/**
* Carries out preprocessing that makes JEuclid handle the document better.
*
* @param doc Document
*/
static void preprocessForJEuclid(Document doc) {
// underbrace and overbrace
NodeList list = doc.getElementsByTagName("mo");
for (int i = 0; i < list.getLength(); i++) {
Element mo = (Element) list.item(i);
String parentName = ((Element) mo.getParentNode()).getTagName();
if (parentName == null) {
continue;
}
if (parentName.equals("munder") && isTextChild(mo, "\ufe38")) {
mo.setAttribute("stretchy", "true");
mo.removeChild(mo.getFirstChild());
mo.appendChild(doc.createTextNode("\u23df"));
} else if (parentName.equals("mover") && isTextChild(mo, "\ufe37")) {
mo.setAttribute("stretchy", "true");
mo.removeChild(mo.getFirstChild());
mo.appendChild(doc.createTextNode("\u23de"));
}
}
// menclose for long division doesn't allow enough top padding. Oh, and
// <mpadded> isn't implemented. And there isn't enough padding to left of
// the bar either. Solve by adding an <mover> with just an <mspace> over#
// the longdiv, contained within an mrow that adds a <mspace> before it.
list = doc.getElementsByTagName("menclose");
for (int i = 0; i < list.getLength(); i++) {
Element menclose = (Element) list.item(i);
// Only for longdiv
if (!"longdiv".equals(menclose.getAttribute("notation"))) {
continue;
}
Element mrow = doc.createElementNS(WebMathsService.NS, "mrow");
Element mover = doc.createElementNS(WebMathsService.NS, "mover");
Element mspace = doc.createElementNS(WebMathsService.NS, "mspace");
Element mspaceW = doc.createElementNS(WebMathsService.NS, "mspace");
boolean previousElement = false;
for (Node previous = menclose.getPreviousSibling();
previous != null;
previous = previous.getPreviousSibling()) {
if (previous.getNodeType() == Node.ELEMENT_NODE) {
previousElement = true;
break;
}
}
if (previousElement) {
mspaceW.setAttribute("width", "4px");
}
menclose.getParentNode().insertBefore(mrow, menclose);
menclose.getParentNode().removeChild(menclose);
mrow.appendChild(mspaceW);
mrow.appendChild(mover);
mover.appendChild(menclose);
mover.appendChild(mspace);
}
}
/** used for cut and paste. */
public void addObjectFromClipboard(String a_value) throws CircularIncludeException {
Reader reader = new StringReader(a_value);
Document document = null;
try {
document = UJAXP.getDocument(reader);
} catch (Exception e) {
e.printStackTrace();
return;
} // try-catch
Element root = document.getDocumentElement();
if (!root.getNodeName().equals("clipboard")) {
return;
} // if
Node child;
for (child = root.getFirstChild(); child != null; child = child.getNextSibling()) {
if (!(child instanceof Element)) {
continue;
} // if
Element element = (Element) child;
IGlyphFactory factory = GlyphFactory.getFactory();
if (XModule.isMatch(element)) {
EModuleInvoke module = (EModuleInvoke) factory.createXModule(element);
addModule(module);
continue;
} // if
if (XContour.isMatch(element)) {
EContour contour = (EContour) factory.createXContour(element);
addContour(contour);
continue;
} // if
if (XInclude.isMatch(element)) {
EIncludeInvoke include = (EIncludeInvoke) factory.createXInclude(element);
addInclude(include);
continue;
} // if
} // while
}
/**
* 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;
}
@Override
protected void initChildren(Element eThis) throws OmException {
Node nPrevious = eThis.getPreviousSibling();
if (nPrevious != null && nPrevious instanceof Text) {
String sText = ((Text) nPrevious).getData();
if (sText.length() > 0 && Character.isWhitespace(sText.charAt(sText.length() - 1)))
bSpaceBefore = true;
}
Node nAfter = eThis.getNextSibling();
if (nAfter != null && nAfter instanceof Text) {
String sText = ((Text) nAfter).getData();
if (sText.length() > 0 && Character.isWhitespace(sText.charAt(0))) bSpaceAfter = true;
}
List<Place> lPlaces = new LinkedList<Place>();
int iPlace = 0;
StringBuffer sbText = new StringBuffer();
for (Node n = eThis.getFirstChild(); n != null; n = n.getNextSibling()) {
if (n instanceof Element) {
Element eplace = (Element) n;
if (!eplace.getTagName().equals("eplace"))
throw new OmFormatException("<equation> may only contain text and <eplace> tags");
Element[] aeChildren = XML.getChildren(eplace);
QComponent qcChild;
boolean bImplicit = false;
if (aeChildren.length != 1) // Treats more than one child as inside <t>
{
qcChild = getQDocument().build(this, eplace, "t");
bImplicit = true;
} else // Treats single child as specific component (auto-sizing works)
qcChild = getQDocument().build(this, aeChildren[0], null);
addChild(qcChild); // Must be stored in standard child array so it
// can be found etc.
