Skip to content

Commit 1651107

Browse files
WilliamKMLaiWilliamKMLai
committed
Resolve Issue #19
added new batch m5d checksum calculator. not to be used in place of existing unix command unless absolutely necessary
1 parent 9b05a77 commit 1651107

3 files changed

Lines changed: 245 additions & 1 deletion

File tree

‎src/main/ScriptManager.java‎

Lines changed: 22 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -30,6 +30,7 @@
3030
import window_interface.Coordinate_Manipulation.GFF_Manipulation.ExpandGFFWindow;
3131
import window_interface.Coordinate_Manipulation.GFF_Manipulation.GFFtoBEDWindow;
3232
import window_interface.Coordinate_Manipulation.GFF_Manipulation.SortGFFWindow;
33+
import window_interface.File_Utilities.MD5ChecksumWindow;
3334
import window_interface.Coordinate_Analysis.BEDPeakAligntoRefWindow;
3435
import window_interface.Coordinate_Analysis.FilterBEDbyProximityWindow;
3536
import window_interface.Sequence_Analysis.DNAShapefromBEDWindow;
@@ -56,7 +57,7 @@ public class ScriptManager {
5657
private void initialize() {
5758
frmScriptManager = new JFrame();
5859
frmScriptManager.setTitle("Script Manager v" + VERSION);
59-
frmScriptManager.setBounds(100, 100, 475, 275);
60+
frmScriptManager.setBounds(100, 100, 500, 275);
6061
frmScriptManager.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
6162
frmScriptManager.setResizable(false);
6263
SpringLayout springLayout = new SpringLayout();
@@ -281,6 +282,26 @@ public void run() {
281282
btnBamToBed.setToolTipText("Convert BAM file to BED file.");
282283
pnlBamConvert.add(btnBamToBed);
283284

285+
JPanel pnlFileUtility = new JPanel();
286+
tabbedPane.addTab("File Utilities", null, pnlFileUtility, null);
287+
288+
JButton btnMD5 = new JButton("MD5 Checksum");
289+
btnMD5.addActionListener(new ActionListener() {
290+
public void actionPerformed(ActionEvent e) {
291+
EventQueue.invokeLater(new Runnable() {
292+
public void run() {
293+
try {
294+
MD5ChecksumWindow frame = new MD5ChecksumWindow();
295+
frame.setVisible(true);
296+
} catch (Exception e) {
297+
e.printStackTrace();
298+
}
299+
}
300+
});
301+
}
302+
});
303+
pnlFileUtility.add(btnMD5);
304+
284305
JPanel pnlCoord_Manip = new JPanel();
285306
tabbedPane.addTab("Coordinate File Manipulation", null, pnlCoord_Manip, null);
286307

‎src/scripts/File_Utilities/MD5Checksum.java‎

Lines changed: 17 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,17 @@
1+
package scripts.File_Utilities;
2+
3+
import java.io.IOException;
4+
import java.nio.file.Files;
5+
import java.nio.file.Paths;
6+
import java.security.MessageDigest;
7+
import java.security.NoSuchAlgorithmException;
8+
import javax.xml.bind.DatatypeConverter;
9+
10+
public class MD5Checksum {
11+
public static String calculateMD5(String input) throws IOException, NoSuchAlgorithmException {
12+
MessageDigest md = MessageDigest.getInstance("MD5");
13+
md.update(Files.readAllBytes(Paths.get(input)));
14+
byte[] digest = md.digest();
15+
return DatatypeConverter.printHexBinary(digest).toLowerCase();
16+
}
17+
}

