org.openscience.chimetojmol.ChimePanel Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of jmol Show documentation
Show all versions of jmol Show documentation
Jmol: an open-source Java viewer for chemical structures in 3D
package org.openscience.chimetojmol;
import java.awt.BorderLayout;
import java.awt.Checkbox;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Pattern;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JFileChooser;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.JTextField;
public class ChimePanel extends JPanel implements ItemListener, ActionListener {
private JTextField chimePath;
private JButton goButton, browseButton;
private JTextArea logArea;
private JScrollPane logScrollPane;
private JFileChooser chooser;
private File oldDir;
private List pages;
private int nDir;
private int nFiles;
//private int nControls;
private Checkbox checkSubs, checkFilenames, checkSigned;
private boolean doSubdirectories;
private boolean doFixFilenames;
private boolean doUseSigned;
private File myDir;
ChimePanel() {
chooser = new JFileChooser();
chooser.setCurrentDirectory(new File("."));
myDir = chooser.getCurrentDirectory();
chooser.setDialogTitle("Select a Directory");
chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
chooser.setAcceptAllFileFilterUsed(false);
setLayout(new BorderLayout());
chimePath = new JTextField(50);
chimePath.addActionListener(this);
chimePath.setText("c:/temp/Teaching");
JPanel pathPanel = new JPanel();
pathPanel.setLayout(new BorderLayout());
pathPanel
.setBorder(BorderFactory
.createTitledBorder("Directory containing Chime-based HTML pages to convert"));
pathPanel.add("West", chimePath);
browseButton = new JButton("browse...");
browseButton.addActionListener(this);
pathPanel.add("East", browseButton);
add("North", pathPanel);
JPanel checkPanel = new JPanel();
checkPanel.setLayout(new BorderLayout());
checkSubs = new Checkbox("include subdirectories");
checkSubs.addItemListener(this);
checkFilenames = new Checkbox("fix file name case");
checkFilenames.addItemListener(this);
checkSigned = new Checkbox("use signed applet");
checkSigned.addItemListener(this);
checkPanel.add("North", checkSubs);
checkPanel.add("Center", checkFilenames);
checkPanel.add("South", checkSigned);
add("Center", checkPanel);
JPanel lowerPanel = new JPanel();
lowerPanel.setLayout(new BorderLayout());
JPanel goPane = new JPanel();
goPane.setSize(30, 10);
goButton = new JButton("Convert Page(s)");
goButton.addActionListener(this);
goPane.add(goButton);
lowerPanel.add("North", goPane);
logArea = new JTextArea(30, 20);
logArea.setMargin(new Insets(5, 5, 5, 5));
logArea.setEditable(false);
logScrollPane = new JScrollPane(logArea);
logScrollPane.setBorder(BorderFactory.createTitledBorder("0 pages"));
lowerPanel.add("South", logScrollPane);
add("South", lowerPanel);
}
public void actionPerformed(ActionEvent e) {
Object source = e.getSource();
if (source == goButton) {
doGo();
} else if (source == browseButton) {
doBrowse();
}
}
public void itemStateChanged(ItemEvent e) {
Object source = e.getSource();
int stateChange = e.getStateChange();
if (source == checkSubs) {
doSubdirectories = (stateChange == ItemEvent.SELECTED);
getFileList();
}
if (source == checkFilenames) {
doFixFilenames = (stateChange == ItemEvent.SELECTED);
}
if (source == checkSigned) {
doUseSigned = (stateChange == ItemEvent.SELECTED);
}
}
private void log(String string) {
logArea.setText(logArea.getText() + string + "\n");
}
void getFileList() {
logArea.setText("");
pages = new ArrayList();
String dir = chimePath.getText();
dir = dir.replace('\\', '/');
while (dir.endsWith("/"))
dir = dir.substring(0, dir.length() - 1);
if (dir.length() < 4)
return;
oldDir = new File(dir);
try {
copyDirectory("", oldDir, new File(oldDir + "_jmol"), true);
} catch (IOException e) {
log(e.getMessage());
}
}
private void doGo() {
getFileList();
try {
copyDirectory("", oldDir, new File(oldDir + "_jmol"), false);
} catch (IOException e) {
logArea.setText(e.getMessage());
}
}
private void doBrowse() {
if (chooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) {
String dir = chooser.getSelectedFile().toString();
chimePath.setText(dir);
getFileList();
}
}
private String rootDir;
private void copyDirectory(String level, File sourceLocation,
File targetLocation, boolean justChecking)
throws IOException {
if (level.equals("")) {
nDir = nFiles = 0;
rootDir = targetLocation.getAbsolutePath();
if (!justChecking) {
deleteDirectory(targetLocation);
targetLocation.mkdir();
addJmolFiles(rootDir);
}
} else if (doFixFilenames) {
targetLocation = new File(fixFileName(targetLocation));
}
if (sourceLocation.isDirectory()) {
if (!doSubdirectories && !level.equals(""))
return;
nDir++;
if (!targetLocation.exists() && !justChecking)
targetLocation.mkdir();
String[] children = sourceLocation.list();
for (int i = 0; i < children.length; i++)
copyDirectory((level.equals("") ? "." : level.equals(".") ? ".."
