - s11) * 1e-9);
+            System.out.println("^^^^ line 77 execution line");
+
+            timedata[3]=String.valueOf((s12 - s11) * 1e-9);
+
+
+            binXStart = 1500;
+            binYStart = 1600;
+            binXEnd = 2000;
+            binYEnd = 2200;
+            s11 = System.nanoTime();
+            blocks = zd.getNormalizedBlocksOverlapping(binXStart, binYStart, binXEnd, binYEnd, norm,false, getDataUnderTheDiagonal);
+            s12 = System.nanoTime();
+            System.out.println((s12 - s11) * 1e-9);
+            System.out.println("^^^^ line 88 execution line");
+
+            timedata[4]=String.valueOf((s12 - s11) * 1e-9);
+
+
+            //change file path for the different versions of juicebox you are testing, and to wherever you want to store the file. I had two different paths.
+            String csvFilePath = "C:\\Users\\Mahdi\\Downloads\\Juicebox2.csv";
+            File f = new File(csvFilePath);
+
+            if (f.exists()){
+                CSVWriter writer = new CSVWriter(new FileWriter(csvFilePath, true));
+
+                writer.writeNext(timedata);
+
+                writer.close();
+            }
+
+            else{
+                FileWriter outputfile = new FileWriter(csvFilePath);
+
+                // create CSVWriter object filewriter object as parameter
+                CSVWriter writer = new CSVWriter(outputfile);
+
+                // adding header to csv
+                String[] header = { "L29", "L49", "L57", "L77", "L88" };
+                writer.writeNext(header);
+
+                // add data to csv
+                writer.writeNext(timedata);
+                writer.close();
+            }
+
+        }
+    }
+}

src/juicebox/MainWindow.java

@@ -420,11 +420,9 @@ public void exitActionPerformed() {
         if (option == 0) {
             setVisible(false);
             dispose();
-            String autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" +
-                    System.nanoTime() + ".review.autosave.assembly";
+            String autoSaveFileName = System.nanoTime() + ".review.autosave.assembly";
             try {
-                autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" +
-                        (SuperAdapter.getDatasetTitle().split(".+?/(?=[^/]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] +
+                autoSaveFileName = SuperAdapter.getDatasetTitle().split("\\.(?=[^\\.]+$)")[0] +
                         ".review.autosave.assembly";
             } catch (Exception e) {
                 System.err.println("Unable to get desired file name");

src/juicebox/assembly/AssemblyStateTracker.java

@@ -48,7 +48,7 @@ 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 = SuperAdapter.getDatasetTitle().split("\\.(?=[^\\.]+$)")[0] + ".review.autosave";
     }
 
     public AssemblyScaffoldHandler getAssemblyHandler() {

src/juicebox/windowui/SaveAssemblyDialog.java

@@ -73,10 +73,10 @@ private void menuOptions() {
                     assemblyFileExporter.exportAssemblyFile();
                 }
 
-                String autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" + (SuperAdapter.getDatasetTitle().split(".+?/(?=[^/]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] + ".review.autosave.assembly";
+                String autoSaveFileName = SuperAdapter.getDatasetTitle().split("\\.(?=[^\\.]+$)")[0] + ".review.autosave.assembly";
                 File autoSaveFile = new File(autoSaveFileName);
                 autoSaveFile.delete();
             }
         }
     }
-}
+}