/**
* Method to convert a List of beans to a List of Array of Strings.
*
* @param beans the List of Beans.
* @param addNewHeader the new String Array for the Header row.
* @param <T> generic value.
* @return the List of Array of String content of the csv.
*/
@SuppressWarnings("unchecked")
public static <T> List<String[]> toStringArray(List<T> beans, String[] addNewHeader) {
List<String[]> records = new ArrayList<>();
// add header record
// records.add(new String[]{"ID","Name","Role","Salary"});
if (addNewHeader != null) records.add(addNewHeader);
for (T bean : beans) {
// beans.stream().map((bean) -> {
List<String> record = new ArrayList<>();
// invoke getter method and convert to String
Class<T> clazz = (Class<T>) bean.getClass();
// T t = ReflectionUtilities.invokeConstructor(clazz);
List<Method> getter = (List<Method>) ReflectionUtilities.findGetters(clazz, true);
for (Method method : getter) {
record.add(String.valueOf(ReflectionUtilities.invokeGetter(bean, method)));
}
// getter.stream().forEach((method) ->
// record.add(String.valueOf(ReflectionUtilities.invokeGetter(bean,method))));
// return record;
// }).forEach((record) -> records.add(ListUtilities.toArray(record)));
records.add(ListUtilities.toArray(record));
}
return records;
}
/**
* Copy from the copy method in StructUtil. Did not want to drag that code in. maybe this actually
* should go to struct.
*
* @param from
* @param to
* @param excludes
* @return
* @throws Exception
*/
public static <T extends struct> T xcopy(struct from, T to, String... excludes) throws Exception {
Arrays.sort(excludes);
for (Field f : from.fields()) {
if (Arrays.binarySearch(excludes, f.getName()) >= 0) continue;
Object o = f.get(from);
if (o == null) continue;
Field tof = to.getField(f.getName());
if (tof != null)
try {
tof.set(to, Converter.cnv(tof.getGenericType(), o));
} catch (Exception e) {
System.out.println(
"Failed to convert "
+ f.getName()
+ " from "
+ from.getClass()
+ " to "
+ to.getClass()
+ " value "
+ o
+ " exception "
+ e);
}
}
return to;
}
/**
* This function returns a map whose entries hold the coordinates of the sequence as keys and the
* coordinates of the target sequences as values.</br> If a coordinate in sequence corresponds to
* a gap in another sequence, then -1 is assigned to that position.</br> For example suppose we
* have the sequences:</br> seq1: AAT-GCT-TCG</br> seq2: G--C-CTCT-C</br> seq3: A-T--GT-AG-</br>
* Then, if we wish to find the mapping of seq1's coordinates to seq2's coordinates, this will
* give us: 0 -> 0, 1 -> -1, 2 -> -1, 3 -> -1, 4 -> 2, 5 -> 3, 6 -> 5, 7 -> -1, 8 -> 6.</br> Also,
* if we wish to find the mapping of seq1's coordinates to seq2's and seq3's coordinates, this
* will give us: 0 -> {0, 0}, 1 -> {-1, -1}, 2 -> {-1, 1}, 3 -> {-1, -1}, 4 -> {2, 2}, 5 -> {3,
* 3}, 6 -> {5, 4}, 7 -> {-1, 5}, 8 -> {6, -1}.
