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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/coverage/CoverageUtilities.java | CoverageUtilities.mergeCoverages | public static GridCoverage2D mergeCoverages( GridCoverage2D valuesMap, GridCoverage2D onMap ) {
RegionMap valuesRegionMap = getRegionParamsFromGridCoverage(valuesMap);
int cs = valuesRegionMap.getCols();
int rs = valuesRegionMap.getRows();
RegionMap onRegionMap = getRegionParamsFromGridCoverage(onMap);
int tmpcs = onRegionMap.getCols();
int tmprs = onRegionMap.getRows();
if (cs != tmpcs || rs != tmprs) {
throw new IllegalArgumentException("The raster maps have to be of equal size to be mapped.");
}
RandomIter valuesIter = RandomIterFactory.create(valuesMap.getRenderedImage(), null);
WritableRaster outWR = renderedImage2WritableRaster(onMap.getRenderedImage(), false);
WritableRandomIter outIter = RandomIterFactory.createWritable(outWR, null);
for( int c = 0; c < cs; c++ ) {
for( int r = 0; r < rs; r++ ) {
double value = valuesIter.getSampleDouble(c, r, 0);
if (!isNovalue(value))
outIter.setSample(c, r, 0, value);
}
}
GridCoverage2D outCoverage = buildCoverage("merged", outWR, onRegionMap, valuesMap.getCoordinateReferenceSystem()); //$NON-NLS-1$
return outCoverage;
} | java | public static GridCoverage2D mergeCoverages( GridCoverage2D valuesMap, GridCoverage2D onMap ) {
RegionMap valuesRegionMap = getRegionParamsFromGridCoverage(valuesMap);
int cs = valuesRegionMap.getCols();
int rs = valuesRegionMap.getRows();
RegionMap onRegionMap = getRegionParamsFromGridCoverage(onMap);
int tmpcs = onRegionMap.getCols();
int tmprs = onRegionMap.getRows();
if (cs != tmpcs || rs != tmprs) {
throw new IllegalArgumentException("The raster maps have to be of equal size to be mapped.");
}
RandomIter valuesIter = RandomIterFactory.create(valuesMap.getRenderedImage(), null);
WritableRaster outWR = renderedImage2WritableRaster(onMap.getRenderedImage(), false);
WritableRandomIter outIter = RandomIterFactory.createWritable(outWR, null);
for( int c = 0; c < cs; c++ ) {
for( int r = 0; r < rs; r++ ) {
double value = valuesIter.getSampleDouble(c, r, 0);
if (!isNovalue(value))
outIter.setSample(c, r, 0, value);
}
}
GridCoverage2D outCoverage = buildCoverage("merged", outWR, onRegionMap, valuesMap.getCoordinateReferenceSystem()); //$NON-NLS-1$
return outCoverage;
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/coverage/CoverageUtilities.java | CoverageUtilities.calculateHypsographic | public static double[][] calculateHypsographic( GridCoverage2D elevationCoverage, int bins, IHMProgressMonitor pm ) {
if (pm == null) {
pm = new DummyProgressMonitor();
}
RegionMap regionMap = getRegionParamsFromGridCoverage(elevationCoverage);
int cols = regionMap.getCols();
int rows = regionMap.getRows();
double xres = regionMap.getXres();
double yres = regionMap.getYres();
/*
* calculate the maximum and minimum value of the raster data
*/
RandomIter elevIter = getRandomIterator(elevationCoverage);
double maxRasterValue = Double.NEGATIVE_INFINITY;
double minRasterValue = Double.POSITIVE_INFINITY;
for( int r = 0; r < rows; r++ ) {
for( int c = 0; c < cols; c++ ) {
double value = elevIter.getSampleDouble(c, r, 0);
if (isNovalue(value)) {
continue;
}
maxRasterValue = max(maxRasterValue, value);
minRasterValue = min(minRasterValue, value);
}
}
/*
* subdivide the whole value range in bins and count the number of pixels in each bin
*/
double binWidth = (maxRasterValue - minRasterValue) / (bins);
double[] pixelPerBinCount = new double[bins];
double[] areaAtGreaterElevation = new double[bins];
pm.beginTask("Performing calculation of hypsographic curve...", rows);
for( int r = 0; r < rows; r++ ) {
for( int c = 0; c < cols; c++ ) {
double value = elevIter.getSampleDouble(c, r, 0);
if (isNovalue(value)) {
continue;
}
for( int k = 0; k < pixelPerBinCount.length; k++ ) {
double thres = minRasterValue + k * binWidth;
if (value >= thres) {
pixelPerBinCount[k] = pixelPerBinCount[k] + 1;
areaAtGreaterElevation[k] = areaAtGreaterElevation[k] + (yres * xres);
}
}
}
pm.worked(1);
}
pm.done();
double[][] hypso = new double[pixelPerBinCount.length][3];
for( int j = 0; j < hypso.length; j++ ) {
hypso[j][0] = minRasterValue + (j * binWidth) + (binWidth / 2.0);
hypso[j][1] = areaAtGreaterElevation[j] / 1000000.0;
}
return hypso;
} | java | public static double[][] calculateHypsographic( GridCoverage2D elevationCoverage, int bins, IHMProgressMonitor pm ) {
if (pm == null) {
pm = new DummyProgressMonitor();
}
RegionMap regionMap = getRegionParamsFromGridCoverage(elevationCoverage);
int cols = regionMap.getCols();
int rows = regionMap.getRows();
double xres = regionMap.getXres();
double yres = regionMap.getYres();
/*
* calculate the maximum and minimum value of the raster data
*/
RandomIter elevIter = getRandomIterator(elevationCoverage);
double maxRasterValue = Double.NEGATIVE_INFINITY;
double minRasterValue = Double.POSITIVE_INFINITY;
for( int r = 0; r < rows; r++ ) {
for( int c = 0; c < cols; c++ ) {
double value = elevIter.getSampleDouble(c, r, 0);
if (isNovalue(value)) {
continue;
}
maxRasterValue = max(maxRasterValue, value);
minRasterValue = min(minRasterValue, value);
}
}
/*
* subdivide the whole value range in bins and count the number of pixels in each bin
*/
double binWidth = (maxRasterValue - minRasterValue) / (bins);
double[] pixelPerBinCount = new double[bins];
double[] areaAtGreaterElevation = new double[bins];
pm.beginTask("Performing calculation of hypsographic curve...", rows);
for( int r = 0; r < rows; r++ ) {
for( int c = 0; c < cols; c++ ) {
double value = elevIter.getSampleDouble(c, r, 0);
if (isNovalue(value)) {
continue;
}
for( int k = 0; k < pixelPerBinCount.length; k++ ) {
double thres = minRasterValue + k * binWidth;
if (value >= thres) {
pixelPerBinCount[k] = pixelPerBinCount[k] + 1;
areaAtGreaterElevation[k] = areaAtGreaterElevation[k] + (yres * xres);
}
}
}
pm.worked(1);
}
pm.done();
double[][] hypso = new double[pixelPerBinCount.length][3];
for( int j = 0; j < hypso.length; j++ ) {
hypso[j][0] = minRasterValue + (j * binWidth) + (binWidth / 2.0);
hypso[j][1] = areaAtGreaterElevation[j] / 1000000.0;
}
return hypso;
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/CompressionUtilities.java | CompressionUtilities.zipFolder | static public void zipFolder( String srcFolder, String destZipFile, boolean addBaseFolder ) throws IOException {
if (new File(srcFolder).isDirectory()) {
try (FileOutputStream fileWriter = new FileOutputStream(destZipFile);
ZipOutputStream zip = new ZipOutputStream(fileWriter)) {
addFolderToZip("", srcFolder, zip, addBaseFolder); //$NON-NLS-1$
}
} else {
throw new IOException(srcFolder + " is not a folder.");
}
} | java | static public void zipFolder( String srcFolder, String destZipFile, boolean addBaseFolder ) throws IOException {
if (new File(srcFolder).isDirectory()) {
try (FileOutputStream fileWriter = new FileOutputStream(destZipFile);
ZipOutputStream zip = new ZipOutputStream(fileWriter)) {
addFolderToZip("", srcFolder, zip, addBaseFolder); //$NON-NLS-1$
}
} else {
throw new IOException(srcFolder + " is not a folder.");
}
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/CompressionUtilities.java | CompressionUtilities.unzipFolder | public static String unzipFolder( String zipFile, String destFolder, boolean addTimeStamp ) throws IOException {
String newFirstName = null;
try (ZipFile zf = new ZipFile(zipFile)) {
Enumeration< ? extends ZipEntry> zipEnum = zf.entries();
String firstName = null;
while( zipEnum.hasMoreElements() ) {
ZipEntry item = (ZipEntry) zipEnum.nextElement();
String itemName = item.getName();
if (firstName == null) {
int firstSlash = itemName.indexOf('/');
if (firstSlash == -1) {
firstSlash = itemName.length();
}
firstName = itemName.substring(0, firstSlash);
newFirstName = firstName;
File baseFile = new File(destFolder + File.separator + firstName);
if (baseFile.exists()) {
if (addTimeStamp) {
newFirstName = firstName + "_"
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} else {
throw new IOException("Not overwriting existing: " + baseFile);
}
}
}
if (firstName == null) {
throw new IOException();
}
itemName = itemName.replaceFirst(firstName, newFirstName);
if (item.isDirectory()) {
File newdir = new File(destFolder + File.separator + itemName);
if (!newdir.mkdir())
throw new IOException();
} else {
String newfilePath = destFolder + File.separator + itemName;
File newFile = new File(newfilePath);
File parentFile = newFile.getParentFile();
if (!parentFile.exists()) {
if (!parentFile.mkdirs())
throw new IOException();
}
InputStream is = zf.getInputStream(item);
FileOutputStream fos = new FileOutputStream(newfilePath);
byte[] buffer = new byte[512];
int readchars = 0;
while( (readchars = is.read(buffer)) != -1 ) {
fos.write(buffer, 0, readchars);
}
is.close();
fos.close();
}
}
}
return newFirstName;
} | java | public static String unzipFolder( String zipFile, String destFolder, boolean addTimeStamp ) throws IOException {
String newFirstName = null;
try (ZipFile zf = new ZipFile(zipFile)) {
Enumeration< ? extends ZipEntry> zipEnum = zf.entries();
String firstName = null;
while( zipEnum.hasMoreElements() ) {
ZipEntry item = (ZipEntry) zipEnum.nextElement();
String itemName = item.getName();
if (firstName == null) {
int firstSlash = itemName.indexOf('/');
if (firstSlash == -1) {
firstSlash = itemName.length();
}
firstName = itemName.substring(0, firstSlash);
newFirstName = firstName;
File baseFile = new File(destFolder + File.separator + firstName);
if (baseFile.exists()) {
if (addTimeStamp) {
newFirstName = firstName + "_"
+ new DateTime().toString(HMConstants.dateTimeFormatterYYYYMMDDHHMMSScompact);
} else {
throw new IOException("Not overwriting existing: " + baseFile);
}
}
}
if (firstName == null) {
throw new IOException();
}
itemName = itemName.replaceFirst(firstName, newFirstName);
if (item.isDirectory()) {
File newdir = new File(destFolder + File.separator + itemName);
if (!newdir.mkdir())
throw new IOException();
} else {
String newfilePath = destFolder + File.separator + itemName;
File newFile = new File(newfilePath);
File parentFile = newFile.getParentFile();
if (!parentFile.exists()) {
if (!parentFile.mkdirs())
throw new IOException();
}
InputStream is = zf.getInputStream(item);
FileOutputStream fos = new FileOutputStream(newfilePath);
byte[] buffer = new byte[512];
int readchars = 0;
while( (readchars = is.read(buffer)) != -1 ) {
fos.write(buffer, 0, readchars);
}
is.close();
fos.close();
}
}
}
return newFirstName;
} | [
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@return the name of the internal base folder or <code>null</code>.