‎src/window_interface/File_Utilities/MD5ChecksumWindow.java‎

Lines changed: 206 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,206 @@
1+
package window_interface.File_Utilities;
2+
3+
import java.io.File;
4+
import java.io.IOException;
5+
import java.io.PrintStream;
6+
import java.security.NoSuchAlgorithmException;
7+
import java.util.Vector;
8+
9+
import javax.swing.JFileChooser;
10+
import javax.swing.JFrame;
11+
import javax.swing.JPanel;
12+
import javax.swing.border.EmptyBorder;
13+
import javax.swing.DefaultListModel;
14+
import javax.swing.JButton;
15+
import javax.swing.JOptionPane;
16+
import javax.swing.ListSelectionModel;
17+
import javax.swing.SpringLayout;
18+
import javax.swing.JScrollPane;
19+
import javax.swing.JList;
20+
import javax.swing.SwingWorker;
21+
import javax.swing.JProgressBar;
22+
import javax.swing.JLabel;
23+
24+
import scripts.File_Utilities.MD5Checksum;
25+
import util.FileSelection;
26+
27+
import java.awt.Component;
28+
import java.awt.Container;
29+
import java.awt.Cursor;
30+
import java.awt.Font;
31+
import java.awt.Color;
32+
import java.awt.event.ActionEvent;
33+
import java.awt.event.ActionListener;
34+
import java.beans.PropertyChangeEvent;
35+
import java.beans.PropertyChangeListener;
36+
37+
@SuppressWarnings("serial")
38+
public class MD5ChecksumWindow extends JFrame implements ActionListener, PropertyChangeListener {
39+
private JPanel contentPane;
40+
protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));
41+
42+
private File OUTPUT_PATH = null;
43+
private PrintStream OUT = null;
44+
final DefaultListModel<String> expList;
45+
Vector<File> Files = new Vector<File>();
46+
47+
private JButton btnLoad;
48+
private JButton btnRemove;
49+
private JButton btnConvert;
50+
51+
private JProgressBar progressBar;
52+
public Task task;
53+
private JLabel lblCurrent;
54+
private JLabel lblDefaultToLocal;
55+
private JButton btnOutput;
56+
57+
class Task extends SwingWorker<Void, Void> {
58+
@Override
59+
public Void doInBackground() throws IOException, NoSuchAlgorithmException {
60+
setProgress(0);
61+
62+
if(OUTPUT_PATH == null) OUT = new PrintStream("md5checksum.txt");
63+
else OUT = new PrintStream(OUTPUT_PATH + File.separator + "md5checksum.txt");
64+
for(int x = 0; x < Files.size(); x++) {
65+
String md5hash = MD5Checksum.calculateMD5(Files.get(x).getAbsolutePath());
66+
OUT.println("MD5 (" + Files.get(x).getName() + ") = " + md5hash);
67+
int percentComplete = (int)(((double)(x + 1) / Files.size()) * 100);
68+
setProgress(percentComplete);
69+
}
70+
setProgress(100);
71+
72+
OUT.close();
73+
JOptionPane.showMessageDialog(null, "Calculation Complete");
74+
return null;
75+
}
76+
77+
public void done() {
78+
massXable(contentPane, true);
79+
setCursor(null); //turn off the wait cursor
80+
}
81+
}
82+
83+
public MD5ChecksumWindow() {
84+
setTitle("MD5 Checksum");
85+
setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
86+
87+
setBounds(125, 125, 450, 300);
88+
contentPane = new JPanel();
89+
contentPane.setBorder(new EmptyBorder(5, 5, 5, 5));
90+
setContentPane(contentPane);
91+
SpringLayout sl_contentPane = new SpringLayout();
92+
contentPane.setLayout(sl_contentPane);
93+
94+
JScrollPane scrollPane = new JScrollPane();
95+
sl_contentPane.putConstraint(SpringLayout.WEST, scrollPane, 5, SpringLayout.WEST, contentPane);
96+
sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
97+
contentPane.add(scrollPane);
98+
99+
expList = new DefaultListModel<String>();
100+
final JList<String> listExp = new JList<String>(expList);
101+
listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
102+
scrollPane.setViewportView(listExp);
103+
104+
btnLoad = new JButton("Load Files");
105+
sl_contentPane.putConstraint(SpringLayout.WEST, btnLoad, 5, SpringLayout.WEST, contentPane);
106+
sl_contentPane.putConstraint(SpringLayout.NORTH, scrollPane, 6, SpringLayout.SOUTH, btnLoad);
107+
btnLoad.addActionListener(new ActionListener() {
108+
public void actionPerformed(ActionEvent e) {
109+
File[] newFiles = FileSelection.getGenericFiles(fc);