*
* @param <T> This could be either the serial number of the sequence (valid range: [0,
* sequences.length-1]) or the sequence names
* @param <E>
* @param seqID The sequence ID (either serial number or name) which we wish to map</br> Note that
* the valid range of serial numbers is [0, sequences.length-1]
* @param targetSeqIDs The (target) sequences IDs (either serial numbers or names)
* @return A map whose keys are the sequence coordinates and values the corresponding coordinates
* of the target sequences
* @throws IllegalArgumentException
* @see GappedAlignmentString
*/
public <T extends Object> Map mapSeqCoords2SeqsCoords(
T generic_seqID, Vector<T> generic_targetSeqIDs)
throws IllegalArgumentException, IndexOutOfBoundsException {
GappedAlignmentString gas_seq;
GappedAlignmentString[] gas_targetSeqs;
String[] speciesNames = species();
// Check if generic_seqID is mistakenly included in the generic_targetSeqIDs set
if (generic_targetSeqIDs.contains(generic_seqID)) generic_targetSeqIDs.remove(generic_seqID);
if (generic_targetSeqIDs.size() + 1 > speciesNames.length)
throw new IndexOutOfBoundsException("You entered more sequences than are in the file.");
Map map = new HashMap();
// Check whether sequence IDs are inputed as serial numbers or as names
String seqsClassName = generic_seqID.getClass().getSimpleName();
// if( generic_seqID.getClass() instanceof java.lang.Integer )
// System.out.println("XAXA");
if (seqsClassName.equals("Integer")) {
Integer seqID = (Integer) generic_seqID;
Integer[] seqIDs = generic_targetSeqIDs.toArray(new Integer[generic_targetSeqIDs.size()]);
if ((StatUtil.findMax(seqIDs).getFirst() > speciesNames.length - 1)
|| (StatUtil.findMin(seqIDs).getFirst() < 0))
throw new IndexOutOfBoundsException(
"The sequence IDs (aka, serial numbers have to lie inside"
+ " the range 0 to speciesNames.length -1");
gas_seq = getGappedAlignment(speciesNames[seqID]);
gas_targetSeqs = new GappedAlignmentString[seqIDs.length];
for (int i = 0; i < seqIDs.length; i++)
gas_targetSeqs[i] = getGappedAlignment(speciesNames[seqIDs[i]]);
} else if (seqsClassName.equals("String")) {
String seqID = (String) generic_seqID;
String[] seqIDs = generic_targetSeqIDs.toArray(new String[generic_targetSeqIDs.size()]);
gas_seq = getGappedAlignment(seqID);
gas_targetSeqs = new GappedAlignmentString[seqIDs.length];
for (int i = 0; i < seqIDs.length; i++) gas_targetSeqs[i] = getGappedAlignment(seqIDs[i]);
} else {
throw new IllegalArgumentException("Sequence IDs should be either of type Integer or String");
}
// Pairwise Alignment
if (gas_targetSeqs.length == 1) {
map = doMapSeq2Seq(gas_seq, gas_targetSeqs);
}
// Multiple Alignment
else {
map = doMapSeq2Seqs(gas_seq, gas_targetSeqs);
}
return map;
} // end of mapSeqCoords2SeqsCoords method
public <T> String post(String resource, T object)
throws JAXBException, CloudException, InternalException {
StringWriter stringWriter = new StringWriter();
JAXBContext jc = JAXBContext.newInstance(object.getClass());
Marshaller m = jc.createMarshaller();
m.marshal(object, stringWriter);
return post(provider.getContext().getAccountNumber(), resource, stringWriter.toString());
}
/**
* Make a copy of a writable object using serialization to a buffer.
*
* @param orig The object to copy
* @return The copied object
*/
public static <T extends Writable> T clone(T orig, Configuration conf) {
try {
@SuppressWarnings("unchecked") // Unchecked cast from Class to Class<T>
T newInst = ReflectionUtils.newInstance((Class<T>) orig.getClass(), conf);
ReflectionUtils.copy(conf, orig, newInst);
return newInst;
} catch (IOException e) {
throw new RuntimeException("Error writing/reading clone buffer", e);
}
}
/** Return the value of an enum of the given type. Prefix allows a shortened form of the enum */
@SuppressWarnings("unchecked")
public <T extends Enum<T>> T getEnum(String prop, String prefix, T dflt) {
Enum<?> v = dflt;
String s = getProperty(prop);
if (s == null || s.length() == 0) return dflt;
if (prefix != null && !s.startsWith(prefix)) s = prefix + s;
Object[] vals = dflt.getClass().getEnumConstants();
if (vals == null) return dflt;
for (int i = 0; i < vals.length; ++i) {
Enum<?> e = (Enum<?>) vals[i];
if (e.name().equalsIgnoreCase(s)) {
v = e;
break;
}
}
return (T) v;
}
@SuppressWarnings("unchecked")
public static <T extends JsonElement> T deepCopy(T from) {
if (from == null) {
throw new IllegalArgumentException("from must not be null");
}
if (from instanceof JsonObject) {
return (T) deepCopyObj((JsonObject) from);
}
if (from instanceof JsonArray) {
return (T) deepCopyArr((JsonArray) from);
}
if (from instanceof JsonNull) {
return (T) JsonNull.INSTANCE;
}
if (from instanceof JsonPrimitive) {
// Nulls and primitives are immutable
return from;
}
throw new AssertionError("Unknown element type " + from.getClass().getName());
}
/**
* Method use OpenCsv Library for
*
* @param clazz the Class of the Bean.
* @param fileInputCsv the File CSV to parse.
* @param separator the char separator.
* @param <T> the generic variable.
* @return the List of Bean parsed from the CSV file.