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/util/Processes1.java | Processes1.setWorkingDirectory | public void setWorkingDirectory(File dir) {
if (!dir.exists()) {
throw new IllegalArgumentException(dir + " doesn't exist.");
}
pb.directory(dir);
} | java | public void setWorkingDirectory(File dir) {
if (!dir.exists()) {
throw new IllegalArgumentException(dir + " doesn't exist.");
}
pb.directory(dir);
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/util/Processes1.java | Processes1.exec | public int exec() throws IOException {
int exitValue = 0;
List<String> argl = new ArrayList<String>();
argl.add(executable.toString());
for (Object a : args) {
if (a != null) {
if (a.getClass() == String.class) {
argl.add(a.toString());
} else if (a.getClass() == String[].class) {
for (String s : (String[]) a) {
if (s != null && !s.isEmpty()) {
argl.add(s);
}
}
}
}
}
pb.command(argl);
if (log != null && log.isLoggable(Level.INFO)) {
log.info("Command : " + pb.command().toString());
}
Process process = pb.start();
CountDownLatch latch = new CountDownLatch(2);
// Thread in_ = new Thread(new Handler(stdin,
// new OutputStreamWriter(process.getOutputStream()), latch));
Thread out_ = new Thread(new Handler(new BufferedReader(
new InputStreamReader(process.getInputStream())), stdout, latch));
Thread err_ = new Thread(new Handler(new BufferedReader(
new InputStreamReader(process.getErrorStream())), stderr, latch));
out_.start();
err_.start();
// in_.start();
try {
latch.await();
exitValue = process.waitFor();
} catch (InterruptedException e) {
// throw new RuntimeException(e);
} finally {
process.getInputStream().close();
process.getOutputStream().close();
process.getErrorStream().close();
process.destroy();
}
return exitValue;
} | java | public int exec() throws IOException {
int exitValue = 0;
List<String> argl = new ArrayList<String>();
argl.add(executable.toString());
for (Object a : args) {
if (a != null) {
if (a.getClass() == String.class) {
argl.add(a.toString());
} else if (a.getClass() == String[].class) {
for (String s : (String[]) a) {
if (s != null && !s.isEmpty()) {
argl.add(s);
}
}
}
}
}
pb.command(argl);
if (log != null && log.isLoggable(Level.INFO)) {
log.info("Command : " + pb.command().toString());
}
Process process = pb.start();
CountDownLatch latch = new CountDownLatch(2);
// Thread in_ = new Thread(new Handler(stdin,
// new OutputStreamWriter(process.getOutputStream()), latch));
Thread out_ = new Thread(new Handler(new BufferedReader(
new InputStreamReader(process.getInputStream())), stdout, latch));
Thread err_ = new Thread(new Handler(new BufferedReader(
new InputStreamReader(process.getErrorStream())), stderr, latch));
out_.start();
err_.start();
// in_.start();
try {
latch.await();
exitValue = process.waitFor();
} catch (InterruptedException e) {
// throw new RuntimeException(e);
} finally {
process.getInputStream().close();
process.getOutputStream().close();
process.getErrorStream().close();
process.destroy();
}
return exitValue;
} | [
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/ValidationPlanResult.java | ValidationPlanResult.addResult | private void addResult(ValidationResult result) {
if (result == null || result.count() == 0) {
return;
}
this.results.add(result);
} | java | private void addResult(ValidationResult result) {
if (result == null || result.count() == 0) {
return;
}
this.results.add(result);
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/ValidationPlanResult.java | ValidationPlanResult.getMessages | public List<ValidationMessage<Origin>> getMessages(String messageKey, Severity severity) {
List<ValidationMessage<Origin>> messages = new ArrayList<ValidationMessage<Origin>>();
for (ValidationResult result : results) {
for (ValidationMessage<Origin> message : result.getMessages()) {
if (messageKey.equals(message.getMessageKey()) && severity.equals(message.getSeverity())) {
messages.add(message);
}
}
}
return messages;
} | java | public List<ValidationMessage<Origin>> getMessages(String messageKey, Severity severity) {
List<ValidationMessage<Origin>> messages = new ArrayList<ValidationMessage<Origin>>();
for (ValidationResult result : results) {
for (ValidationMessage<Origin> message : result.getMessages()) {
if (messageKey.equals(message.getMessageKey()) && severity.equals(message.getSeverity())) {
messages.add(message);
}
}
}
return messages;
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] | 4127f5e1a17540239f5810136153fbd6737fa262 | https://github.com/enasequence/sequencetools/blob/4127f5e1a17540239f5810136153fbd6737fa262/src/main/java/uk/ac/ebi/embl/api/validation/ValidationPlanResult.java#L213-L226 | train |
TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/utils/SerializationUtilities.java | SerializationUtilities.serialize | public static byte[] serialize( Object obj ) throws IOException {
try (ByteArrayOutputStream bos = new ByteArrayOutputStream()) {
ObjectOutputStream out = new ObjectOutputStream(bos);
out.writeObject(obj);
out.close();
return bos.toByteArray();
}
} | java | public static byte[] serialize( Object obj ) throws IOException {
try (ByteArrayOutputStream bos = new ByteArrayOutputStream()) {
ObjectOutputStream out = new ObjectOutputStream(bos);
out.writeObject(obj);
out.close();
return bos.toByteArray();
}
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/utils/SerializationUtilities.java | SerializationUtilities.deSerialize | public static <T> T deSerialize( byte[] bytes, Class<T> adaptee ) throws Exception {
ObjectInputStream in = new ObjectInputStream(new ByteArrayInputStream(bytes));
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/utils/SerializationUtilities.java | SerializationUtilities.serializeToDisk | public static void serializeToDisk( File file, Object obj ) throws IOException {
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/utils/SerializationUtilities.java | SerializationUtilities.deSerializeFromDisk | public static <T> T deSerializeFromDisk( File file, Class<T> adaptee ) throws Exception {
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long length = raf.length();
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/energybalance/OmsEnergyBalance.java | OmsEnergyBalance.checkParametersAndRunEnergyBalance | private void checkParametersAndRunEnergyBalance( double[] rain, double[][] T, double[][] V, double[][] P, double[][] RH,
double month, double day, double hour, double[] Abasin, double[][][] A, double[][][] EI, double[][] DTd,
double[][] DTm, double[][] canopy ) {
double Dt = ((double) tTimestep / (double) pInternaltimestep) * 60.0;
/*
* some hardcoded variables
*/
boolean hasNoStations = false;
double zmes_T = 2.0; // quota misura temperatura,pressione e umidita'
double zmes_U = 2.0; // quota misura velocita' vento [m]
double z0T = 0.005; // [m] roughness length della temperatura
double z0U = 0.05; // [m] roughness length del vento
double K = ka * ka / ((log(zmes_U / z0U)) * (log(zmes_T / z0T)));
double eps = 0.98; // emissivita' neve
double Lc = 0.05; // ritenzione capillare
double Ksat = 3.0; // 5.55; // conducibilita' idraulica della neve a saturazione
double Ks = 5.55E-5; // conducibilita' termica superficiale della neve
double aep = 50.0; // albedo extinction parameter (kg/m2==mm)
double rho_g = 1600; // densita' del suolo [kg/m3]
double De = 0.4; // suolo termicamente attivo
double C_g = 890.0; // capacita' termica del suolo [J/(kg K)]
double albedo_land = 0.2;
double Ts_min = -20.0;
double Ts_max = 20.0;
// TODO check parameters and add to the model parameter
latitude = 46.6 * Math.PI / 180.0; // [rad]
longitude = 10.88 * Math.PI / 180.0; // [rad]
standard_time = -1.0; // differenza rispetto a UMT [h]
/*
* start calculations
*/
sun(hour, day);
for( int i = 0; i < basinNum; i++ ) {
calculateEnergyBalance(i, month, hasNoStations, V[i], canopy, T[i], P[i], RH[i], rain, pTrain, pTsnow, Dt, A, Abasin,
EI, DTd[i], DTm[i], K, eps, Lc, pRhosnow, Ksat, rho_g, De, C_g, aep, albedo_land, Ks, Ts_min, Ts_max);
}
} | java | private void checkParametersAndRunEnergyBalance( double[] rain, double[][] T, double[][] V, double[][] P, double[][] RH,
double month, double day, double hour, double[] Abasin, double[][][] A, double[][][] EI, double[][] DTd,
double[][] DTm, double[][] canopy ) {
double Dt = ((double) tTimestep / (double) pInternaltimestep) * 60.0;
/*
* some hardcoded variables
*/
boolean hasNoStations = false;
double zmes_T = 2.0; // quota misura temperatura,pressione e umidita'
double zmes_U = 2.0; // quota misura velocita' vento [m]
double z0T = 0.005; // [m] roughness length della temperatura
double z0U = 0.05; // [m] roughness length del vento
double K = ka * ka / ((log(zmes_U / z0U)) * (log(zmes_T / z0T)));
double eps = 0.98; // emissivita' neve
double Lc = 0.05; // ritenzione capillare
double Ksat = 3.0; // 5.55; // conducibilita' idraulica della neve a saturazione
double Ks = 5.55E-5; // conducibilita' termica superficiale della neve
double aep = 50.0; // albedo extinction parameter (kg/m2==mm)
double rho_g = 1600; // densita' del suolo [kg/m3]
double De = 0.4; // suolo termicamente attivo
double C_g = 890.0; // capacita' termica del suolo [J/(kg K)]
double albedo_land = 0.2;
double Ts_min = -20.0;
double Ts_max = 20.0;
// TODO check parameters and add to the model parameter
latitude = 46.6 * Math.PI / 180.0; // [rad]
longitude = 10.88 * Math.PI / 180.0; // [rad]
standard_time = -1.0; // differenza rispetto a UMT [h]
/*
* start calculations
*/
sun(hour, day);
for( int i = 0; i < basinNum; i++ ) {
calculateEnergyBalance(i, month, hasNoStations, V[i], canopy, T[i], P[i], RH[i], rain, pTrain, pTsnow, Dt, A, Abasin,
EI, DTd[i], DTm[i], K, eps, Lc, pRhosnow, Ksat, rho_g, De, C_g, aep, albedo_land, Ks, Ts_min, Ts_max);
}
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@param Abasin area of the different basins (as defined through the features/geometries)
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/energybalance/OmsEnergyBalance.java#L689-L730 | train |
TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/sld/RequestUtils.java | RequestUtils.getBufferedXMLReader | public static BufferedReader getBufferedXMLReader(InputStream stream, int xmlLookahead)
throws IOException {
// create a buffer so we can reset the input stream
BufferedInputStream input = new BufferedInputStream(stream);
input.mark(xmlLookahead);
// create object to hold encoding info
EncodingInfo encoding = new EncodingInfo();
// call this method to set the encoding info
XmlCharsetDetector.getCharsetAwareReader(input, encoding);
// call this method to create the reader
Reader reader = XmlCharsetDetector.createReader(input, encoding);
// rest the input
input.reset();
return getBufferedXMLReader(reader, xmlLookahead);
} | java | public static BufferedReader getBufferedXMLReader(InputStream stream, int xmlLookahead)
throws IOException {
// create a buffer so we can reset the input stream
BufferedInputStream input = new BufferedInputStream(stream);
input.mark(xmlLookahead);
// create object to hold encoding info
EncodingInfo encoding = new EncodingInfo();
// call this method to set the encoding info
XmlCharsetDetector.getCharsetAwareReader(input, encoding);
// call this method to create the reader
Reader reader = XmlCharsetDetector.createReader(input, encoding);
// rest the input
input.reset();
return getBufferedXMLReader(reader, xmlLookahead);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/sld/RequestUtils.java | RequestUtils.getBufferedXMLReader | public static BufferedReader getBufferedXMLReader(Reader reader, int xmlLookahead)
throws IOException {
// ensure the reader is a buffered reader
if (!(reader instanceof BufferedReader)) {
reader = new BufferedReader(reader);
}
// mark the input stream
reader.mark(xmlLookahead);
return (BufferedReader) reader;
} | java | public static BufferedReader getBufferedXMLReader(Reader reader, int xmlLookahead)
throws IOException {
// ensure the reader is a buffered reader
if (!(reader instanceof BufferedReader)) {
reader = new BufferedReader(reader);
}
// mark the input stream
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/math/interpolation/LeastSquaresInterpolator.java | LeastSquaresInterpolator.validateCoefficients | private void validateCoefficients() {
if (coefsValid)
return;
if (n >= 2) {
double xBar = (double) sumX / n;
double yBar = (double) sumY / n;
a1 = (double) ((n * sumXY - sumX * sumY) / (n * sumXX - sumX * sumX));
a0 = (double) (yBar - a1 * xBar);
} else {
a0 = a1 = Double.NaN;
}
coefsValid = true;
} | java | private void validateCoefficients() {
if (coefsValid)
return;
if (n >= 2) {
double xBar = (double) sumX / n;
double yBar = (double) sumY / n;
a1 = (double) ((n * sumXY - sumX * sumY) / (n * sumXX - sumX * sumX));
a0 = (double) (yBar - a1 * xBar);
} else {
a0 = a1 = Double.NaN;
}
coefsValid = true;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/io/dxfdwg/libs/dxf/DxfFile.java | DxfFile.initializeDXF_SCHEMA | public static synchronized void initializeDXF_SCHEMA( CoordinateReferenceSystem crs ) {
if (DXF_POINTSCHEMA != null && DXF_POINTSCHEMA.getAttributeCount() != 0)
return;
SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder();
b.setName("dxfpointfile");
b.setCRS(crs);
b.add("the_geom", Point.class);
b.add("LAYER", String.class);
b.add("LTYPE", String.class);
b.add("ELEVATION", Double.class);
b.add("THICKNESS", Double.class);
b.add("COLOR", Integer.class);
b.add("TEXT", String.class);
b.add("TEXT_HEIGHT", Double.class);
b.add("TEXT_STYLE", String.class);
DXF_POINTSCHEMA = b.buildFeatureType();
b = new SimpleFeatureTypeBuilder();
b.setName("dxflinefile");
b.setCRS(crs);
