public void save(File f) throws IOException {
PrintStream ps = new PrintStream(new FileOutputStream(f));
String[] genes = genes();
Vector<Map<String, Double>> maps = new Vector<Map<String, Double>>();
for (int j = 0; j < coefs.size(); j++) {
maps.add(coefs.get(j).geneValues(args.compare));
}
ps.print("gene");
for (int i = 0; i < coefs.size(); i++) {
ps.print(" " + keys.get(i));
}
ps.println();
for (int i = 0; i < genes.length; i++) {
ps.print(String.format("%s", genes[i]));
for (int j = 0; j < coefs.size(); j++) {
Map<String, Double> map = maps.get(j);
Double value = map.containsKey(genes[i]) ? map.get(genes[i]) : null;
ps.print(String.format(" %s", value != null ? String.format("%.2f", value) : "N/A"));
}
ps.println();
}
ps.println();
ps.close();
}
public void normalize() {
for (int i = 0; i < samples.size(); i++) {
TreeSet<Column.Entry> entries = new TreeSet<Column.Entry>();
for (int j = 0; j < cols.size(); j++) {
Column c = cols.get(j);
if (c.values.get(i) != null) {
entries.add(c.entry(i));
}
}
int ns = entries.size();
int j = 0;
for (Column.Entry e : entries) {
int cidx = ids.get(e.id());
float ff = (float) j / (float) ns;
cols.get(cidx).values.set(i, ff);
}
if (i > 0) {
if (i % 100 == 0) {
System.out.print(".");
System.out.flush();
}
}
}
System.out.println();
}
public void saveFile(File f) throws IOException {
PrintStream ps = new PrintStream(new FileOutputStream(f));
ps.print("ID");
for (Column c : cols) {
ps.print(String.format("\t%s", c.id));
}
ps.println();
for (int i = 0; i < samples.size(); i++) {
ps.print(samples.get(i));
for (int j = 0; j < cols.size(); j++) {
Float ff = cols.get(j).values.get(i);
if (ff == null) {
ps.print("\tnull");
} else {
ps.print(String.format("\t%.2f", ff));
}
}
ps.println();
if (i > 0) {
if (i % 100 == 0) {
System.out.print(".");
System.out.flush();
}
}
}
System.out.println();
ps.close();
}
Woman ExtractMax() {
Woman maxV = A.get(1);
A.set(1, A.get(BinaryHeapSize));
BinaryHeapSize--; // virtual decrease
shiftDown(1);
return maxV;
}
// keyboard discovery code
private void _mapKey(char charCode, int keyindex, boolean shift, boolean altgraph) {
log("_mapKey: " + charCode);
// if character is not in map, add it
if (!charMap.containsKey(new Integer(charCode))) {
log("Notified: " + (char) charCode);
KeyEvent event =
new KeyEvent(
applet(),
0,
0,
(shift ? KeyEvent.SHIFT_MASK : 0) + (altgraph ? KeyEvent.ALT_GRAPH_MASK : 0),
((Integer) vkKeys.get(keyindex)).intValue(),
(char) charCode);
charMap.put(new Integer(charCode), event);
log("Mapped char " + (char) charCode + " to KeyEvent " + event);
if (((char) charCode) >= 'a' && ((char) charCode) <= 'z') {
// put shifted version of a-z in automatically
int uppercharCode = (int) Character.toUpperCase((char) charCode);
event =
new KeyEvent(
applet(),
0,
0,
KeyEvent.SHIFT_MASK + (altgraph ? KeyEvent.ALT_GRAPH_MASK : 0),
((Integer) vkKeys.get(keyindex)).intValue(),
(char) uppercharCode);
charMap.put(new Integer(uppercharCode), event);
log("Mapped char " + (char) uppercharCode + " to KeyEvent " + event);
}
}
}
/**
* Gets a list of all the devices found on the bus matching the specified serial number. Only
* devices exactly matching the specified serial number will be returned. In theory, there ought
* to be only one device matching a given serial number, but this method returns a vector in order
* to be consistent with the other search methods, and in unlikely event that multiple devices do
* share the same serial number.
