/**
* Prompt to confirm that the user wants to delete the JShellItem from the file system. If so,
* remove it. If -f is supplied, do not prompt and confirm. If the root directory is specified,
* its contents but not itself will be subject to deletion.
*
* @param paths the JShellItem to be removed.
*/
public void rm(List<String> paths) throws Exception {
// Loop through the user inputs.
for (String path : paths) {
// Initialize the current JShellItem.
JShellItem item = getItemAtPath(path, 0);
if (item == null) {
System.out.printf("%s: does not exist.\n", path);
} else {
// Keep track of the size of that JShellItem.
int size = item.getSize();
if (size > 0) {
List<String> recursiveList = recurseOnPath(path, true);
rm(recursiveList.subList(0, size + 1));
if (item.getSize() == 0) {
rm(recursiveList.subList(size + 1, size + 2));
}
} else {
if (item.getPath().equals("/")) {
return;
}
// Check the -f option.
if (!currentOptions_.equals("f")) {
System.out.printf(
"Really remove %s from %s? (y/n) ",
item.getName(), item.getParentDirectory().getPath());
// Read the user input.
ArrayList<String> in = readInput();
// If 'y'
if (in.toString().equals("[y]")) {
item.getParentDirectory().removeItem(item);
// if not 'n', ask again.
} else if (!in.toString().equals("[n]")) {
List<String> tempStore = new ArrayList<String>();
tempStore.add(path);
rm(tempStore);
}
// If -f is specified.
} else {
item.getParentDirectory().removeItem(item);
}
}
}
}
}
/**
* Converts a map of results to a String JSON representation for it
*
* @param map a map that matches properties with an ArrayList of values
* @return the JSON representation for the map, as a String
*/
private String mapToString(Map<String, ArrayList<String>> map) {
StringBuilder result = new StringBuilder("{");
for (Map.Entry<String, ArrayList<String>> entry : map.entrySet()) {
ArrayList<String> value = entry.getValue();
if (value.size() == 1)
result.append(String.format("\"%s\" : %s,\n", entry.getKey(), value.get(0)));
else result.append(String.format("\"%s\" : %s,\n", entry.getKey(), value.toString()));
}
result.setCharAt(result.length() - 2, '}');
return result.toString();
}
public static String pSet(Integer n) {
String str1 = "";
for (int i = 1; i <= n; i++) {
str1 += i;
}
char[] array1 = str1.toCharArray();
ArrayList list = new ArrayList();
int length = array1.length;
int totalElements = (int) Math.pow(2, length);
for (int i = 0; i < totalElements; i++) {
String binString = Integer.toBinaryString(i);
int stringValue = binString.length();
String subset = binString;
for (int j = stringValue; j < length; j++) {
subset = "0" + subset;
}
ArrayList innerSet = new ArrayList();
for (int k = 0; k < subset.length(); k++) {
if (subset.charAt(k) == '1') innerSet.add(array1[k]);
}
list.add(innerSet);
}
return list.toString();
}
public void addObjectValue(String name, String[] al) {
ArrayList al1 = new ArrayList();
for (int i = 0; i < al.length; i++) {
// this.theArrayAdapter.add(name + ":" + al[i]);
al1.add(al[i]);
}
String f = al1.toString().replace('[', '{');
String f2 = f.replace(']', '}');
this.theArrayAdapter.add(name + ":" + f2);
}
private int vita_sociale(FileAccess file_acc, ArrayList<InetAddress> l_peers) {
int contattato_ok = 0;
int problemi = 0;
System.out.println("@ vista sociale attivata con lista !" + l_peers.toString());
for (InetAddress i : l_peers)
if (!i.getHostAddress().equals("192.168.0.10")) {
System.out.println("@ confronto gli ip di: " + i.getHostAddress() + " con 192.168.0.10");
contattato_ok = contatta_Peer(file_acc, i, 4000);
if (contattato_ok != 0) {
System.out.println(
"# il tentativo di creazione di connessione con il peer "
+ i.getHostAddress()
+ " ha fallito");
problemi = 1;
}
} else
System.out.println("Evito di contattare il mio stesso indirizzo"); // TODO togliere questo
