diff smart_toolShed/SMART/Java/WindowsRegistry.java @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/WindowsRegistry.java	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,387 @@
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.prefs.Preferences;
+
+public class WindowsRegistry {
+  public static final int HKEY_CURRENT_USER = 0x80000001;
+  public static final int HKEY_LOCAL_MACHINE = 0x80000002;
+  public static final int REG_SUCCESS = 0;
+  public static final int REG_NOTFOUND = 2;
+  public static final int REG_ACCESSDENIED = 5;
+
+  private static final int KEY_ALL_ACCESS = 0xf003f;
+  private static final int KEY_READ = 0x20019;
+  private static Preferences userRoot = Preferences.userRoot();
+  private static Preferences systemRoot = Preferences.systemRoot();
+  private static Class<? extends Preferences> userClass = userRoot.getClass();
+  private static Method regOpenKey = null;
+  private static Method regCloseKey = null;
+  private static Method regQueryValueEx = null;
+  private static Method regEnumValue = null;
+  private static Method regQueryInfoKey = null;
+  private static Method regEnumKeyEx = null;
+  private static Method regCreateKeyEx = null;
+  private static Method regSetValueEx = null;
+  private static Method regDeleteKey = null;
+  private static Method regDeleteValue = null;
+
+  static {
+    try {
+      regOpenKey = userClass.getDeclaredMethod("WindowsRegOpenKey",
+          new Class[] { int.class, byte[].class, int.class });
+      regOpenKey.setAccessible(true);
+      regCloseKey = userClass.getDeclaredMethod("WindowsRegCloseKey",
+          new Class[] { int.class });
+      regCloseKey.setAccessible(true);
+      regQueryValueEx = userClass.getDeclaredMethod("WindowsRegQueryValueEx",
+          new Class[] { int.class, byte[].class });
+      regQueryValueEx.setAccessible(true);
+      regEnumValue = userClass.getDeclaredMethod("WindowsRegEnumValue",
+          new Class[] { int.class, int.class, int.class });
+      regEnumValue.setAccessible(true);
+      regQueryInfoKey = userClass.getDeclaredMethod("WindowsRegQueryInfoKey1",
+          new Class[] { int.class });
+      regQueryInfoKey.setAccessible(true);
+      regEnumKeyEx = userClass.getDeclaredMethod(  
+          "WindowsRegEnumKeyEx", new Class[] { int.class, int.class,  
+              int.class });  
+      regEnumKeyEx.setAccessible(true);
+      regCreateKeyEx = userClass.getDeclaredMethod(  
+          "WindowsRegCreateKeyEx", new Class[] { int.class,  
+              byte[].class });  
+      regCreateKeyEx.setAccessible(true);  
+      regSetValueEx = userClass.getDeclaredMethod(  
+          "WindowsRegSetValueEx", new Class[] { int.class,  
+              byte[].class, byte[].class });  
+      regSetValueEx.setAccessible(true); 
+      regDeleteValue = userClass.getDeclaredMethod(  
+          "WindowsRegDeleteValue", new Class[] { int.class,  
+              byte[].class });  
+      regDeleteValue.setAccessible(true); 
+      regDeleteKey = userClass.getDeclaredMethod(  
+          "WindowsRegDeleteKey", new Class[] { int.class,  
+              byte[].class });  
+      regDeleteKey.setAccessible(true); 
+    }
+    catch (Exception e) {
+      e.printStackTrace();
+    }
+  }
+
+  private WindowsRegistry() {  }
+
+  /**
+   * Read a value from key and value name
+   * @param hkey   HKEY_CURRENT_USER/HKEY_LOCAL_MACHINE
+   * @param key
+   * @param valueName
+   * @return the value
+   * @throws IllegalArgumentException
+   * @throws IllegalAccessException
+   * @throws InvocationTargetException
+   */
+  public static String readString(int hkey, String key, String valueName) 
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    if (hkey == HKEY_LOCAL_MACHINE) {
+      return readString(systemRoot, hkey, key, valueName);
+    }
+    else if (hkey == HKEY_CURRENT_USER) {
+      return readString(userRoot, hkey, key, valueName);
+    }
+    else {
+      throw new IllegalArgumentException("hkey=" + hkey);
+    }
+  }
+
+  /**
+   * Read value(s) and value name(s) form given key 
+   * @param hkey  HKEY_CURRENT_USER/HKEY_LOCAL_MACHINE
+   * @param key
+   * @return the value name(s) plus the value(s)
+   * @throws IllegalArgumentException
+   * @throws IllegalAccessException
+   * @throws InvocationTargetException
+   */
+  public static Map<String, String> readStringValues(int hkey, String key) 
