@Override
protected Transferable createTransferable(JComponent c) {
JTextPane aTextPane = (JTextPane) c;
HTMLEditorKit kit = ((HTMLEditorKit) aTextPane.getEditorKit());
StyledDocument sdoc = aTextPane.getStyledDocument();
int sel_start = aTextPane.getSelectionStart();
int sel_end = aTextPane.getSelectionEnd();
int i = sel_start;
StringBuilder output = new StringBuilder();
while (i < sel_end) {
Element e = sdoc.getCharacterElement(i);
Object nameAttr = e.getAttributes().getAttribute(StyleConstants.NameAttribute);
int start = e.getStartOffset(), end = e.getEndOffset();
if (nameAttr == HTML.Tag.BR) {
output.append("\n");
} else if (nameAttr == HTML.Tag.CONTENT) {
if (start < sel_start) {
start = sel_start;
}
if (end > sel_end) {
end = sel_end;
}
try {
String str = sdoc.getText(start, end - start);
output.append(str);
} catch (BadLocationException ble) {
Debug.error(me + "Copy-paste problem!\n%s", ble.getMessage());
}
}
i = end;
}
return new StringSelection(output.toString());
}
private void updateTemplateFromEditor(PrintfTemplate template) {
ArrayList params = new ArrayList();
String format = null;
int text_length = editorPane.getDocument().getLength();
try {
format = editorPane.getDocument().getText(0, text_length);
} catch (BadLocationException ex1) {
}
Element section_el = editorPane.getDocument().getDefaultRootElement();
// Get number of paragraphs.
int num_para = section_el.getElementCount();
for (int p_count = 0; p_count < num_para; p_count++) {
Element para_el = section_el.getElement(p_count);
// Enumerate the content elements
int num_cont = para_el.getElementCount();
for (int c_count = 0; c_count < num_cont; c_count++) {
Element content_el = para_el.getElement(c_count);
AttributeSet attr = content_el.getAttributes();
// Get the name of the style applied to this content element; may be null
String sn = (String) attr.getAttribute(StyleConstants.NameAttribute);
// Check if style name match
if (sn != null && sn.startsWith("Parameter")) {
// we extract the label.
JLabel l = (JLabel) StyleConstants.getComponent(attr);
if (l != null) {
params.add(l.getName());
}
}
}
}
template.setFormat(format);
template.setTokens(params);
}
/**
* Highlight lines to start or end delimiter.
*
* @param content the content to parse
* @param line the line number
* @throws BadLocationException if offsets are wrong
*/
protected void highlightLinesAfter(String content, int line) throws BadLocationException {
int offset = m_RootElement.getElement(line).getEndOffset();
// Start/End delimiter not found, nothing to do
int startDelimiter = -1;
int endDelimiter = -1;
if (getMultiLineComment()) {
startDelimiter = indexOf(content, getMultiLineCommentStart(), offset);
endDelimiter = indexOf(content, getMultiLineCommentEnd(), offset);
}
if (startDelimiter < 0) startDelimiter = content.length();
if (endDelimiter < 0) endDelimiter = content.length();
int delimiter = Math.min(startDelimiter, endDelimiter);
if (delimiter < offset) return;
// Start/End delimiter found, reapply highlighting
int endLine = m_RootElement.getElementIndex(delimiter);
for (int i = line + 1; i < endLine; i++) {
Element branch = m_RootElement.getElement(i);
Element leaf = m_Self.getCharacterElement(branch.getStartOffset());
AttributeSet as = leaf.getAttributes();
if (as.isEqual(DEFAULT_COMMENT)) applyHighlighting(content, i);
}
}
@Override
public void mouseClicked(MouseEvent me) {
Element el = doc.getCharacterElement(viewToModel(me.getPoint()));
if (el == null) return;
AttributeSet as = el.getAttributes();
if (as.isDefined("ip")) {
String ip = (String) as.getAttribute("ip");
ScriptException se = (ScriptException) as.getAttribute("exception");
Node node = net.getAtIP(ip);
if (node == null) {
Utility.displayError("Error", "Computer does not exist");
return;
}
String errorString =
"--ERROR--\n"
+ "Error at line number "
+ se.getLineNumber()
+ " and column number "
+ se.getColumnNumber()
+ "\n"
+ se.getMessage();
new ScriptDialog(
parentFrame,
str -> {
if (str != null) {
node.setScript(str);
}
},
node.getScript(),
errorString)
.setVisible(true);
}
}
@Override
public void mouseMoved(MouseEvent me) {
Element el = doc.getCharacterElement(viewToModel(me.getPoint()));
if (el == null) return;
AttributeSet as = el.getAttributes();
if (as.isDefined("ip")) {
setCursor(handCursor);
} else {
setCursor(defaultCursor);
}
}
void editorPane_keyPressed(KeyEvent e) {
StyledDocument doc = editorPane.getStyledDocument();
int pos = editorPane.getCaretPosition();
int code = e.getKeyCode();
Element el;
switch (code) {
case KeyEvent.VK_BACK_SPACE:
case KeyEvent.VK_DELETE:
case KeyEvent.VK_LEFT:
case KeyEvent.VK_KP_LEFT:
if (pos == 0) return;
// we want to get the element to the left of position.
el = doc.getCharacterElement(pos - 1);
break;
case KeyEvent.VK_RIGHT:
case KeyEvent.VK_KP_RIGHT:
// we want to get the element to the right of position.
el = doc.getCharacterElement(pos + 1);
break;
default:
return; // bail we don't handle it.
