Do some things that I haven't finished yet

src/eu/steffo/cleaver/Main.java

@@ -2,7 +2,7 @@ package eu.steffo.cleaver;
 
 import javax.swing.*;
 import eu.steffo.cleaver.gui.CleaverFrame;
-import eu.steffo.cleaver.logic.Job;
+import eu.steffo.cleaver.logic.job.Job;
 
 import java.util.ArrayList;
 

src/eu/steffo/cleaver/Test.java

@@ -1,8 +1,6 @@
 package eu.steffo.cleaver;
 
-import eu.steffo.cleaver.logic.ChopJob;
-import eu.steffo.cleaver.logic.Job;
-import eu.steffo.cleaver.logic.split.SplitFileOutputStream;
+import eu.steffo.cleaver.logic.stream.output.CleaverSplitFileOutputStream;
 
 import java.io.IOException;
 import java.io.OutputStream;
@@ -10,7 +8,7 @@ import java.io.OutputStream;
 //TODO: delet this
 public class Test {
     public static void main(String[] args) {
-        OutputStream stream = new SplitFileOutputStream("test", 64);
+        OutputStream stream = new CleaverSplitFileOutputStream("test", 64);
         for(int i = 0; i < 256; i++) {
             try {
                 stream.write(i);

src/eu/steffo/cleaver/gui/CleaverFrame.java

@@ -3,8 +3,7 @@ package eu.steffo.cleaver.gui;
 import eu.steffo.cleaver.gui.panels.ChopAndStitchPanel;
 import eu.steffo.cleaver.gui.panels.JobsButtonsPanel;
 import eu.steffo.cleaver.gui.panels.JobsTablePanel;
-import eu.steffo.cleaver.logic.Job;
-import eu.steffo.cleaver.logic.progress.NotStartedProgress;
+import eu.steffo.cleaver.logic.job.Job;
 
 import java.awt.*;
 import java.awt.event.ActionEvent;

src/eu/steffo/cleaver/gui/panels/ChopAndStitchPanel.java

@@ -1,6 +1,7 @@
 package eu.steffo.cleaver.gui.panels;
 
-import eu.steffo.cleaver.logic.Job;
+import eu.steffo.cleaver.logic.job.Job;
+import eu.steffo.cleaver.logic.job.ChopJob;
 
 import javax.swing.*;
 import java.awt.event.ActionListener;
@@ -48,7 +49,7 @@ public class ChopAndStitchPanel extends JPanel {
      * @param jobs The {@link ArrayList} of jobs that should be manipulated.
      * @param onProgressChange The function that should be invoked when the {@link Job} {@link eu.steffo.cleaver.logic.progress.Progress Progress} changes.
      * @see ChopPanel#createAndAddJobs(ArrayList, Runnable)
-     * @see eu.steffo.cleaver.logic.ChopJob
+     * @see ChopJob
      * @see eu.steffo.cleaver.gui.CleaverFrame
      */
     public void createAndAddChopJobs(ArrayList<Job> jobs, Runnable onProgressChange) {
@@ -60,7 +61,7 @@ public class ChopAndStitchPanel extends JPanel {
      * @param jobs The {@link ArrayList} of jobs that should be manipulated.
      * @param onProgressChange The function that should be invoked when the {@link Job} {@link eu.steffo.cleaver.logic.progress.Progress Progress} changes.
      * @see StitchPanel#createAndAddJobs(ArrayList, Runnable)
-     * @see eu.steffo.cleaver.logic.ChopJob
+     * @see ChopJob
      * @see eu.steffo.cleaver.gui.CleaverFrame
      */
     public void createAndAddStitchJobs(ArrayList<Job> jobs, Runnable onProgressChange) {

src/eu/steffo/cleaver/gui/panels/ChopPanel.java

@@ -4,11 +4,11 @@ import eu.steffo.cleaver.gui.panels.rows.CreateJobButtonRow;
 import eu.steffo.cleaver.gui.panels.rows.option.CompressRow;
 import eu.steffo.cleaver.gui.panels.rows.option.CryptRow;
 import eu.steffo.cleaver.gui.panels.rows.option.SplitRow;
-import eu.steffo.cleaver.logic.ChopJob;
-import eu.steffo.cleaver.logic.Job;
-import eu.steffo.cleaver.logic.compress.CompressConfig;
-import eu.steffo.cleaver.logic.crypt.CryptConfig;
-import eu.steffo.cleaver.logic.split.SplitConfig;
+import eu.steffo.cleaver.logic.job.ChopJob;
+import eu.steffo.cleaver.logic.job.Job;
+import eu.steffo.cleaver.logic.config.CompressConfig;
+import eu.steffo.cleaver.logic.config.CryptConfig;
+import eu.steffo.cleaver.logic.config.SplitConfig;
 
 import javax.swing.*;
 import java.awt.event.ActionListener;

src/eu/steffo/cleaver/gui/panels/JobsTablePanel.java

@@ -1,9 +1,9 @@
 package eu.steffo.cleaver.gui.panels;
 
-import eu.steffo.cleaver.logic.Job;
-import eu.steffo.cleaver.logic.compress.CompressConfig;
-import eu.steffo.cleaver.logic.crypt.CryptConfig;
-import eu.steffo.cleaver.logic.split.SplitConfig;
+import eu.steffo.cleaver.logic.job.Job;
+import eu.steffo.cleaver.logic.config.CompressConfig;
+import eu.steffo.cleaver.logic.config.CryptConfig;
+import eu.steffo.cleaver.logic.config.SplitConfig;
 
 import javax.swing.*;
 import javax.swing.table.AbstractTableModel;

src/eu/steffo/cleaver/gui/panels/StitchPanel.java

@@ -4,8 +4,8 @@ import eu.steffo.cleaver.errors.ChpFileError;
 import eu.steffo.cleaver.errors.ProgrammingError;
 import eu.steffo.cleaver.gui.panels.rows.CreateJobButtonRow;
 import eu.steffo.cleaver.gui.panels.rows.option.KeyRow;
-import eu.steffo.cleaver.logic.Job;
-import eu.steffo.cleaver.logic.StitchJob;
+import eu.steffo.cleaver.logic.job.Job;
+import eu.steffo.cleaver.logic.job.StitchJob;
 
 import javax.swing.*;
 import javax.swing.filechooser.FileNameExtensionFilter;

src/eu/steffo/cleaver/gui/panels/rows/option/CompressRow.java

@@ -1,6 +1,6 @@
 package eu.steffo.cleaver.gui.panels.rows.option;
 