return problemi;
}
private List<String> getIgnoreSignFieldNames(Class<? extends RopRequest> requestType) {
if (logger.isDebugEnabled()) {
logger.debug("获取" + requestType.getCanonicalName() + "需要签名的属性");
}
final ArrayList<String> igoreSignFieldNames = new ArrayList<String>(10);
ReflectionUtils.doWithFields(
requestType,
new ReflectionUtils.FieldCallback() {
public void doWith(Field field) throws IllegalArgumentException, IllegalAccessException {
igoreSignFieldNames.add(field.getName());
}
},
new ReflectionUtils.FieldFilter() {
public boolean matches(Field field) {
IgnoreSign ignoreSign = field.getAnnotation(IgnoreSign.class);
return ignoreSign != null;
}
});
if (logger.isDebugEnabled()) {
logger.debug(requestType.getCanonicalName() + "需要签名的属性:" + igoreSignFieldNames.toString());
}
return igoreSignFieldNames;
}
public Allele getLikelihoods(
RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, AlignmentContext> contexts,
AlignmentContextUtils.ReadOrientation contextType,
GenotypePriors priors,
Map<String, MultiallelicGenotypeLikelihoods> GLs,
Allele alternateAlleleToUse,
boolean useBAQedPileup) {
if (tracker == null) return null;
GenomeLoc loc = ref.getLocus();
Allele refAllele, altAllele;
VariantContext vc = null;
if (!ref.getLocus().equals(lastSiteVisited)) {
// starting a new site: clear allele list
alleleList.clear();
lastSiteVisited = ref.getLocus();
indelLikelihoodMap.set(new HashMap<PileupElement, LinkedHashMap<Allele, Double>>());
haplotypeMap.clear();
if (getAlleleListFromVCF) {
for (final VariantContext vc_input : tracker.getValues(UAC.alleles, loc)) {
if (vc_input != null
&& allowableTypes.contains(vc_input.getType())
&& ref.getLocus().getStart() == vc_input.getStart()) {
vc = vc_input;
break;
}
}
// ignore places where we don't have a variant
if (vc == null) return null;
alleleList.clear();
if (ignoreSNPAllelesWhenGenotypingIndels) {
// if there's an allele that has same length as the reference (i.e. a SNP or MNP), ignore
// it and don't genotype it
for (Allele a : vc.getAlleles())
if (a.isNonReference() && a.getBases().length == vc.getReference().getBases().length)
continue;
else alleleList.add(a);
} else {
for (Allele a : vc.getAlleles()) alleleList.add(a);
}
} else {
alleleList = computeConsensusAlleles(ref, contexts, contextType);
if (alleleList.isEmpty()) return null;
}
}
// protect against having an indel too close to the edge of a contig
if (loc.getStart() <= HAPLOTYPE_SIZE) return null;
// check if there is enough reference window to create haplotypes (can be an issue at end of
// contigs)
if (ref.getWindow().getStop() < loc.getStop() + HAPLOTYPE_SIZE) return null;
if (!(priors instanceof DiploidIndelGenotypePriors))
throw new StingException(
"Only diploid-based Indel priors are supported in the DINDEL GL model");
if (alleleList.isEmpty()) return null;
refAllele = alleleList.get(0);
altAllele = alleleList.get(1);
// look for alt allele that has biggest length distance to ref allele
int maxLenDiff = 0;
for (Allele a : alleleList) {
if (a.isNonReference()) {
int lenDiff = Math.abs(a.getBaseString().length() - refAllele.getBaseString().length());
if (lenDiff > maxLenDiff) {
maxLenDiff = lenDiff;
altAllele = a;
}
}
}
final int eventLength = altAllele.getBaseString().length() - refAllele.getBaseString().length();
final int hsize = (int) ref.getWindow().size() - Math.abs(eventLength) - 1;
final int numPrefBases = ref.getLocus().getStart() - ref.getWindow().getStart() + 1;
haplotypeMap =
Haplotype.makeHaplotypeListFromAlleles(
alleleList, loc.getStart(), ref, hsize, numPrefBases);
// For each sample, get genotype likelihoods based on pileup
// compute prior likelihoods on haplotypes, and initialize haplotype likelihood matrix with
// them.