110+
if(newFiles != null) {
111+
for(int x = 0; x < newFiles.length; x++) {
112+
Files.add(newFiles[x]);
113+
expList.addElement(newFiles[x].getName());
114+
}
115+
}
116+
}
117+
});
118+
contentPane.add(btnLoad);
119+
120+
btnRemove = new JButton("Remove Files");
121+
sl_contentPane.putConstraint(SpringLayout.NORTH, btnLoad, 0, SpringLayout.NORTH, btnRemove);
122+
sl_contentPane.putConstraint(SpringLayout.NORTH, btnRemove, 0, SpringLayout.NORTH, contentPane);
123+
sl_contentPane.putConstraint(SpringLayout.EAST, btnRemove, -5, SpringLayout.EAST, contentPane);
124+
btnRemove.addActionListener(new ActionListener() {
125+
public void actionPerformed(ActionEvent arg0) {
126+
while(listExp.getSelectedIndex() > -1) {
127+
Files.remove(listExp.getSelectedIndex());
128+
expList.remove(listExp.getSelectedIndex());
129+
}
130+
}
131+
});
132+
contentPane.add(btnRemove);
133+
134+
btnConvert = new JButton("Calculate");
135+
sl_contentPane.putConstraint(SpringLayout.SOUTH, scrollPane, -62, SpringLayout.NORTH, btnConvert);
136+
sl_contentPane.putConstraint(SpringLayout.WEST, btnConvert, 167, SpringLayout.WEST, contentPane);
137+
sl_contentPane.putConstraint(SpringLayout.SOUTH, btnConvert, 0, SpringLayout.SOUTH, contentPane);
138+
sl_contentPane.putConstraint(SpringLayout.EAST, btnConvert, -175, SpringLayout.EAST, contentPane);
139+
contentPane.add(btnConvert);
140+
141+
progressBar = new JProgressBar();
142+
sl_contentPane.putConstraint(SpringLayout.NORTH, progressBar, 3, SpringLayout.NORTH, btnConvert);
143+
sl_contentPane.putConstraint(SpringLayout.EAST, progressBar, -5, SpringLayout.EAST, contentPane);
144+
progressBar.setStringPainted(true);
145+
contentPane.add(progressBar);
146+
147+
btnConvert.setActionCommand("start");
148+
149+
lblCurrent = new JLabel("Current Output:");
150+
sl_contentPane.putConstraint(SpringLayout.NORTH, lblCurrent, 37, SpringLayout.SOUTH, scrollPane);
151+
sl_contentPane.putConstraint(SpringLayout.WEST, lblCurrent, 0, SpringLayout.WEST, scrollPane);
152+
lblCurrent.setFont(new Font("Lucida Grande", Font.BOLD, 13));
153+
contentPane.add(lblCurrent);
154+
155+
lblDefaultToLocal = new JLabel("Default to Local Directory");
156+
sl_contentPane.putConstraint(SpringLayout.NORTH, lblDefaultToLocal, 1, SpringLayout.NORTH, lblCurrent);
157+
sl_contentPane.putConstraint(SpringLayout.WEST, lblDefaultToLocal, 6, SpringLayout.EAST, lblCurrent);
158+
lblDefaultToLocal.setBackground(Color.WHITE);
159+
contentPane.add(lblDefaultToLocal);
160+
161+
btnOutput = new JButton("Output Directory");
162+
btnOutput.addActionListener(new ActionListener() {
163+
public void actionPerformed(ActionEvent e) {
164+
OUTPUT_PATH = FileSelection.getOutputDir(fc);
165+
if(OUTPUT_PATH != null) {
166+
lblDefaultToLocal.setText(OUTPUT_PATH.getAbsolutePath());
167+
}
168+
}
169+
});
170+
sl_contentPane.putConstraint(SpringLayout.NORTH, btnOutput, 6, SpringLayout.SOUTH, scrollPane);
171+
sl_contentPane.putConstraint(SpringLayout.WEST, btnOutput, 150, SpringLayout.WEST, contentPane);
172+
sl_contentPane.putConstraint(SpringLayout.EAST, btnOutput, -150, SpringLayout.EAST, contentPane);
173+
contentPane.add(btnOutput);
174+
btnConvert.addActionListener(this);
175+
}
176+
177+
@Override
178+
public void actionPerformed(ActionEvent arg0) {
179+
massXable(contentPane, false);
180+
setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
181+
182+
task = new Task();
183+
task.addPropertyChangeListener(this);
184+
task.execute();
185+
}
186+
187+
/**
188+
* Invoked when task's progress property changes.
189+
*/
190+
public void propertyChange(PropertyChangeEvent evt) {
191+
if ("progress" == evt.getPropertyName()) {
192+
int progress = (Integer) evt.getNewValue();
193+
progressBar.setValue(progress);
194+
}
195+
}
196+
197+
public void massXable(Container con, boolean status) {
198+
for(Component c : con.getComponents()) {
199+
c.setEnabled(status);
200+
if(c instanceof Container) { massXable((Container)c, status); }
201+
}
202+
}
203+
}
204+
205+
206+

0 commit comments

Comments
 (0)