*
* @param serialNumber the serial number to search for.
* @return An array of all the devices found. If no devices were found matching the specified
* serial number, the array will be empty (i.e. contain zero items).
*/
public USBDevice[] getDeviceBySerialNumber(long serialNumber) {
Vector<USBDevice> devices = new Vector<USBDevice>();
for (int index = 0; index < deviceList.size(); index++) {
if (deviceList.get(index).getSerialNumber() == serialNumber)
devices.add(deviceList.get(index));
} // for( int index ...
return devices.toArray(new USBDevice[0]);
} // getDeviceBySerialNumber()
// ParserListener methods
public void noteEvent(Note note) {
if (layer >= staves) {
return;
}
// System.out.println(note.getMusicString() + " " + note.getMillisDuration() + " " +
// note.getDecimalDuration());
Vector<Chord> currChords = chords[layer];
Iterator<NotePanel> currNote = currNotes[layer];
if (!currNote.hasNext()) {
System.err.println("Received noteEvent, but no PostScript notes are left");
return;
}
if (note.getMillisDuration() > 0) {
NotePanel notePanel = currNote.next();
// time the last chord ended
long tempTime = 0;
for (int i = currChords.size() - 1; i >= 0; --i) {
if (!currChords.get(i).isTie()) {
tempTime = currChords.get(i).getTime() + currChords.get(i).getDuration();
break;
}
}
if (notePanel.isTie) {
Chord chord = new Chord();
// for each note in the last chord, set the next note as a tied note
for (int i = 0; i < currChords.lastElement().size(); ++i) {
notePanel.setTie(true).setTime(Math.min(tempTime, time - 1)).setTempo(tempo);
chord.addNote(notePanel);
notePanel = currNote.next();
}
currChords.add(chord);
}
while (notePanel.isRest) {
notePanel
.setTime(Math.min(tempTime, time - 1)) // hack, in case the rest should be trimmed
.setTempo(tempo);
tempTime += notePanel.getDuration();
Chord chord = new Chord(notePanel);
currChords.add(chord);
// System.out.println("REST: " + notePanel.getMusicString() + " " +
// notePanel.getDuration());
notePanel = currNote.next();
}
notePanel.setNote(note).setTime(time).setTempo(tempo);
if (currChords.isEmpty() || currChords.lastElement().getTime() != time) {
Chord chord = new Chord(notePanel);
currChords.add(chord);
} else {
currChords.lastElement().addNote(notePanel);
}
}
}
/**
* Show a dialog for printing the current drawing.
*
* @param fff the parent frame which will be used for dialogs and message boxes.
* @param CCr the CircuitPanel containing the drawing to be exported.
*/
public void printDrawing(JFrame fff, CircuitPanel CCr) {
cc = CCr;
DialogPrint dp = new DialogPrint(fff);
dp.setMirror(printMirror);
dp.setFit(printFitToPage);
dp.setBW(printBlackWhite);
dp.setLandscape(printLandscape);
dp.setVisible(true);
// Get some information about the printing options.
printMirror = dp.getMirror();
printFitToPage = dp.getFit();
printLandscape = dp.getLandscape();
printBlackWhite = dp.getBW();
Vector<LayerDesc> ol = cc.dmp.getLayers();
if (dp.shouldPrint()) {
if (printBlackWhite) {
Vector<LayerDesc> v = new Vector<LayerDesc>();
// Here we create an alternative array of layers in
// which all colors are pitch black. This may be
// useful for PCB's.
for (int i = 0; i < LayerDesc.MAX_LAYERS; ++i)
v.add(
new LayerDesc(
new ColorSwing(Color.black),
((LayerDesc) ol.get(i)).getVisible(),
"B/W",
((LayerDesc) ol.get(i)).getAlpha()));
cc.dmp.setLayers(v);
}
PrinterJob job = PrinterJob.getPrinterJob();
job.setPrintable(this);
boolean ok = job.printDialog();
if (ok) {
try {
PrintRequestAttributeSet aset = new HashPrintRequestAttributeSet();
// Set the correct printing orientation.
