Fixed/Added JavaDoc in numerous places

src/main/java/com/jcraft/jsch/ChannelDirectTCPIP.java

@@ -183,11 +183,11 @@ public void run(){
     //System.err.println("connect end");
   }
 
-  /** {@inheritDoc} */
+  @Override
   public void setInputStream(InputStream in){
     io.setInputStream(in);
   }
-  /** {@inheritDoc} */
+  @Override
   public void setOutputStream(OutputStream out){
     io.setOutputStream(out);
   }

src/main/java/com/jcraft/jsch/ChannelSftp.java

@@ -2810,6 +2810,9 @@ public String realpath(String path) throws SftpException{
     }
   }
 
+  /**
+   * Filesystem listing class
+   */
   public class LsEntry implements Comparable{
     private  String filename;
     private  String longname;
@@ -2819,13 +2822,56 @@ public class LsEntry implements Comparable{
       setLongname(longname);
       setAttrs(attrs);
     }
+
+    /**
+     * Get the file name from the listing entry
+     * @return A string representing the file name.
+     */
     public String getFilename(){return filename;};
+
+    /**
+     * Set the file name for the listing entry
+     * @param filename The filename to be set on the listing entry
+     */
     void setFilename(String filename){this.filename = filename;};
+
+    /**
+     * Get long version of the file name for the listing entry
+     * @return A String containing the long name of the listing entry
+     */
     public String getLongname(){return longname;};
+
+    /**
+     * Set the long file name for the listing entry
+     * @param longname The long file name to be set on the listing entry
+     */
     void setLongname(String longname){this.longname = longname;};
+
+    /**
+     * Get file attributes for this listing entry
+     * @return The file attributes as a {@link SftpATTRS} object
+     */
     public SftpATTRS getAttrs(){return attrs;};
+
+    /**
+     * Set the file attributes for this listing entry
+     * @param attrs An instance of {@link SftpATTRS} with the attributes to be set
+     */
     void setAttrs(SftpATTRS attrs) {this.attrs = attrs;};
+
+    /**
+     * Return the long version of the file name for this listing entry
+     * @return The long file name
+     */
     public String toString(){ return longname; }
+
+    /**
+     * Compare 2 listing entries and return the differential value
+     * @param o The object with which to compare this listing entry
+     * @return An integer which is less-than-zero for items sorted higher than this entry, greater-than-zero for items
+     *          to be sorted lower than this entry, and 0 if the items are equal
+     * @throws ClassCastException If the provided object is not of type {@link LsEntry}
+     */
     public int compareTo(Object o) throws ClassCastException{
       if(o instanceof LsEntry){
         return filename.compareTo(((LsEntry)o).getFilename());

src/main/java/com/jcraft/jsch/ChannelSubsystem.java

@@ -40,9 +40,10 @@ public class ChannelSubsystem extends ChannelSession{
   boolean pty=false;
   boolean want_reply=true;
   String subsystem="";
-  /** {@inheritDoc} */
+  @Override
   public void setXForwarding(boolean foo){ xforwading=true; }
-  /** {@inheritDoc} */
+
+  @Override
   public void setPty(boolean foo){ pty=foo; }
   /**
    * <p>setWantReply.</p>

src/main/java/com/jcraft/jsch/CipherNone.java

@@ -60,7 +60,7 @@ public class CipherNone implements Cipher{
    */
   public void init(int mode, byte[] key, byte[] iv) throws Exception{
   }
-  /** {@inheritDoc} */
+  @Override
   public void update(byte[] foo, int s1, int len, byte[] bar, int s2) throws Exception{
   }
   /**

src/main/java/com/jcraft/jsch/DHG1.java

@@ -152,7 +152,7 @@ public void init(Session session,
     state=SSH_MSG_KEXDH_REPLY;
   }
 
-  /** {@inheritDoc} */
+  @Override
   public boolean next(Buffer _buf) throws Exception{
     int i,j;
 

src/main/java/com/jcraft/jsch/DHGEX.java

@@ -130,7 +130,7 @@ public void init(Session session,
     state=SSH_MSG_KEX_DH_GEX_GROUP;
   }
 