-import eu.steffo.cleaver.logic.compress.CompressConfig;
+import eu.steffo.cleaver.logic.config.CompressConfig;
 
 import javax.swing.*;
 

src/eu/steffo/cleaver/gui/panels/rows/option/CryptRow.java

@@ -1,6 +1,6 @@
 package eu.steffo.cleaver.gui.panels.rows.option;
 
-import eu.steffo.cleaver.logic.crypt.CryptConfig;
+import eu.steffo.cleaver.logic.config.CryptConfig;
 
 import javax.swing.*;
 

src/eu/steffo/cleaver/gui/panels/rows/option/KeyRow.java

@@ -1,9 +1,11 @@
 package eu.steffo.cleaver.gui.panels.rows.option;
 
+import eu.steffo.cleaver.logic.config.CryptConfig;
+
 import javax.swing.*;
 
 /**
- * A {@link OptionRow} allowing the {@link eu.steffo.cleaver.logic.crypt.CryptConfig configuration of the crypt step} of the file stitch process.
+ * A {@link OptionRow} allowing the {@link CryptConfig configuration of the crypt step} of the file stitch process.
  *
  * This configuration is used only if the selected *.chp file specifies that the *.cXX are encrypted.
  *

src/eu/steffo/cleaver/gui/panels/rows/option/SplitRow.java

@@ -1,8 +1,8 @@
 package eu.steffo.cleaver.gui.panels.rows.option;
 
-import eu.steffo.cleaver.logic.split.SplitByPartsConfig;
-import eu.steffo.cleaver.logic.split.SplitBySizeConfig;
-import eu.steffo.cleaver.logic.split.SplitConfig;
+import eu.steffo.cleaver.logic.config.SplitByPartsConfig;
+import eu.steffo.cleaver.logic.config.SplitBySizeConfig;
+import eu.steffo.cleaver.logic.config.SplitConfig;
 
 import javax.swing.*;
 import javax.swing.event.DocumentEvent;

src/eu/steffo/cleaver/logic/compress/CompressConfig.java

@@ -1,25 +0,0 @@
-package eu.steffo.cleaver.logic.compress;
-
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-
-/**
- * A class containing the configuration for the compression step of a {@link eu.steffo.cleaver.logic.Job Job}.
- */
-public class CompressConfig {
-    @Override
-    public String toString() {
-        return "Yes (Deflate)";
-    }
-
-    /**
-     * Create a {@link Element} representing this CompressConfig (to be used in *.chp metadata files).
-     * @param doc The {@link Document} the {@link Element} should be created in.
-     * @return The created {@link Element}.
-     * @see eu.steffo.cleaver.logic.ChopJob
-     * @see eu.steffo.cleaver.logic.StitchJob
-     */
-    public Element toElement(Document doc) {
-        return doc.createElement("Compress");
-    }
-}

src/eu/steffo/cleaver/logic/compress/package-info.java

@@ -1,4 +0,0 @@
-/**
- * The package containing classes related to the (de)compression functionality.
- */
-package eu.steffo.cleaver.logic.compress;

src/eu/steffo/cleaver/logic/config/CompressConfig.java

@@ -0,0 +1,13 @@
+package eu.steffo.cleaver.logic.config;
+
+import eu.steffo.cleaver.logic.job.Job;
+
+/**
+ * A class containing the configuration for the compression step of a {@link Job Job}.
+ */
+public class CompressConfig {
+    @Override
+    public String toString() {
+        return "Yes (Deflate)";
+    }
+}

src/eu/steffo/cleaver/logic/config/CryptConfig.java

@@ -0,0 +1,30 @@
+package eu.steffo.cleaver.logic.config;
+
+import eu.steffo.cleaver.logic.job.Job;
+
+/**
+ * A class containing the configuration for the encryption/decryption step of a {@link Job Job}.
+ */
+public class CryptConfig {
+    protected final String key;
+
+    /**
+     * Construct a new CryptConfig with a specific encryption key.
+     * @param key The encryption key.
+     */
+    public CryptConfig(String key) {
+        this.key = key;
+    }
+
+    /**
+     * @return The encryption key.
+     */
+    public String getKey() {
+        return key;
+    }
+
+    @Override
+    public String toString() {
+        return "••••••••";
+    }
+}

src/eu/steffo/cleaver/logic/config/MergeConfig.java

@@ -1,4 +1,4 @@
-package eu.steffo.cleaver.logic.split;
+package eu.steffo.cleaver.logic.config;
 
 /**
  * A {@link SplitConfig} created by reading a *.chp file, containing the number of parts and their size, but not the resulting file size.

src/eu/steffo/cleaver/logic/config/SplitByPartsConfig.java

@@ -1,4 +1,4 @@
-package eu.steffo.cleaver.logic.split;
+package eu.steffo.cleaver.logic.config;
 
 public class SplitByPartsConfig extends SplitConfig {
     /**

src/eu/steffo/cleaver/logic/config/SplitBySizeConfig.java

@@ -1,4 +1,4 @@
-package eu.steffo.cleaver.logic.split;
+package eu.steffo.cleaver.logic.config;
 