if (printLandscape) {
aset.add(OrientationRequested.LANDSCAPE);
} else {
aset.add(OrientationRequested.PORTRAIT);
}
job.print(aset);
} catch (PrinterException ex) {
// The job did not successfully complete
JOptionPane.showMessageDialog(fff, Globals.messages.getString("Print_uncomplete"));
}
}
cc.dmp.setLayers(ol);
}
}
void Update(Woman mother) {
Woman temp;
int i = getNameIndex(mother.name);
temp = A.get(i);
temp.dilation = A.get(i).dilation + mother.dilation;
temp.name = A.get(i).name;
temp.order = A.get(i).order;
A.set(i, temp);
shiftUp(i);
shiftDown(i);
}
public static void main(String[] args) throws Exception {
int V, E, s, a, b, w;
File f = new File("in_06.txt");
Scanner sc = new Scanner(f);
V = sc.nextInt();
E = sc.nextInt();
s = sc.nextInt();
AdjList.clear();
for (int i = 0; i < V; i++) {
Vector<IntegerPair> Neighbor = new Vector<IntegerPair>();
AdjList.add(Neighbor); // add neighbor list to Adjacency List
}
for (int i = 0; i < E; i++) {
a = sc.nextInt();
b = sc.nextInt();
w = sc.nextInt();
AdjList.get(a).add(new IntegerPair(b, w)); // first time using weight
}
// as an example, we start from this source (see Figure 1.15)
Vector<Integer> dist = new Vector<Integer>();
dist.addAll(Collections.nCopies(V, INF));
dist.set(s, 0);
// Bellman Ford routine
for (int i = 0; i < V - 1; i++) // relax all E edges V-1 times, O(V)
for (int u = 0; u < V; u++) { // these two loops = O(E)
Iterator it = AdjList.get(u).iterator();
while (it.hasNext()) { // relax these edges
IntegerPair v = (IntegerPair) it.next();
dist.set(v.first(), Math.min(dist.get(v.first()), dist.get(u) + v.second()));
}
}
boolean negative_cycle_exist = false;
for (int u = 0; u < V; u++) { // one more pass to check
Iterator it = AdjList.get(u).iterator();
while (it.hasNext()) { // relax these edges
IntegerPair v = (IntegerPair) it.next();
if (dist.get(v.first()) > dist.get(u) + v.second()) // should be false, but if possible
negative_cycle_exist = true; // then negative cycle exists!
}
}
System.out.printf("Negative Cycle Exist? %s\n", negative_cycle_exist ? "Yes" : "No");
if (!negative_cycle_exist)
for (int i = 0; i < V; i++) System.out.printf("SSSP(%d, %d) = %d\n", s, i, dist.get(i));
}
public static int find(
Vector<String> fileNames, String name, Vector<String> fileTypes, String type) {
int pos = -1;
// necessario procurar um por um porque pode ter arquivos
// com o mesmo nome mas com tipo diferentes
for (int i = 0; i < fileNames.size(); i++) {
if (fileNames.get(i).equals(name) && fileTypes.get(i).equals(type)) {
pos = i;
}
}
return pos;
}
/**
* Gets a list of all the devices found on the bus matching the specified product ID range. Any
* device with a product ID greater than or equal to <i>minProductID</i> and less than or equal to
* <i>maxProductID</i> will be returned. You can obtain the entire list of devices detected by
* passing a value of 0 for <i>minProductID</i> and a value of 0xffff for <i>maxProductID</i>.
* Then you can search the list obtained using your own search criteria.
*
* @param minProductID the minimum product ID to search for.
* @param maxProductID the maximum product ID to search for.
* @return An array of all the devices found. If no devices were found matching the specified
* product ID range, the array will be empty (i.e. contain zero items).