-  /** {@inheritDoc} */
+  @Override
   public boolean next(Buffer _buf) throws Exception{
     int i,j;
     switch(state){

src/main/java/com/jcraft/jsch/HostKey.java

@@ -47,8 +47,19 @@ public class HostKey{
   public static final int SSHRSA=2;
   static final int UNKNOWN=3;
 
+  /**
+   * The name of the host
+   */
   protected String host;
+
+  /**
+   * The type of key
+   */
   protected int type;
+
+  /**
+   * The bytes of the host key
+   */
   protected byte[] key;
 
   /**

src/main/java/com/jcraft/jsch/IdentityFile.java

@@ -932,7 +932,7 @@ private byte a2b(byte c){
     return (byte)(c-'A'+10);
   }
 
-  /** {@inheritDoc} */
+  @Override
   public boolean equals(Object o){
     if(!(o instanceof IdentityFile)) return super.equals(o);
     IdentityFile foo=(IdentityFile)o;

src/main/java/com/jcraft/jsch/KeyExchange.java

@@ -68,10 +68,29 @@ public abstract class KeyExchange{
   /** Constant <code>STATE_END=0</code> */
   public static final int STATE_END=0;
 
+  /**
+   * A JSch {@link Session} instance
+   */
   protected Session session=null;
+
+  /**
+   * The SHA hash for the key
+   */
   protected HASH sha=null;
+
+  /**
+   * TODO
+   */
   protected byte[] K=null;
+
+  /**
+   * TODO
+   */
   protected byte[] H=null;
+
+  /**
+   * TODO
+   */
   protected byte[] K_S=null;
 
   /**

src/main/java/com/jcraft/jsch/KnownHosts.java

@@ -229,7 +229,7 @@ public int check(String host, byte[] key){
 
     return result;
   }
-  /** {@inheritDoc} */
+  @Override
   public void add(HostKey hostkey, UserInfo userinfo){
     int type=hostkey.type;
     String host=hostkey.getHost();
@@ -304,7 +304,7 @@ public void add(HostKey hostkey, UserInfo userinfo){
   public HostKey[] getHostKey(){
     return getHostKey(null, null);
   }
-  /** {@inheritDoc} */
+  @Override
   public HostKey[] getHostKey(String host, String type){
     synchronized(pool){
       int count=0;
@@ -332,7 +332,7 @@ public HostKey[] getHostKey(String host, String type){
       return foo;
     }
   }
-  /** {@inheritDoc} */
+  @Override
   public void remove(String host, String type){
     remove(host, type, null);
   }

src/main/java/com/jcraft/jsch/ProxyHTTP.java

@@ -88,7 +88,7 @@ public void setUserPasswd(String user, String passwd){
     this.user=user;
     this.passwd=passwd;
   }
-  /** {@inheritDoc} */
+  @Override
   public void connect(SocketFactory socket_factory, String host, int port, int timeout) throws JSchException{
     try{
       if(socket_factory==null){

src/main/java/com/jcraft/jsch/ProxySOCKS4.java

@@ -93,7 +93,7 @@ public void setUserPasswd(String user, String passwd){
     this.user=user;
     this.passwd=passwd;
   }
-  /** {@inheritDoc} */
+  @Override
   public void connect(SocketFactory socket_factory, String host, int port, int timeout) throws JSchException{
     try{
       if(socket_factory==null){

src/main/java/com/jcraft/jsch/ProxySOCKS5.java

@@ -93,7 +93,7 @@ public void setUserPasswd(String user, String passwd){
     this.user=user;
     this.passwd=passwd;
   }
-  /** {@inheritDoc} */
+  @Override
   public void connect(SocketFactory socket_factory, String host, int port, int timeout) throws JSchException{
     try{
       if(socket_factory==null){

src/main/java/com/jcraft/jsch/Request.java

@@ -1,68 +1,96 @@
 /* -*-mode:java; c-basic-offset:2; indent-tabs-mode:nil -*- */
 /*
-Copyright (c) 2002-2010 ymnk, JCraft,Inc. All rights reserved.
+ Copyright (c) 2002-2010 ymnk, JCraft,Inc. All rights reserved.
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+ 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.
+ 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.
+ 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. The names of the authors may not be used to endorse or promote products
-     derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED 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 JCRAFT,
-INC. OR ANY CONTRIBUTORS TO THIS SOFTWARE 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.
-*/
+ 3. The names of the authors may not be used to endorse or promote products
+ derived from this software without specific prior written permission.
 