// initialize the GenotypeLikelihoods
GLs.clear();
for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);
ReadBackedPileup pileup = null;
if (context.hasExtendedEventPileup()) pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup()) pileup = context.getBasePileup();
if (pileup != null) {
final double[] genotypeLikelihoods =
pairModel.computeReadHaplotypeLikelihoods(
pileup, haplotypeMap, ref, eventLength, getIndelLikelihoodMap());
GLs.put(
sample.getKey(),
new MultiallelicGenotypeLikelihoods(
sample.getKey(), alleleList, genotypeLikelihoods, getFilteredDepth(pileup)));
if (DEBUG) {
System.out.format("Sample:%s Alleles:%s GL:", sample.getKey(), alleleList.toString());
for (int k = 0; k < genotypeLikelihoods.length; k++)
System.out.format("%1.4f ", genotypeLikelihoods[k]);
System.out.println();
}
}
}
return refAllele;
}
/**
* Assign a {@link FloatingIP} from the given {@link FloatingNetwork} to the given {@link Port}.
* It will either assign an existing floating IP or it will create and assign a new floating IP.
*
* @param port the {@link Port} to which a floating IP to be assigned.
* @param floatingNetworkUuid the network uuid of the floating network from which a floating IP to
* be chosen/created
* @return the assigned Floating IP
*/
private FloatingIP assignFloatingIP(Port port, String floatingNetworkUuid) {
// checking whether if there are any available floating IPs in the external network
// if there are any we don't need to create a new one
ArrayList<FloatingIP> unassignedFloatingIPs =
getUnassignedFloatingIPsByNetworkUuid(floatingNetworkUuid);
// we should remove all predefined floating IPs from unassigned list
// otherwise, these predefined floating IPs can be associated to some other interfaces
if (unassignedFloatingIPs != null) {
if (log.isDebugEnabled()) {
String msg =
String.format(
"Unassigned floating IPs from the network %s - %s",
floatingNetworkUuid, unassignedFloatingIPs.toString());
log.debug(msg);
}
Iterator<FloatingIP> unassginedFloatingIPsIterator = unassignedFloatingIPs.iterator();
while (unassginedFloatingIPsIterator.hasNext()) {
FloatingIP floatingIP = unassginedFloatingIPsIterator.next();
List<String> allPredefinedFloatingIPs =
getAllPredefinedFloatingIPs(iaasProvider.getNetworkInterfaces());
if (allPredefinedFloatingIPs != null && !allPredefinedFloatingIPs.isEmpty()) {
if (log.isDebugEnabled()) {
String msg =
String.format(
"Predefined floating IPs - %s found in cartridge",
allPredefinedFloatingIPs.toString());
log.debug(msg);
}
Iterator<String> predefinedFloatingIPsIterator = allPredefinedFloatingIPs.iterator();
while (predefinedFloatingIPsIterator.hasNext()) {
String floatingIPAddress = predefinedFloatingIPsIterator.next();
if (floatingIP.getFloatingIpAddress() != null
&& floatingIP.getFloatingIpAddress().equals(floatingIPAddress)) {
unassginedFloatingIPsIterator.remove();
if (log.isDebugEnabled()) {
String msg =
String.format(
"Removed predefined floating IP %s from available floating IPs",
floatingIPAddress);
log.debug(msg);
}
}
}
}
}
}
if (unassignedFloatingIPs == null || unassignedFloatingIPs.isEmpty()) {
return createAndAssignFloatingIP(port, floatingNetworkUuid);
}
if (log.isDebugEnabled()) {
String msg =
String.format(
"Available floating IPs from the network %s - %s",
floatingNetworkUuid, unassignedFloatingIPs.toString());
log.debug(msg);
}
// shuffle and get the last for randomness