* @throws IllegalArgumentException
*/
public USBDevice[] getDeviceByProductID(int minProductID, int maxProductID) {
if (minProductID < MIN_PRODUCT_ID
|| minProductID > MAX_PRODUCT_ID
|| maxProductID < minProductID
|| maxProductID > MAX_PRODUCT_ID)
throw new IllegalArgumentException(
"Invalid product IDs: " + minProductID + ", " + maxProductID);
Vector<USBDevice> devices = new Vector<USBDevice>();
for (int index = 0; index < deviceList.size(); index++) {
final int productID = deviceList.get(index).getProductID();
if (productID >= minProductID && productID <= maxProductID)
devices.add(deviceList.get(index));
} // for( int index ...
return devices.toArray(new USBDevice[0]);
} // getDeviceByProductID()
public void outputBinary(DataOutputStream dos) throws IOException {
dos.writeUTF(id);
dos.writeInt(values.size());
int i = 0, j = 0;
while (i < values.size()) {
for (j = i; j < values.size() && values.get(j) != null; j++) {}
int count = j - i - 1;
dos.writeInt(count);
for (j = 1; j <= count && i + j < values.size(); j++) {
dos.writeFloat(values.get(i + j));
}
i = j + 1;
}
}
public void nick_name(String msg) {
try {
String name = msg.substring(13);
this.setName(name);
Vector v = father.onlineList;
boolean isRepeatedName = false;
int size = v.size();
for (int i = 0; i < size; i++) {
ServerAgentThread tempSat = (ServerAgentThread) v.get(i);
if (tempSat.getName().equals(name)) {
isRepeatedName = true;
break;
}
}
if (isRepeatedName == true) {
dout.writeUTF("<#NAME_REPEATED#>");
din.close();
dout.close();
sc.close();
flag = false;
} else {
v.add(this);
father.refreshList();
String nickListMsg = "";
StringBuilder nickListMsgSb = new StringBuilder();
size = v.size();
for (int i = 0; i < size; i++) {
ServerAgentThread tempSat = (ServerAgentThread) v.get(i);
nickListMsgSb.append("!");
nickListMsgSb.append(tempSat.getName());
}
nickListMsgSb.append("<#NICK_LIST#>");
nickListMsg = nickListMsgSb.toString();
Vector tempv = father.onlineList;
size = tempv.size();
for (int i = 0; i < size; i++) {
ServerAgentThread tempSat = (ServerAgentThread) tempv.get(i);
tempSat.dout.writeUTF(nickListMsg);
if (tempSat != this) {
tempSat.dout.writeUTF("<#MSG#>" + this.getName() + "is now online....");
}
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Gets a list of all the devices found on the bus matching the specified set of product IDs. Any
* device with a product ID equal to one of the products listed in <i>productIDs[]</i> will be
* returned. You can search for devices by product name using {@link #productNameToID( String[]
* productName ) productNameToID()}, like so:
*
* <pre>USBDevice[] devices = deviceManager.getDeviceByProductID(
* deviceManager.productNameToID( new String[] { "USB-AO16-16A", "USB-AO16-16" } ) );</pre>
*
* @param productIDs an array containing one or more product IDs to search for.
* @return An array of all the devices found. If no devices were found matching the specified set
* of product IDs, the array will be empty (i.e. contain zero items).
* @throws IllegalArgumentException
*/
public USBDevice[] getDeviceByProductID(int[] productIDs) {
if (productIDs == null || productIDs.length < 1)
throw new IllegalArgumentException("Invalid product ID array");
for (int index = 0; index < productIDs.length; index++) {
if (productIDs[index] < MIN_PRODUCT_ID || productIDs[index] > MAX_PRODUCT_ID)
throw new IllegalArgumentException("Invalid product ID: " + productIDs[index]);
} // for( int index ...
int[] sortedProductIDs = productIDs.clone();
Arrays.sort(sortedProductIDs);
Vector<USBDevice> devices = new Vector<USBDevice>();
for (int index = 0; index < deviceList.size(); index++) {
final int productID = deviceList.get(index).getProductID();
if (Arrays.binarySearch(sortedProductIDs, productID) >= 0) devices.add(deviceList.get(index));
} // for( int index ...
return devices.toArray(new USBDevice[0]);
} // getDeviceByProductID()
private MultipleAlignment(Vector<String> ord, String[] seqs) {
this();
for (int i = 0; i < ord.size(); i++) {
GappedAlignmentString gap = new GappedAlignmentString(seqs[i].toCharArray());
addGappedAlignment(ord.get(i), gap);
}
}
/**
* Gets the urlClassLoader that enables to access to the objects jar files.