b.add("the_geom", LineString.class);
b.add("LAYER", String.class);
b.add("LTYPE", String.class);
b.add("ELEVATION", Double.class);
b.add("THICKNESS", Double.class);
b.add("COLOR", Integer.class);
b.add("TEXT", String.class);
b.add("TEXT_HEIGHT", Double.class);
b.add("TEXT_STYLE", String.class);
DXF_LINESCHEMA = b.buildFeatureType();
b = new SimpleFeatureTypeBuilder();
b.setName("dxfpolygonfile");
b.setCRS(crs);
b.add("the_geom", Polygon.class);
b.add("LAYER", String.class);
b.add("LTYPE", String.class);
b.add("ELEVATION", Double.class);
b.add("THICKNESS", Double.class);
b.add("COLOR", Integer.class);
b.add("TEXT", String.class);
b.add("TEXT_HEIGHT", Double.class);
b.add("TEXT_STYLE", String.class);
DXF_POLYGONSCHEMA = b.buildFeatureType();
} | java | public static synchronized void initializeDXF_SCHEMA( CoordinateReferenceSystem crs ) {
if (DXF_POINTSCHEMA != null && DXF_POINTSCHEMA.getAttributeCount() != 0)
return;
SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder();
b.setName("dxfpointfile");
b.setCRS(crs);
b.add("the_geom", Point.class);
b.add("LAYER", String.class);
b.add("LTYPE", String.class);
b.add("ELEVATION", Double.class);
b.add("THICKNESS", Double.class);
b.add("COLOR", Integer.class);
b.add("TEXT", String.class);
b.add("TEXT_HEIGHT", Double.class);
b.add("TEXT_STYLE", String.class);
DXF_POINTSCHEMA = b.buildFeatureType();
b = new SimpleFeatureTypeBuilder();
b.setName("dxflinefile");
b.setCRS(crs);
b.add("the_geom", LineString.class);
b.add("LAYER", String.class);
b.add("LTYPE", String.class);
b.add("ELEVATION", Double.class);
b.add("THICKNESS", Double.class);
b.add("COLOR", Integer.class);
b.add("TEXT", String.class);
b.add("TEXT_HEIGHT", Double.class);
b.add("TEXT_STYLE", String.class);
DXF_LINESCHEMA = b.buildFeatureType();
b = new SimpleFeatureTypeBuilder();
b.setName("dxfpolygonfile");
b.setCRS(crs);
b.add("the_geom", Polygon.class);
b.add("LAYER", String.class);
b.add("LTYPE", String.class);
b.add("ELEVATION", Double.class);
b.add("THICKNESS", Double.class);
b.add("COLOR", Integer.class);
b.add("TEXT", String.class);
b.add("TEXT_HEIGHT", Double.class);
b.add("TEXT_STYLE", String.class);
DXF_POLYGONSCHEMA = b.buildFeatureType();
} | [
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/gears/src/main/java/org/hortonmachine/gears/io/dxfdwg/libs/dxf/DxfFile.java#L115-L161 | train |
TheHortonMachine/hortonmachine | gears/src/main/java/oms3/compiler/JavaFileManagerClassLoader.java | JavaFileManagerClassLoader.readClassData | private byte[] readClassData(JavaFileObject classFile) throws IOException {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
byte[] buf = new byte[4096];
InputStream classStream = classFile.openInputStream();
int n = classStream.read(buf);
while (n > 0) {
bos.write(buf, 0, n);
n = classStream.read(buf);
}
classStream.close();
return bos.toByteArray();
} | java | private byte[] readClassData(JavaFileObject classFile) throws IOException {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
byte[] buf = new byte[4096];
InputStream classStream = classFile.openInputStream();
int n = classStream.read(buf);
while (n > 0) {
bos.write(buf, 0, n);
n = classStream.read(buf);
}
classStream.close();
return bos.toByteArray();
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.getAllMarksArray | public static String[] getAllMarksArray() {
Set<String> keySet = markNamesToDef.keySet();
return (String[]) keySet.toArray(new String[keySet.size()]);
} | java | public static String[] getAllMarksArray() {
Set<String> keySet = markNamesToDef.keySet();
return (String[]) keySet.toArray(new String[keySet.size()]);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.substituteMark | public static void substituteMark( Rule rule, String wellKnownMarkName ) {
PointSymbolizer pointSymbolizer = StyleUtilities.pointSymbolizerFromRule(rule);
Mark oldMark = SLD.mark(pointSymbolizer);
Graphic graphic = SLD.graphic(pointSymbolizer);
graphic.graphicalSymbols().clear();
Mark mark = StyleUtilities.sf.createMark();
mark.setWellKnownName(StyleUtilities.ff.literal(wellKnownMarkName));
if (oldMark != null) {
mark.setFill(oldMark.getFill());
mark.setStroke(oldMark.getStroke());
}
graphic.graphicalSymbols().add(mark);
} | java | public static void substituteMark( Rule rule, String wellKnownMarkName ) {
PointSymbolizer pointSymbolizer = StyleUtilities.pointSymbolizerFromRule(rule);
Mark oldMark = SLD.mark(pointSymbolizer);
Graphic graphic = SLD.graphic(pointSymbolizer);
graphic.graphicalSymbols().clear();
Mark mark = StyleUtilities.sf.createMark();
mark.setWellKnownName(StyleUtilities.ff.literal(wellKnownMarkName));
if (oldMark != null) {
mark.setFill(oldMark.getFill());
mark.setStroke(oldMark.getStroke());
}
graphic.graphicalSymbols().add(mark);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.substituteExternalGraphics | public static void substituteExternalGraphics( Rule rule, URL externalGraphicsUrl ) {
String urlString = externalGraphicsUrl.toString();
String format = "";
if (urlString.toLowerCase().endsWith(".png")) {
format = "image/png";
} else if (urlString.toLowerCase().endsWith(".jpg")) {
format = "image/jpg";
} else if (urlString.toLowerCase().endsWith(".svg")) {
format = "image/svg+xml";
} else {
urlString = "";
try {
externalGraphicsUrl = new URL("file:");
} catch (MalformedURLException e) {
e.printStackTrace();
}
}
PointSymbolizer pointSymbolizer = StyleUtilities.pointSymbolizerFromRule(rule);
Graphic graphic = SLD.graphic(pointSymbolizer);
graphic.graphicalSymbols().clear();
ExternalGraphic exGraphic = sf.createExternalGraphic(externalGraphicsUrl, format);
graphic.graphicalSymbols().add(exGraphic);
} | java | public static void substituteExternalGraphics( Rule rule, URL externalGraphicsUrl ) {
String urlString = externalGraphicsUrl.toString();
String format = "";
if (urlString.toLowerCase().endsWith(".png")) {
format = "image/png";
} else if (urlString.toLowerCase().endsWith(".jpg")) {
format = "image/jpg";
} else if (urlString.toLowerCase().endsWith(".svg")) {
format = "image/svg+xml";
} else {
urlString = "";
try {
externalGraphicsUrl = new URL("file:");
} catch (MalformedURLException e) {
e.printStackTrace();
}
}
PointSymbolizer pointSymbolizer = StyleUtilities.pointSymbolizerFromRule(rule);
Graphic graphic = SLD.graphic(pointSymbolizer);
graphic.graphicalSymbols().clear();
ExternalGraphic exGraphic = sf.createExternalGraphic(externalGraphicsUrl, format);
graphic.graphicalSymbols().add(exGraphic);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.changeMarkSize | public static void changeMarkSize( Rule rule, int newSize ) {
PointSymbolizer pointSymbolizer = StyleUtilities.pointSymbolizerFromRule(rule);
Graphic graphic = SLD.graphic(pointSymbolizer);
graphic.setSize(ff.literal(newSize));
// Mark oldMark = SLDs.mark(pointSymbolizer);
// oldMark.setSize(ff.literal(newSize));
// Graphic graphic = SLDs.graphic(pointSymbolizer);
} | java | public static void changeMarkSize( Rule rule, int newSize ) {
PointSymbolizer pointSymbolizer = StyleUtilities.pointSymbolizerFromRule(rule);
Graphic graphic = SLD.graphic(pointSymbolizer);
graphic.setSize(ff.literal(newSize));
// Mark oldMark = SLDs.mark(pointSymbolizer);
// oldMark.setSize(ff.literal(newSize));
// Graphic graphic = SLDs.graphic(pointSymbolizer);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.changeRotation | public static void changeRotation( Rule rule, int newRotation ) {
PointSymbolizer pointSymbolizer = StyleUtilities.pointSymbolizerFromRule(rule);
Graphic graphic = SLD.graphic(pointSymbolizer);
graphic.setRotation(ff.literal(newRotation));
// Mark oldMark = SLDs.mark(pointSymbolizer);
// oldMark.setSize(ff.literal(newRotation));
} | java | public static void changeRotation( Rule rule, int newRotation ) {
PointSymbolizer pointSymbolizer = StyleUtilities.pointSymbolizerFromRule(rule);
Graphic graphic = SLD.graphic(pointSymbolizer);
graphic.setRotation(ff.literal(newRotation));
// Mark oldMark = SLDs.mark(pointSymbolizer);
// oldMark.setSize(ff.literal(newRotation));
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.setOffset | @SuppressWarnings({"rawtypes", "unchecked"})
public static void setOffset( Symbolizer symbolizer, String text ) {
if (text.indexOf(',') == -1) {
return;
}
String[] split = text.split(",");
if (split.length != 2) {
return;
}
double xOffset = Double.parseDouble(split[0]);
double yOffset = Double.parseDouble(split[1]);
Expression geometry = symbolizer.getGeometry();
if (geometry != null) {
if (geometry instanceof FilterFunction_offset) {
FilterFunction_offset offsetFunction = (FilterFunction_offset) geometry;
List parameters = offsetFunction.getParameters();
parameters.set(1, ff.literal(xOffset));
parameters.set(2, ff.literal(yOffset));
}
} else {
Function function = ff.function("offset", ff.property("the_geom"), ff.literal(xOffset), ff.literal(yOffset));
symbolizer.setGeometry(function);
}
} | java | @SuppressWarnings({"rawtypes", "unchecked"})
public static void setOffset( Symbolizer symbolizer, String text ) {
if (text.indexOf(',') == -1) {
return;
}
String[] split = text.split(",");
if (split.length != 2) {
return;
}
double xOffset = Double.parseDouble(split[0]);
double yOffset = Double.parseDouble(split[1]);
Expression geometry = symbolizer.getGeometry();
if (geometry != null) {
if (geometry instanceof FilterFunction_offset) {
FilterFunction_offset offsetFunction = (FilterFunction_offset) geometry;
List parameters = offsetFunction.getParameters();
parameters.set(1, ff.literal(xOffset));
parameters.set(2, ff.literal(yOffset));
}
} else {
Function function = ff.function("offset", ff.property("the_geom"), ff.literal(xOffset), ff.literal(yOffset));
symbolizer.setGeometry(function);
}
} | [
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java#L721-L745 | train |
TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.styleToString | public static String styleToString( Style style ) throws Exception {
StyledLayerDescriptor sld = sf.createStyledLayerDescriptor();
UserLayer layer = sf.createUserLayer();
layer.setLayerFeatureConstraints(new FeatureTypeConstraint[]{null});
sld.addStyledLayer(layer);
layer.addUserStyle(style);
SLDTransformer aTransformer = new SLDTransformer();
aTransformer.setIndentation(4);
String xml = aTransformer.transform(sld);
return xml;
} | java | public static String styleToString( Style style ) throws Exception {
StyledLayerDescriptor sld = sf.createStyledLayerDescriptor();
UserLayer layer = sf.createUserLayer();
layer.setLayerFeatureConstraints(new FeatureTypeConstraint[]{null});
sld.addStyledLayer(layer);
layer.addUserStyle(style);
SLDTransformer aTransformer = new SLDTransformer();
aTransformer.setIndentation(4);
String xml = aTransformer.transform(sld);
return xml;
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.createStyleFromGraphic | public static StyleWrapper createStyleFromGraphic( File graphicsPath ) throws IOException {
String name = graphicsPath.getName();
ExternalGraphic exGraphic = null;
if (name.toLowerCase().endsWith(".png")) {
exGraphic = sf.createExternalGraphic(graphicsPath.toURI().toURL(), "image/png");
} else if (name.toLowerCase().endsWith(".svg")) {
exGraphic = sf.createExternalGraphic(graphicsPath.toURI().toURL(), "image/svg+xml");
} else if (name.toLowerCase().endsWith(".sld")) {
StyledLayerDescriptor sld = readStyle(graphicsPath);
Style style = SldUtilities.getDefaultStyle(sld);
return new StyleWrapper(style);
}
if (exGraphic == null) {
throw new IOException("Style could not be created!");
}
Graphic gr = sf.createDefaultGraphic();
gr.graphicalSymbols().clear();
gr.graphicalSymbols().add(exGraphic);
Expression size = ff.literal(20);
gr.setSize(size);
Rule rule = sf.createRule();
PointSymbolizer pointSymbolizer = sf.createPointSymbolizer(gr, null);
rule.symbolizers().add(pointSymbolizer);
FeatureTypeStyle featureTypeStyle = sf.createFeatureTypeStyle();
featureTypeStyle.rules().add(rule);
Style namedStyle = sf.createStyle();
namedStyle.featureTypeStyles().add(featureTypeStyle);
namedStyle.setName(FilenameUtils.removeExtension(name));
return new StyleWrapper(namedStyle);
} | java | public static StyleWrapper createStyleFromGraphic( File graphicsPath ) throws IOException {
String name = graphicsPath.getName();
ExternalGraphic exGraphic = null;
if (name.toLowerCase().endsWith(".png")) {
exGraphic = sf.createExternalGraphic(graphicsPath.toURI().toURL(), "image/png");
} else if (name.toLowerCase().endsWith(".svg")) {
exGraphic = sf.createExternalGraphic(graphicsPath.toURI().toURL(), "image/svg+xml");
} else if (name.toLowerCase().endsWith(".sld")) {
StyledLayerDescriptor sld = readStyle(graphicsPath);
Style style = SldUtilities.getDefaultStyle(sld);
return new StyleWrapper(style);
}
if (exGraphic == null) {
throw new IOException("Style could not be created!");
}
Graphic gr = sf.createDefaultGraphic();
gr.graphicalSymbols().clear();
gr.graphicalSymbols().add(exGraphic);
Expression size = ff.literal(20);
gr.setSize(size);
Rule rule = sf.createRule();
PointSymbolizer pointSymbolizer = sf.createPointSymbolizer(gr, null);
rule.symbolizers().add(pointSymbolizer);
FeatureTypeStyle featureTypeStyle = sf.createFeatureTypeStyle();
featureTypeStyle.rules().add(rule);
Style namedStyle = sf.createStyle();
namedStyle.featureTypeStyles().add(featureTypeStyle);
namedStyle.setName(FilenameUtils.removeExtension(name));
return new StyleWrapper(namedStyle);
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.getDash | public static float[] getDash( String dashStr ) {
if (dashStr == null) {
return null;
}
String[] dashSplit = dashStr.split(","); //$NON-NLS-1$
int size = dashSplit.length;