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    if (hkey == HKEY_LOCAL_MACHINE) {
+      return readStringValues(systemRoot, hkey, key);
+    }
+    else if (hkey == HKEY_CURRENT_USER) {
+      return readStringValues(userRoot, hkey, key);
+    }
+    else {
+      throw new IllegalArgumentException("hkey=" + hkey);
+    }
+  }
+
+  /**
+   * Read the value name(s) from a given key
+   * @param hkey  HKEY_CURRENT_USER/HKEY_LOCAL_MACHINE
+   * @param key
+   * @return the value name(s)
+   * @throws IllegalArgumentException
+   * @throws IllegalAccessException
+   * @throws InvocationTargetException
+   */
+  public static List<String> readStringSubKeys(int hkey, String key) 
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    if (hkey == HKEY_LOCAL_MACHINE) {
+      return readStringSubKeys(systemRoot, hkey, key);
+    }
+    else if (hkey == HKEY_CURRENT_USER) {
+      return readStringSubKeys(userRoot, hkey, key);
+    }
+    else {
+      throw new IllegalArgumentException("hkey=" + hkey);
+    }
+  }
+
+  /**
+   * Create a key
+   * @param hkey  HKEY_CURRENT_USER/HKEY_LOCAL_MACHINE
+   * @param key
+   * @throws IllegalArgumentException
+   * @throws IllegalAccessException
+   * @throws InvocationTargetException
+   */
+  public static void createKey(int hkey, String key) 
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    int [] ret;
+    if (hkey == HKEY_LOCAL_MACHINE) {
+      ret = createKey(systemRoot, hkey, key);
+      regCloseKey.invoke(systemRoot, new Object[] { new Integer(ret[0]) });
+    }
+    else if (hkey == HKEY_CURRENT_USER) {
+      ret = createKey(userRoot, hkey, key);
+      regCloseKey.invoke(userRoot, new Object[] { new Integer(ret[0]) });
+    }
+    else {
+      throw new IllegalArgumentException("hkey=" + hkey);
+    }
+    if (ret[1] != REG_SUCCESS) {
+      throw new IllegalArgumentException("rc=" + ret[1] + "  key=" + key);
+    }
+  }
+
+  /**
+   * Write a value in a given key/value name
+   * @param hkey
+   * @param key
+   * @param valueName
+   * @param value
+   * @throws IllegalArgumentException
+   * @throws IllegalAccessException
+   * @throws InvocationTargetException
+   */
+  public static void writeStringValue
+    (int hkey, String key, String valueName, String value) 
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    if (hkey == HKEY_LOCAL_MACHINE) {
+      writeStringValue(systemRoot, hkey, key, valueName, value);
+    }
+    else if (hkey == HKEY_CURRENT_USER) {
+      writeStringValue(userRoot, hkey, key, valueName, value);
+    }
+    else {
+      throw new IllegalArgumentException("hkey=" + hkey);
+    }
+  }
+
+  /**
+   * Delete a given key
+   * @param hkey
+   * @param key
+   * @throws IllegalArgumentException
+   * @throws IllegalAccessException
+   * @throws InvocationTargetException
+   */
+  public static void deleteKey(int hkey, String key) 
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    int rc = -1;
+    if (hkey == HKEY_LOCAL_MACHINE) {
+      rc = deleteKey(systemRoot, hkey, key);
+    }
+    else if (hkey == HKEY_CURRENT_USER) {
+      rc = deleteKey(userRoot, hkey, key);
+    }
+    if (rc != REG_SUCCESS) {
+      throw new IllegalArgumentException("rc=" + rc + "  key=" + key);
+    }
+  }
+
+  /**
+   * delete a value from a given key/value name
+   * @param hkey
+   * @param key
+   * @param value
+   * @throws IllegalArgumentException
+   * @throws IllegalAccessException
+   * @throws InvocationTargetException
+   */
+  public static void deleteValue(int hkey, String key, String value) 
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    int rc = -1;
+    if (hkey == HKEY_LOCAL_MACHINE) {
+      rc = deleteValue(systemRoot, hkey, key, value);
+    }
+    else if (hkey == HKEY_CURRENT_USER) {
+      rc = deleteValue(userRoot, hkey, key, value);
+    }
+    if (rc != REG_SUCCESS) {
+      throw new IllegalArgumentException("rc=" + rc + "  key=" + key + "  value=" + value);
+    }
+  }
+
+  // =====================
+
+  private static int deleteValue
+    (Preferences root, int hkey, String key, String value)
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    int[] handles = (int[]) regOpenKey.invoke(root, new Object[] {
+        new Integer(hkey), toCstr(key), new Integer(KEY_ALL_ACCESS) });
+    if (handles[1] != REG_SUCCESS) {