// See if width/height is specified
int iWidth, iHeight;
if (eplace.hasAttribute("width") && eplace.hasAttribute("height")) {
try {
iWidth = Integer.parseInt(eplace.getAttribute("width"));
iHeight = Integer.parseInt(eplace.getAttribute("height"));
} catch (NumberFormatException nfe) {
throw new OmFormatException("<equation> <eplace>: width= and height= must be integers");
}
} else {
Dimension d = qcChild.getApproximatePixelSize();
if (d == null)
throw new OmFormatException(
"<equation> <eplace>: Except for components that support automatic "
+ "size estimation and fixing, <eplace> must include width= and height=");
iWidth = d.width;
iHeight = d.height;
}
Place p = new Place();
p.sID = "p" + (iPlace++);
p.qc = qcChild;
p.iWidth = iWidth;
p.iHeight = iHeight;
p.bImplicit = bImplicit;
if (!eplace.hasAttribute("label"))
throw new OmFormatException("<equation> <eplace>: Must include label=");
if (eplace.hasAttribute("label")) p.sLabel = eplace.getAttribute("label");
else p.sLabel = null;
if (eplace.hasAttribute("for")) p.sLabelFor = eplace.getAttribute("for");
else if (qcChild instanceof Labelable) p.sLabelFor = qcChild.getID();
lPlaces.add(p);
// Add in the equation format text representing the placeholder
sbText.append("\\placeholder{" + p.sID + "}{" + p.iWidth + "," + p.iHeight + "}");
} else if (n instanceof Text) {
sbText.append(n.getNodeValue());
}
}
sEquation = sbText.toString();
apPlaces = lPlaces.toArray(new Place[0]);
}
/**
* creates a new image
*
* @param svgHandle a svg handle
* @param resourceId the id of the resource from which the image will be created
*/
protected void createNewImage(SVGHandle svgHandle, String resourceId) {
if (svgHandle != null && resourceId != null && !resourceId.equals("")) {
Element resourceElement = null;
resourceElement =
svgHandle.getScrollPane().getSVGCanvas().getDocument().getElementById(resourceId);
final String fresourceId = resourceId;
if (resourceElement != null) {
final SVGHandle fhandle = svgHandle;
// creating the canvas and setting its properties
final JSVGCanvas canvas =
new JSVGCanvas() {
@Override
public void dispose() {
removeKeyListener(listener);
removeMouseMotionListener(listener);
removeMouseListener(listener);
disableInteractions = true;
selectableText = false;
userAgent = null;
bridgeContext.dispose();
super.dispose();
}
};
// the element to be added
Element elementToAdd = null;
canvas.setDocumentState(JSVGComponent.ALWAYS_STATIC);
canvas.setDisableInteractions(true);
// creating the new document
final String svgNS = SVGDOMImplementation.SVG_NAMESPACE_URI;
final SVGDocument doc = (SVGDocument) resourceElement.getOwnerDocument().cloneNode(false);
// creating the root element
final Element root =
(Element)
doc.importNode(resourceElement.getOwnerDocument().getDocumentElement(), false);
doc.appendChild(root);
// removing all the attributes of the root element
NamedNodeMap attributes = doc.getDocumentElement().getAttributes();
for (int i = 0; i < attributes.getLength(); i++) {
if (attributes.item(i) != null) {
doc.getDocumentElement().removeAttribute(attributes.item(i).getNodeName());
}
}
// adding the new attributes for the root
root.setAttributeNS(null, "width", imageSize.width + "");
root.setAttributeNS(null, "height", imageSize.height + "");
root.setAttributeNS(null, "viewBox", "0 0 " + imageSize.width + " " + imageSize.height);
// the defs element that will contain the cloned resource node
final Element defs = (Element) doc.importNode(resourceElement.getParentNode(), true);
root.appendChild(defs);
if (resourceElement.getNodeName().equals("linearGradient")