float[] dash = new float[size];
try {
for( int i = 0; i < dash.length; i++ ) {
dash[i] = Float.parseFloat(dashSplit[i].trim());
}
return dash;
} catch (NumberFormatException e) {
return null;
}
} | java | public static float[] getDash( String dashStr ) {
if (dashStr == null) {
return null;
}
String[] dashSplit = dashStr.split(","); //$NON-NLS-1$
int size = dashSplit.length;
float[] dash = new float[size];
try {
for( int i = 0; i < dash.length; i++ ) {
dash[i] = Float.parseFloat(dashSplit[i].trim());
}
return dash;
} catch (NumberFormatException e) {
return null;
}
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.getDashString | public static String getDashString( float[] dashArray ) {
StringBuilder sb = null;
for( float f : dashArray ) {
if (sb == null) {
sb = new StringBuilder(String.valueOf(f));
} else {
sb.append(",");
sb.append(String.valueOf(f));
}
}
return sb.toString();
} | java | public static String getDashString( float[] dashArray ) {
StringBuilder sb = null;
for( float f : dashArray ) {
if (sb == null) {
sb = new StringBuilder(String.valueOf(f));
} else {
sb.append(",");
sb.append(String.valueOf(f));
}
}
return sb.toString();
} | [
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java#L984-L995 | train |
TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.sld2awtJoin | public static int sld2awtJoin( String sldJoin ) {
if (sldJoin.equals(lineJoinNames[1])) {
return BasicStroke.JOIN_BEVEL;
} else if (sldJoin.equals("") || sldJoin.equals(lineJoinNames[2])) {
return BasicStroke.JOIN_MITER;
} else if (sldJoin.equals(lineJoinNames[3])) {
return BasicStroke.JOIN_ROUND;
} else {
throw new IllegalArgumentException("unsupported line join");
}
} | java | public static int sld2awtJoin( String sldJoin ) {
if (sldJoin.equals(lineJoinNames[1])) {
return BasicStroke.JOIN_BEVEL;
} else if (sldJoin.equals("") || sldJoin.equals(lineJoinNames[2])) {
return BasicStroke.JOIN_MITER;
} else if (sldJoin.equals(lineJoinNames[3])) {
return BasicStroke.JOIN_ROUND;
} else {
throw new IllegalArgumentException("unsupported line join");
}
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/StyleUtilities.java | StyleUtilities.sld2awtCap | public static int sld2awtCap( String sldCap ) {
if (sldCap.equals("") || sldCap.equals(lineCapNames[1])) {
return BasicStroke.CAP_BUTT;
} else if (sldCap.equals(lineCapNames[2])) {
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} else if (sldCap.equals(lineCapNames[3])) {
return BasicStroke.CAP_SQUARE;
} else {
throw new IllegalArgumentException("unsupported line cap");
}
} | java | public static int sld2awtCap( String sldCap ) {
if (sldCap.equals("") || sldCap.equals(lineCapNames[1])) {
return BasicStroke.CAP_BUTT;
} else if (sldCap.equals(lineCapNames[2])) {
return BasicStroke.CAP_ROUND;
} else if (sldCap.equals(lineCapNames[3])) {
return BasicStroke.CAP_SQUARE;
} else {
throw new IllegalArgumentException("unsupported line cap");
}
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/TransformationUtils.java | TransformationUtils.scaleToWidth | public static Envelope scaleToWidth( Envelope original, double newWidth ) {
double width = original.getWidth();
double factor = newWidth / width;
double newHeight = original.getHeight() * factor;
return new Envelope(original.getMinX(), original.getMinX() + newWidth, original.getMinY(),
original.getMinY() + newHeight);
} | java | public static Envelope scaleToWidth( Envelope original, double newWidth ) {
double width = original.getWidth();
double factor = newWidth / width;
double newHeight = original.getHeight() * factor;
return new Envelope(original.getMinX(), original.getMinX() + newWidth, original.getMinY(),
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/util/Times.java | Times.getDayOfYear | public static int getDayOfYear(Calendar cal, int type) {
int jday = cal.get(Calendar.DAY_OF_YEAR);
int mo = cal.get(java.util.Calendar.MONTH) + 1;
if (type == CALENDAR_YEAR) {
return jday;
} else if (type == SOLAR_YEAR) {
int day = cal.get(Calendar.DAY_OF_MONTH);
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} else if (type == WATER_YEAR) {
return (mo > 9) ? (jday - (isLeapYear(cal.get(Calendar.YEAR)) ? 274 : 273)) : (jday + 92);
}
throw new IllegalArgumentException("getDayOfYear() type argument unknown");
} | java | public static int getDayOfYear(Calendar cal, int type) {
int jday = cal.get(Calendar.DAY_OF_YEAR);
int mo = cal.get(java.util.Calendar.MONTH) + 1;
if (type == CALENDAR_YEAR) {
return jday;
} else if (type == SOLAR_YEAR) {
int day = cal.get(Calendar.DAY_OF_MONTH);
return (mo == 12 && day > 21) ? (day - 21) : (jday + 10);
} else if (type == WATER_YEAR) {
return (mo > 9) ? (jday - (isLeapYear(cal.get(Calendar.YEAR)) ? 274 : 273)) : (jday + 92);
}
throw new IllegalArgumentException("getDayOfYear() type argument unknown");
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/util/Times.java | Times.deltaHours | public static double deltaHours(int calUnit, int increments) {
if (calUnit == Calendar.DATE) {
return 24 * increments;
} else if (calUnit == Calendar.HOUR) {
return increments;
} else if (calUnit == Calendar.MINUTE) {
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} else if (calUnit == Calendar.SECOND) {
return increments / 3600;
}
return -1;
} | java | public static double deltaHours(int calUnit, int increments) {
if (calUnit == Calendar.DATE) {
return 24 * increments;
} else if (calUnit == Calendar.HOUR) {
return increments;
} else if (calUnit == Calendar.MINUTE) {
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return -1;
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/check/feature/FeatureValidationCheck.java | FeatureValidationCheck.reportError | protected ValidationMessage<Origin> reportError(Origin origin, String messageKey,
Object... params) {
return reportMessage(Severity.ERROR, origin, messageKey, params);
} | java | protected ValidationMessage<Origin> reportError(Origin origin, String messageKey,
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return reportMessage(Severity.ERROR, origin, messageKey, params);
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/check/feature/FeatureValidationCheck.java | FeatureValidationCheck.reportFeatureError | protected ValidationMessage<Origin> reportFeatureError(Origin origin, String messageKey, Feature feature,
Object... params) {
ValidationMessage<Origin> message = reportMessage(Severity.ERROR, origin, messageKey, params);
appendLocusTadAndGeneIDToMessage(feature, message);
return message;
} | java | protected ValidationMessage<Origin> reportFeatureError(Origin origin, String messageKey, Feature feature,
Object... params) {
ValidationMessage<Origin> message = reportMessage(Severity.ERROR, origin, messageKey, params);
appendLocusTadAndGeneIDToMessage(feature, message);
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/check/feature/FeatureValidationCheck.java | FeatureValidationCheck.appendLocusTadAndGeneIDToMessage | public static void appendLocusTadAndGeneIDToMessage(Feature feature, ValidationMessage<Origin> message) {
if (SequenceEntryUtils.isQualifierAvailable(Qualifier.LOCUS_TAG_QUALIFIER_NAME, feature)) {
Qualifier locusTag = SequenceEntryUtils.getQualifier(Qualifier.LOCUS_TAG_QUALIFIER_NAME, feature);
if (locusTag.isValue()) {
message.appendCuratorMessage("locus tag = " + locusTag.getValue());
}
}
if (SequenceEntryUtils.isQualifierAvailable(Qualifier.GENE_QUALIFIER_NAME, feature)) {
Qualifier geneName = SequenceEntryUtils.getQualifier(Qualifier.GENE_QUALIFIER_NAME, feature);
if (geneName.isValue()) {
message.appendCuratorMessage("gene = " + geneName.getValue());
}
}
} | java | public static void appendLocusTadAndGeneIDToMessage(Feature feature, ValidationMessage<Origin> message) {
if (SequenceEntryUtils.isQualifierAvailable(Qualifier.LOCUS_TAG_QUALIFIER_NAME, feature)) {
Qualifier locusTag = SequenceEntryUtils.getQualifier(Qualifier.LOCUS_TAG_QUALIFIER_NAME, feature);
if (locusTag.isValue()) {
message.appendCuratorMessage("locus tag = " + locusTag.getValue());
}
}
if (SequenceEntryUtils.isQualifierAvailable(Qualifier.GENE_QUALIFIER_NAME, feature)) {
Qualifier geneName = SequenceEntryUtils.getQualifier(Qualifier.GENE_QUALIFIER_NAME, feature);
if (geneName.isValue()) {
message.appendCuratorMessage("gene = " + geneName.getValue());
}
}
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/check/feature/FeatureValidationCheck.java | FeatureValidationCheck.reportWarning | protected ValidationMessage<Origin> reportWarning(Origin origin, String messageKey,
Object... params) {
return reportMessage(Severity.WARNING, origin, messageKey, params);
} | java | protected ValidationMessage<Origin> reportWarning(Origin origin, String messageKey,
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/check/feature/FeatureValidationCheck.java | FeatureValidationCheck.reportMessage | protected ValidationMessage<Origin> reportMessage(Severity severity, Origin origin,
String messageKey, Object... params) {
ValidationMessage<Origin> message = EntryValidations.createMessage(origin, severity, messageKey, params);
message.getMessage();
// System.out.println("message = " + message.getMessage());
result.append(message);
return message;
} | java | protected ValidationMessage<Origin> reportMessage(Severity severity, Origin origin,
String messageKey, Object... params) {
ValidationMessage<Origin> message = EntryValidations.createMessage(origin, severity, messageKey, params);
message.getMessage();
// System.out.println("message = " + message.getMessage());
result.append(message);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/v/smoothing/OmsLineSmootherMcMaster.java | OmsLineSmootherMcMaster.isAlone | private boolean isAlone( Geometry geometryN ) {
Coordinate[] coordinates = geometryN.getCoordinates();
if (coordinates.length > 1) {
Coordinate first = coordinates[0];
Coordinate last = coordinates[coordinates.length - 1];
for( SimpleFeature line : linesList ) {
Geometry lineGeom = (Geometry) line.getDefaultGeometry();
int numGeometries = lineGeom.getNumGeometries();
for( int i = 0; i < numGeometries; i++ ) {
Geometry subGeom = lineGeom.getGeometryN(i);
Coordinate[] lineCoordinates = subGeom.getCoordinates();
if (lineCoordinates.length < 2) {
continue;
} else {
Coordinate tmpFirst = lineCoordinates[0];
Coordinate tmpLast = lineCoordinates[lineCoordinates.length - 1];
if (tmpFirst.distance(first) < SAMEPOINTTHRESHOLD || tmpFirst.distance(last) < SAMEPOINTTHRESHOLD
|| tmpLast.distance(first) < SAMEPOINTTHRESHOLD || tmpLast.distance(last) < SAMEPOINTTHRESHOLD) {
return false;
}
}
}
}
}
// 1 point line or no connection, mark it as alone for removal
return true;
} | java | private boolean isAlone( Geometry geometryN ) {
Coordinate[] coordinates = geometryN.getCoordinates();
if (coordinates.length > 1) {
Coordinate first = coordinates[0];
Coordinate last = coordinates[coordinates.length - 1];
for( SimpleFeature line : linesList ) {
Geometry lineGeom = (Geometry) line.getDefaultGeometry();
int numGeometries = lineGeom.getNumGeometries();
for( int i = 0; i < numGeometries; i++ ) {
Geometry subGeom = lineGeom.getGeometryN(i);
Coordinate[] lineCoordinates = subGeom.getCoordinates();
if (lineCoordinates.length < 2) {
continue;
} else {
Coordinate tmpFirst = lineCoordinates[0];
Coordinate tmpLast = lineCoordinates[lineCoordinates.length - 1];
if (tmpFirst.distance(first) < SAMEPOINTTHRESHOLD || tmpFirst.distance(last) < SAMEPOINTTHRESHOLD
|| tmpLast.distance(first) < SAMEPOINTTHRESHOLD || tmpLast.distance(last) < SAMEPOINTTHRESHOLD) {
return false;
}
}
}
}
}
// 1 point line or no connection, mark it as alone for removal
return true;
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/v/smoothing/OmsLineSmootherMcMaster.java | OmsLineSmootherMcMaster.defaultSmoothShapefile | public static void defaultSmoothShapefile( String shapePath, String outPath ) throws Exception {
PrintStreamProgressMonitor pm = new PrintStreamProgressMonitor(System.out, System.err);
SimpleFeatureCollection initialFC = OmsShapefileFeatureReader.readShapefile(shapePath);
OmsLineSmootherMcMaster smoother = new OmsLineSmootherMcMaster();
smoother.pm = pm;
smoother.pLimit = 10;
smoother.inVector = initialFC;
smoother.pLookahead = 13;
// smoother.pSlide = 1;
smoother.pDensify = 0.2;
smoother.pSimplify = 0.01;
smoother.process();
SimpleFeatureCollection smoothedFeatures = smoother.outVector;
OmsShapefileFeatureWriter.writeShapefile(outPath, smoothedFeatures, pm);
} | java | public static void defaultSmoothShapefile( String shapePath, String outPath ) throws Exception {
PrintStreamProgressMonitor pm = new PrintStreamProgressMonitor(System.out, System.err);
SimpleFeatureCollection initialFC = OmsShapefileFeatureReader.readShapefile(shapePath);
OmsLineSmootherMcMaster smoother = new OmsLineSmootherMcMaster();
smoother.pm = pm;
smoother.pLimit = 10;
smoother.inVector = initialFC;
smoother.pLookahead = 13;
// smoother.pSlide = 1;
smoother.pDensify = 0.2;
smoother.pSimplify = 0.01;
smoother.process();
SimpleFeatureCollection smoothedFeatures = smoother.outVector;
OmsShapefileFeatureWriter.writeShapefile(outPath, smoothedFeatures, pm);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/clustering/GvmVectorSpace.java | GvmVectorSpace.magnitudeSqr | @Override
public double magnitudeSqr( Object pt ) {
double sum = 0.0;
double[] coords = coords(pt);
for( int i = 0; i < dimensions; i++ ) {
double c = coords[i];
sum += c * c;
}
return sum;
} | java | @Override
public double magnitudeSqr( Object pt ) {
double sum = 0.0;
double[] coords = coords(pt);
for( int i = 0; i < dimensions; i++ ) {
double c = coords[i];
sum += c * c;
}
return sum;