: level + "/.."), new File(sourceLocation, children[i]), new File(
targetLocation, children[i]), justChecking);
} else {
if (!copyFile(level, sourceLocation, targetLocation, justChecking))
log("Hmm..." + sourceLocation + " --> " + targetLocation);
nFiles++;
}
showProgress();
}
private void addJmolFiles(String rootDir) {
File dir = myDir;
if (!new File(dir, "Jmol.js").exists())
dir = oldDir;
File dest = new File(rootDir);
String[] list = dir.list();
for (int i = 0; i < list.length; i++) {
String f = list[i];
if (!f.equals("Jmol.js")) {
if (!f.startsWith("JmolApplet") || !f.endsWith(".jar")
|| doUseSigned != (f.indexOf("AppletSigned") >= 0))
continue;
}
justTransferFile(new File(dir, f), new File(dest, f), null);
}
transferResource(dir, "chimebtn16.bin", dest, "chimebtn16.png");
transferResource(dir, "ChimeToJmol.js", dest, "ChimeToJmol.js");
}
private void transferResource(File dir, String name, File dest, String nameOut) {
File file = new File(dir, name);
File fileOut = new File(dest, nameOut);
if (file.exists())
justTransferFile(file, fileOut, null);
else
justTransferFile(null, fileOut, getResourceStream(name));
}
public static boolean deleteDirectory(File directory) {
if (directory == null)
return false;
if (!directory.exists())
return true;
if (!directory.isDirectory())
return false;
String[] list = directory.list();
if (list != null) {
for (int i = 0; i < list.length; i++) {
File entry = new File(directory, list[i]);
if (entry.isDirectory()) {
if (!deleteDirectory(entry))
return false;
} else {
if (!entry.delete())
return false;
}
}
}
return directory.delete();
}
private String fixFileName(File f) {
return (rootDir + "/" + f.getAbsolutePath().substring(rootDir.length()).toLowerCase()).replace('\\','/');
}
private void showProgress() {
String s = pages.size() + " pages/"
+ (nDir > 1 ? nDir + " directories/" : "") + nFiles + " files";
logScrollPane.setBorder(BorderFactory.createTitledBorder(s));
}
private boolean copyFile(String level, File f1, File f2, boolean justChecking) {
String name = f1.getName().toLowerCase();
if (name.endsWith(".htm") || name.endsWith(".html")) {
if (justChecking) {
pages.add(f1);
log(f1.getAbsolutePath());
return true;
}
log("---\n" + f1.getAbsolutePath() + " --> " + f2.getAbsolutePath());
return processFile(level, f1, f2, true, true);
}
if (justChecking)
return true;
if (name.endsWith(".spt")) {
log("---\n" + f1.getAbsolutePath() + " --> " + f2.getAbsolutePath());
return processFile(level, f1, f2, false, true);
}
return justTransferFile(f1, f2, null);
}
private boolean justTransferFile(File f1, File f2, InputStream in) {
try {
if (f1 != null)
in = new FileInputStream(f1);
OutputStream out = new FileOutputStream(f2);
byte[] buf = new byte[1024];
int len;
while ((len = in.read(buf)) > 0) {
out.write(buf, 0, len);
}
in.close();
out.close();
} catch (Exception e) {
return false;
}
return true;
}
private static Pattern embed1 = Pattern.compile("";
s += opener + " src=\"" + level + "/ChimeToJmol.js\">";
s += opener + ">jmolInitialize('" + level + "'," + doUseSigned + ");chimebtn = '" + level
+ "/chimebtn16.png';";
int i = data.toLowerCase().indexOf("");
if (i < 0) {
data = "" + data;
i = 0;
}
data = data.substring(0, i + 6) + s + "\n" + data.substring(i + 6);
data = embed1.matcher(data).replaceAll("= 0) {
if (term == '\n') {
i1 = data.indexOf(term, i + 1);
} else {
i1 = i + what.length();
if (i1 == data.length())
break;
boolean stopDQuote = data.charAt(i1) == '"';
boolean stopSQuote = data.charAt(i1) == '\'';
boolean stopSpace = (!stopDQuote && !stopSQuote);
if (stopDQuote || stopSQuote)
i1++;
if (stopSpace)
while(i1 < data.length() && Character.isWhitespace(data.charAt(i1)))
i1++;
out: for (; i1 < data.length(); i1++) {
if (stopSpace && Character.isWhitespace(data.charAt(i1)))
break;
switch (data.charAt(i1)) {
case '"':
if (stopDQuote)
break out;
break;
case '\'':
if (stopSQuote)
break out;
break;
case '>':
break out;
}
}
}
String s;
if (isScript) {
// slight potential for error here when ; is quoted
s = fixFileNames(data.substring(i, i1).replace(';','\n'), false).replace('\n', ';');
} else {
s = lcdata.substring(i, i1);
}
log(data.substring(i, i1) + " --> " + s);
dataOut.append(data.substring(pt0, i)).append(s);
pt0 = i1;
}
dataOut.append(data.substring(pt0, data.length()));
return dataOut.toString();
}
/**
* @param data
* @param isHtml
* @return fixed Chime commands
*/
private String fixChime(String data, boolean isHtml) {
// (JavaScript will do this)
return data;
}
private String getFileContents(File f) {
StringBuffer sb = new StringBuffer(8192);
String line;
try {
BufferedReader br = new BufferedReader(new FileReader(f));
while ((line = br.readLine()) != null)
sb.append(line).append('\n');
br.close();
} catch (IOException e) {
return null;
}
return sb.toString();
}
private boolean putFileContents(File f, String html) {
FileWriter fstream;
try {
fstream = new FileWriter(f, false);
BufferedWriter out = new BufferedWriter(fstream);
out.write(html);
out.close();
} catch (IOException e) {
return false;
}
return true;
}
static InputStream getResourceStream(String fileName) {
URL url = null;
fileName = "org/openscience/chimetojmol/" + fileName;
try {
if ((url = ClassLoader.getSystemResource(fileName)) == null)
return null;
return (InputStream) url.getContent();
} catch (Exception e) {
return null;
}
}
}