 /**
  * A {@link SplitConfig} for splitting a file in parts of a specific part size.

src/eu/steffo/cleaver/logic/config/SplitConfig.java

@@ -0,0 +1,29 @@
+package eu.steffo.cleaver.logic.config;
+
+import eu.steffo.cleaver.logic.job.Job;
+
+/**
+ * A class containing the configuration for the split/merge step of a {@link Job Job}.
+ */
+public abstract class SplitConfig {
+    /**
+     * @return The size in bytes of a single part of the file.
+     */
+    public abstract long getPartSize();
+
+    /**
+     * @return The number of parts the file should be split in.
+     */
+    public abstract int getPartCount();
+
+    /**
+     * @return The total size of the original file.
+     */
+    public abstract long getTotalSize();
+
+    /**
+     * @return The string representation of the {@link SplitConfig}, to be used in the jobs table.
+     * @see eu.steffo.cleaver.gui.panels.JobsTablePanel
+     */
+    public abstract String toString();
+}

src/eu/steffo/cleaver/logic/crypt/CryptConfig.java

@@ -1,42 +0,0 @@
-package eu.steffo.cleaver.logic.crypt;
-
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-
-/**
- * A class containing the configuration for the encryption/decryption step of a {@link eu.steffo.cleaver.logic.Job Job}.
- */
-public class CryptConfig {
-    protected final String key;
-
-    /**
-     * Construct a new CryptConfig with a specific encryption key.
-     * @param key The encryption key.
-     */
-    public CryptConfig(String key) {
-        this.key = key;
-    }
-
-    /**
-     * @return The encryption key.
-     */
-    public String getKey() {
-        return key;
-    }
-
-    @Override
-    public String toString() {
-        return "••••••••";
-    }
-
-    /**
-     * Create a {@link Element} representing this CryptConfig (to be used in *.chp metadata files).
-     * @param doc The {@link Document} the {@link Element} should be created in.
-     * @return The created {@link Element}.
-     * @see eu.steffo.cleaver.logic.ChopJob
-     * @see eu.steffo.cleaver.logic.StitchJob
-     */
-    public Element toElement(Document doc) {
-        return doc.createElement("Crypt");
-    }
-}

src/eu/steffo/cleaver/logic/crypt/CryptOutputStream.java

@@ -1,122 +0,0 @@
-package eu.steffo.cleaver.logic.crypt;
-
-import eu.steffo.cleaver.errors.ProgrammingError;
-
-import javax.crypto.Cipher;
-import javax.crypto.NoSuchPaddingException;
-import javax.crypto.SecretKey;
-import javax.crypto.SecretKeyFactory;
-import javax.crypto.spec.PBEKeySpec;
-import javax.crypto.spec.SecretKeySpec;
-import java.io.FilterOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.security.InvalidKeyException;
-import java.security.NoSuchAlgorithmException;
-import java.security.SecureRandom;
-import java.security.spec.InvalidKeySpecException;
-import java.security.spec.KeySpec;
-
-public class CryptOutputStream extends FilterOutputStream {
-    private Cipher cipher;
-
-    /**
-     * @return The algorithm used for the encryption.
-     */
-    public String getAlgorithm() {
-        return "AES";
-    }
-
-    /**
-     * @return The mode of operation used for the encryption.
-     */
-    public String getModeOfOperation() {
-        return "CFB8";
-    }
-
-    /**
-     * @return The padding used for the encryption.
-     */
-    public String getPadding() {
-        return "PKCS5Padding";
-    }
-
-    /**
-     * @return The secret key algorithm used in the generation of the final key.
-     */
-    public String getKeyAlgorithm() {
-        return "PBKDF2WithHmacSHA1";
-    }
-
-    /**
-     * @return The full transformation string as required by {@link Cipher#getInstance(String)}.
-     */
-    public String getTransformationString() {
-        return String.format("%s/%s/%s", getAlgorithm(), getModeOfOperation(), getPadding());
-    }
-
-    /**
-     * Create a new CryptOutputStream with default {@link Cipher} parameters.
-     * (AES algorithm in operation mode CFB8 with PKCS5 padding)
-     *
-     * Does not use this as {@literal try} and {@literal catch} are not supported.
-     *
-     * @param out The {@link OutputStream} to connect this {@link FilterOutputStream} to.
-     * @param key The desired encryption key.
-     */
-    public CryptOutputStream(OutputStream out, String key) throws InvalidKeyException {
-        super(out);
-
-        //Setup the cipher object
-        try {
-            cipher = Cipher.getInstance(getTransformationString());
-        } catch (NoSuchAlgorithmException | NoSuchPaddingException e) {
-            //Should never happen, as it's predefined
-            e.printStackTrace();
-            return;
-        }
-
-        //Create the salt
-        byte[] salt = new byte[8];
-        SecureRandom secureRandom = new SecureRandom();
-        secureRandom.nextBytes(salt);
-
-        //Create the KeySpec
-        //Using the recommended 65536 as iteration count
-        KeySpec spec = new PBEKeySpec(key.toCharArray(), salt, 65536, 256);
-
-        SecretKeyFactory factory;
-        try {
-             factory = SecretKeyFactory.getInstance(getKeyAlgorithm());
-        } catch (NoSuchAlgorithmException e) {
-            //Should never happen, as it's predefined
-            e.printStackTrace();
-            return;
-        }
-
-        //Create the pbkdf secret key
-        SecretKey pbkdf;
-        try {
-             pbkdf = factory.generateSecret(spec);
-        } catch (InvalidKeySpecException e) {
-            //Should never happen, as it's predefined
-            e.printStackTrace();
-            return;
-        }
-
-        //"Convert" the secret key to a AES secret key
-        SecretKey aes = new SecretKeySpec(pbkdf.getEncoded(), getAlgorithm());
-
-        //Init the cipher instance
-        cipher.init(Cipher.ENCRYPT_MODE, aes);
-    }
-
-    @Override
-    public void write(int decryptedInt) throws IOException {
-        byte[] decryptedByte = new byte[1];
-        decryptedByte[0] = (byte)decryptedInt;
-        byte[] encryptedByte = cipher.update(decryptedByte);
-        int encryptedInt = encryptedByte[0];
-        super.write(encryptedInt);
-    }
-}