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codahale/xsalsa20poly1305 | src/main/java/com/codahale/xsalsa20poly1305/Keys.java | Keys.generateSecretKey | public static byte[] generateSecretKey() {
final byte[] k = new byte[KEY_LEN];
final SecureRandom random = new SecureRandom();
random.nextBytes(k);
return k;
} | java | public static byte[] generateSecretKey() {
final byte[] k = new byte[KEY_LEN];
final SecureRandom random = new SecureRandom();
random.nextBytes(k);
return k;
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/checksum/CRC32.java | CRC32.initialize | private static void initialize()
{
for (int i = 0; i < 256; ++i)
{
long crc = i;
for (int j = 8; j > 0; j--)
{
if ((crc & 1) == 1)
crc = (crc >>> 1) ^ polynomial;
else
crc >>>= 1;
}
values[i] = crc;
}
init_done = true;
} | java | private static void initialize()
{
for (int i = 0; i < 256; ++i)
{
long crc = i;
for (int j = 8; j > 0; j--)
{
if ((crc & 1) == 1)
crc = (crc >>> 1) ^ polynomial;
else
crc >>>= 1;
}
values[i] = crc;
}
init_done = true;
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/checksum/CRC32.java | CRC32.calculateCRC32 | public static long calculateCRC32(byte[] buffer, int offset, int length)
{
if (!init_done)
{
initialize();
}
for (int i = offset; i < offset + length; i++)
{
long tmp1 = (crc >>> 8) & 0x00FFFFFFL;
long tmp2 = values[(int) ((crc ^ Character.toUpperCase((char) buffer[i])) & 0xff)];
crc = tmp1 ^ tmp2;
// System.out.println("CRC: "+crc);
}
return crc;
} | java | public static long calculateCRC32(byte[] buffer, int offset, int length)
{
if (!init_done)
{
initialize();
}
for (int i = offset; i < offset + length; i++)
{
long tmp1 = (crc >>> 8) & 0x00FFFFFFL;
long tmp2 = values[(int) ((crc ^ Character.toUpperCase((char) buffer[i])) & 0xff)];
crc = tmp1 ^ tmp2;
// System.out.println("CRC: "+crc);
}
return crc;
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/dsl/Model.java | Model.getClassLoader | private synchronized URLClassLoader getClassLoader() {
if (modelClassLoader == null) {
List<File> jars = res.filterFiles("jar"); // jars as defined in
List<File> cli_jars = getExtraResources(); // cli extra jars
List<File> dirs = res.filterDirectories(); // testing
List<URL> urls = new ArrayList<URL>();
try {
for (int i = 0; i < jars.size(); i++) {
urls.add(jars.get(i).toURI().toURL());
if (log.isLoggable(Level.CONFIG)) {
log.config("classpath entry from simulation: " + jars.get(i));
}
}
for (int i = 0; i < dirs.size(); i++) {
urls.add(dirs.get(i).toURI().toURL());
if (log.isLoggable(Level.CONFIG)) {
log.config("dir entry: " + dirs.get(i));
}
}
for (int i = 0; i < cli_jars.size(); i++) {
urls.add(cli_jars.get(i).toURI().toURL());
if (log.isLoggable(Level.CONFIG)) {
log.config("classpath entry from CLI: " + cli_jars.get(i));
}
}
urls.add(new URL("file:" + System.getProperty("oms.prj") + "/dist/"));
if (log.isLoggable(Level.CONFIG)) {
log.config("Sim loading classpath : " + "file:" + System.getProperty("oms.prj") + "/dist/");
}
} catch (MalformedURLException ex) {
throw new ComponentException("Illegal resource:" + ex.getMessage());
}
modelClassLoader = new URLClassLoader(urls.toArray(new URL[0]),
Thread.currentThread().getContextClassLoader());
}
return modelClassLoader;
} | java | private synchronized URLClassLoader getClassLoader() {
if (modelClassLoader == null) {
List<File> jars = res.filterFiles("jar"); // jars as defined in
List<File> cli_jars = getExtraResources(); // cli extra jars
List<File> dirs = res.filterDirectories(); // testing
List<URL> urls = new ArrayList<URL>();
try {
for (int i = 0; i < jars.size(); i++) {
urls.add(jars.get(i).toURI().toURL());
if (log.isLoggable(Level.CONFIG)) {
log.config("classpath entry from simulation: " + jars.get(i));
}
}
for (int i = 0; i < dirs.size(); i++) {
urls.add(dirs.get(i).toURI().toURL());
if (log.isLoggable(Level.CONFIG)) {
log.config("dir entry: " + dirs.get(i));
}
}
for (int i = 0; i < cli_jars.size(); i++) {
urls.add(cli_jars.get(i).toURI().toURL());
if (log.isLoggable(Level.CONFIG)) {
log.config("classpath entry from CLI: " + cli_jars.get(i));
}
}
urls.add(new URL("file:" + System.getProperty("oms.prj") + "/dist/"));
if (log.isLoggable(Level.CONFIG)) {
log.config("Sim loading classpath : " + "file:" + System.getProperty("oms.prj") + "/dist/");
}
} catch (MalformedURLException ex) {
throw new ComponentException("Illegal resource:" + ex.getMessage());
}
modelClassLoader = new URLClassLoader(urls.toArray(new URL[0]),
Thread.currentThread().getContextClassLoader());
}
return modelClassLoader;
} | [
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/utils/CommonQueries.java | CommonQueries.getDistanceBetween | public static double getDistanceBetween( IHMConnection connection, Coordinate p1, Coordinate p2, int srid ) throws Exception {
if (srid < 0) {
srid = 4326;
}
GeometryFactory gf = new GeometryFactory();
LineString lineString = gf.createLineString(new Coordinate[]{p1, p2});
String sql = "select GeodesicLength(LineFromText(\"" + lineString.toText() + "\"," + srid + "));";
try (IHMStatement stmt = connection.createStatement(); IHMResultSet rs = stmt.executeQuery(sql);) {
if (rs.next()) {
double length = rs.getDouble(1);
return length;
}
throw new RuntimeException("Could not calculate distance.");
}
} | java | public static double getDistanceBetween( IHMConnection connection, Coordinate p1, Coordinate p2, int srid ) throws Exception {
if (srid < 0) {
srid = 4326;
}
GeometryFactory gf = new GeometryFactory();
LineString lineString = gf.createLineString(new Coordinate[]{p1, p2});
String sql = "select GeodesicLength(LineFromText(\"" + lineString.toText() + "\"," + srid + "));";
try (IHMStatement stmt = connection.createStatement(); IHMResultSet rs = stmt.executeQuery(sql);) {
if (rs.next()) {
double length = rs.getDouble(1);
return length;
}
throw new RuntimeException("Could not calculate distance.");
}
} | [
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/debrisvandre/OmsDebrisVandre.java | OmsDebrisVandre.moveToNextTriggerpoint | private boolean moveToNextTriggerpoint( RandomIter triggerIter, RandomIter flowIter, int[] flowDirColRow ) {
double tmpFlowValue = flowIter.getSampleDouble(flowDirColRow[0], flowDirColRow[1], 0);
if (tmpFlowValue == 10) {
return false;
}
if (!ModelsEngine.go_downstream(flowDirColRow, tmpFlowValue))
throw new ModelsIllegalargumentException("Unable to go downstream: " + flowDirColRow[0] + "/" + flowDirColRow[1],
this, pm);
while( isNovalue(triggerIter.getSampleDouble(flowDirColRow[0], flowDirColRow[1], 0)) ) {
tmpFlowValue = flowIter.getSampleDouble(flowDirColRow[0], flowDirColRow[1], 0);
if (tmpFlowValue == 10) {
return false;
}
if (!ModelsEngine.go_downstream(flowDirColRow, tmpFlowValue))
throw new ModelsIllegalargumentException("Unable to go downstream: " + flowDirColRow[0] + "/" + flowDirColRow[1],
this, pm);
}
return true;
} | java | private boolean moveToNextTriggerpoint( RandomIter triggerIter, RandomIter flowIter, int[] flowDirColRow ) {
double tmpFlowValue = flowIter.getSampleDouble(flowDirColRow[0], flowDirColRow[1], 0);
if (tmpFlowValue == 10) {
return false;
}
if (!ModelsEngine.go_downstream(flowDirColRow, tmpFlowValue))
throw new ModelsIllegalargumentException("Unable to go downstream: " + flowDirColRow[0] + "/" + flowDirColRow[1],
this, pm);
while( isNovalue(triggerIter.getSampleDouble(flowDirColRow[0], flowDirColRow[1], 0)) ) {
tmpFlowValue = flowIter.getSampleDouble(flowDirColRow[0], flowDirColRow[1], 0);
if (tmpFlowValue == 10) {
return false;
}
if (!ModelsEngine.go_downstream(flowDirColRow, tmpFlowValue))
throw new ModelsIllegalargumentException("Unable to go downstream: " + flowDirColRow[0] + "/" + flowDirColRow[1],
this, pm);
}
return true;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/io/dxfdwg/libs/dwg/utils/ByteUtils.java | ByteUtils.memclr | public static void memclr( byte[] array, int offset, int length ) {
for( int i = 0; i < length; ++i, ++offset )
array[offset] = 0;
} | java | public static void memclr( byte[] array, int offset, int length ) {
for( int i = 0; i < length; ++i, ++offset )
array[offset] = 0;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/io/dxfdwg/libs/dwg/utils/ByteUtils.java | ByteUtils.zero_pad | public static byte[] zero_pad( byte[] original, int block_size ) {
if ((original.length % block_size) == 0) {
return original;
}
byte[] result = new byte[round_up(original.length, block_size)];
memcpy(result, 0, original, 0, original.length);
// Unnecessary - jvm sets bytes to 0.
// memclr (result, original.length, result.length - original.length);
return result;
} | java | public static byte[] zero_pad( byte[] original, int block_size ) {
if ((original.length % block_size) == 0) {
return original;
}
byte[] result = new byte[round_up(original.length, block_size)];
memcpy(result, 0, original, 0, original.length);
// Unnecessary - jvm sets bytes to 0.
// memclr (result, original.length, result.length - original.length);
return result;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/DataUtilities.java | DataUtilities.isSupportedVectorExtension | public static boolean isSupportedVectorExtension( String name ) {
for( String ext : supportedVectors ) {
if (name.toLowerCase().endsWith(ext)) {
return true;
}
}
return false;
} | java | public static boolean isSupportedVectorExtension( String name ) {
for( String ext : supportedVectors ) {
if (name.toLowerCase().endsWith(ext)) {
return true;
}
}
return false;
} | [
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/gears/src/main/java/org/hortonmachine/gears/utils/DataUtilities.java#L37-L44 | train |
TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/DataUtilities.java | DataUtilities.isSupportedRasterExtension | public static boolean isSupportedRasterExtension( String name ) {
for( String ext : supportedRasters ) {
if (name.toLowerCase().endsWith(ext)) {
return true;
}
}
return false;
} | java | public static boolean isSupportedRasterExtension( String name ) {
for( String ext : supportedRasters ) {
if (name.toLowerCase().endsWith(ext)) {
return true;
}
}
return false;
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/io/rasterreader/OmsRasterReader.java | OmsRasterReader.readRaster | public static GridCoverage2D readRaster( String path ) throws Exception {
OmsRasterReader reader = new OmsRasterReader();
reader.file = path;
reader.process();
GridCoverage2D geodata = reader.outRaster;
return geodata;
} | java | public static GridCoverage2D readRaster( String path ) throws Exception {
OmsRasterReader reader = new OmsRasterReader();
reader.file = path;
reader.process();
GridCoverage2D geodata = reader.outRaster;
return geodata;
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/dsl/cosu/Matrix.java | Matrix.swap | private void swap(int i, int j) {
double[] temp = data[i];
data[i] = data[j];
data[j] = temp;
} | java | private void swap(int i, int j) {
double[] temp = data[i];
data[i] = data[j];
data[j] = temp;
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/dsl/cosu/Matrix.java | Matrix.transpose | public Matrix transpose() {
Matrix A = new Matrix(N, M);
for (int i = 0; i < M; i++) {
for (int j = 0; j < N; j++) {
A.data[j][i] = data[i][j];
}
}
return A;
} | java | public Matrix transpose() {
Matrix A = new Matrix(N, M);
for (int i = 0; i < M; i++) {
for (int j = 0; j < N; j++) {
A.data[j][i] = data[i][j];
}
}
return A;
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/dsl/cosu/Matrix.java | Matrix.solve | public Matrix solve(Matrix rhs) {
if (M != N || rhs.M != N || rhs.N != 1) {
throw new RuntimeException("Illegal matrix dimensions.");
}
// create copies of the data
Matrix A = new Matrix(this);
Matrix b = new Matrix(rhs);
// Gaussian elimination with partial pivoting
for (int i = 0; i < N; i++) {
// find pivot row and swap
int max = i;
for (int j = i + 1; j < N; j++) {
if (Math.abs(A.data[j][i]) > Math.abs(A.data[max][i])) {
max = j;
}
}
A.swap(i, max);
b.swap(i, max);
// singular
if (A.data[i][i] == 0.0) {
throw new RuntimeException("Matrix is singular.");
}
// pivot within b
for (int j = i + 1; j < N; j++) {
b.data[j][0] -= b.data[i][0] * A.data[j][i] / A.data[i][i];
}
// pivot within A
for (int j = i + 1; j < N; j++) {
double m = A.data[j][i] / A.data[i][i];
for (int k = i + 1; k < N; k++) {
A.data[j][k] -= A.data[i][k] * m;
}
A.data[j][i] = 0.0;
}
}
// back substitution
Matrix x = new Matrix(N, 1);
for (int j = N - 1; j >= 0; j--) {
double t = 0.0;
for (int k = j + 1; k < N; k++) {
t += A.data[j][k] * x.data[k][0];
}
x.data[j][0] = (b.data[j][0] - t) / A.data[j][j];
}
return x;
} | java | public Matrix solve(Matrix rhs) {
if (M != N || rhs.M != N || rhs.N != 1) {
throw new RuntimeException("Illegal matrix dimensions.");
}
// create copies of the data
Matrix A = new Matrix(this);
Matrix b = new Matrix(rhs);
// Gaussian elimination with partial pivoting
for (int i = 0; i < N; i++) {
// find pivot row and swap
int max = i;
for (int j = i + 1; j < N; j++) {
if (Math.abs(A.data[j][i]) > Math.abs(A.data[max][i])) {
max = j;
}
}
A.swap(i, max);
b.swap(i, max);
// singular
if (A.data[i][i] == 0.0) {
throw new RuntimeException("Matrix is singular.");
}
// pivot within b
for (int j = i + 1; j < N; j++) {
b.data[j][0] -= b.data[i][0] * A.data[j][i] / A.data[i][i];
}
// pivot within A
for (int j = i + 1; j < N; j++) {
double m = A.data[j][i] / A.data[i][i];
for (int k = i + 1; k < N; k++) {
A.data[j][k] -= A.data[i][k] * m;
}
A.data[j][i] = 0.0;
}
}
// back substitution
Matrix x = new Matrix(N, 1);
for (int j = N - 1; j >= 0; j--) {
double t = 0.0;
for (int k = j + 1; k < N; k++) {
t += A.data[j][k] * x.data[k][0];
}
x.data[j][0] = (b.data[j][0] - t) / A.data[j][j];