}
AttributeSet attr = el.getAttributes();
String el_name = (String) attr.getAttribute(StyleConstants.NameAttribute);
int el_range = el.getEndOffset() - el.getStartOffset() - 1;
if (el_name.startsWith("Parameter") && StyleConstants.getComponent(attr) != null) {
try {
switch (code) {
case KeyEvent.VK_BACK_SPACE:
case KeyEvent.VK_DELETE:
doc.remove(el.getStartOffset(), el_range);
break;
case KeyEvent.VK_LEFT:
case KeyEvent.VK_KP_LEFT:
editorPane.setCaretPosition(pos - el_range);
break;
case KeyEvent.VK_RIGHT:
case KeyEvent.VK_KP_RIGHT:
editorPane.setCaretPosition(pos + (el_range));
break;
}
} catch (BadLocationException ex) {
}
}
}
/*
* Determine the Y offset for the current row
*/
private int getOffsetY(int rowStartOffset, FontMetrics fontMetrics) throws BadLocationException {
// Get the bounding rectangle of the row
Rectangle r = component.modelToView(rowStartOffset);
int lineHeight = fontMetrics.getHeight();
int y = r.y + r.height;
int descent = 0;
// The text needs to be positioned above the bottom of the bounding
// rectangle based on the descent of the font(s) contained on the row.
if (r.height == lineHeight) {
// default font is being used
descent = fontMetrics.getDescent();
} else {
// We need to check all the attributes for font changes
if (fonts == null) {
fonts = new HashMap<String, FontMetrics>();
}
Element root = component.getDocument().getDefaultRootElement();
int index = root.getElementIndex(rowStartOffset);
Element line = root.getElement(index);
for (int i = 0; i < line.getElementCount(); i++) {
Element child = line.getElement(i);
AttributeSet as = child.getAttributes();
String fontFamily = (String) as.getAttribute(StyleConstants.FontFamily);
Integer fontSize = (Integer) as.getAttribute(StyleConstants.FontSize);
String key = fontFamily + fontSize;
FontMetrics fm = fonts.get(key);
if (fm == null) {
Font font = new Font(fontFamily, Font.PLAIN, fontSize);
fm = component.getFontMetrics(font);
fonts.put(key, fm);
}
descent = Math.max(descent, fm.getDescent());
}
}
return y - descent;
}
public void write(Writer out, Document doc, int pos, int len, Map<String, String> copiedImgs)
throws IOException, BadLocationException {
Debug.log(9, "SikuliEditorKit.write %d %d", pos, len);
DefaultStyledDocument sdoc = (DefaultStyledDocument) doc;
int i = pos;
String absPath;
while (i < pos + len) {
Element e = sdoc.getCharacterElement(i);
int start = e.getStartOffset(), end = e.getEndOffset();
if (e.getName().equals(StyleConstants.ComponentElementName)) {
// A image argument to be filled
AttributeSet attr = e.getAttributes();
Component com = StyleConstants.getComponent(attr);
out.write(com.toString());
if (copiedImgs != null
&& (com instanceof EditorPatternButton || com instanceof EditorPatternLabel)) {
if (com instanceof EditorPatternButton) {
absPath = ((EditorPatternButton) com).getFilename();
} else {
absPath = ((EditorPatternLabel) com).getFile();
}
String fname = (new File(absPath)).getName();
copiedImgs.put(fname, absPath);
Debug.log(3, "save image for copy&paste: " + fname + " -> " + absPath);
}
} else {
if (start < pos) {
start = pos;
}
if (end > pos + len) {
end = pos + len;
}
out.write(doc.getText(start, end - start));
}
i = end;
}
out.close();
}
private void processPanelLayout(Session session, Element element, HashMap additionalInformation) {
String nodeName = element.getNodeName();
String panelName = nodeName;
NamedNodeMap tNodeMap = element.getAttributes();
for (int i = 0; i < tNodeMap.getLength(); i++) {
Node node = tNodeMap.item(i);
String name = node.getNodeName();
if (name.equals("dividerFractions")) {
String value = node.getNodeValue();
String[] tokens = value.split(",");
double[] divs = new double[tokens.length];
try {
for (int j = 0; j < tokens.length; j++) {
divs[j] = Double.parseDouble(tokens[j]);
}
session.setDividerFractions(divs);
} catch (NumberFormatException e) {
log.error("Error parsing divider locations", e);
}
}
}
}
/**
* Process a track element. This should return a single track, but could return multiple tracks
* since the uniqueness of the track id is not enforced.