src/eu/steffo/cleaver/logic/crypt/package-info.java

@@ -1,4 +0,0 @@
-/**
- * The package containing classes related to the encryption/decryption functionality.
- */
-package eu.steffo.cleaver.logic.crypt;

src/eu/steffo/cleaver/logic/job/ChopJob.java

@@ -1,15 +1,15 @@
-package eu.steffo.cleaver.logic;
+package eu.steffo.cleaver.logic.job;
 
 import eu.steffo.cleaver.errors.ProgrammingError;
-import eu.steffo.cleaver.logic.compress.CompressConfig;
-import eu.steffo.cleaver.logic.crypt.CryptConfig;
-import eu.steffo.cleaver.logic.crypt.CryptOutputStream;
+import eu.steffo.cleaver.logic.config.CompressConfig;
+import eu.steffo.cleaver.logic.config.CryptConfig;
+import eu.steffo.cleaver.logic.stream.output.CleaverCryptOutputStream;
 import eu.steffo.cleaver.logic.progress.ErrorProgress;
 import eu.steffo.cleaver.logic.progress.FinishedProgress;
 import eu.steffo.cleaver.logic.progress.Progress;
 import eu.steffo.cleaver.logic.progress.WorkingProgress;
-import eu.steffo.cleaver.logic.split.SplitConfig;
-import eu.steffo.cleaver.logic.split.SplitFileOutputStream;
+import eu.steffo.cleaver.logic.config.SplitConfig;
+import eu.steffo.cleaver.logic.stream.output.CleaverSplitFileOutputStream;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
@@ -95,7 +95,7 @@ public class ChopJob extends Job {
             OutputStream outputStream;
 
             if(splitConfig != null) {
-                outputStream = new SplitFileOutputStream(file.getAbsolutePath(), splitConfig.getPartSize());
+                outputStream = new CleaverSplitFileOutputStream(file.getAbsolutePath(), splitConfig.getPartSize());
             }
             else {
                 outputStream = new FileOutputStream(String.format("%s.c0", file.getAbsolutePath()));
@@ -106,7 +106,7 @@ public class ChopJob extends Job {
             }
 
             if(cryptConfig != null) {
-                outputStream = new CryptOutputStream(outputStream, cryptConfig.getKey());
+                outputStream = new CleaverCryptOutputStream(outputStream, cryptConfig.getKey());
             }
 
             //Create the .chp file

src/eu/steffo/cleaver/logic/job/Job.java

@@ -1,13 +1,13 @@
-package eu.steffo.cleaver.logic;
+package eu.steffo.cleaver.logic.job;
 
 import java.io.File;
 import javax.swing.SwingUtilities;
 
-import eu.steffo.cleaver.logic.compress.CompressConfig;
-import eu.steffo.cleaver.logic.crypt.CryptConfig;
+import eu.steffo.cleaver.logic.config.CompressConfig;
+import eu.steffo.cleaver.logic.config.CryptConfig;
 import eu.steffo.cleaver.logic.progress.NotStartedProgress;
 import eu.steffo.cleaver.logic.progress.Progress;
-import eu.steffo.cleaver.logic.split.SplitConfig;
+import eu.steffo.cleaver.logic.config.SplitConfig;
 
 /**
  * A {@link Thread} that allows access to the basic .

src/eu/steffo/cleaver/logic/job/StitchJob.java

@@ -1,16 +1,18 @@
-package eu.steffo.cleaver.logic;
+package eu.steffo.cleaver.logic.job;
 
 import eu.steffo.cleaver.errors.ChpFileError;
 import eu.steffo.cleaver.errors.ProgrammingError;
-import eu.steffo.cleaver.logic.compress.CompressConfig;
-import eu.steffo.cleaver.logic.crypt.CryptConfig;
-import eu.steffo.cleaver.logic.crypt.CryptInputStream;
+import eu.steffo.cleaver.logic.config.CompressConfig;
+import eu.steffo.cleaver.logic.config.CryptConfig;
+import eu.steffo.cleaver.logic.config.MergeConfig;
+import eu.steffo.cleaver.logic.config.SplitConfig;
+import eu.steffo.cleaver.logic.stream.input.CryptInputStream;
 import eu.steffo.cleaver.logic.progress.ErrorProgress;
 import eu.steffo.cleaver.logic.progress.FinishedProgress;
 import eu.steffo.cleaver.logic.progress.Progress;
 import eu.steffo.cleaver.logic.progress.WorkingProgress;
-import eu.steffo.cleaver.logic.split.*;
 
+import eu.steffo.cleaver.logic.stream.input.CleaverSplitFileInputStream;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
@@ -21,7 +23,6 @@ import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import java.io.*;
-import java.util.zip.DeflaterInputStream;
 import java.util.zip.InflaterInputStream;
 
 /**
@@ -190,7 +191,7 @@ public class StitchJob extends Job {
             OutputStream outputStream = new FileOutputStream(resultFile);
 
             if (splitConfig != null) {
-                inputStream = new SplitFileInputStream(resultFile.getPath(), splitConfig.getPartSize());
+                inputStream = new CleaverSplitFileInputStream(resultFile.getPath(), splitConfig.getPartSize());
             }
             else {
                 inputStream = new FileInputStream(String.format("%s.c0", resultFile.getAbsolutePath()));

src/eu/steffo/cleaver/logic/job/package-info.java

@@ -0,0 +1,4 @@
+/**
+ * The package containing all possible {@link eu.steffo.cleaver.logic.job.Job Jobs}.
+ */
+package eu.steffo.cleaver.logic.job;

src/eu/steffo/cleaver/logic/progress/ErrorProgress.java

@@ -1,7 +1,9 @@
 package eu.steffo.cleaver.logic.progress;
 