+      return handles[1];  // can be REG_NOTFOUND, REG_ACCESSDENIED
+    }
+    int rc =((Integer) regDeleteValue.invoke(root,  
+        new Object[] { 
+          new Integer(handles[0]), toCstr(value) 
+          })).intValue();
+    regCloseKey.invoke(root, new Object[] { new Integer(handles[0]) });
+    return rc;
+  }
+
+  private static int deleteKey(Preferences root, int hkey, String key) 
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    int rc =((Integer) regDeleteKey.invoke(root,  
+        new Object[] { new Integer(hkey), toCstr(key) })).intValue();
+    return rc;  // can REG_NOTFOUND, REG_ACCESSDENIED, REG_SUCCESS
+  }
+
+  private static String readString(Preferences root, int hkey, String key, String value)
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    int[] handles = (int[]) regOpenKey.invoke(root, new Object[] {
+        new Integer(hkey), toCstr(key), new Integer(KEY_READ) });
+    if (handles[1] != REG_SUCCESS) {
+      return null; 
+    }
+    byte[] valb = (byte[]) regQueryValueEx.invoke(root, new Object[] {
+        new Integer(handles[0]), toCstr(value) });
+    regCloseKey.invoke(root, new Object[] { new Integer(handles[0]) });
+    return (valb != null ? new String(valb).trim() : null);
+  }
+
+  private static Map<String,String> readStringValues
+    (Preferences root, int hkey, String key)
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    HashMap<String, String> results = new HashMap<String,String>();
+    int[] handles = (int[]) regOpenKey.invoke(root, new Object[] {
+        new Integer(hkey), toCstr(key), new Integer(KEY_READ) });
+    if (handles[1] != REG_SUCCESS) {
+      return null;
+    }
+    int[] info = (int[]) regQueryInfoKey.invoke(root,
+        new Object[] { new Integer(handles[0]) });
+
+    int count = info[2]; // count  
+    int maxlen = info[3]; // value length max
+    for(int index=0; index<count; index++)  {
+      byte[] name = (byte[]) regEnumValue.invoke(root, new Object[] {
+          new Integer
+            (handles[0]), new Integer(index), new Integer(maxlen + 1)});
+      String value = readString(hkey, key, new String(name));
+      results.put(new String(name).trim(), value);
+    }
+    regCloseKey.invoke(root, new Object[] { new Integer(handles[0]) });
+    return results;
+  }
+
+  private static List<String> readStringSubKeys
+    (Preferences root, int hkey, String key)
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    List<String> results = new ArrayList<String>();
+    int[] handles = (int[]) regOpenKey.invoke(root, new Object[] {
+        new Integer(hkey), toCstr(key), new Integer(KEY_READ) 
+        });
+    if (handles[1] != REG_SUCCESS) {
+      return null;
+    }
+    int[] info = (int[]) regQueryInfoKey.invoke(root,
+        new Object[] { new Integer(handles[0]) });
+
+    int count = info[2]; // count  
+    int maxlen = info[3]; // value length max
+    for(int index=0; index<count; index++)  {
+      byte[] name = (byte[]) regEnumKeyEx.invoke(root, new Object[] {
+          new Integer
+            (handles[0]), new Integer(index), new Integer(maxlen + 1)
+          });
+      results.add(new String(name).trim());
+    }
+    regCloseKey.invoke(root, new Object[] { new Integer(handles[0]) });
+    return results;
+  }
+
+  private static int [] createKey(Preferences root, int hkey, String key)
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    return  (int[]) regCreateKeyEx.invoke(root,
+        new Object[] { new Integer(hkey), toCstr(key) });
+  }
+
+  private static void writeStringValue 
+    (Preferences root, int hkey, String key, String valueName, String value) 
+    throws IllegalArgumentException, IllegalAccessException,
+    InvocationTargetException 
+  {
+    int[] handles = (int[]) regOpenKey.invoke(root, new Object[] {
+        new Integer(hkey), toCstr(key), new Integer(KEY_ALL_ACCESS) });
+
+    regSetValueEx.invoke(root,  
+        new Object[] { 
+          new Integer(handles[0]), toCstr(valueName), toCstr(value) 
+          }); 
+    regCloseKey.invoke(root, new Object[] { new Integer(handles[0]) });
+  }
+
+  // utility
+  private static byte[] toCstr(String str) {
+    byte[] result = new byte[str.length() + 1];
+
+    for (int i = 0; i < str.length(); i++) {
+      result[i] = (byte) str.charAt(i);
+    }
+    result[str.length()] = 0;
+    return result;
+  }
+}
+