|| resourceElement.getNodeName().equals("radialGradient")
|| resourceElement.getNodeName().equals("pattern")) {
// the rectangle that will be drawn
final Element rect = doc.createElementNS(svgNS, "rect");
rect.setAttributeNS(null, "x", "0");
rect.setAttributeNS(null, "y", "0");
rect.setAttributeNS(null, "width", imageSize.width + "");
rect.setAttributeNS(null, "height", imageSize.height + "");
elementToAdd = rect;
// setting that the rectangle uses the resource
String id = resourceElement.getAttribute("id");
if (id == null) {
id = "";
}
rect.setAttributeNS(null, "style", "fill:url(#" + id + ");");
// getting the cloned resource node
Node cur = null;
Element clonedResourceElement = null;
String id2 = "";
for (cur = defs.getFirstChild(); cur != null; cur = cur.getNextSibling()) {
if (cur instanceof Element) {
id2 = ((Element) cur).getAttribute("id");
if (id2 != null && id.equals(id2)) {
clonedResourceElement = (Element) cur;
}
}
}
if (clonedResourceElement != null) {
// getting the root element of the initial resource
// element
Element initialRoot = resourceElement.getOwnerDocument().getDocumentElement();
// getting the width and height of the initial root
// element
double initialWidth = 0, initialHeight = 0;
try {
initialWidth =
EditorToolkit.getPixelledNumber(initialRoot.getAttributeNS(null, "width"));
initialHeight =
EditorToolkit.getPixelledNumber(initialRoot.getAttributeNS(null, "height"));
} catch (DOMException ex) {
ex.printStackTrace();
}
if (resourceElement.getNodeName().equals("linearGradient")) {
if (resourceElement.getAttributeNS(null, "gradientUnits").equals("userSpaceOnUse")) {
double x1 = 0, y1 = 0, x2 = 0, y2 = 0;
// normalizing the values for the vector to fit
// the rectangle
try {
x1 = Double.parseDouble(resourceElement.getAttributeNS(null, "x1"));
y1 = Double.parseDouble(resourceElement.getAttributeNS(null, "y1"));
x2 = Double.parseDouble(resourceElement.getAttributeNS(null, "x2"));
y2 = Double.parseDouble(resourceElement.getAttributeNS(null, "y2"));
x1 = x1 / initialWidth * imageSize.width;
y1 = y1 / initialHeight * imageSize.height;
x2 = x2 / initialWidth * imageSize.width;
y2 = y2 / initialHeight * imageSize.height;
} catch (NumberFormatException | DOMException ex) {
ex.printStackTrace();
}
clonedResourceElement.setAttributeNS(null, "x1", format.format(x1));
clonedResourceElement.setAttributeNS(null, "y1", format.format(y1));
clonedResourceElement.setAttributeNS(null, "x2", format.format(x2));
clonedResourceElement.setAttributeNS(null, "y2", format.format(y2));
}
} else if (resourceElement.getNodeName().equals("radialGradient")) {
if (resourceElement.getAttributeNS(null, "gradientUnits").equals("userSpaceOnUse")) {
double cx = 0, cy = 0, r = 0, fx = 0, fy = 0;
// normalizing the values for the circle to fit
// the rectangle
try {
cx = Double.parseDouble(resourceElement.getAttributeNS(null, "cx"));
cy = Double.parseDouble(resourceElement.getAttributeNS(null, "cy"));
r = Double.parseDouble(resourceElement.getAttributeNS(null, "r"));
fx = Double.parseDouble(resourceElement.getAttributeNS(null, "fx"));
fy = Double.parseDouble(resourceElement.getAttributeNS(null, "fy"));
cx = cx / initialWidth * imageSize.width;
cy = cy / initialHeight * imageSize.height;
r =
r
/ (Math.abs(
Math.sqrt(Math.pow(initialWidth, 2) + Math.pow(initialHeight, 2))))
* Math.abs(
Math.sqrt(
Math.pow(imageSize.width, 2) + Math.pow(imageSize.width, 2)));
fx = fx / initialWidth * imageSize.width;
fy = fy / initialHeight * imageSize.height;
} catch (NumberFormatException | DOMException ex) {
ex.printStackTrace();