+import eu.steffo.cleaver.logic.job.Job;
+
 /**
- * A {@link Progress} that specifies that a {@link eu.steffo.cleaver.logic.Job} stopped because an exception occoured.
+ * A {@link Progress} that specifies that a {@link Job} stopped because an exception occoured.
  */
 public class ErrorProgress extends Progress {
     private final Throwable error;
@@ -15,7 +17,7 @@ public class ErrorProgress extends Progress {
     }
 
     /**
-     * @return The error encountered by the {@link eu.steffo.cleaver.logic.Job}.
+     * @return The error encountered by the {@link Job}.
      */
     public Throwable getError() {
         return error;

src/eu/steffo/cleaver/logic/progress/FinishedProgress.java

@@ -1,7 +1,9 @@
 package eu.steffo.cleaver.logic.progress;
 
+import eu.steffo.cleaver.logic.job.Job;
+
 /**
- * A {@link Progress} that specifies that a {@link eu.steffo.cleaver.logic.Job} has finished.
+ * A {@link Progress} that specifies that a {@link Job} has finished.
  */
 public class FinishedProgress extends Progress {
     @Override

src/eu/steffo/cleaver/logic/progress/NotStartedProgress.java

@@ -1,7 +1,9 @@
 package eu.steffo.cleaver.logic.progress;
 
+import eu.steffo.cleaver.logic.job.Job;
+
 /**
- * A {@link Progress} that specifies that a {@link eu.steffo.cleaver.logic.Job} hasn't started yet.
+ * A {@link Progress} that specifies that a {@link Job} hasn't started yet.
  */
 public class NotStartedProgress extends Progress {
     @Override

src/eu/steffo/cleaver/logic/progress/WorkingProgress.java

@@ -1,7 +1,9 @@
 package eu.steffo.cleaver.logic.progress;
 
+import eu.steffo.cleaver.logic.job.Job;
+
 /**
- * A {@link Progress} that specifies that a {@link eu.steffo.cleaver.logic.Job} is currently running and has progressed to {@link #progress} %.
+ * A {@link Progress} that specifies that a {@link Job} is currently running and has progressed to {@link #progress} %.
  */
 public class WorkingProgress extends Progress {
     public final float progress;

src/eu/steffo/cleaver/logic/split/SplitConfig.java

@@ -1,59 +0,0 @@
-package eu.steffo.cleaver.logic.split;
-
-import org.w3c.dom.Attr;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-
-/**
- * A class containing the configuration for the split/merge step of a {@link eu.steffo.cleaver.logic.Job Job}.
- */
-public abstract class SplitConfig {
-    //TODO REBUILD ERRORS
-    /**
-     * Create a {@link Element} representing this SplitConfig (to be used in *.chp metadata files).
-     *
-     * @param doc The {@link Document} the {@link Element} should be created in.
-     * @return The created {@link Element}.
-     *
-     * @see eu.steffo.cleaver.logic.ChopJob
-     * @see eu.steffo.cleaver.logic.StitchJob
-     */
-    public Element toElement(Document doc) {
-        Element element = doc.createElement("Split");
-
-        Attr partSizeAttr = doc.createAttribute("part-size");
-        partSizeAttr.setValue(Long.toString(getPartSize()));
-        element.setAttributeNode(partSizeAttr);
-
-        Attr partCountAttr = doc.createAttribute("parts");
-        partCountAttr.setValue(Long.toString(getPartCount()));
-        element.setAttributeNode(partCountAttr);
-
-        Attr totalSizeAttr = doc.createAttribute("total-size");
-        totalSizeAttr.setValue(Long.toString(getPartCount()));
-        element.setAttributeNode(totalSizeAttr);
-
-        return element;
-    }
-
-    /**
-     * @return The size in bytes of a single part of the file.
-     */
-    public abstract long getPartSize();
-
-    /**
-     * @return The number of parts the file should be split in.
-     */
-    public abstract int getPartCount();
-
-    /**
-     * @return The total size of the original file.
-     */
-    public abstract long getTotalSize();
-
-    /**
-     * @return The string representation of the {@link SplitConfig}, to be used in the jobs table.
-     * @see eu.steffo.cleaver.gui.panels.JobsTablePanel
-     */
-    public abstract String toString();
-}

src/eu/steffo/cleaver/logic/split/package-info.java

@@ -1,4 +0,0 @@
-/**
- * The package containing classes related to the file splitting/merging functionality.
- */
-package eu.steffo.cleaver.logic.split;

src/eu/steffo/cleaver/logic/stream/ICleaverStream.java

@@ -0,0 +1,4 @@
+package eu.steffo.cleaver.logic.stream;
+
+public interface ICleaverStream {
+}

src/eu/steffo/cleaver/logic/stream/input/CleaverSplitFileInputStream.java

@@ -1,10 +1,10 @@
-package eu.steffo.cleaver.logic.split;
+package eu.steffo.cleaver.logic.stream.input;
 