*
* @param session
* @param element
* @param additionalInformation
* @return
*/
private List<Track> processTrack(
Session session, Element element, HashMap additionalInformation) {
String id = getAttribute(element, SessionAttribute.ID.getText());
// TODo -- put in utility method, extacts attributes from element **Definitely need to do this
HashMap<String, String> tAttributes = new HashMap();
HashMap<String, String> drAttributes = null;
NamedNodeMap tNodeMap = element.getAttributes();
for (int i = 0; i < tNodeMap.getLength(); i++) {
Node node = tNodeMap.item(i);
String value = node.getNodeValue();
if (value != null && value.length() > 0) {
tAttributes.put(node.getNodeName(), value);
}
}
if (element.hasChildNodes()) {
drAttributes = new HashMap();
Node childNode = element.getFirstChild();
Node sibNode = childNode.getNextSibling();
String sibName = sibNode.getNodeName();
if (sibName.equals(SessionElement.DATA_RANGE.getText())) {
NamedNodeMap drNodeMap = sibNode.getAttributes();
for (int i = 0; i < drNodeMap.getLength(); i++) {
Node node = drNodeMap.item(i);
String value = node.getNodeValue();
if (value != null && value.length() > 0) {
drAttributes.put(node.getNodeName(), value);
}
}
}
}
// Get matching tracks.
List<Track> matchedTracks = trackDictionary.get(id);
if (matchedTracks == null) {
log.info("Warning. No tracks were found with id: " + id + " in session file");
} else {
for (final Track track : matchedTracks) {
// Special case for sequence & gene tracks, they need to be removed before being placed.
if (version >= 4 && track == geneTrack || track == seqTrack) {
igv.removeTracks(Arrays.asList(track));
}
track.restorePersistentState(tAttributes);
if (drAttributes != null) {
DataRange dr = track.getDataRange();
dr.restorePersistentState(drAttributes);
track.setDataRange(dr);
}
}
trackDictionary.remove(id);
}
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
return matchedTracks;
}
private void initialize(Element elem) {
synchronized (this) {
loading = true;
fWidth = fHeight = 0;
}
int width = 0;
int height = 0;
boolean customWidth = false;
boolean customHeight = false;
try {
fElement = elem;
// Request image from document's cache:
AttributeSet attr = elem.getAttributes();
if (isURL()) {
URL src = getSourceURL();
if (src != null) {
Dictionary cache = (Dictionary) getDocument().getProperty(IMAGE_CACHE_PROPERTY);
if (cache != null) fImage = (Image) cache.get(src);
else fImage = Toolkit.getDefaultToolkit().getImage(src);
}
} else {
/** ****** Code to load from relative path ************ */
String src = (String) fElement.getAttributes().getAttribute(HTML.Attribute.SRC);
System.out.println("before src: " + src);
src = processSrcPath(src);
System.out.println("after src: " + src);
fImage = Toolkit.getDefaultToolkit().createImage(src);
try {
waitForImage();
} catch (InterruptedException e) {
fImage = null;
}
/** *************************************************** */
}
// Get height/width from params or image or defaults:
height = getIntAttr(HTML.Attribute.HEIGHT, -1);
customHeight = (height > 0);
if (!customHeight && fImage != null) height = fImage.getHeight(this);
if (height <= 0) height = DEFAULT_HEIGHT;
width = getIntAttr(HTML.Attribute.WIDTH, -1);
customWidth = (width > 0);
if (!customWidth && fImage != null) width = fImage.getWidth(this);
if (width <= 0) width = DEFAULT_WIDTH;
// Make sure the image starts loading:
if (fImage != null)
if (customWidth && customHeight)
Toolkit.getDefaultToolkit().prepareImage(fImage, height, width, this);
else Toolkit.getDefaultToolkit().prepareImage(fImage, -1, -1, this);
/**
* ****************************************************** // Rob took this out. Changed scope
* of src. if( DEBUG ) { if( fImage != null ) System.out.println("ImageInfo: new on "+src+ "
* ("+fWidth+"x"+fHeight+")"); else System.out.println("ImageInfo: couldn't get image at "+
* src); if(isLink()) System.out.println(" It's a link! Border = "+ getBorder());
* //((AbstractDocument.AbstractElement)elem).dump(System.out,4); }
* ******************************************************
*/
} finally {
synchronized (this) {
loading = false;
if (customWidth || fWidth == 0) {
fWidth = width;
}
if (customHeight || fHeight == 0) {
fHeight = height;
}
}
}
}