Encode

scripts/mac.app/Contents/MacOS/main.c

@@ -0,0 +1,146 @@
+//
+//  main.c
+//  igv-launcher
+//
+//  Created by James Robinson on 9/14/24.
+//
+//  Launch IGV on MacOS (https://github.com/igvteam/igv).
+//
+//  Code adapted from https://incenp.org/notes/2023/universal-java-app-on-macos.html
+//
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <limits.h>
+#include <string.h>
+#include <err.h>
+#include <mach-o/dyld.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <CoreFoundation/CoreFoundation.h>
+
+
+/* Remove the last n components of a pathname. The pathname
+ * is modified in place. Returns 0 if the requested number
+ * of components have been removed, -1 otherwise. */
+static int remove_last_component(char *buffer , unsigned n)
+{
+    char *last_slash = NULL;
+    while ( n-- > 0 ) {
+        if ( (last_slash = strrchr(buffer, '/')) )
+            *last_slash = '\0';
+    }
+    return last_slash ? 0 : -1;
+}
+
+/*
+ * Test if a given path exists and if it is a  directory.
+ * It returns 1 if given path is directory and  exists
+ * otherwise returns 0.
+ */
+static int isDirectoryExists(const char *path)
+{
+    struct stat stats;
+    stat(path, &stats);
+
+    // Check for file existence
+    if (S_ISDIR(stats.st_mode))
+        return 1;
+
+    return 0;
+}
+
+static int simpleLauncher(int argc, char **argv)
+{
+    char app_path[PATH_MAX];
+    uint32_t path_size = PATH_MAX;
+    int ret = 0;
+
+    (void) argc;
+    (void) argv;
+
+    /* Get the path to the "Contents" directory. */
+    if ( _NSGetExecutablePath(app_path, &path_size) == -1 )
+        err(EXIT_FAILURE, "Cannot get application directory");
+    if ( remove_last_component(app_path, 2) == -1 )
+        errx(EXIT_FAILURE, "Cannot get application directory");
+
+    /* Move to that directory. */
+    if ( chdir(app_path) == -1 )
+        err(EXIT_FAILURE, "Cannot change current directory");
+
+    char* cmd;
+
+    /* See if there is a bundled JDK */
+    if(isDirectoryExists("jdk-21")) {
+        char jdkPath[2048] = {'\0'};
+        snprintf(jdkPath, sizeof(jdkPath), "%s/jdk-21", app_path);
+
+        setenv("JAVA_HOME", jdkPath, true);
+
+        char javaPath[2048] = {'\0'};
+        snprintf(javaPath, sizeof(javaPath), "%s/bin/java", jdkPath);
+        cmd = javaPath;
+
+        printf("Using bundled JDK");
+
+        //PATH=$JAVA_HOME/bin:$PATH
+    } else {
+
+        cmd = "java";
+        printf("Using System JDK\n");
+    }
+
+    /* Get user defined extra arguments, if any */
+    char extraArgumentsPath[2048] = {'\0'};
+    const char *homeDir = getenv("HOME");
+    snprintf(extraArgumentsPath, sizeof(extraArgumentsPath), "%s/.igv/java_arguments", homeDir);
+
+    if(access(extraArgumentsPath, F_OK) == 0) {
+        char extraArguments[2048] = {'\0'};
+        snprintf(extraArguments, sizeof(extraArguments), "@%s", extraArgumentsPath);
+
+        /* Run IGV with user extra arguments */
+
+
+        char* args[] = {
+            "java",
+            "-showversion",
+            "--module-path=Java/lib",
+            "-Xmx8g",
+            "@Java/igv.args",
+            "-Xdock:name=IGV",
+            "-Xdock:icon=Resources/IGV_64.png",
+            "-Dapple.laf.useScreenMenuBar=true",
+            extraArguments,
+            "--module=org.igv/org.broad.igv.ui.Main",
+            NULL};
+
+        ret = execvp(cmd, args);
+        return ret;
+
+    } else {
+
+        /* Run IGV without user extra arguments */
+
+        char* args[] = {
+            "java",
+            "-showversion",
+            "--module-path=Java/lib",
+            "-Xmx8g",
+            "@Java/igv.args",
+            "-Xdock:name=IGV",
+            "-Xdock:icon=Resources/IGV_64.png",
+            "--module=org.igv/org.broad.igv.ui.Main",
+            NULL};
+
+        ret = execvp(cmd, args);
+        return ret;
+    }
+}
+
+int main(int argc, char **argv)
+{
+    return simpleLauncher(argc, argv);
+}

src/main/java/org/broad/igv/util/encode/DCCEncodeUtils.java → src/main/java/org/broad/igv/encode/DCCEncodeUtils.java

