/* * ProteinIIApp.java * * Created on March 22, 2008, 6:09 PM * * To change this template, choose Tools | Template Manager * and open the template in the editor. */ /** * * @author roland */ import java.awt.*; import java.awt.event.*; import java.applet.*; public class ProteinIIApp extends Applet implements ActionListener { /******************************************* * Data Members Used in the Applet Display * *******************************************/ private TextField // To accept user input SeqLength, // To out sequence length Sum, // To output sum of DIVW's InstIndex; // To output II value private TextArea Sequence; private Button Calculate, // This button to initiate II calculation Clear; // Clear the panel to prepare for new input /******************************************************* * Some constants and tables used in the computations. * *******************************************************/ private static final int numAminoAcids = 20; private static final double scalingFactor = 10.0; private static final double[][] DIVW_val = { {1.0, 1.0, 24.68, 24.68, 1.0, 1.0, 1.0, 13.34, 1.0, 1.0, 1.0, 1.0, -14.03, 1.0, 1.0, -7.49, 1.0, -9.37, -14.03, 13.34}, // row W {24.68, 1.0, 33.6, 33.6, 1.0, 1.0, -6.54, 1.0, 1.0, 1.0, 20.26, 20.26, 33.6, 1.0, 1.0, -6.54, 1.0, 1.0, 1.0, 20.26}, // row C {1.0, 1.0, -1.88, 58.28, 24.68, 1.0, -6.54, 1.0, 1.0, -6.54, 1.0, 44.94, -1.88, 1.0, 1.0, 1.0, 44.94, 1.0, 13.34, 1.0}, // row M {-1.88, 1.0, 1.0, 1.0, 44.94, -9.37, 1.0, 24.68, 44.94, 1.0, 1.0, -1.88, -6.54, 24.68, 1.0, 1.0, 1.0, -9.37, 1.0, 1.0}, // row H {-9.37, 1.0, 44.94, 13.34, 13.34, 1.0, 1.0, 1.0, 1.0, -15.91, 24.68, 13.34, -7.49, 1.0, -6.54, 1.0, 1.0, -7.49, 24.68, 1.0}, // row Y {1.0, 1.0, 1.0, 1.0, 33.6, 1.0, 1.0, 1.0, 1.0, 1.0, 13.34, 20.26, 1.0, -14.03, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0}, // row F {1.0, -6.54, 1.0, 1.0, -6.54, -6.54, 20.26, 1.0, 1.0, 1.0, 20.26, 20.26, 1.0, 1.0, 20.26, -6.54, 44.94, 1.0, 1.0, 1.0}, // row Q {-9.37, -1.88, 1.0, 1.0, 1.0, -14.03, -6.54, 1.0, 44.94, 1.0, 1.0, -1.88, -7.49, 24.68, 1.0, 1.0, 1.0, -14.03, 1.0, 1.0}, // row N {1.0, 1.0, 1.0, 13.34, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, -1.88, 1.0, -7.49, 44.94, -7.49, 1.0, 1.0, 1.0, 20.26}, // row I {58.28, 1.0, 1.0, 20.26, -6.54, 1.0, 20.26, 13.34, 1.0, 58.28, 1.0, 20.26, 1.0, 1.0, 1.0, 1.0, 44.94, -7.49, 1.0, 1.0}, // row R {1.0, 1.0, 1.0, 1.0, 1.0, -6.54, 1.0, 1.0, 1.0, -6.54, 1.0, 1.0, -14.03, -7.49, 1.0, 1.0, 20.26, 1.0, 1.0, 1.0}, // row D {-1.88, -6.54, -6.54, 1.0, 1.0, 20.26, 20.26, 1.0, 1.0, -6.54, -6.54, 20.26, 1.0, 1.0, 18.38, 20.26, 20.26, 1.0, 20.26, 1.0}, // row P {-14.03, 1.0, 1.0, 1.0, 1.0, 13.34, -6.54, -14.03, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 20.26, 1.0, 1.0, -7.49, 1.0, 1.0}, // row T {1.0, 1.0, 33.6, 1.0, 1.0, 1.0, 24.68, 1.0, -7.49, 33.6, 1.0, -6.54, 1.0, 1.0, 1.0, -7.49, 1.0, -7.49, 1.0, -7.49}, // row K {-14.03, 44.94, 1.0, -6.54, 1.0, 1.0, 20.26, 1.0, 20.26, 1.0, 20.26, 20.26, 1.0, 1.0, 33.6,1.0, 20.26, 1.0, 1.0, 1.0}, // row E {1.0, 1.0, 1.0, 1.0, -6.54, 1.0, 1.0, 1.0, 1.0, 1.0, -14.03, 20.26, -7.49, -1.88, 1.0, 1.0, 1.0, -7.49, 1.0, 1.0}, // row V {1.0, 33.6, 1.0, 1.0, 1.0, 1.0, 20.26, 1.0, 1.0, 20.26, 1.0, 44.94, 1.0, 1.0, 20.26, 1.0, 20.26, 1.0, 1.0, 1.0}, // row S {13.34, 1.0, 1.0, 1.0, -7.49, 1.0, 1.0, -7.49, -7.49, 1.0, 1.0, 1.0, -7.49, -7.49, -6.54, 1.0, 1.0, 13.34, -7.49, 1.0}, // row G {1.0, 44.94, 1.0, -7.49, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, -7.49, 20.26, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0}, // row A {24.68, 1.0, 1.0, 1.0, 1.0, 1.0, 33.6, 1.0, 1.0, 20.26, 1.0, 20.26, 1.0, -7.49, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0} /* row L */ }; private static final char[] aminoLetters = {'W', 'C', 'M', 'H', 'Y', 'F', 'Q', 'N', 'I', 'R', 'D', 'P', 'T', 'K', 'E', 'V', 'S', 'G', 'A', 'L'}; /** Initialization method that will be called after the applet is loaded * into the browser. */ public void