/** Draw atom */
void drawAtom(Graphics g, int iz) {
int i = zOrder[iz];
Atom atom = atoms[i];
if (atom == null) return;
double zMin = screenXYZ[zOrder[0]][2]; // fartherest from the viewer
double zMax = screenXYZ[zOrder[np - 1]][2]; // closest to the viewer
int greyScale = Atom.nBalls - 1;
if (zMin != zMax) // zMin == zMax means the two-dimensional case
greyScale = (int) (Atom.nBalls * (screenXYZ[i][2] - zMin) / (zMax - zMin) - 1e-6);
// the atom closest to the viewer has a greyScale of Atom.nBalls - 1
// the atom fartherest from the viewer has a greyScale of 0
double radius = ballSize * atom.relRadius * real2Screen;
atom.paint(g, screenXYZ[i][0], screenXYZ[i][1], greyScale, radius);
}
static void reqGetSelectionOwner(Client c) throws IOException {
int foo;
int selection;
IO io = c.client;
selection = io.readInt();
c.length -= 2;
if (!Atom.valid(selection)) {
c.errorValue = selection;
c.errorReason = 5; // BadAtom
return;
}
synchronized (io) {
io.writeByte(1);
Selection s = getSelection(selection);
io.writePad(1);
io.writeShort(c.seq);
io.writeInt(0);
if (s != null) {
io.writeInt(s.wid);
} else {
io.writeInt(0);
}
io.writePad(20);
io.flush();
}
}
static void reqConvertSelection(Client c) throws IOException {
int foo;
int selection, requestor, target, property, time;
boolean paramsOkay = true;
IO io = c.client;
requestor = io.readInt();
Window w = c.lookupWindow(requestor);
if (w == null) {
c.errorValue = requestor;
c.errorReason = 3; // BadWindow;
}
selection = io.readInt();
paramsOkay = Atom.valid(selection);
target = io.readInt();
paramsOkay &= Atom.valid(target);
property = io.readInt();
if (property != 0) {
paramsOkay &= Atom.valid(property);
}
time = io.readInt();
c.length -= 6;
if (c.errorReason != 0) {
return;
}
if (paramsOkay) {
Selection s = getSelection(selection);
if (s != null && s.client != null) {
c.cevent.mkSelectionRequest(time, s.wid, requestor, selection, target, property);
if (s.client.sendEvent(c.cevent, 1, Event.NoEventMask, Event.NoEventMask, null) != 0)
return;
}
c.cevent.mkSelectionNotify(time, requestor, selection, target, 0);
c.sendEvent(c.cevent, 1, Event.NoEventMask, Event.NoEventMask, null);
return;
} else {
// System.out.println("error!!");
c.errorValue = property;
c.errorReason = 5; // BadAtom
return;
}
}
private void removeUnnecessaryData() {
Set<AtomType> clear = Sets.newHashSet();
List<Atom> atoms = Lists.newArrayList();
List<AtomType> atomTypes = structure.getAtomTypes();
for (Section section : structure.getSections()) {
if (section.getSectionType().equals(SectionType.STRUCTUREDATA)) {
atoms.addAll(section.getAtoms());
}
}
for (AtomType atomType : atomTypes) {
AtomType delete = atomType;
for (Atom atom : atoms) {
if (atomType.getName().contains(atom.getType())) {
delete = null;
}
}
if (delete != null) {
clear.add(delete);
}
}
clear.forEach(atomTypes::remove);
}
static void reqSetSelectionOwner(Client c) throws IOException {
int foo;
int selection;
IO io = c.client;
foo = io.readInt();
c.length -= 2;
Window w = null;
if (foo != 0) {
w = c.lookupWindow(foo);
if (w == null) {
c.errorValue = foo;
c.errorReason = 3; // BadWindow
return;
}
}
selection = io.readInt();
foo = io.readInt();
c.length -= 2;
int time = 0;
time = (int) System.currentTimeMillis();
time = foo; // ??