@@ -23,7 +23,7 @@
  * THE SOFTWARE.
  */
 
-package org.broad.igv.util.encode;
+package org.broad.igv.encode;
 
 /**
  * Created by jrobinso on 6/4/15.

src/main/java/org/broad/igv/util/encode/EncodeFileRecord.java → src/main/java/org/broad/igv/encode/EncodeFileRecord.java

@@ -23,7 +23,7 @@
  * THE SOFTWARE.
  */
 
-package org.broad.igv.util.encode;
+package org.broad.igv.encode;
 
 import java.io.File;
 import java.util.Collection;
@@ -70,11 +70,8 @@ public Collection<String> getAttributeNames() {
         return attributes.keySet();
     }
 
-    public boolean containsText(String filter) {
-        for (String value : attributes.values()) {
-            if (value.contains(filter)) return true;
-        }
-        return false;
+    public Map<String, String> getAttributes() {
+        return attributes;
     }
 
     boolean isSelected() {
@@ -108,14 +105,4 @@ public String getTrackName() {
 
     }
 
-    /**
-     * Test if record has a eough of meta-data to be interpretable
-     *
-     * @return
-     */
-    public boolean hasMetaData() {
-
-        return  (attributes.containsKey("cell")) || (attributes.containsKey("antibody"));
-
-    }
 }

src/main/java/org/broad/igv/util/encode/EncodeTableModel.java → src/main/java/org/broad/igv/encode/EncodeTableModel.java

@@ -23,41 +23,16 @@
  * THE SOFTWARE.
  */
 
-package org.broad.igv.util.encode;
+package org.broad.igv.encode;
 
-import javax.swing.*;
 import javax.swing.table.AbstractTableModel;
 import javax.swing.table.TableModel;
 import javax.swing.table.TableRowSorter;
 import javax.swing.table.TableStringConverter;
 import java.util.ArrayList;
-import java.util.Collections;
-import java.util.LinkedHashSet;
 import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 /**
- * //wgEncodeBroadHistoneGm12878H3k4me1StdSig.bigWig
- * // size=346M;
- * // dateSubmitted=2009-01-05;
- * // dataType=ChipSeq;
- * // cell=GM12878;
- * // antibody=H3K4me1;
- * // control=std;
- * // expId=33;
- * // setType=exp;
- * // controlId=GM12878/Input/std;
- * // subId=2804;
- * // dataVersion=ENCODE Jan 2011 Freeze;
- * // dateResubmitted=2010-11-05;
- * // grant=Bernstein;
- * // lab=Broad;
- * // view=Signal;
- * // type=bigWig;
- * // dccAccession=wgEncodeEH000033;
- * // origAssembly=hg18
- *
  * @author jrobinso
  *         Date: 10/31/13
  *         Time: 10:09 PM
@@ -68,7 +43,7 @@ public class EncodeTableModel extends AbstractTableModel {
     private List<EncodeFileRecord> records;
     private final TableRowSorter<EncodeTableModel> sorter;
 
-    public EncodeTableModel(String [] headings, List<EncodeFileRecord> records) {
+    public EncodeTableModel(List<String> headings, List<EncodeFileRecord> records) {
 
         this.records = records;
 
@@ -80,11 +55,10 @@ public EncodeTableModel(String [] headings, List<EncodeFileRecord> records) {
                 tmp.add(heading);
             }
         }
-        //tmp.add("path");
-        columnHeadings = tmp.toArray(new String[tmp.size()]);
 
+        columnHeadings = tmp.toArray(new String[tmp.size()]);
 
-        sorter = new TableRowSorter<EncodeTableModel>(this);
+        sorter = new TableRowSorter<>(this);
 
         sorter.setStringConverter(new TableStringConverter() {
             @Override
@@ -149,6 +123,8 @@ public void setValueAt(Object value, int row, int col) {
         fireTableCellUpdated(row, col);
     }
 
+
+
     public List<EncodeFileRecord> getRecords() {
         return records;
     }