*
* @return an URLClassLoader
*/
public URLClassLoader getObjectsClassLoader() {
if (objectsClassLoader == null) {
try {
if (isExecutionMode()) {
URL[] listUrl = new URL[1];
listUrl[0] = instance.getTangaraPath().toURI().toURL();
objectsClassLoader = new URLClassLoader(listUrl);
} else {
File f = new File(instance.getTangaraPath().getParentFile(), "objects");
File[] list = f.listFiles();
Vector<URL> vector = new Vector<URL>();
for (int i = 0; i < list.length; i++) {
if (list[i].getName().endsWith(".jar")) vector.add(list[i].toURI().toURL());
}
File flib =
new File(
instance.getTangaraPath().getParentFile().getAbsolutePath().replace("\\", "/")
+ "/objects/lib");
File[] listflib = flib.listFiles();
for (int j = 0; j < listflib.length; j++) {
if (listflib[j].getName().endsWith(".jar")) vector.add(listflib[j].toURI().toURL());
}
URL[] listUrl = new URL[vector.size()];
for (int j = 0; j < vector.size(); j++) listUrl[j] = vector.get(j);
objectsClassLoader = new URLClassLoader(listUrl);
}
} catch (Exception e1) {
displayError("URL MAL FORMED " + e1);
return null;
}
}
return objectsClassLoader;
}
private void addLine(TableLine l) {
for (int i = 0; i < l.values.length; i++) {
cols.get(i).values.add(l.values[i]);
}
samples.add(l.id);
sampleIndices.put(l.id, samples.size() - 1);
}
/**
* Registers a reaction on this tuple space.
*
* @param rxn The reaction to register
* @param listener The reaction callback function
*/
public void registerReaction(Reaction rxn, ReactionListener listener) {
reactions.add(new RegisteredReaction(rxn, listener));
for (int i = 0; i < ts.size(); i++) {
Tuple t = (Tuple) ts.get(i);
if (rxn.getTemplate().matches(t)) listener.reactionFired(t);
}
}
public Tuple rdp(Tuple template) {
for (int i = 0; i < ts.size(); i++) {
Tuple tuple = (Tuple) ts.get(i);
if (template.matches(tuple)) return tuple;
}
return null;
}
public Matrix matrix(boolean centered) {
String[] genes = genes();
Matrix matrix = new Matrix(genes.length, coefs.size());
for (int j = 0; j < coefs.size(); j++) {
Map<String, Double> values = coefs.get(j).geneValues(args.compare);
double sum = 0.0;
for (int i = 0; i < genes.length; i++) {
Double value = values.get(genes[i]);
if (value != null) {
matrix.set(i, j, value);
sum += value;
} else {
matrix.set(i, j, 0.0);
}
}
if (centered) {
sum /= (double) genes.length;
for (int i = 0; i < genes.length; i++) {
matrix.set(i, j, matrix.get(i, j) - sum);
}
}
}
return matrix;
}
/*................................................................................................*/
private TreeVector fillBlock(Taxa taxa) { // TODO: fill in
TreeVector filledVector = new TreeVector(taxa);
int vectorTreeCount = 0;
for (int fillers = 0; fillers < fillerTasks.size(); fillers++) {
if (fillerTasks.get(fillers) instanceof SampleOneTreeFromFile) {
((SampleOneTreeFromFile) fillerTasks.get(fillers))
.resetTreesToSample(); // One unnecessary resetting of bits on first call
TreeVector tempTreeVector = new TreeVector(taxa);
((TreeBlockFiller) fillerTasks.get(fillers)).fillTreeBlock(tempTreeVector, 1);
if (tempTreeVector.getNumberOfTrees() < 1) {
logln(
"Not enough trees were supplied by "
+ ((TreeBlockFiller) fillerTasks.get(fillers)).getName()
+ "; "
+ tempTreeVector.getNumberOfTrees()
+ " provided, one requested.");
;
}
if (tempTreeVector.getNumberOfTrees() > 0) {
int treeCount = 0;
while (treeCount < 1
&& treeCount
< tempTreeVector
.getNumberOfTrees()) { // Check so we don't ask for more trees that are there.