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 
-public class SplitFileInputStream extends InputStream {
+public class CleaverSplitFileInputStream extends InputStream {
     private final String fileBaseName;
     private long currentByteCount;
     private long maximumByteCount;
@@ -20,7 +20,7 @@ public class SplitFileInputStream extends InputStream {
      * @param fileBaseName The name of the files without the extension. If it is {@literal example}, the opened files will be {@literal example.c1}, {@literal example.c2}, and so on.
      * @param maximumByteCount The number of bytes that should be read from a file before switching to the next one.
      */
-    public SplitFileInputStream(String fileBaseName, long maximumByteCount) {
+    public CleaverSplitFileInputStream(String fileBaseName, long maximumByteCount) {
         this.fileBaseName = fileBaseName;
         this.maximumByteCount = maximumByteCount;
         this.currentByteCount = 0;

src/eu/steffo/cleaver/logic/stream/input/CryptInputStream.java

@@ -1,4 +1,4 @@
-package eu.steffo.cleaver.logic.crypt;
+package eu.steffo.cleaver.logic.stream.input;
 
 import javax.crypto.Cipher;
 import javax.crypto.NoSuchPaddingException;

src/eu/steffo/cleaver/logic/stream/input/ICleaverInputStream.java

@@ -0,0 +1,6 @@
+package eu.steffo.cleaver.logic.stream.input;
+
+import eu.steffo.cleaver.logic.stream.ICleaverStream;
+
+public interface ICleaverInputStream extends ICleaverStream {
+}

src/eu/steffo/cleaver/logic/stream/output/CleaverCompressOutputStream.java

@@ -0,0 +1,98 @@
+package eu.steffo.cleaver.logic.stream.output;
+
+import org.w3c.dom.Attr;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+import java.io.OutputStream;
+import java.util.zip.Deflater;
+import java.util.zip.DeflaterOutputStream;
+
+public class CleaverCompressOutputStream extends DeflaterOutputStream implements ICleaverOutputStream {
+    /**
+     * Construct a new CleaverCompressOutputStream and ensure the passed {@link OutputStream} implements {@link ICleaverOutputStream}.
+     * @see DeflaterOutputStream#DeflaterOutputStream(OutputStream, Deflater, int, boolean)
+     */
+    public CleaverCompressOutputStream(OutputStream out, Deflater def, int size, boolean syncFlush) {
+        super(out, def, size, syncFlush);
+        if(!(out instanceof ICleaverOutputStream)) {
+            throw new IllegalArgumentException("The OutputStream passed to the CleaverCompressOutputStream must implement ICleaverOutputStream.");
+        }
+    }
+
+    /**
+     * Construct a new CleaverCompressOutputStream and ensure the passed {@link OutputStream} implements {@link ICleaverOutputStream}.
+     * @see DeflaterOutputStream#DeflaterOutputStream(OutputStream, Deflater, int)
+     */
+    public CleaverCompressOutputStream(OutputStream out, Deflater def, int size) {
+        super(out, def, size);
+        if(!(out instanceof ICleaverOutputStream)) {
+            throw new IllegalArgumentException("The OutputStream passed to the CleaverCompressOutputStream must implement ICleaverOutputStream.");
+        }
+    }
+
+    /**
+     * Construct a new CleaverCompressOutputStream and ensure the passed {@link OutputStream} implements {@link ICleaverOutputStream}.
+     * @see DeflaterOutputStream#DeflaterOutputStream(OutputStream, Deflater, boolean)
+     */
+    public CleaverCompressOutputStream(OutputStream out, Deflater def, boolean syncFlush) {
+        super(out, def, syncFlush);
+        if(!(out instanceof ICleaverOutputStream)) {
+            throw new IllegalArgumentException("The OutputStream passed to the CleaverCompressOutputStream must implement ICleaverOutputStream.");
+        }
+    }
+
+    /**
+     * Construct a new CleaverCompressOutputStream and ensure the passed {@link OutputStream} implements {@link ICleaverOutputStream}.
+     * @see DeflaterOutputStream#DeflaterOutputStream(OutputStream, Deflater)
+     */
+    public CleaverCompressOutputStream(OutputStream out, Deflater def) {
+        super(out, def);
+        if(!(out instanceof ICleaverOutputStream)) {
+            throw new IllegalArgumentException("The OutputStream passed to the CleaverCompressOutputStream must implement ICleaverOutputStream.");
+        }
+    }
+
+    /**
+     * Construct a new CleaverCompressOutputStream and ensure the passed {@link OutputStream} implements {@link ICleaverOutputStream}.
+     * @see DeflaterOutputStream#DeflaterOutputStream(OutputStream, boolean)
+     */
+    public CleaverCompressOutputStream(OutputStream out, boolean syncFlush) {
+        super(out, syncFlush);
+        if(!(out instanceof ICleaverOutputStream)) {
+            throw new IllegalArgumentException("The OutputStream passed to the CleaverCompressOutputStream must implement ICleaverOutputStream.");
+        }
+    }
+
+    /**
+     * Construct a new CleaverCompressOutputStream and ensure the passed {@link OutputStream} implements {@link ICleaverOutputStream}.
+     * @see DeflaterOutputStream#DeflaterOutputStream(OutputStream)
+     */
+    public CleaverCompressOutputStream(OutputStream out) {
+        super(out);
+        if(!(out instanceof ICleaverOutputStream)) {
+            throw new IllegalArgumentException("The OutputStream passed to the CleaverCompressOutputStream must implement ICleaverOutputStream.");
+        }
+    }
+
+    /**
+     * @return The name of the used compression algorithm (currently only {@literal Deflate}).
+     */
+    public String getAlgorithm() {
+        return "Deflate";
+    }
+
+    @Override
+    public Element toElement(Document doc) {
+        Element element = doc.createElement("Compress");
+
+        Element child = ((ICleaverOutputStream)out).toElement(doc);
+        element.appendChild(child);
+
+        Attr algorithmAttr = doc.createAttribute("algorithm");
+        algorithmAttr.setValue(getAlgorithm());
+        element.setAttributeNode(algorithmAttr);
+
+        return element;
+    }
+}