}
return x;
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/dsl/cosu/Matrix.java | Matrix.print | public void print() {
for (int i = 0; i < M; i++) {
for (int j = 0; j < N; j++) {
System.out.printf("%9.4f ", data[i][j]);
}
System.out.println();
}
} | java | public void print() {
for (int i = 0; i < M; i++) {
for (int j = 0; j < N; j++) {
System.out.printf("%9.4f ", data[i][j]);
}
System.out.println();
}
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/mbtiles/MBTilesDb.java | MBTilesDb.createTables | public void createTables( boolean makeIndexes ) throws Exception {
database.executeInsertUpdateDeleteSql("DROP TABLE IF EXISTS " + TABLE_TILES);
database.executeInsertUpdateDeleteSql("DROP TABLE IF EXISTS " + TABLE_METADATA);
database.executeInsertUpdateDeleteSql(CREATE_TILES);
database.executeInsertUpdateDeleteSql(CREATE_METADATA);
if (makeIndexes) {
createIndexes();
}
} | java | public void createTables( boolean makeIndexes ) throws Exception {
database.executeInsertUpdateDeleteSql("DROP TABLE IF EXISTS " + TABLE_TILES);
database.executeInsertUpdateDeleteSql("DROP TABLE IF EXISTS " + TABLE_METADATA);
database.executeInsertUpdateDeleteSql(CREATE_TILES);
database.executeInsertUpdateDeleteSql(CREATE_METADATA);
if (makeIndexes) {
createIndexes();
}
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/mbtiles/MBTilesDb.java | MBTilesDb.fillMetadata | public void fillMetadata( float n, float s, float w, float e, String name, String format, int minZoom, int maxZoom )
throws Exception {
// type = baselayer
// version = 1.1
// descritpion = name
String query = toMetadataQuery("name", name);
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("description", name);
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("format", format);
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("minZoom", minZoom + "");
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("maxZoom", maxZoom + "");
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("type", "baselayer");
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("version", "1.1");
database.executeInsertUpdateDeleteSql(query);
// left, bottom, right, top
query = toMetadataQuery("bounds", w + "," + s + "," + e + "," + n);
database.executeInsertUpdateDeleteSql(query);
} | java | public void fillMetadata( float n, float s, float w, float e, String name, String format, int minZoom, int maxZoom )
throws Exception {
// type = baselayer
// version = 1.1
// descritpion = name
String query = toMetadataQuery("name", name);
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("description", name);
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("format", format);
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("minZoom", minZoom + "");
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("maxZoom", maxZoom + "");
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("type", "baselayer");
database.executeInsertUpdateDeleteSql(query);
query = toMetadataQuery("version", "1.1");
database.executeInsertUpdateDeleteSql(query);
// left, bottom, right, top
query = toMetadataQuery("bounds", w + "," + s + "," + e + "," + n);
database.executeInsertUpdateDeleteSql(query);
} | [
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/mbtiles/MBTilesDb.java | MBTilesDb.addTile | public synchronized void addTile( int x, int y, int z, byte[] imageBytes ) throws Exception {
database.execOnConnection(connection -> {
try (IHMPreparedStatement pstmt = connection.prepareStatement(insertTileSql);) {
pstmt.setInt(1, z);
pstmt.setInt(2, x);
pstmt.setInt(3, y);
pstmt.setBytes(4, imageBytes);
pstmt.executeUpdate();
return "";
}
});
} | java | public synchronized void addTile( int x, int y, int z, byte[] imageBytes ) throws Exception {
database.execOnConnection(connection -> {
try (IHMPreparedStatement pstmt = connection.prepareStatement(insertTileSql);) {
pstmt.setInt(1, z);
pstmt.setInt(2, x);
pstmt.setInt(3, y);
pstmt.setBytes(4, imageBytes);
pstmt.executeUpdate();
return "";
}
});
} | [
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/mbtiles/MBTilesDb.java | MBTilesDb.addTilesInBatch | public synchronized void addTilesInBatch( List<Tile> tilesList ) throws Exception {
database.execOnConnection(connection -> {
boolean autoCommit = connection.getAutoCommit();
connection.setAutoCommit(false);
try (IHMPreparedStatement pstmt = connection.prepareStatement(insertTileSql);) {
for( Tile tile : tilesList ) {
pstmt.setInt(1, tile.z);
pstmt.setInt(2, tile.x);
pstmt.setInt(3, tile.y);
pstmt.setBytes(4, tile.imageBytes);
pstmt.addBatch();
}
pstmt.executeBatch();
return "";
} finally {
connection.setAutoCommit(autoCommit);
}
});
} | java | public synchronized void addTilesInBatch( List<Tile> tilesList ) throws Exception {
database.execOnConnection(connection -> {
boolean autoCommit = connection.getAutoCommit();
connection.setAutoCommit(false);
try (IHMPreparedStatement pstmt = connection.prepareStatement(insertTileSql);) {
for( Tile tile : tilesList ) {
pstmt.setInt(1, tile.z);
pstmt.setInt(2, tile.x);
pstmt.setInt(3, tile.y);
pstmt.setBytes(4, tile.imageBytes);
pstmt.addBatch();
}
pstmt.executeBatch();
return "";
} finally {
connection.setAutoCommit(autoCommit);
}
});
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/mbtiles/MBTilesDb.java | MBTilesDb.getTile | public byte[] getTile( int tx, int tyOsm, int zoom ) throws Exception {
int ty = tyOsm;
if (tileRowType.equals("tms")) {
int[] tmsTileXY = MercatorUtils.osmTile2TmsTile(tx, tyOsm, zoom);
ty = tmsTileXY[1];
}
int _ty = ty;
return database.execOnConnection(connection -> {
try (IHMPreparedStatement statement = connection.prepareStatement(SELECTQUERY)) {
statement.setInt(1, zoom);
statement.setInt(2, tx);
statement.setInt(3, _ty);
IHMResultSet resultSet = statement.executeQuery();
if (resultSet.next()) {
byte[] imageBytes = resultSet.getBytes(1);
return imageBytes;
}
}
return null;
});
} | java | public byte[] getTile( int tx, int tyOsm, int zoom ) throws Exception {
int ty = tyOsm;
if (tileRowType.equals("tms")) {
int[] tmsTileXY = MercatorUtils.osmTile2TmsTile(tx, tyOsm, zoom);
ty = tmsTileXY[1];
}
int _ty = ty;
return database.execOnConnection(connection -> {
try (IHMPreparedStatement statement = connection.prepareStatement(SELECTQUERY)) {
statement.setInt(1, zoom);
statement.setInt(2, tx);
statement.setInt(3, _ty);
IHMResultSet resultSet = statement.executeQuery();
if (resultSet.next()) {
byte[] imageBytes = resultSet.getBytes(1);
return imageBytes;
}
}
return null;
});
} | [
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/dbs/src/main/java/org/hortonmachine/dbs/mbtiles/MBTilesDb.java#L266-L286 | train |
TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/mbtiles/MBTilesDb.java | MBTilesDb.getBounds | public Envelope getBounds() throws Exception {
checkMetadata();
String boundsWSEN = metadataMap.get("bounds");
String[] split = boundsWSEN.split(",");
double w = Double.parseDouble(split[0]);
double s = Double.parseDouble(split[1]);
double e = Double.parseDouble(split[2]);
double n = Double.parseDouble(split[3]);
return new Envelope(w, e, s, n);
} | java | public Envelope getBounds() throws Exception {
checkMetadata();
String boundsWSEN = metadataMap.get("bounds");
String[] split = boundsWSEN.split(",");
double w = Double.parseDouble(split[0]);
double s = Double.parseDouble(split[1]);
double e = Double.parseDouble(split[2]);
double n = Double.parseDouble(split[3]);
return new Envelope(w, e, s, n);
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/mbtiles/MBTilesDb.java | MBTilesDb.getBoundsInTileIndex | public int[] getBoundsInTileIndex( int zoomlevel ) throws Exception {
String sql = "select min(tile_column), max(tile_column), min(tile_row), max(tile_row) from tiles where zoom_level="
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return database.execOnConnection(connection -> {
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int minTx = resultSet.getInt(1);
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int minTy = resultSet.getInt(3);
int maxTy = resultSet.getInt(4);
return new int[]{minTx, maxTx, minTy, maxTy};
}
}
return null;
});
} | java | public int[] getBoundsInTileIndex( int zoomlevel ) throws Exception {
String sql = "select min(tile_column), max(tile_column), min(tile_row), max(tile_row) from tiles where zoom_level="
+ zoomlevel;
return database.execOnConnection(connection -> {
try (IHMStatement statement = connection.createStatement(); IHMResultSet resultSet = statement.executeQuery(sql);) {
if (resultSet.next()) {
int minTx = resultSet.getInt(1);
int maxTx = resultSet.getInt(2);
int minTy = resultSet.getInt(3);
int maxTy = resultSet.getInt(4);
return new int[]{minTx, maxTx, minTy, maxTy};
}
}
return null;
});
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/Compound.java | Compound.out2in | public void out2in(Object from, String from_out, Object... tos) {
for (Object co : tos) {
out2in(from, from_out, co, from_out);
}
} | java | public void out2in(Object from, String from_out, Object... tos) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/Compound.java | Compound.in2in | public void in2in(String in, Object to, String to_in) {
controller.mapIn(in, to, to_in);
} | java | public void in2in(String in, Object to, String to_in) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/Compound.java | Compound.in2in | public void in2in(String in, Object... to) {
for (Object cmd : to) {
in2in(in, cmd, in);
}
} | java | public void in2in(String in, Object... to) {
for (Object cmd : to) {
in2in(in, cmd, in);
}
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/Compound.java | Compound.field2in | public void field2in(Object o, String field, Object to, String to_in) {
controller.mapInField(o, field, to, to_in);
} | java | public void field2in(Object o, String field, Object to, String to_in) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/Compound.java | Compound.field2in | public void field2in(Object o, String field, Object to) {
field = field.trim();
if (field.indexOf(' ') > 0) { // maybe multiple field names given
String[] fields = field.split("\\s+");
for (String f : fields) {
field2in(o, f, to, f);
}
} else {
field2in(o, field, to, field);
}
} | java | public void field2in(Object o, String field, Object to) {
field = field.trim();
if (field.indexOf(' ') > 0) { // maybe multiple field names given
String[] fields = field.split("\\s+");
for (String f : fields) {
field2in(o, f, to, f);
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} else {
field2in(o, field, to, field);
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/Compound.java | Compound.out2field | public void out2field(Object from, String from_out, Object o, String field) {
controller.mapOutField(from, from_out, o, field);
} | java | public void out2field(Object from, String from_out, Object o, String field) {
controller.mapOutField(from, from_out, o, field);
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/Compound.java | Compound.out2field | public void out2field(Object from, String from_out, Object o) {
out2field(from, from_out, o, from_out);
} | java | public void out2field(Object from, String from_out, Object o) {
out2field(from, from_out, o, from_out);
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/Compound.java | Compound.out2out | public void out2out(String out, Object to, String to_out) {
controller.mapOut(out, to, to_out);
} | java | public void out2out(String out, Object to, String to_out) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/Compound.java | Compound.connect | @Deprecated
public void connect(Object from, String from_out, Object to, String to_in) {
controller.connect(from, from_out, to, to_in);
} | java | @Deprecated
public void connect(Object from, String from_out, Object to, String to_in) {
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/check/sequence/SequenceValidationCheck.java | SequenceValidationCheck.reportError | protected void reportError(ValidationResult result, String messageKey,
Object... params) {
reportMessage(result, Severity.ERROR, messageKey, params);
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/check/sequence/SequenceValidationCheck.java | SequenceValidationCheck.reportWarning | protected void reportWarning(ValidationResult result, String messageKey,
Object... params) {
reportMessage(result, Severity.WARNING, messageKey, params);
} | java | protected void reportWarning(ValidationResult result, String messageKey,
Object... params) {
reportMessage(result, Severity.WARNING, messageKey, params);
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/check/sequence/SequenceValidationCheck.java | SequenceValidationCheck.reportMessage | protected void reportMessage(ValidationResult result, Severity severity,
String messageKey, Object... params) {
result.append(EntryValidations.createMessage(origin, severity, messageKey, params));
} | java | protected void reportMessage(ValidationResult result, Severity severity,
String messageKey, Object... params) {
result.append(EntryValidations.createMessage(origin, severity, messageKey, params));
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/insolation/OmsInsolation.java | OmsInsolation.calcInsolation | private void calcInsolation( double lambda, WritableRaster demWR, WritableRaster gradientWR, WritableRaster insolationWR,
int day, double dx ) {
// calculating the day angle
// double dayang = 2 * Math.PI * (day - 1) / 365.0;
double dayangb = (360 / 365.25) * (day - 79.436);
dayangb = Math.toRadians(dayangb);
// Evaluate the declination of the sun.
delta = getDeclination(dayangb);
// Evaluate the radiation in this day.