if (Atom.valid(selection)) {
int i = 0;
Selection s = getSelection(selection);
if (s != null) {
if (s.client != null && (w == null || (s.client != c))) {
if (s.client != null) {
c.cevent.mkSelectionClear(time, s.wid, s.selection);
s.client.sendEvent(c.cevent, 1, Event.NoEventMask, Event.NoEventMask, null);
}
}
s.window = w;
s.wid = (w != null ? w.id : 0);
s.lastTimeChanged = time;
s.client = (w != null ? c : null);
} else {
// System.out.println("add");
addSelection(selection, time, w, c);
}
return;
} else {
c.errorValue = selection;
c.errorReason = 5;
return;
}
}
static void reqRotateProperties(Client c) throws IOException {
int foo, propty;
IO io = c.client;
foo = io.readInt();
Window w = c.lookupWindow(foo);
c.length -= 2;
if (w == null) {
c.errorValue = foo;
c.errorReason = 3; // BadWindow;
return;
}
int n = (short) io.readShort();
int delta = (short) io.readShort();
c.length--;
if (n == 0) {
return;
}
int[] atoms = new int[n];
Property[] props = new Property[n];
Property p;
int i = 0;
while (n != 0) {
atoms[i] = io.readInt();
c.length--;
if (!Atom.valid(atoms[i])) {
c.errorValue = atoms[i];
c.errorReason = 5; // BadAtom
return;
}
p = w.getProperty();
while (p != null) {
if (p.propertyName == atoms[i]) {
props[i] = p;
break;
}
p = p.next;
}
if (p == null) {
c.errorReason = 8; // BadMatch
return;
}
i++;
n--;
}
for (int j = 0; j < atoms.length; j++) {
for (int k = j + 1; k < atoms.length; k++) {
if (atoms[j] == atoms[k]) {
c.errorReason = 8; // BadMatch
return;
}
}
}
if (((delta < 0 ? -1 * delta : delta) % atoms.length) != 0) {
while (delta < 0) {
delta += atoms.length;
}
for (i = 0; i < atoms.length; i++) {
c.cevent.mkPropertyNotify(
w.id,
props[i].propertyName,
(int) System.currentTimeMillis(),
// Property.PropertyNewValue
0);
w.sendEvent(c.cevent, 1, null);
props[i].propertyName = atoms[(i + delta) % atoms.length];
}
}
}
public QTFastStartRAF(FileAccessor accessor, boolean enable) throws IOException {
input = accessor;
if (enable) {
String name = accessor.getName();
boolean log;
String fail = null;
synchronized (tested) {
log = !tested.contains(name);
if (log) {
tested.add(name);
}
}
try {
Atom ah = null;
Atom ftypAtom = null;
boolean gotFtyp = false;
boolean gotMdat = false;
boolean justCopy = false;
while (input.getFilePointer() < input.length()) {
ah = new Atom(input);
// System.out.println( "got " + ah.type +", size=" + ah.size );
if (!isValidTopLevelAtom(ah)) {
throw new IOException("Non top level QT atom found (" + ah.type + "). File invalid?");
}
if (gotFtyp && !gotMdat && ah.type.equalsIgnoreCase(ATOM_MOOV)) {
justCopy = true;
break;
}
// store ftyp atom to buffer
if (ah.type.equalsIgnoreCase(ATOM_FTYP)) {
ftypAtom = ah;
ftypAtom.fillBuffer(input);
gotFtyp = true;
} else if (ah.type.equalsIgnoreCase(ATOM_MDAT)) {
gotMdat = true;
input.skipBytes((int) ah.size);
} else {
input.skipBytes((int) ah.size);
}
}
if (justCopy) {
transparent = true;
return;
}
if (ftypAtom == null) {
throw new IOException("No FTYP atom found");
}
if (ah == null || !ah.type.equalsIgnoreCase(ATOM_MOOV)) {
throw new IOException("Last QT atom was not the MOOV atom.");
}
input.seek(ah.offset);
Atom moovAtom = ah;
moovAtom.fillBuffer(input);