filledVector.addElement(tempTreeVector.getTree(treeCount), false);
if (filledVector != null && tempTreeVector != null) {
if (filledVector.getTree(vectorTreeCount) != null
&& tempTreeVector.getName() != null) {
if (filledVector.getTree(vectorTreeCount).getName() != null)
logln(
filledVector.getTree(vectorTreeCount).getName()
+ " added from "
+ tempTreeVector.getName());
}
}
treeCount++;
vectorTreeCount++;
}
}
tempTreeVector.dispose(); // disposed to reduce memory demands
// (fillerTask.get(fillers)).
}
}
return filledVector;
}
/**
* Generates XML description of the OD.<br>
* If the print stream is specified, then XML buffer is written to the stream.
*
* @param out print stream.
* @throws IOException
*/
public void xmlDump(PrintStream out) throws IOException {
if (out == null) out = System.out;
out.print("<od begin=\"" + origin.getId() + "\" end=\"" + destination.getId() + "\">\n");
out.print("<PathList>\n");
for (int i = 0; i < pathList.size(); i++) pathList.get(i).xmlDump(out);
out.print("</PathList>\n</od>\n");
return;
}
private static void printpath(int u) {
if (u == s) {
System.out.printf("%d", u);
return;
}
printpath(p.get(u));
System.out.printf(" %d", u);
}
private void checkRxns(Tuple t) {
for (int i = 0; i < reactions.size(); i++) {
RegisteredReaction rr = (RegisteredReaction) reactions.get(i);
if (rr.getReaction().getTemplate().matches(t)) {
rr.getListener().reactionFired(t);
}
}
}
/**
* @param j The ungapped index into the multiple alignment.
* @return An array of characters, corresponding to a particular column from the multiple
* alignment.
*/
public char[] alignedChars(int j) {
char[] array = new char[ordering.size()];
for (int i = 0; i < ordering.size(); i++) {
String species = ordering.get(i);
array[i] = gappedAlignments.get(species).gappedChar(j);
}
return array;
}
void print() {
System.out.println();
System.out.println();
System.out.println("PRINTING MAP ELEMENTS");
for (Map.Entry<String, Woman> entry : B.entrySet()) {
System.out.println(entry.getKey() + "/" + entry.getValue().index);
}
System.out.println();
System.out.println("PRINTING VECTOR ELEMENTS");
for (int i = 0; i < A.size(); i++) {
System.out.println(i + " " + A.get(i).name + " " + A.get(i).index + " " + A.get(i).dilation);
}
System.out.println();
System.out.println();
}
/**
* Checks if there is a gap in position <tt>gi</tt> in at least one of the aligned sequences
*
* @param gi Position to be queried for the presence of a gap
* @return <tt>true</tt> if there is no gap in any of the aligned sequences</br> <tt>false</tt> if
* there is at least one.
*/
public boolean isPresent(int gi) {
for (int i = 0; i < ordering.size(); i++) {
if (gappedAlignments.get(ordering.get(i)).isGap(gi)) {
return false;
}
}
return true;
}
public Tuple[] rdgp(Tuple template) {
Vector matchingTuples = new Vector();
for (int i = 0; i < ts.size(); i++) {
Tuple tuple = (Tuple) ts.get(i);
if (template.matches(tuple)) matchingTuples.add(tuple);
}
if (matchingTuples.size() == 0) return null;
return (Tuple[]) matchingTuples.toArray(new Tuple[0]);
}
/**
* Deregisters a reaction.
*
* @param r The reaction to register.
* @return true if successful, false otherwise.
*/
public boolean deregisterReaction(Reaction r) {
for (int i = 0; i < reactions.size(); i++) {
RegisteredReaction rxn = (RegisteredReaction) reactions.get(i);
if (rxn.rxn.equals(r)) {
reactions.remove(i);
return true;
}
}
return false;
}