Collections.shuffle(unassignedFloatingIPs);
FloatingIP selectedFloatingIP = Iterables.getLast(unassignedFloatingIPs);
if (log.isDebugEnabled()) {
String msg =
String.format(
"Floating IP %s is selected among %s from the network %s",
selectedFloatingIP.getFloatingIpAddress(),
unassignedFloatingIPs.toString(),
floatingNetworkUuid);
log.debug(msg);
}
return updateFloatingIP(selectedFloatingIP, port);
}
public String toString() {
return historia.toString();
}
@Override
public String toString() {
return original.toString();
}
public void onMessage(
String channel, String sender, String login, String hostname, String message) {
if (message.equalsIgnoreCase("!goaway")) {
if (sender.equals(BotOP) || sender.equals(BotOP2)) {
partChannel(channel, "Fine, I'll leave quietly.");
} else {
sendMessage(channel, "Only the main operator can use this command.");
}
}
if (message.contains("!game")) {
String[] parts = message.split(" ");
if (parts[1].equalsIgnoreCase("genesis")) {
if (parts[2].equals("1")) {
sendMessage(channel, "Name: Sonic the Hedgehog; Release date: 1991-06-23;");
}
if (parts[2].equals("2")) {
sendMessage(channel, "Name: Sonic the Hedgehog 2; Release date: 1992-11-24;");
}
if (parts[2].equals("3")) {
sendMessage(
channel,
"Name: Sonic the Hedgehog 3 (and Knuckles); Release date: 1994-02-02 (1994-08-18)");
}
if (parts[2].equalsIgnoreCase("spinball")) {
sendMessage(channel, "Name: Sonic Spinball; Initial US Release date: 1993-11-23;");
}
if (parts[2].equalsIgnoreCase("3dblast")) {
sendMessage(channel, "Name: Sonic 3D Blast; Genesis release date: 1996-11-12;");
}
}
if (parts[1].equalsIgnoreCase("saturn")) {
if (parts[2].equalsIgnoreCase("r")) {
sendMessage(channel, "Name: Sonic R; Release date: 1997-11-18;");
}
if (parts[2].equalsIgnoreCase("3dblast")) {
sendMessage(channel, "Name: Sonic 3D Blast; Saturn release date: 1996-11-20;");
}
}
if (parts[1].equalsIgnoreCase("dreamcast")) {
if (parts[2].equalsIgnoreCase("adventure")) {
if (parts.length == 4) {
if (parts[3].equals("2")) {
sendMessage(channel, "Name: Sonic Adventure 2; Release date: 2001-06-19;");
}
} else {
sendMessage(channel, "Name: Sonic Adventure; Release date: 1998-12-23;");
}
}
if (parts[2].equalsIgnoreCase("shuffle")) {
sendMessage(channel, "Name: Sonic Shuffle; Release date: 2000-11-14;");
}
}
}
if (message.equalsIgnoreCase("!didit")) {
if (jokesPub) {
sendMessage(channel, "I DID IT! \\o/");
} else {
if (sender.equals(BotOP) || sender.equalsIgnoreCase(BotOP2) || checkMod(sender)) {
sendMessage(channel, "I DID IT! \\o/");
} else {
return;
}
}
}
if (message.equalsIgnoreCase("!isayhey")) {
if (channel.equals("")) {
return;
} else {
if (jokesPub) {
sendMessage(channel, "What's going on?");
} else {
if (sender.equals(BotOP) || sender.equals("BotOP2") || checkMod(sender)) {
sendMessage(channel, "What's going on?");
} else {
return;
}
}
}
}
if (message.equals("!jokes")) {
if (sender.equals(BotOP) || sender.equals(BotOP2) || checkMod(sender)) {
jokesPub = !jokesPub;
sendMessage(channel, "Joke commands toggled!");
} else {
sendMessage(channel, "Only the current operator can toggle joke commands!");
}
}
if (message.equalsIgnoreCase("!source")) {
sendMessage(
channel, sender + ": My source code is at http://www.github.com/MineRobber9000/KintoBot");
sendMessage(
channel,
sender + ": It may not be up to date though, my creator works on my code a lot.");
}
if (message.contains("!kb")) {