if (isCompressedMoovAtom(moovAtom)) {
throw new IOException("Compressed MOOV qt atoms are not supported");
}
patchMoovAtom(moovAtom);
body_start = ftypAtom.offset + ftypAtom.size;
body_end = moovAtom.offset;
header = new byte[ftypAtom.buffer.length + moovAtom.buffer.length];
System.arraycopy(ftypAtom.buffer, 0, header, 0, ftypAtom.buffer.length);
System.arraycopy(
moovAtom.buffer, 0, header, ftypAtom.buffer.length, moovAtom.buffer.length);
if (accessor.length() != header.length + (body_end - body_start)) {
throw (new IOException("Inconsistent: file size has changed"));
}
} catch (Throwable e) {
// e.printStackTrace();
fail = Debug.getNestedExceptionMessage(e);
transparent = true;
} finally {
input.seek(0);
if (log) {
String message;
if (fail == null) {
message = transparent ? "Not required" : "Required";
} else {
message = "Failed - " + fail;
}
Debug.outNoStack("MOOV relocation for " + accessor.getName() + ": " + message);
}
}
} else {
transparent = true;
}
}
public void writeMeat() {
try {
for (int i = 0; i < aList.size(); i++) {
w.write("{");
w.newLine();
Atom tempA = aList.get(i);
w.write("\t" + "\"" + "vertexNum" + "\":" + tempA.getVertexNum() + "\",");
w.newLine();
w.write("\t" + "\"" + "atomicNum" + "\":" + tempA.getAtomicNum() + "\",");
w.newLine();
w.write("\t" + "\"" + "atomicWeight" + "\":" + tempA.getAtomicWeight() + "\",");
w.newLine();
w.write("\t" + "\"" + "electroNeg" + "\":" + tempA.getElectroNeg() + "\",");
w.newLine();
w.write("\t" + "\"" + "atomName" + "\":" + tempA.getAtomName() + "\",");
w.newLine();
w.write("\t" + "\"" + "adjacentBonds" + "\": {");
w.newLine();
for (int z = 0; z < tempA.getAdjacentBonds().size(); z++) {
w.write("\t\t" + "[");
w.newLine();
w.write(
"\t\t\t"
+ "\""
+ "edgeNum"
+ "\":"
+ tempA.getAdjacentBonds().get(z).getEdgeNum()
+ "\",");
w.newLine();
w.write(
"\t\t\t"
+ "\""
+ "bondType"
+ "\":"
+ tempA.getAdjacentBonds().get(z).getBondType()
+ "\",");
w.newLine();
w.write(
"\t\t\t"
+ "\""
+ "exist"
+ "\":"
+ tempA.getAdjacentBonds().get(z).getExist()
+ "\",");
w.newLine();
w.write("\t\t\t" + "\"" + "weight" + "\":" + tempA.getAdjacentBonds().get(z).getWeight());
w.newLine();
w.write("\t\t" + "]");
w.newLine();
}
w.write("\t" + "}");
w.newLine();
}
for (int p = 0; p < bList.size(); p++) {
Bond tempB = bList.get(p);
w.write("{");
w.newLine();
w.write("\t" + "\"" + "edgeNum" + "\":" + tempB.getEdgeNum() + "\",");
w.newLine();
w.write("\t" + "\"" + "bondType" + "\":" + tempB.getBondType() + "\",");
w.newLine();
w.write("\t" + "\"" + "exist" + "\":" + tempB.getExist() + "\",");
w.newLine();
w.write("\t" + "\"" + "weight" + tempB.getWeight() + "\":");
w.newLine();
w.write("\t" + "\"" + "adjacentAtoms" + "\": {");
w.newLine();
w.write("\t\t" + "\"" + "vertexNum" + "\":" + "\",");
w.newLine();
w.write("\t\t" + "\"" + "atomicNum" + "\":" + "\",");
w.newLine();
w.write("\t\t" + "\"" + "atomicWeight" + "\":" + "\",");
w.newLine();
w.write("\t\t" + "\"" + "electroNeg" + "\":" + "\",");
w.newLine();
w.write("\t\t" + "\"" + "atomName" + "\":" + "\",");
w.newLine();
}
w.write("\t" + "}");
w.newLine();
} catch (IOException e) {
System.out.println("error writing meat of file");
}
}