init() { setBackground(Color.white); //Set white background setLayout(null); resize(575, 270); Sequence = new TextArea("", 5, 100, 1); Sequence.setBounds(165, 55, 400, 80); Sequence.setEditable(true); add(Sequence); SeqLength = new TextField(); SeqLength.setBounds(165, 145, 165, 25); add(SeqLength); // Sum = new TextField(); // Sum.setBounds(130, 95, 165, 25); // add(Sum); InstIndex = new TextField(); InstIndex.setBounds(165, 175, 165, 25); add(InstIndex); Calculate = new Button("Calculate"); Calculate.setBounds(165, 215, 100, 45); add(Calculate); Clear = new Button("Clear"); Clear.setBounds (290, 215, 100, 45); add(Clear); // Sequence.addActionListener(this); Calculate.addActionListener(this); Clear.addActionListener(this); } /** Method: paint * Purpose: Draw the outline of calculator *(this method can auto. draw when develop Applet, but it isn't Applet's method) * Parameters: Graphics * Returns: None */ public void paint(Graphics graphic) { graphic.setColor(Color.black); graphic.drawRoundRect(0, 0, 574, 269, 15, 15); // graphic.drawRect(574, 249, 15, 15); graphic.setColor(Color.white); graphic.fillRoundRect(1, 1, 573, 268, 15, 15); //graphic.fillRect(573, 248, 15, 15); graphic.setColor(Color.black); Font f1 = new Font("Arial", Font.BOLD, 24); graphic.setFont(f1); graphic.drawString("Protein Instability Index Calculator", 85, 30); Font f2 = new Font("Arial", Font.BOLD, 14); graphic.setFont(f2); graphic.drawString("Amino Acid Sequence", 10, 75); graphic.drawString("Sequence Length", 10, 165); // graphic.drawString("Sum of DIVW's", 10, 105); graphic.drawString("Instability Index", 10, 195); } /** Method: actionPerformed * Purpose: Event-handling * Parameters: Action event * Returns: None */ public void actionPerformed(ActionEvent event) { if (event.getSource() instanceof Button) { Button clickedButton = (Button) event.getSource(); if (clickedButton == Calculate) { ComputeII(); } else if (clickedButton == Clear) { ClearSequence(); } } } /** Method: ClearSequence * Purpose: Clear Sequence TextField objects * Parameters: None * Returns: None */ private void ClearSequence() { Sequence.setText(""); InstIndex.setText(""); SeqLength.setText(""); Sum.setText(""); } private void ComputeII() { String aminoSequence = Sequence.getText(); aminoSequence = parseProtein(aminoSequence); int seqLength = aminoSequence.length(); double DIVWsum = getDIVWsum(aminoSequence, seqLength); double II = (scalingFactor * DIVWsum) / (double)(seqLength); // Print the calculated values. printVals(aminoSequence, seqLength, DIVWsum, II); } private int getIndex(char letter) { for (int index = 0; index < numAminoAcids; ++index) { if (aminoLetters[index] == letter) { return index; } } return numAminoAcids; } private String parseProtein(String protein) { String returnString = ""; char currentChar; protein = protein.toUpperCase(); for (int i = 0; i < protein.length(); ++i) { currentChar = protein.charAt(i); if (getIndex(currentChar) != numAminoAcids) { //returnString.append(currentChar); returnString += currentChar; } } return returnString; } private double getDIVWsum(String protein, int sLength) { int row = 0, col = 0; double sum = 0.0; protein = protein.toUpperCase(); for (int current = 0; current < sLength - 1; ++current) { row = getIndex(protein.charAt(current)); col = getIndex(protein.charAt(current + 1)); sum += DIVW_val[row][col]; } return sum; } private void printVals(String protein, int sLength, double sum, double instIndex) { String fs; //int perLine = 30, index; //String line; //print("\nhas length " + sLength); //print("\nThe sum of the DIVW's is " + sum + // "\nThe instability index ( II ) for this protein is " + instIndex); //println("\n"); if(sLength != 0){ fs = String.format("%.2f", instIndex); // InstIndex.setText(String.valueOf(instIndex)); InstIndex.setText(fs); SeqLength.setText(String.valueOf(sLength)); Sum.setText(String.valueOf(sum)); } if(sLength == 0){ Sequence.setText("Enter a sequence."); InstIndex.setText(""); } } }