}
clonedResourceElement.setAttributeNS(null, "cx", format.format(cx));
clonedResourceElement.setAttributeNS(null, "cy", format.format(cy));
clonedResourceElement.setAttributeNS(null, "r", format.format(r));
clonedResourceElement.setAttributeNS(null, "fx", format.format(fx));
clonedResourceElement.setAttributeNS(null, "fy", format.format(fy));
}
} else if (resourceElement.getNodeName().equals("pattern")) {
if (resourceElement.getAttributeNS(null, "patternUnits").equals("userSpaceOnUse")) {
double x = 0, y = 0, w = 0, h = 0;
// normalizing the values for the vector to fit
// the rectangle
try {
String xString = resourceElement.getAttributeNS(null, "x");
if (!xString.equals("")) {
x = Double.parseDouble(xString);
}
String yString = resourceElement.getAttributeNS(null, "y");
if (!yString.equals("")) {
y = Double.parseDouble(yString);
}
String wString = resourceElement.getAttributeNS(null, "w");
if (!wString.equals("")) {
w = Double.parseDouble(wString);
}
String hString = resourceElement.getAttributeNS(null, "h");
if (!hString.equals("")) {
h = Double.parseDouble(hString);
}
x = x / initialWidth * imageSize.width;
y = y / initialHeight * imageSize.height;
w = w / initialWidth * imageSize.width;
h = h / initialHeight * imageSize.height;
} catch (NumberFormatException | DOMException ex) {
ex.printStackTrace();
}
clonedResourceElement.setAttributeNS(null, "x", format.format(x));
clonedResourceElement.setAttributeNS(null, "y", format.format(y));
clonedResourceElement.setAttributeNS(null, "width", format.format(w));
clonedResourceElement.setAttributeNS(null, "height", format.format(h));
}
}
}
} else if (resourceElement.getNodeName().equals("marker")) {
// the line that will be drawn
final Element line = doc.createElementNS(svgNS, "line");
line.setAttributeNS(null, "x1", (((double) imageSize.width) / 2) + "");
line.setAttributeNS(null, "y1", (((double) imageSize.height) / 2) + "");
line.setAttributeNS(null, "x2", ((double) imageSize.width / 2) + "");
line.setAttributeNS(null, "y2", imageSize.height + "");
elementToAdd = line;
// setting that the line uses the resource
String id = resourceElement.getAttribute("id");
if (id == null) id = "";
line.setAttributeNS(
null, "style", "stroke:none;fill:none;marker-start:url(#" + id + ");");
}
root.appendChild(elementToAdd);
// adding a rendering listener to the canvas
GVTTreeRendererAdapter gVTTreeRendererAdapter =
new GVTTreeRendererAdapter() {
@Override
public void gvtRenderingCompleted(GVTTreeRendererEvent evt) {
Image bufferedImage = canvas.getOffScreen();
if (bufferedImage != null) {
Graphics g = bufferedImage.getGraphics();
Color borderColor = MetalLookAndFeel.getSeparatorForeground();
g.setColor(borderColor);
g.drawRect(0, 0, imageSize.width - 1, imageSize.height - 1);
}
setImage(fhandle, fresourceId, bufferedImage);
// refreshing the panels that have been created when no
// image was available for them
Image image = null;
for (ResourceRepresentation resourceRepresentation :
new LinkedList<ResourceRepresentation>(resourceRepresentationList)) {
if (resourceRepresentation != null) {
resourceRepresentation.refreshRepresentation();
image = resourceRepresentation.getImage();
if (image != null) {
resourceRepresentationList.remove(resourceRepresentation);
}
}
}
canvas.removeGVTTreeRendererListener(this);
canvas.stopProcessing();
canvas.dispose();
}
};
canvas.addGVTTreeRendererListener(gVTTreeRendererAdapter);
// setting the document for the canvas
canvas.setSVGDocument(doc);
canvas.setBackground(Color.white);
canvas.setBounds(1, 1, imageSize.width, imageSize.height);
}
}
}