delete unuse class
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/bitwise/BitwiseOperation.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/bitwise/BitwiseOperation.java
deleted file mode 100644
index 8d90e92..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/bitwise/BitwiseOperation.java
+++ /dev/null
@@ -1,115 +0,0 @@
-package edu.uci.ics.genomix.pregelix.bitwise;
-
-public class BitwiseOperation {
-
- public static byte[] shiftBitsLeft(byte[] bytes, final int leftShifts) {
- assert leftShifts >= 1 && leftShifts <= 7;
-
- byte[] resultBytes = new byte[bytes.length];
- for(int i = 0; i < bytes.length; i++)
- resultBytes[i] = bytes[i];
- final int rightShifts = 8 - leftShifts;
-
- byte previousByte = resultBytes[bytes.length - 1]; // keep the byte before modification
- resultBytes[resultBytes.length - 1] = (byte) (((resultBytes[resultBytes.length - 1] & 0xff) << leftShifts));
- for (int i = resultBytes.length - 2; i >= 0; i--) {
- byte tmp = resultBytes[i];
- resultBytes[i] = (byte) (((resultBytes[i] & 0xff) << leftShifts) | ((previousByte & 0xff) >> rightShifts));
- previousByte = tmp;
- }
- return resultBytes;
- }
-
- public static byte[] shiftBitsRight(byte[] bytes, final int rightShifts) {
- assert rightShifts >= 1 && rightShifts <= 7;
-
- byte[] resultBytes = new byte[bytes.length];
- for(int i = 0; i < bytes.length; i++)
- resultBytes[i] = bytes[i];
- final int leftShifts = 8 - rightShifts;
-
- byte previousByte = resultBytes[0]; // keep the byte before modification
- resultBytes[0] = (byte) (((resultBytes[0] & 0xff) >> rightShifts));
- for (int i = 1; i < resultBytes.length; i++) {
- byte tmp = resultBytes[i];
- resultBytes[i] = (byte) (((resultBytes[i] & 0xff) >> rightShifts) | ((previousByte & 0xff) << leftShifts));
- previousByte = tmp;
- }
- return resultBytes;
- }
-
- public static byte convertBinaryStringToByte(String input){
- int tmpInt = Integer.parseInt(input,2);
- byte tmpByte = (byte) tmpInt;
- return tmpByte;
- }
-
- public static byte[] convertBinaryStringToBytes(String input){
- input = complementString(input);
- int numOfBytes = input.length() / 8;
- byte[] bytes = new byte[numOfBytes];
- for(int i = 0; i < numOfBytes; ++i)
- {
- bytes[i] = convertBinaryStringToByte(input.substring(8 * i, 8 * i + 8));
- }
- return bytes;
- }
-
- public static String complementString(String input){
- int remaining = input.length() % 8;
- if(remaining == 0)
- return input;
- for(int i = 0; i < 8 - remaining; i++)
- input += "0";
- return input;
- }
-
- public static String convertByteToBinaryString(byte b){
- StringBuilder sb = new StringBuilder(Byte.SIZE);
- for( int i = 0; i < Byte.SIZE; i++ )
- sb.append((b << i % Byte.SIZE & 0x80) == 0 ? '0' : '1');
- return sb.toString();
- }
-
- public static String convertBytesToBinaryString(byte[] bytes){
- StringBuilder sb = new StringBuilder(bytes.length * Byte.SIZE);
- for( int i = 0; i < Byte.SIZE * bytes.length; i++ )
- sb.append((bytes[i / Byte.SIZE] << i % Byte.SIZE & 0x80) == 0 ? '0' : '1');
- return sb.toString();
- }
-
- public static String convertBytesToBinaryStringKmer(byte[] bytes, int k){
- StringBuilder sb = new StringBuilder(bytes.length * Byte.SIZE);
- for( int i = 0; i < Byte.SIZE * bytes.length; i++ )
- sb.append((bytes[i / Byte.SIZE] << i % Byte.SIZE & 0x80) == 0 ? '0' : '1');
- return sb.toString().substring(0,2*k);
- }
-
- public static byte[] addLastTwoBits(byte[] bytes, int lengthOfChainVertex, String newBits){
- String originalBytes = convertBytesToBinaryString(bytes).substring(0,2*lengthOfChainVertex);
- originalBytes += newBits;
- return convertBinaryStringToBytes(originalBytes);
- }
-
- public static String getLastTwoBits(byte[] bytes, int k){
- String sb = convertBytesToBinaryString(bytes);
- int num = k / 4;
- int extraBit = k % 4;
- if(extraBit >= 1)
- return sb.substring(8*num + 2*(extraBit-1),8*num + 2*extraBit);
- else
- return sb.substring(8*num - 2, 8*num);
- }
-
- public static byte[] mergeTwoBytesArray(byte[] b1, int size1, byte[] b2, int size2){
- String s1 = convertBytesToBinaryStringKmer(b1,size1);
- String s2 = convertBytesToBinaryStringKmer(b2,size2);
- return convertBinaryStringToBytes(s1 + s2);
- }
-
- public static byte replaceLastFourBits(byte b1, byte b2){
- String s1 = convertByteToBinaryString(b1);
- String s2 = convertByteToBinaryString(b2);
- return convertBinaryStringToByte(s1.substring(0,4) + s2.substring(4,8));
- }
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/Proba.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/Proba.java
deleted file mode 100644
index 6bd66e5..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/Proba.java
+++ /dev/null
@@ -1,69 +0,0 @@
-package edu.uci.ics.genomix.pregelix.graph;
-
-import java.io.File;
-
-public class Proba
-{
- public static void main(String[] args)
- {
- Proba p = new Proba();
- p.start();
-// p.start2();
- }
-
- /**
- * Construct a DOT graph in memory, convert it
- * to image and store the image in the file system.
- */
- private void start()
- {
- GraphViz gv = new GraphViz();
- gv.addln(gv.start_graph());
- gv.addln("A -> B;");
- gv.addln("B -> C;");
- gv.addln("C -> D;");
- gv.addln("D -> E;");
- gv.addln("E -> A;");
- gv.addln(gv.end_graph());
- System.out.println(gv.getDotSource());
-
-// String type = "gif";
-// String type = "dot";
-// String type = "fig"; // open with xfig
-// String type = "pdf";
- String type = "ps";
-// String type = "svg"; // open with inkscape
-// String type = "png";
-// String type = "plain";
- File out = new File("graph_out." + type); // Linux
-// File out = new File("c:/eclipse.ws/graphviz-java-api/out." + type); // Windows
- gv.writeGraphToFile( gv.getGraph( gv.getDotSource(), type ), out );
- }
-
- /**
- * Read the DOT source from a file,
- * convert to image and store the image in the file system.
- */
- private void start2()
- {
- String dir = "/home/jabba/eclipse2/laszlo.sajat/graphviz-java-api"; // Linux
- String input = dir + "/sample/simple.dot";
-// String input = "c:/eclipse.ws/graphviz-java-api/sample/simple.dot"; // Windows
-
- GraphViz gv = new GraphViz();
- gv.readSource(input);
- System.out.println(gv.getDotSource());
-
- String type = "gif";
-// String type = "dot";
-// String type = "fig"; // open with xfig
-// String type = "pdf";
-// String type = "ps";
-// String type = "svg"; // open with inkscape
-// String type = "png";
-// String type = "plain";
- File out = new File("/tmp/simple." + type); // Linux
-// File out = new File("c:/eclipse.ws/graphviz-java-api/tmp/simple." + type); // Windows
- gv.writeGraphToFile( gv.getGraph( gv.getDotSource(), type ), out );
- }
-}