if (sender.equals(BotOP)) {
String[] parts = message.split(" ");
if (parts[1].equalsIgnoreCase("dumpvars")) {
sendMessage(
channel,
"The sender is "
+ sender
+ ", the channel was "
+ channel
+ ", the login variable was "
+ login
+ ", the hostname is "
+ hostname
+ ", and the message was "
+ message
+ ".");
}
if (parts[1].equalsIgnoreCase("botop2")) {
if (parts[2].equalsIgnoreCase("clear")) {
BotOP2 = "";
} else {
BotOP2 = parts[2];
}
}
if (parts[1].equalsIgnoreCase("mods")) {
if (parts.length == 4) {
switch (parts[2]) {
case "add":
mods.add(parts[3]);
break;
case "rm":
mods.remove(parts[3]);
break;
}
} else {
if (parts[2].equalsIgnoreCase("wipe")) {
mods = new ArrayList<String>();
} else {
sendMessage(channel, "Mods: " + mods.toString());
}
}
if (parts[2].equalsIgnoreCase("check")) {
if (checkMod(parts[3])) {
sendMessage(channel, BotOP + ": Yes, " + parts[3] + " is a mod.");
} else {
sendMessage(channel, BotOP + ": No, " + parts[3] + " is not a mod.");
}
}
}
if (parts[1].equalsIgnoreCase("passop")) {
BotOP = parts[2];
}
} else {
sendMessage(channel, "Only the current main operator can configure KintoBot.");
}
}
}
public String toString() {
return "[" + this.weight + "]: " + traversals.toString();
}
private ArrayList<InetAddress> contatta_Tracker(Descrittore descr) {
InetAddress server = null;
ObjectInputStream data_in;
ObjectOutputStream data_out;
InputStream in;
OutputStream out;
ArrayList<InetAddress> lista = null;
/* socket per la comunicazione TCP */
SSLSocketFactory factory = null;
SSLSocket socket = null;
// ###### preparo l'indirizzo
try {
server = InetAddress.getByName("192.168.0.10");
} catch (UnknownHostException e1) {
e1.printStackTrace();
}
// ###### creo il socket
if (descr == null) {
System.out.println("## contatta_tracker di Download ha ricevuto parametro null ! ");
return null;
}
System.out.println(
"@ provo a contattare via TCP il Tracker a "
+ server.toString()
+ " porta "
+ descr.getTcp());
try {
factory = (SSLSocketFactory) SSLSocketFactory.getDefault();
socket = (SSLSocket) factory.createSocket(server, descr.getTcp());
} catch (IOException e1) {
System.out.println("# eccezione nella creazione socket verso il Tracker TCP");
e1.printStackTrace();
}
System.out.println("@ socket creato ");
if (factory == null || socket == null) {
System.out.println("## la connessione ssl di Download ha ritornato null ! ");
return null;
}
try {
System.out.println("@ out_stream ");
out = socket.getOutputStream();
System.out.println("@ out ");
data_out = new ObjectOutputStream(out);
System.out.println("@ in_stream ");
in = socket.getInputStream();
System.out.println("@ in ");
data_in = new ObjectInputStream(in);
System.out.println("@ Downloader: streams ok ");
data_out.writeObject(descr); // TODO Perchè ?
data_out.flush();
System.out.println("@ descrittore mandato ");
lista = (ArrayList<InetAddress>) data_in.readObject();
if (lista == null)
System.out.println(
"@ ritornata lista vuota dal tracker riguardo : "
+ descr.nome); // TODO sarebbe un caso plausibile
else System.out.println("@ lista ricevuta : " + lista.toString());
} catch (IOException e) {
System.out.println("# eccezione I/O nella creazione socket verso il Tracker TCP");
e.printStackTrace();
} catch (ClassNotFoundException e) {
System.out.println("# eccezione C N F nella creazione socket verso il Tracker TCP");
e.printStackTrace();
}
return lista;
}