double ss = Math.acos(-Math.tan(delta) * Math.tan(lambda));
double hour = -ss + (Math.PI / 48.0);
while( hour <= ss - (Math.PI / 48) ) {
omega = hour;
// calculating the vector related to the sun
double sunVector[] = calcSunVector();
double zenith = calcZenith(sunVector[2]);
double[] inverseSunVector = calcInverseSunVector(sunVector);
double[] normalSunVector = calcNormalSunVector(sunVector);
int height = demWR.getHeight();
int width = demWR.getWidth();
WritableRaster sOmbraWR = calculateFactor(height, width, sunVector, inverseSunVector, normalSunVector, demWR, dx);
double mr = 1 / (sunVector[2] + 0.15 * Math.pow((93.885 - zenith), (-1.253)));
for( int j = 0; j < height; j++ ) {
for( int i = 0; i < width; i++ ) {
// evaluate the radiation.
calcRadiation(i, j, demWR, sOmbraWR, insolationWR, sunVector, gradientWR, mr);
}
}
hour = hour + Math.PI / 24.0;
}
} | java | private void calcInsolation( double lambda, WritableRaster demWR, WritableRaster gradientWR, WritableRaster insolationWR,
int day, double dx ) {
// calculating the day angle
// double dayang = 2 * Math.PI * (day - 1) / 365.0;
double dayangb = (360 / 365.25) * (day - 79.436);
dayangb = Math.toRadians(dayangb);
// Evaluate the declination of the sun.
delta = getDeclination(dayangb);
// Evaluate the radiation in this day.
double ss = Math.acos(-Math.tan(delta) * Math.tan(lambda));
double hour = -ss + (Math.PI / 48.0);
while( hour <= ss - (Math.PI / 48) ) {
omega = hour;
// calculating the vector related to the sun
double sunVector[] = calcSunVector();
double zenith = calcZenith(sunVector[2]);
double[] inverseSunVector = calcInverseSunVector(sunVector);
double[] normalSunVector = calcNormalSunVector(sunVector);
int height = demWR.getHeight();
int width = demWR.getWidth();
WritableRaster sOmbraWR = calculateFactor(height, width, sunVector, inverseSunVector, normalSunVector, demWR, dx);
double mr = 1 / (sunVector[2] + 0.15 * Math.pow((93.885 - zenith), (-1.253)));
for( int j = 0; j < height; j++ ) {
for( int i = 0; i < width; i++ ) {
// evaluate the radiation.
calcRadiation(i, j, demWR, sOmbraWR, insolationWR, sunVector, gradientWR, mr);
}
}
hour = hour + Math.PI / 24.0;
}
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/CrsUtilities.java | CrsUtilities.isCrsValid | public static boolean isCrsValid( CoordinateReferenceSystem crs ) {
if (crs instanceof AbstractSingleCRS) {
AbstractSingleCRS aCrs = (AbstractSingleCRS) crs;
Datum datum = aCrs.getDatum();
ReferenceIdentifier name = datum.getName();
String code = name.getCode();
if (code.equalsIgnoreCase("Unknown")) {
return false;
}
}
return true;
} | java | public static boolean isCrsValid( CoordinateReferenceSystem crs ) {
if (crs instanceof AbstractSingleCRS) {
AbstractSingleCRS aCrs = (AbstractSingleCRS) crs;
Datum datum = aCrs.getDatum();
ReferenceIdentifier name = datum.getName();
String code = name.getCode();
if (code.equalsIgnoreCase("Unknown")) {
return false;
}
}
return true;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/CrsUtilities.java | CrsUtilities.writeProjectionFile | @SuppressWarnings("nls")
public static void writeProjectionFile( String filePath, String extention, CoordinateReferenceSystem crs )
throws IOException {
/*
* fill a prj file
*/
String prjPath = null;
if (extention != null && filePath.toLowerCase().endsWith("." + extention)) {
int dotLoc = filePath.lastIndexOf(".");
prjPath = filePath.substring(0, dotLoc);
prjPath = prjPath + ".prj";
} else {
if (!filePath.endsWith(".prj")) {
prjPath = filePath + ".prj";
} else {
prjPath = filePath;
}
}
try (BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(prjPath))) {
bufferedWriter.write(crs.toWKT());
}
} | java | @SuppressWarnings("nls")
public static void writeProjectionFile( String filePath, String extention, CoordinateReferenceSystem crs )
throws IOException {
/*
* fill a prj file
*/
String prjPath = null;
if (extention != null && filePath.toLowerCase().endsWith("." + extention)) {
int dotLoc = filePath.lastIndexOf(".");
prjPath = filePath.substring(0, dotLoc);
prjPath = prjPath + ".prj";
} else {
if (!filePath.endsWith(".prj")) {
prjPath = filePath + ".prj";
} else {
prjPath = filePath;
}
}
try (BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(prjPath))) {
bufferedWriter.write(crs.toWKT());
}
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/CrsUtilities.java | CrsUtilities.reproject | public static void reproject( CoordinateReferenceSystem from, CoordinateReferenceSystem to, Object[] geometries )
throws Exception {
MathTransform mathTransform = CRS.findMathTransform(from, to);
for( int i = 0; i < geometries.length; i++ ) {
geometries[i] = JTS.transform((Geometry) geometries[i], mathTransform);
}
} | java | public static void reproject( CoordinateReferenceSystem from, CoordinateReferenceSystem to, Object[] geometries )
throws Exception {
MathTransform mathTransform = CRS.findMathTransform(from, to);
for( int i = 0; i < geometries.length; i++ ) {
geometries[i] = JTS.transform((Geometry) geometries[i], mathTransform);
}
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/CrsUtilities.java | CrsUtilities.reproject | public static void reproject( CoordinateReferenceSystem from, CoordinateReferenceSystem to, Coordinate[] coordinates )
throws Exception {
MathTransform mathTransform = CRS.findMathTransform(from, to);
for( int i = 0; i < coordinates.length; i++ ) {
coordinates[i] = JTS.transform(coordinates[i], coordinates[i], mathTransform);
}
} | java | public static void reproject( CoordinateReferenceSystem from, CoordinateReferenceSystem to, Coordinate[] coordinates )
throws Exception {
MathTransform mathTransform = CRS.findMathTransform(from, to);
for( int i = 0; i < coordinates.length; i++ ) {
coordinates[i] = JTS.transform(coordinates[i], coordinates[i], mathTransform);
}
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/CrsUtilities.java | CrsUtilities.getMetersAsWGS84 | public static double getMetersAsWGS84( double meters, Coordinate c ) {
GeodeticCalculator gc = new GeodeticCalculator(DefaultGeographicCRS.WGS84);
gc.setStartingGeographicPoint(c.x, c.y);
gc.setDirection(90, meters);
Point2D destinationGeographicPoint = gc.getDestinationGeographicPoint();
double degrees = Math.abs(destinationGeographicPoint.getX() - c.x);
return degrees;
} | java | public static double getMetersAsWGS84( double meters, Coordinate c ) {
GeodeticCalculator gc = new GeodeticCalculator(DefaultGeographicCRS.WGS84);
gc.setStartingGeographicPoint(c.x, c.y);
gc.setDirection(90, meters);
Point2D destinationGeographicPoint = gc.getDestinationGeographicPoint();
double degrees = Math.abs(destinationGeographicPoint.getX() - c.x);
return degrees;
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/r/houghes/HoughCircles.java | HoughCircles.createHoughPixels | private void createHoughPixels( double[][][] houghValues, byte houghPixels[] ) {
double d = -1D;
for( int j = 0; j < height; j++ ) {
for( int k = 0; k < width; k++ ) {
if (houghValues[k][j][0] > d) {
d = houghValues[k][j][0];
}
}
}
for( int l = 0; l < height; l++ ) {
for( int i = 0; i < width; i++ ) {
houghPixels[i + l * width] = (byte) Math.round((houghValues[i][l][0] * 255D) / d);
}
}
} | java | private void createHoughPixels( double[][][] houghValues, byte houghPixels[] ) {
double d = -1D;
for( int j = 0; j < height; j++ ) {
for( int k = 0; k < width; k++ ) {
if (houghValues[k][j][0] > d) {
d = houghValues[k][j][0];
}
}
}
for( int l = 0; l < height; l++ ) {
for( int i = 0; i < width; i++ ) {
houghPixels[i + l * width] = (byte) Math.round((houghValues[i][l][0] * 255D) / d);
}
}
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/r/houghes/HoughCircles.java | HoughCircles.drawCircles | public void drawCircles( double[][][] houghValues, byte[] circlespixels ) {
// Copy original input pixels into output
// circle location display image and
// combine with saturation at 100
int roiaddr = 0;
for( int y = offy; y < offy + height; y++ ) {
for( int x = offx; x < offx + width; x++ ) {
// Copy;
circlespixels[roiaddr] = imageValues[x + offset * y];
// Saturate
if (circlespixels[roiaddr] != 0)
circlespixels[roiaddr] = 100;
else
circlespixels[roiaddr] = 0;
roiaddr++;
}
}
// Copy original image to the circlespixels image.
// Changing pixels values to 100, so that the marked
// circles appears more clear. Must be improved in
// the future to show the resuls in a colored image.
// for(int i = 0; i < width*height ;++i ) {
// if(imageValues[i] != 0 )
// if(circlespixels[i] != 0 )
// circlespixels[i] = 100;
// else
// circlespixels[i] = 0;
// }
// if (centerPoints == null) {
// if (useThreshold)
// getCenterPointsByThreshold(threshold);
// else
Coordinate[] centerPoints = getCenterPoints(houghValues, maxCircles);
// }
byte cor = -1;
// Redefine these so refer to ROI coordinates exclusively
int offset = width;
int offx = 0;
int offy = 0;
for( int l = 0; l < maxCircles; l++ ) {
int i = (int) centerPoints[l].x;
int j = (int) centerPoints[l].y;
// Draw a gray cross marking the center of each circle.
for( int k = -10; k <= 10; ++k ) {
int p = (j + k + offy) * offset + (i + offx);
if (!outOfBounds(j + k + offy, i + offx))
circlespixels[(j + k + offy) * offset + (i + offx)] = cor;
if (!outOfBounds(j + offy, i + k + offx))
circlespixels[(j + offy) * offset + (i + k + offx)] = cor;
}
for( int k = -2; k <= 2; ++k ) {
if (!outOfBounds(j - 2 + offy, i + k + offx))
circlespixels[(j - 2 + offy) * offset + (i + k + offx)] = cor;
if (!outOfBounds(j + 2 + offy, i + k + offx))
circlespixels[(j + 2 + offy) * offset + (i + k + offx)] = cor;
if (!outOfBounds(j + k + offy, i - 2 + offx))
circlespixels[(j + k + offy) * offset + (i - 2 + offx)] = cor;
if (!outOfBounds(j + k + offy, i + 2 + offx))
circlespixels[(j + k + offy) * offset + (i + 2 + offx)] = cor;
}
}
} | java | public void drawCircles( double[][][] houghValues, byte[] circlespixels ) {
// Copy original input pixels into output
// circle location display image and
// combine with saturation at 100
int roiaddr = 0;
for( int y = offy; y < offy + height; y++ ) {
for( int x = offx; x < offx + width; x++ ) {
// Copy;
circlespixels[roiaddr] = imageValues[x + offset * y];
// Saturate
if (circlespixels[roiaddr] != 0)
circlespixels[roiaddr] = 100;
else
circlespixels[roiaddr] = 0;
roiaddr++;
}
}
// Copy original image to the circlespixels image.
// Changing pixels values to 100, so that the marked
// circles appears more clear. Must be improved in
// the future to show the resuls in a colored image.
// for(int i = 0; i < width*height ;++i ) {
// if(imageValues[i] != 0 )
// if(circlespixels[i] != 0 )
// circlespixels[i] = 100;
// else
// circlespixels[i] = 0;
// }
// if (centerPoints == null) {
// if (useThreshold)
// getCenterPointsByThreshold(threshold);
// else
Coordinate[] centerPoints = getCenterPoints(houghValues, maxCircles);
// }
byte cor = -1;
// Redefine these so refer to ROI coordinates exclusively
int offset = width;
int offx = 0;
int offy = 0;
for( int l = 0; l < maxCircles; l++ ) {
int i = (int) centerPoints[l].x;
int j = (int) centerPoints[l].y;
// Draw a gray cross marking the center of each circle.
for( int k = -10; k <= 10; ++k ) {
int p = (j + k + offy) * offset + (i + offx);
if (!outOfBounds(j + k + offy, i + offx))
circlespixels[(j + k + offy) * offset + (i + offx)] = cor;
if (!outOfBounds(j + offy, i + k + offx))
circlespixels[(j + offy) * offset + (i + k + offx)] = cor;
}
for( int k = -2; k <= 2; ++k ) {
if (!outOfBounds(j - 2 + offy, i + k + offx))
circlespixels[(j - 2 + offy) * offset + (i + k + offx)] = cor;
if (!outOfBounds(j + 2 + offy, i + k + offx))
circlespixels[(j + 2 + offy) * offset + (i + k + offx)] = cor;
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circlespixels[(j + k + offy) * offset + (i - 2 + offx)] = cor;
if (!outOfBounds(j + k + offy, i + 2 + offx))
circlespixels[(j + k + offy) * offset + (i + 2 + offx)] = cor;
}
}
} | [
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/entry/sequence/AbstractSequence.java | AbstractSequence.getSequence | public String getSequence(Long beginPosition, Long endPosition)
{
byte[] sequenceByte = getSequenceByte(beginPosition, endPosition);
if (sequenceByte != null)
return new String(sequenceByte);
return null;
} | java | public String getSequence(Long beginPosition, Long endPosition)
{
byte[] sequenceByte = getSequenceByte(beginPosition, endPosition);
if (sequenceByte != null)
return new String(sequenceByte);
return null;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/math/matrixes/SquareMatrix.java | SquareMatrix.set | private void set(Matrix m)
{
this.nRows = this.nCols = Math.min(m.nRows, m.nCols);
this.values = m.values;
} | java | private void set(Matrix m)
{
this.nRows = this.nCols = Math.min(m.nRows, m.nCols);
this.values = m.values;
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/math/matrixes/SquareMatrix.java | SquareMatrix.set | protected void set(double values[][])
{
super.set(values);
nRows = nCols = Math.min(nRows, nCols);
} | java | protected void set(double values[][])
{
super.set(values);
nRows = nCols = Math.min(nRows, nCols);
} | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/PrintUtilities.java | PrintUtilities.printMatrixData | public static void printMatrixData(double[][] matrix) {
int cols = matrix[0].length;
int rows = matrix.length;
for (int r = 0; r < rows; r++) {
for (int c = 0; c < cols; c++) {
printer.print(matrix[r][c]);
printer.print(separator);
}
printer.println();
}
} | java | public static void printMatrixData(double[][] matrix) {
int cols = matrix[0].length;
int rows = matrix.length;
for (int r = 0; r < rows; r++) {
for (int c = 0; c < cols; c++) {
printer.print(matrix[r][c]);
printer.print(separator);
}
printer.println();
}
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/PrintUtilities.java | PrintUtilities.envelope2WKT | public static String envelope2WKT(org.locationtech.jts.geom.Envelope env) {
GeometryFactory gf = GeometryUtilities.gf();
Geometry geometry = gf.toGeometry(env);
return geometry.toText();
} | java | public static String envelope2WKT(org.locationtech.jts.geom.Envelope env) {
GeometryFactory gf = GeometryUtilities.gf();
Geometry geometry = gf.toGeometry(env);
return geometry.toText();
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/sld/RewindableInputStream.java | RewindableInputStream.read | public int read() throws IOException {
int b = 0;
// Byte to be read is already in out buffer, simply returning it
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return fData[fOffset++] & 0xff;
}
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* This situation is not handled currently.
