Renamed Java packages to match our contiki-os.org domain. Note that this commit does not affect external dependencies

like /tools/mspsim.

This is a very simple modification that affects a very large number of files in Contiki: Cooja,
/platform/cooja, Collect-view, Coffe-manager, and Cooja simulation files (.csc).

I've gone through Contiki to update all references I could find. Nevertheless, this commit will likely
break external dependencies, like saved Cooja simulation files.

tools/coffee-manager/org/contikios/coffee/CoffeeHeader.java

@@ -0,0 +1,203 @@
+/*
+ * Copyright (c) 2009, Swedish Institute of Computer Science
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ * @author Nicolas Tsiftes
+ *
+ */
+
+package org.contikios.coffee;
+
+class CoffeeHeader {
+	private final CoffeeConfiguration conf;
+	private final int page;
+
+	private static final int HDR_FLAG_VALID		= 0x1;
+	private static final int HDR_FLAG_ALLOCATED	= 0x2;
+	private static final int HDR_FLAG_OBSOLETE	= 0x4;
+	private static final int HDR_FLAG_MODIFIED	= 0x8;
+	private static final int HDR_FLAG_LOG		= 0x10;
+	private static final int HDR_FLAG_ISOLATED	= 0x20;
+
+	int logPage;
+	int logRecords;
+	int logRecordSize;
+	int maxPages;
+	String name;
+
+	private int flags;
+
+	public CoffeeHeader(CoffeeFS coffeeFS, int page) {
+		this.page = page;
+		conf = coffeeFS.getConfiguration();
+	}
+
+	public CoffeeHeader(CoffeeFS coffeeFS, int page, byte[] bytes) {
+		this(coffeeFS, page);
+
+		processRawHeader(bytes);
+	}
+
+	private int getInt(byte[] bytes, int index) {
+	    return (bytes[index] & 0xff) + ((bytes[index + 1] & 0xff) << 8);
+	}
+
+	private void processRawHeader(byte[] bytes) {
+		int index = 0;
+
+		logPage = getPageValue(bytes, 0);
+		index += conf.pageTypeSize;
+
+		logRecords = getInt(bytes, index);
+		index += 2;
+
+		logRecordSize = getInt(bytes, index);
+		index += 2;
+
+		maxPages = getPageValue(bytes, index);
+		index += conf.pageTypeSize;
+
+		index++; // Skip deprecated EOF hint field.
+
+		flags = bytes[index] & 0xff;
+		index++;
+
+		name = new String(bytes).substring(index,
+				index + conf.nameLength);
+		int nullCharOffset = name.indexOf(0);
+		if (nullCharOffset >= 0) {
+			name = name.substring(0, nullCharOffset);
+		}
+	}
+
+	private byte[] setPageValue(int page) {
+		byte[] bytes = new byte[conf.pageTypeSize];
+
+		for (int i = conf.pageTypeSize - 1; i >= 0; i--) {
+			bytes[i] = (byte) (page >> (8 * i));
+		}
+		return bytes;
+	}
+
+	private int getPageValue(byte[] bytes, int offset) {
+		int page = 0;
+		for (int i = 0; i < conf.pageTypeSize; i++) {
+			page |= (bytes[offset + i] & 0xff) << (8 * i);
+		}
+		return page;
+	}
+
+	public byte[] toRawHeader() {
+		byte[] bytes = new byte[2 * conf.pageTypeSize + 
+					conf.nameLength + 6];
+		int index = 0;
+
+		System.arraycopy(setPageValue(logPage), 0, bytes, 0, 
+			conf.pageTypeSize);
+		index += conf.pageTypeSize;
+
+		bytes[index++] = (byte) (logRecords >> 8);
+		bytes[index++] = (byte) logRecords;
+
+		bytes[index++] = (byte) (logRecordSize >> 8);
+		bytes[index++] = (byte) logRecordSize;
+
+		System.arraycopy(setPageValue(maxPages), 0, bytes, index,
+			conf.pageTypeSize);
+		index += conf.pageTypeSize;
+
+		bytes[index++] = 0; // Deprecated EOF hint field.
+		bytes[index++] = (byte) flags;
+
+		byte[] nameBytes = name.getBytes();
+		int copyLength = nameBytes.length > conf.nameLength ?
+					conf.nameLength : nameBytes.length;
+		System.arraycopy(nameBytes, 0, bytes, index, copyLength);
+
+		return bytes;
+	}
+
+	public int rawLength() {
+		return 2 * conf.pageTypeSize + conf.nameLength + 6;
+	}
+
+	public int getPage() {
+		return page;
+	}
+
+	public boolean isValid() {
+		return (flags & HDR_FLAG_VALID) != 0;
+	}
+
+	public boolean isAllocated() {
+		return (flags & HDR_FLAG_ALLOCATED) != 0;
+	}
+
+	public boolean isObsolete() {
+		return (flags & HDR_FLAG_OBSOLETE) != 0;
+	}
+
+	public boolean isModified() {
+		return (flags & HDR_FLAG_MODIFIED) != 0;
+	}
+
+	public boolean isIsolated() {
+		return (flags & HDR_FLAG_ISOLATED) != 0;
+	}
+
+	public boolean isLog() {
+		return (flags & HDR_FLAG_LOG) != 0;
+	}
+
+	public boolean isFree() {
+		return !isAllocated();
+	}
+
+	public boolean isActive() {
+		return isAllocated() && !isObsolete() && !isIsolated();
+	}
+
+	public void allocate() {
+	    flags |= HDR_FLAG_ALLOCATED;
+	}
+
+	public void makeObsolete() {
+	    flags |= HDR_FLAG_OBSOLETE;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public void setReservedSize(int pages) {
+		maxPages = pages;
+	}
+
+	public int getReservedSize() {
+		return maxPages;
+	}
+}