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED 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 JCRAFT,
+ INC. OR ANY CONTRIBUTORS TO THIS SOFTWARE 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.
+ */
 package com.jcraft.jsch;
 
-abstract class Request{
-  private boolean reply=false;
-  private Session session=null;
-  private Channel channel=null;
-  void request(Session session, Channel channel) throws Exception{
-    this.session=session;
-    this.channel=channel;
-    if(channel.connectTimeout>0){
+abstract class Request {
+
+  private boolean reply = false;
+  private Session session = null;
+  private Channel channel = null;
+
+  /**
+   * Make a request on the given session and channel
+   *
+   * @param session The {@link Session} on which to make the request
+   * @param channel The {@link Channel} on which to make the request
+   */
+  void request(Session session, Channel channel) {
+    this.session = session;
+    this.channel = channel;
+    if (channel.connectTimeout > 0) {
       setReply(true);
     }
   }
-  boolean waitForReply(){ return reply; }
-  void setReply(boolean reply){ this.reply=reply; }
-  void write(Packet packet) throws Exception{
-    if(reply){
-      channel.reply=-1;
+
+  /**
+   * Return TRUE if this {@link Request} is set to wait for a reply
+   */
+  boolean waitForReply() {
+    return reply;
+  }
+
+  /**
+   * Set the reply behavior for this {@link Request}
+   *
+   * @param reply Set to TRUE if the {@link Request} should wait for a reply
+   */
+  void setReply(boolean reply) {
+    this.reply = reply;
+  }
+
+  /**
+   * Write a packet to the associated session and channel
+   *
+   * @param packet The packet to be written to the session/channel
+   */
+  void write(Packet packet) throws Exception {
+    if (reply) {
+      channel.reply = -1;
     }
     session.write(packet);
-    if(reply){
-      long start=System.currentTimeMillis();
-      long timeout=channel.connectTimeout;
-      while(channel.isConnected() && channel.reply==-1){
-	try{Thread.sleep(10);}
-	catch(Exception ee){
-	}
-        if(timeout>0L &&
-           (System.currentTimeMillis()-start)>timeout){
-          channel.reply=0;
+    if (reply) {
+      long start = System.currentTimeMillis();
+      long timeout = channel.connectTimeout;
+      while (channel.isConnected() && channel.reply == -1) {
+        try {
+          Thread.sleep(10);
+        } catch (Exception ee) {
+        }
+        if (timeout > 0L
+            && (System.currentTimeMillis() - start) > timeout) {
+          channel.reply = 0;
           throw new JSchException("channel request: timeout");
         }
       }
 
-      if(channel.reply==0){
-	throw new JSchException("failed to send channel request");
+      if (channel.reply == 0) {
+        throw new JSchException("failed to send channel request");
       }
     }
   }

src/main/java/com/jcraft/jsch/RequestAgentForwarding.java

@@ -30,7 +30,7 @@ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 package com.jcraft.jsch;
 
 class RequestAgentForwarding extends Request{
-  /** {@inheritDoc} */
+  @Override
   public void request(Session session, Channel channel) throws Exception{
     super.request(session, channel);
 

src/main/java/com/jcraft/jsch/RequestEnv.java

@@ -36,7 +36,7 @@ void setEnv(byte[] name, byte[] value){
     this.name=name;
     this.value=value;
   }
-  /** {@inheritDoc} */
+  @Override
   public void request(Session session, Channel channel) throws Exception{
     super.request(session, channel);