*/
if (fOffset == fEndOffset) {
return -1;
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/*
* Ok, we should actually read data from underlying stream, but
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*/
if (fOffset == fData.length) {
byte[] newData = new byte[fOffset << 1];
System.arraycopy(fData, 0, newData, 0, fOffset);
fData = newData;
}
// Reading byte from the underlying stream, storing it in buffer and
// then returning it.
b = fInputStream.read();
if (b == -1) {
fEndOffset = fOffset;
return -1;
}
fData[fLength++] = (byte) b;
fOffset++;
return b & 0xff;
} | java | public int read() throws IOException {
int b = 0;
// Byte to be read is already in out buffer, simply returning it
if (fOffset < fLength) {
return fData[fOffset++] & 0xff;
}
/*
* End of the stream is reached.
* I also believe that in certain cases fOffset can point to the
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* This situation is not handled currently.
*/
if (fOffset == fEndOffset) {
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}
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*/
if (fOffset == fData.length) {
byte[] newData = new byte[fOffset << 1];
System.arraycopy(fData, 0, newData, 0, fOffset);
fData = newData;
}
// Reading byte from the underlying stream, storing it in buffer and
// then returning it.
b = fInputStream.read();
if (b == -1) {
fEndOffset = fOffset;
return -1;
}
fData[fLength++] = (byte) b;
fOffset++;
return b & 0xff;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/style/sld/RewindableInputStream.java | RewindableInputStream.close | public void close() throws IOException {
if (fInputStream != null) {
fInputStream.close();
fInputStream = null;
fData = null;
}
} | java | public void close() throws IOException {
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/translation/TranslationResult.java | TranslationResult.getTranslation | public String getTranslation() {
if (codons == null) {
return "";
}
StringBuilder translation = new StringBuilder();
for (Codon codon : codons) {
translation.append(codon.getAminoAcid());
}
return translation.toString();
} | java | public String getTranslation() {
if (codons == null) {
return "";
}
StringBuilder translation = new StringBuilder();
for (Codon codon : codons) {
translation.append(codon.getAminoAcid());
}
return translation.toString();
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/translation/TranslationResult.java | TranslationResult.getConceptualTranslation | public String getConceptualTranslation() {
if (codons == null) {
return "";
}
StringBuilder translation = new StringBuilder();
for (int i = 0 ; i < conceptualTranslationCodons ; ++i) {
Codon codon = codons.get(i);
translation.append(codon.getAminoAcid());
}
return translation.toString();
} | java | public String getConceptualTranslation() {
if (codons == null) {
return "";
}
StringBuilder translation = new StringBuilder();
for (int i = 0 ; i < conceptualTranslationCodons ; ++i) {
Codon codon = codons.get(i);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/r/filter/OmsKernelFilter.java | OmsKernelFilter.gaussianSmooth | public static double[] gaussianSmooth( double[] values, int kernelRadius ) throws Exception {
int size = values.length;
double[] newValues = new double[values.length];
double[] kernelData2D = makeGaussianKernel(kernelRadius);
for( int i = 0; i < kernelRadius; i++ ) {
newValues[i] = values[i];
}
for( int r = kernelRadius; r < size - kernelRadius; r++ ) {
double kernelSum = 0.0;
double outputValue = 0.0;
int k = 0;
for( int kc = -kernelRadius; kc <= kernelRadius; kc++, k++ ) {
double value = values[r + kc];
if (!isNovalue(value)) {
outputValue = outputValue + value * kernelData2D[k];
kernelSum = kernelSum + kernelData2D[k];
}
}
newValues[r] = outputValue / kernelSum;
}
for( int i = size - kernelRadius; i < size; i++ ) {
newValues[i] = values[i];
}
return newValues;
} | java | public static double[] gaussianSmooth( double[] values, int kernelRadius ) throws Exception {
int size = values.length;
double[] newValues = new double[values.length];
double[] kernelData2D = makeGaussianKernel(kernelRadius);
for( int i = 0; i < kernelRadius; i++ ) {
newValues[i] = values[i];
}
for( int r = kernelRadius; r < size - kernelRadius; r++ ) {
double kernelSum = 0.0;
double outputValue = 0.0;
int k = 0;
for( int kc = -kernelRadius; kc <= kernelRadius; kc++, k++ ) {
double value = values[r + kc];
if (!isNovalue(value)) {
outputValue = outputValue + value * kernelData2D[k];
kernelSum = kernelSum + kernelData2D[k];
}
}
newValues[r] = outputValue / kernelSum;
}
for( int i = size - kernelRadius; i < size; i++ ) {
newValues[i] = values[i];
}
return newValues;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/r/filter/OmsKernelFilter.java | OmsKernelFilter.averageSmooth | public static double[] averageSmooth( double[] values, int lookAhead ) throws Exception {
int size = values.length;
double[] newValues = new double[values.length];
for( int i = 0; i < lookAhead; i++ ) {
newValues[i] = values[i];
}
for( int i = lookAhead; i < size - lookAhead; i++ ) {
double sum = 0.0;
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}
}
newValues[i] = sum / k;
}
for( int i = size - lookAhead; i < size; i++ ) {
newValues[i] = values[i];
}
return newValues;
} | java | public static double[] averageSmooth( double[] values, int lookAhead ) throws Exception {
int size = values.length;
double[] newValues = new double[values.length];
for( int i = 0; i < lookAhead; i++ ) {
newValues[i] = values[i];
}
for( int i = lookAhead; i < size - lookAhead; i++ ) {
double sum = 0.0;
int k = 0;
for( int l = -lookAhead; l <= lookAhead; l++ ) {
double value = values[i + l];
if (!isNovalue(value)) {
sum = sum + value;
k++;
}
}
newValues[i] = sum / k;
}
for( int i = size - lookAhead; i < size; i++ ) {
newValues[i] = values[i];
}
return newValues;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/ENU.java | ENU.wgs84ToEnu | public Coordinate wgs84ToEnu( Coordinate cLL ) {
checkZ(cLL);
Coordinate cEcef = wgs84ToEcef(cLL);
Coordinate enu = ecefToEnu(cEcef);
return enu;
} | java | public Coordinate wgs84ToEnu( Coordinate cLL ) {
checkZ(cLL);
Coordinate cEcef = wgs84ToEcef(cLL);
Coordinate enu = ecefToEnu(cEcef);
return enu;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/ENU.java | ENU.enuToWgs84 | public Coordinate enuToWgs84( Coordinate enu ) {
checkZ(enu);
Coordinate cEcef = enuToEcef(enu);
Coordinate wgs84 = ecefToWgs84(cEcef);
return wgs84;
} | java | public Coordinate enuToWgs84( Coordinate enu ) {
checkZ(enu);
Coordinate cEcef = enuToEcef(enu);
Coordinate wgs84 = ecefToWgs84(cEcef);
return wgs84;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/ENU.java | ENU.convertGeometryFromEnuToWgs84 | public void convertGeometryFromEnuToWgs84( Geometry geometryEnu ) {
Coordinate[] coordinates = geometryEnu.getCoordinates();
for( int i = 0; i < coordinates.length; i++ ) {
Coordinate wgs84 = enuToWgs84(coordinates[i]);
coordinates[i].x = wgs84.x;
coordinates[i].y = wgs84.y;
coordinates[i].z = wgs84.z;
}
} | java | public void convertGeometryFromEnuToWgs84( Geometry geometryEnu ) {
Coordinate[] coordinates = geometryEnu.getCoordinates();
for( int i = 0; i < coordinates.length; i++ ) {
Coordinate wgs84 = enuToWgs84(coordinates[i]);
coordinates[i].x = wgs84.x;
coordinates[i].y = wgs84.y;
coordinates[i].z = wgs84.z;
}
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/ENU.java | ENU.convertGeometryFromWgsToEnu | public void convertGeometryFromWgsToEnu( Geometry geometryWgs ) {
Coordinate[] coordinates = geometryWgs.getCoordinates();
for( int i = 0; i < coordinates.length; i++ ) {
Coordinate enu = wgs84ToEnu(coordinates[i]);
coordinates[i].x = enu.x;
coordinates[i].y = enu.y;
coordinates[i].z = enu.z;
}
} | java | public void convertGeometryFromWgsToEnu( Geometry geometryWgs ) {
Coordinate[] coordinates = geometryWgs.getCoordinates();
for( int i = 0; i < coordinates.length; i++ ) {
Coordinate enu = wgs84ToEnu(coordinates[i]);
coordinates[i].x = enu.x;
coordinates[i].y = enu.y;
coordinates[i].z = enu.z;
}
} | [
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... | Converts a geometry from WGS to ENU.
<p>Note that the geometry is internally converted. Use clone() if you need a copy.</p>
@param geometryWgs | [
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/gears/src/main/java/org/hortonmachine/gears/utils/ENU.java#L249-L257 | train |
TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/ENU.java | ENU.convertEnvelopeFromWgsToEnu | public Envelope convertEnvelopeFromWgsToEnu( Envelope envelopeWgs ) {
Polygon polygonEnu = GeometryUtilities.createPolygonFromEnvelope(envelopeWgs);
convertGeometryFromWgsToEnu(polygonEnu);
Envelope envelopeEnu = polygonEnu.getEnvelopeInternal();
return envelopeEnu;
} | java | public Envelope convertEnvelopeFromWgsToEnu( Envelope envelopeWgs ) {
Polygon polygonEnu = GeometryUtilities.createPolygonFromEnvelope(envelopeWgs);
convertGeometryFromWgsToEnu(polygonEnu);
Envelope envelopeEnu = polygonEnu.getEnvelopeInternal();
return envelopeEnu;
} | [
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... | Converts an envelope from WGS to ENU.
@param envelopeWgs
@return the converted envelope. | [
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/gears/src/main/java/org/hortonmachine/gears/utils/ENU.java#L265-L270 | train |
TheHortonMachine/hortonmachine | apps/src/main/java/org/hortonmachine/nww/gui/NwwPanel.java | NwwPanel.goTo | public synchronized Position goTo( Double lon, Double lat, Double elev, Double azimuth, boolean animate ) {
View view = getWwd().getView();
view.stopAnimations();
view.stopMovement();
Position eyePosition;
if (lon == null || lat == null) {
Position currentEyePosition = wwd.getView().getCurrentEyePosition();
if (currentEyePosition != null) {
lat = currentEyePosition.latitude.degrees;
lon = currentEyePosition.longitude.degrees;
} else {
return null;
}
}
if (elev == null) {
// use the current
elev = wwd.getView().getCurrentEyePosition().getAltitude();
}
if (Double.isNaN(elev)) {
if (!Double.isNaN(lastElevation)) {
elev = lastElevation;
} else {
elev = NwwUtilities.DEFAULT_ELEV;
}
}
eyePosition = NwwUtilities.toPosition(lat, lon, elev);
if (animate) {
view.goTo(eyePosition, elev);
} else {
view.setEyePosition(eyePosition);
}
if (azimuth != null) {
Angle heading = Angle.fromDegrees(azimuth);
view.setHeading(heading);
}
lastElevation = elev;
return eyePosition;
} | java | public synchronized Position goTo( Double lon, Double lat, Double elev, Double azimuth, boolean animate ) {
View view = getWwd().getView();
view.stopAnimations();
view.stopMovement();
Position eyePosition;
if (lon == null || lat == null) {
Position currentEyePosition = wwd.getView().getCurrentEyePosition();
if (currentEyePosition != null) {
lat = currentEyePosition.latitude.degrees;
lon = currentEyePosition.longitude.degrees;
} else {
return null;
}
}
if (elev == null) {
// use the current
elev = wwd.getView().getCurrentEyePosition().getAltitude();
}
if (Double.isNaN(elev)) {
if (!Double.isNaN(lastElevation)) {
elev = lastElevation;
} else {
elev = NwwUtilities.DEFAULT_ELEV;
}
}
eyePosition = NwwUtilities.toPosition(lat, lon, elev);
if (animate) {
view.goTo(eyePosition, elev);
} else {
view.setEyePosition(eyePosition);
}
if (azimuth != null) {
Angle heading = Angle.fromDegrees(azimuth);
view.setHeading(heading);
}
lastElevation = elev;
return eyePosition;
} | [
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"vie... | Move to a given location.
@param lon
the longitude.
@param lat
the latitude.
@param elev
the eye elevation.
@param azimuth
if supplied, the map is rotated to follow that angle.
@param animate
if <code>true</code>, it animates to the position. | [
"Move",
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/apps/src/main/java/org/hortonmachine/nww/gui/NwwPanel.java#L208-L247 | train |
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