package com.ibm.compbio;
public abstract class DynamicProgramming {
private Cell prevCell;
private int score;
private int row;
private int col;
protected String sequence1;
protected String sequence2;
protected Cell[][] scoreTable;
protected boolean tableIsFilledIn;
protected boolean isInitialized;
public Cell(int row, int col) {
this.row = row;
this.col = col;
}
/**
* @param score
* the score to set
*/
public void setScore(int score) {
this.score = score;
}
/**
* @return the score
*/
public int getScore() {
return score;
}
/**
* @param prevCell
* the prevCell to set
*/
public void setPrevCell(Cell prevCell) {
this.prevCell = prevCell;
}
/**
* @return the row
*/
public int getRow() {
return row;
}
/**
* @return the col
*/
public int getCol() {
return col;
}
/**
* @return the prevCell
*/
public Cell getPrevCell() {
return prevCell;
}
/*
* (non-Javadoc)
*
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
return "Cell(" + row + ", " + col + "): score=" + score + ", prevCell="
+ prevCell + "]";
}
public DynamicProgramming(String sequence1, String sequence2) {
this.sequence1 = sequence1;
this.sequence2 = sequence2;
scoreTable = new Cell[sequence2.length() + 1][sequence1.length() + 1];
}
public int[][] getScoreTable() {
ensureTableIsFilledIn();
int[][] matrix = new int[scoreTable.length][scoreTable[0].length];
for (int i = 0; i < matrix.length; i++) {
for (int j = 0; j < matrix[i].length; j++) {
matrix[i][j] = scoreTable[i][j].getScore();
}
}
return matrix;
}
protected void initializeScores() {
for (int i = 0; i < scoreTable.length; i++) {
for (int j = 0; j < scoreTable[i].length; j++) {
scoreTable[i][j].setScore(getInitialScore(i, j));
}
}
}
protected void initializePointers() {
for (int i = 0; i < scoreTable.length; i++) {
for (int j = 0; j < scoreTable[i].length; j++) {
scoreTable[i][j].setPrevCell(getInitialPointer(i, j));
}
}
}
protected void initialize() {
for (int i = 0; i < scoreTable.length; i++) {
for (int j = 0; j < scoreTable[i].length; j++) {
scoreTable[i][j] = new Cell(i, j);
}
}
initializeScores();
initializePointers();
isInitialized = true;
}
protected abstract Cell getInitialPointer(int row, int col);
protected abstract int getInitialScore(int row, int col);
protected abstract void fillInCell(Cell currentCell, Cell cellAbove,
Cell cellToLeft, Cell cellAboveLeft);
protected void fillIn() {
for (int row = 1; row < scoreTable.length; row++) {
for (int col = 1; col < scoreTable[row].length; col++) {
Cell currentCell = scoreTable[row][col];
Cell cellAbove = scoreTable[row - 1][col];
Cell cellToLeft = scoreTable[row][col - 1];
Cell cellAboveLeft = scoreTable[row - 1][col - 1];
fillInCell(currentCell, cellAbove, cellToLeft, cellAboveLeft);
}
}
tableIsFilledIn = true;
}
abstract protected Object getTraceback();
public void printScoreTable() {
ensureTableIsFilledIn();
for (int i = 0; i < sequence2.length() + 2; i++) {
for (int j = 0; j < sequence1.length() + 2; j++) {
if (i == 0) {
if (j == 0 || j == 1) {
System.out.print(" ");
} else {
if (j == 2) {
System.out.print(" ");
} else {
System.out.print(" ");
}
System.out.print(sequence1.charAt(j - 2));
}
} else if (j == 0) {
if (i == 1) {
System.out.print(" ");
} else {
System.out.print(" " + sequence2.charAt(i - 2));
}
} else {
String toPrint;
Cell currentCell = scoreTable[i - 1][j - 1];
Cell prevCell = currentCell.getPrevCell();
if (prevCell != null) {
if (currentCell.getCol() == prevCell.getCol() + 1
&& currentCell.getRow() == prevCell.getRow() + 1) {
toPrint = "\\";
} else if (currentCell.getCol() == prevCell.getCol() + 1) {
toPrint = "-";
} else {
toPrint = "|";
}
} else {
toPrint = " ";
}
int score = currentCell.getScore();
String s = String.format("%1$3d", score);
toPrint += s;
System.out.print(toPrint);
}
System.out.print(' ');
}
System.out.println();
}
}
protected void ensureTableIsFilledIn() {
if (!isInitialized) {
initialize();
}
if (!tableIsFilledIn) {
fillIn();
}
}
}I have an error at line 19, which says, "invalid method declaration; return type required". However if I enter a return for that error, there is more error. May I know how to solve this error?