*/
public static <T> List<T> parseCSVFileAsList(Class<T> clazz, File fileInputCsv, char separator) {
try {
List<T> beans;
try ( // create CSVReader object
CSVReader reader = new CSVReader(new FileReader(fileInputCsv), separator)) {
beans = new ArrayList<>();
// read line by line
String[] record;
// skip header row
String[] headers = reader.readNext();
// read content
while ((record = reader.readNext()) != null) {
T t = ReflectionUtilities.invokeConstructor(clazz);
for (int i = 0; i < record.length; i++) {
String nameMethod = "set" + org.apache.commons.lang3.StringUtils.capitalize(headers[i]);
// invoke setter method
if (ReflectionUtilities.checkMethod(clazz, nameMethod)) {
ReflectionUtilities.invokeSetter(t, nameMethod, record[i]);
} else {
logger.warn(
"Not exists the Method with name:"
+ nameMethod
+ " on the Bean:"
+ t.getClass().getName());
}
}
beans.add(t);
}
}
return beans;
} catch (IOException e) {
logger.error(
"Can't parse the CSV file:" + fileInputCsv.getAbsolutePath() + " -> " + e.getMessage(),
e);
return new ArrayList<>();
}
}
public <T> T map(Object source, T target, Object mappingCase) {
if (source != null && target != null) map(source, target, target.getClass(), mappingCase);
return target;
}
public void applyInputsToObject(Object obj) {
T config = this.getConfig();
if (config == null) {
return;
}
Field[] toObjectFields = obj.getClass().getSuperclass().getDeclaredFields();
Field[] fromObjectFields = config.getClass().getDeclaredFields();
for (int to = 0; to < toObjectFields.length; to++) {
String inputToName = toObjectFields[to].getName();
// Only input starting fields are used in configuration file
if (inputToName.startsWith("input")) {
for (int from = 0; from < fromObjectFields.length; from++) {
String inputFromName = fromObjectFields[from].getName();
if (toObjectFields[to].getType() == fromObjectFields[from].getType()
&& inputFromName.compareTo(inputToName) == 0) {
try {
if (toObjectFields[to].getType() == Calendar.class
&& inputToName.compareTo("inputEndingDate") == 0) {
Calendar currentDate = Calendar.getInstance();
toObjectFields[to].set(obj, currentDate);
continue;
}
toObjectFields[to].set(obj, fromObjectFields[from].get(config));
} catch (IllegalArgumentException ex) {
Logger.getLogger(ConfigLoader.class.getName()).log(Level.SEVERE, null, ex);
return;
} catch (IllegalAccessException ex) {
Logger.getLogger(ConfigLoader.class.getName()).log(Level.SEVERE, null, ex);
return;
}
}
}
}
}
toObjectFields = obj.getClass().getDeclaredFields();
fromObjectFields = config.getClass().getDeclaredFields();
for (int to = 0; to < toObjectFields.length; to++) {
String inputToName = toObjectFields[to].getName();
// Only input starting fields are used in configuration file
if (inputToName.startsWith("input")) {
for (int from = 0; from < fromObjectFields.length; from++) {
String inputFromName = fromObjectFields[from].getName();
if (toObjectFields[to].getType() == fromObjectFields[from].getType()
&& inputFromName.compareTo(inputToName) == 0) {
try {
if (toObjectFields[to].getType() == Calendar.class
&& inputToName.compareTo("inputEndingDate") == 0) {
Calendar currentDate = Calendar.getInstance();
toObjectFields[to].set(obj, currentDate);
continue;
}
toObjectFields[to].set(obj, fromObjectFields[from].get(config));
} catch (IllegalArgumentException ex) {
Logger.getLogger(ConfigLoader.class.getName()).log(Level.SEVERE, null, ex);
return;
} catch (IllegalAccessException ex) {
Logger.getLogger(ConfigLoader.class.getName()).log(Level.SEVERE, null, ex);
return;
}
}
}
}
}
}
public <T> T get(String path, Class<T> c) {
Log.d(TAG, "get " + path); // NON-NLS
File f = new File(getFullCachePath(path));
if (!f.exists()) {
Log.w(TAG, "file: " + f.toString() + " not exists"); // NON-NLS
return null;
}
T object;
try {
StringBuffer fileData = new StringBuffer();
BufferedReader reader = new BufferedReader(new FileReader(f));
char[] buf = new char[1024];
int numRead = 0;
while ((numRead = reader.read(buf)) != -1) {
String readData = String.valueOf(buf, 0, numRead);
fileData.append(readData);
}
reader.close();
String json = fileData.toString();
Log.d(TAG, "cache: " + json); // NON-NLS
object = getGson().fromJson(json, c);
} catch (FileNotFoundException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (StreamCorruptedException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IOException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (JsonSyntaxException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IllegalArgumentException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (RuntimeException e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (Exception e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
}
if (object.getClass().toString().equals(c.toString())) return object;
else return null;
}