src/eu/steffo/cleaver/logic/stream/output/CleaverCryptOutputStream.java

@@ -0,0 +1,174 @@
+package eu.steffo.cleaver.logic.stream.output;
+
+import org.w3c.dom.Attr;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+import javax.crypto.*;
+import javax.crypto.spec.IvParameterSpec;
+import javax.crypto.spec.PBEKeySpec;
+import javax.crypto.spec.SecretKeySpec;
+import java.io.FilterOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.security.InvalidAlgorithmParameterException;
+import java.security.InvalidKeyException;
+import java.security.NoSuchAlgorithmException;
+import java.security.SecureRandom;
+import java.security.spec.InvalidKeySpecException;
+import java.security.spec.KeySpec;
+
+public class CleaverCryptOutputStream extends FilterOutputStream implements ICleaverOutputStream {
+    private Cipher cipher;
+
+    /**
+     * The algorithm used for the encryption (<a href="https://en.wikipedia.org/wiki/Advanced_Encryption_Standard">Advanced Encryption Standard</a>).
+     */
+    public static final String ENCRYPTION_ALGORITHM = "AES";
+
+    /**
+     * The mode of operation used for the encryption (<a href="https://en.wikipedia.org/wiki/Block_cipher_mode_of_operation#Cipher_Feedback_(CFB)">Cipher FeedBack</a> with 8-bit blocks).
+     */
+    public static final String MODE_OF_OPERATION = "CFB8";
+
+    /**
+     * The padding standard used for the encryption (<a href="https://en.wikipedia.org/wiki/PKCS">PKCS#5</a>).
+     */
+    public static final String PADDING = "PKCS5Padding";
+
+    /**
+     * The size in bytes of the <a href="https://en.wikipedia.org/wiki/Salt_(cryptography)">salt</a>.
+     */
+    public static final int SALT_SIZE = 8;
+
+    /**
+     * The name of the key derivation algorithm to be used (<a href="https://en.wikipedia.org/wiki/PBKDF2">Password-Based Key Derivation Function 2</a> with <a href="https://en.wikipedia.org/wiki/HMAC">HMAC</a>-<a href="https://it.wikipedia.org/wiki/Secure_Hash_Algorithm>SHA512</a>).
+     */
+    public static final String KEY_DERIVATION_ALGORITHM = "PBKDF2WithHmacSHA512";
+
+    /**
+     * The iteration count for the {@link #KEY_DERIVATION_ALGORITHM}.
+     */
+    public static final int KEY_ITERATION_COUNT = 65535;
+
+    /**
+     * The length in bits of the key to be generated with the {@link #KEY_DERIVATION_ALGORITHM}.
+     */
+    public static final int KEY_LENGTH = 512;
+
+    /**
+     * @return The full transformation string as required by {@link Cipher#getInstance(String)}.
+     */
+    public String getTransformationString() {
+        return String.format("%s/%s/%s", ENCRYPTION_ALGORITHM, MODE_OF_OPERATION, PADDING);
+    }
+
+    /**
+     * Generate an array of secure random bytes.
+     * @param size The size of the array.
+     * @return The generated array of secure random bytes.
+     * @see SecureRandom
+     */
+    protected byte[] generateSecure(int size) {
+        byte[] salt = new byte[8];
+        SecureRandom secureRandom = new SecureRandom();
+        secureRandom.nextBytes(salt);
+        return salt;
+    }
+
+    /**
+     * Generate a new <a href="https://en.wikipedia.org/wiki/Initialization_vector">Initialization Vector</a> with the specified size.
+     * @param size The size of the initialization vector.
+     * @return The generated IV.
+     */
+    protected IvParameterSpec generateIV(int size) {
+        return new IvParameterSpec(generateSecure(size));
+    }
+
+    /**
+     * Generate a key starting from a character array.
+     * @throws NoSuchAlgorithmException If the {@link #KEY_DERIVATION_ALGORITHM} is invalid.
+     * @throws InvalidKeySpecException If the generated {@link KeySpec} is invalid.
+     */
+    private SecretKey generatePasswordKey(char[] key) throws NoSuchAlgorithmException, InvalidKeySpecException {
+        KeySpec spec = new PBEKeySpec(key, generateSecure(SALT_SIZE), KEY_ITERATION_COUNT, KEY_LENGTH);
+        SecretKeyFactory factory = SecretKeyFactory.getInstance(KEY_DERIVATION_ALGORITHM);
+        return factory.generateSecret(spec);
+    }
+
+    /**
+     * Create and initialize the {@link Cipher} {@link #cipher} to be used by the CleaverCryptOutputStream.
+     * @param key The string to be used in the {@link Cipher} as encryption key.
+     * @throws NoSuchPaddingException If the {@link #PADDING} is invalid.
+     * @throws NoSuchAlgorithmException If the {@link #ENCRYPTION_ALGORITHM} is invalid.
+     * @throws InvalidKeySpecException If the generated {@link KeySpec} is invalid.
+     */
+    private void createCipher(char[] key) throws NoSuchPaddingException, NoSuchAlgorithmException, InvalidKeySpecException, InvalidAlgorithmParameterException, InvalidKeyException {
+        //Setup the cipher object
+        cipher = Cipher.getInstance(getTransformationString());
+
+        //"Convert" the secret key to a AES secret key
+        SecretKey aes = new SecretKeySpec(generatePasswordKey(key).getEncoded(), ENCRYPTION_ALGORITHM);
+
+        //Init the cipher instance
+        cipher.init(Cipher.ENCRYPT_MODE, aes, generateIV(1));
+    }
+
+    /**
+     * Create a new CleaverCryptOutputStream with default {@link Cipher} parameters (AES algorithm in operation mode CFB8 with PKCS5 padding).
+     *
+     * @param out The {@link OutputStream} to connect this {@link FilterOutputStream} to.
+     * @param key The desired encryption key.
+     */
+    public CleaverCryptOutputStream(OutputStream out, String key) {
+        super(out);
+        try {
+            createCipher(key.toCharArray());
+        } catch (NoSuchPaddingException | NoSuchAlgorithmException | InvalidKeySpecException | InvalidAlgorithmParameterException | InvalidKeyException e) {
+            e.printStackTrace();
+        }
+    }
+
+    @Override
+    public void write(int decryptedInt) throws IOException {
+        byte[] decryptedByte = new byte[1];
+        decryptedByte[0] = (byte)decryptedInt;
+        byte[] encryptedByte = cipher.update(decryptedByte);
+        int encryptedInt = encryptedByte[0];
+        super.write(encryptedInt);
+    }
+
+    @Override
+    public Element toElement(Document doc) {
+        Element element = doc.createElement("Crypt");
+
+        Element child = ((ICleaverOutputStream)out).toElement(doc);
+        element.appendChild(child);
+
+        Attr algorithmAttr = doc.createAttribute("algorithm");
+        algorithmAttr.setValue(ENCRYPTION_ALGORITHM);
+        element.setAttributeNode(algorithmAttr);
+
+        Attr modeOfOperationAttr = doc.createAttribute("mode-of-operation");
+        modeOfOperationAttr.setValue(MODE_OF_OPERATION);
+        element.setAttributeNode(modeOfOperationAttr);
+
+        Attr paddingAttr = doc.createAttribute("padding");
+        paddingAttr.setValue(PADDING);
+        element.setAttributeNode(paddingAttr);
+
+        Attr keyAlgorithmAttr = doc.createAttribute("key-algorithm");
+        keyAlgorithmAttr.setValue(KEY_DERIVATION_ALGORITHM);
+        element.setAttributeNode(keyAlgorithmAttr);
+
+        Attr iterationCountAttr = doc.createAttribute("iteration-count");
+        iterationCountAttr.setValue(Integer.toString(KEY_ITERATION_COUNT));
+        element.setAttributeNode(iterationCountAttr);
+
+        Attr keyLengthAttr = doc.createAttribute("key-length");
+        keyLengthAttr.setValue(Integer.toString(KEY_LENGTH));
+        element.setAttributeNode(keyLengthAttr);
+
+        return element;
+    }
+}

src/eu/steffo/cleaver/logic/stream/output/CleaverSplitFileOutputStream.java

@@ -1,4 +1,8 @@
-package eu.steffo.cleaver.logic.split;
+package eu.steffo.cleaver.logic.stream.output;
+
+import org.w3c.dom.Attr;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 
 import java.io.FileOutputStream;
 import java.io.IOException;
@@ -9,10 +13,11 @@ import java.io.OutputStream;
  *
  * Bytes are written to a file until its length reaches {@link #maximumByteCount}, then the program switches to the following file (.c2 if .c1 is full, .c3 if .c2 is full, and so on).
  */
-public class SplitFileOutputStream extends OutputStream {
+public class CleaverSplitFileOutputStream extends OutputStream implements ICleaverOutputStream {
     private final String fileBaseName;
     private long currentByteCount;
     private long maximumByteCount;
+    private long totalByteCount;
     private int currentFileCount;
 
     /**
@@ -21,11 +26,11 @@ public class SplitFileOutputStream extends OutputStream {
     protected FileOutputStream currentFileOutputStream;
 
     /**
-     * Construct a SplitFileOutputStream.
+     * Construct a CleaverSplitFileOutputStream.
      * @param fileBaseName The name of the files without the extension. If it is {@literal example}, the created files will be {@literal example.c1}, {@literal example.c2}, and so on.
      * @param maximumByteCount The number of bytes that should be written to a file before switching to the next one.
      */
-    public SplitFileOutputStream(String fileBaseName, long maximumByteCount) {
+    public CleaverSplitFileOutputStream(String fileBaseName, long maximumByteCount) {
         this.fileBaseName = fileBaseName;
         this.maximumByteCount = maximumByteCount;
         this.currentByteCount = 0;
@@ -49,11 +54,13 @@ public class SplitFileOutputStream extends OutputStream {
 
     @Override
     public void write(int b) throws IOException {
+        // Can be optimized using the modulo operation, not doing it now for clarity
         if(currentFileOutputStream == null || currentByteCount >= maximumByteCount) {
             createNextFileOutputStream();
         }
         currentFileOutputStream.write(b);
         currentByteCount += 1;
+        totalByteCount += 1;
     }
 
     @Override
@@ -88,4 +95,31 @@ public class SplitFileOutputStream extends OutputStream {
     public int getCurrentFileCount() {
         return currentFileCount;
     }
+
+    /**
+     * @return The number of bytes that have already been written.
+     */
+    public long getTotalByteCount() {
+        return totalByteCount;
+    }
+
+    @Override
+    public Element toElement(Document doc) {
+        Element element = doc.createElement("Split");
+        element.setTextContent(fileBaseName);
+
+        Attr partSizeAttr = doc.createAttribute("part-size");
+        partSizeAttr.setValue(Long.toString(maximumByteCount));
+        element.setAttributeNode(partSizeAttr);
+
+        Attr partCountAttr = doc.createAttribute("parts");
+        partCountAttr.setValue(Long.toString(currentFileCount));
+        element.setAttributeNode(partCountAttr);
+
+        Attr totalSizeAttr = doc.createAttribute("total-size");
+        totalSizeAttr.setValue(Long.toString(totalByteCount));
+        element.setAttributeNode(totalSizeAttr);
+
+        return element;
+    }
 }

src/eu/steffo/cleaver/logic/stream/output/ICleaverOutputStream.java

@@ -0,0 +1,15 @@
+package eu.steffo.cleaver.logic.stream.output;
+
+import eu.steffo.cleaver.logic.stream.ICleaverStream;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+public interface ICleaverOutputStream extends ICleaverStream {
+    /**
+     * Create a {@link Element} representing the stream (to be used in *.chp metadata files).
+     *
+     * @param doc The {@link Document} the {@link Element} should be created in.
+     * @return The created {@link Element}.
+     */
+    public Element toElement(Document doc);
+}