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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/r/cutout/OmsCutOut.java | OmsCutOut.cut | public static GridCoverage2D cut( GridCoverage2D raster, GridCoverage2D mask ) throws Exception {
OmsCutOut cutDrain = new OmsCutOut();
cutDrain.inRaster = raster;
cutDrain.inMask = mask;
cutDrain.process();
return cutDrain.outRaster;
} | java | public static GridCoverage2D cut( GridCoverage2D raster, GridCoverage2D mask ) throws Exception {
OmsCutOut cutDrain = new OmsCutOut();
cutDrain.inRaster = raster;
cutDrain.inMask = mask;
cutDrain.process();
return cutDrain.outRaster;
} | [
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/ValidationResult.java | ValidationResult.addMessage | private void addMessage(ValidationMessage<Origin> message) {
if (message == null) {
return;
}
if( null != defaultOrigin ) {
message.addOrigin( defaultOrigin );
}
this.messages.add(message);
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if (message == null) {
return;
}
if( null != defaultOrigin ) {
message.addOrigin( defaultOrigin );
}
this.messages.add(message);
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/ValidationResult.java | ValidationResult.count | public int count(Severity severity) {
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return result;
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for (ValidationMessage<Origin> message : messages) {
if (severity.equals(message.getSeverity())) {
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return result;
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int result = 0;
if (severity == null) {
return result;
}
for (ValidationMessage<Origin> message : messages) {
if (severity.equals(message.getSeverity())) {
result++;
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return result;
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/ValidationResult.java | ValidationResult.removeMessage | public void removeMessage(String messageId) {
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for (ValidationMessage<Origin> message : messages) {
if (messageId.equals(message.getMessageKey())) {
toRemove.add(message);
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Collection<ValidationMessage<Origin>> toRemove = new ArrayList<ValidationMessage<Origin>>();
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if (messageId.equals(message.getMessageKey())) {
toRemove.add(message);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/io/las/index/strtree/BoundablePair.java | BoundablePair.compareTo | public int compareTo( Object o ) {
BoundablePair nd = (BoundablePair) o;
if (distance < nd.distance)
return -1;
if (distance > nd.distance)
return 1;
return 0;
} | java | public int compareTo( Object o ) {
BoundablePair nd = (BoundablePair) o;
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return -1;
if (distance > nd.distance)
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return 0;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/math/interpolation/splines/Bspline.java | Bspline.b | double b( int i, double t ) {
switch( i ) {
case -2:
return (((-t + 3) * t - 3) * t + 1) / 6;
case -1:
return (((3 * t - 6) * t) * t + 4) / 6;
case 0:
return (((-3 * t + 3) * t + 3) * t + 1) / 6;
case 1:
return (t * t * t) / 6;
... | java | double b( int i, double t ) {
switch( i ) {
case -2:
return (((-t + 3) * t - 3) * t + 1) / 6;
case -1:
return (((3 * t - 6) * t) * t + 4) / 6;
case 0:
return (((-3 * t + 3) * t + 3) * t + 1) / 6;
case 1:
return (t * t * t) / 6;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/math/interpolation/splines/Bspline.java | Bspline.p | private Coordinate p( int i, double t ) {
double px = 0;
double py = 0;
for( int j = -2; j <= 1; j++ ) {
Coordinate coordinate = pts.get(i + j);
px += b(j, t) * coordinate.x;
py += b(j, t) * coordinate.y;
}
return new Coordinate(px, py);
} | java | private Coordinate p( int i, double t ) {
double px = 0;
double py = 0;
for( int j = -2; j <= 1; j++ ) {
Coordinate coordinate = pts.get(i + j);
px += b(j, t) * coordinate.x;
py += b(j, t) * coordinate.y;
}
return new Coordinate(px, py);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/sorting/OddEvenSortAlgorithm.java | OddEvenSortAlgorithm.oddEvenSort | public static void oddEvenSort( List<Double> listToBeSorted, List<Double> listThatFollowsTheSort ) {
for( int i = 0; i < listToBeSorted.size() / 2; i++ ) {
for( int j = 0; j + 1 < listToBeSorted.size(); j += 2 )
if (listToBeSorted.get(j) > listToBeSorted.get(j + 1)) {
... | java | public static void oddEvenSort( List<Double> listToBeSorted, List<Double> listThatFollowsTheSort ) {
for( int i = 0; i < listToBeSorted.size() / 2; i++ ) {
for( int j = 0; j + 1 < listToBeSorted.size(); j += 2 )
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... | [
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/math/integration/SimpsonIntegral.java | SimpsonIntegral.simpson | protected double simpson() {
double s = 0f;
double st = 0f;
double ost = 0f;
double os = 0f;
for( int i = 1; i < maxsteps; i++ ) {
st = trapezoid(i);
s = (4f * st - ost) / 3f;
if (i > 5) {
if (Math.abs(s - os) < accuracy * Ma... | java | protected double simpson() {
double s = 0f;
double st = 0f;
double ost = 0f;
double os = 0f;
for( int i = 1; i < maxsteps; i++ ) {
st = trapezoid(i);
s = (4f * st - ost) / 3f;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/math/integration/SimpsonIntegral.java | SimpsonIntegral.trapezoid | protected double trapezoid( int n ) {
double x = 0;
double tnm = 0;
double sum = 0;
double del = 0;
int it = 0;
int j = 0;
if (n == 1) {
strapezoid = 0.5f * (upperlimit - lowerlimit)
* (equation(lowerlimit) + equation(upperlimit));... | java | protected double trapezoid( int n ) {
double x = 0;
double tnm = 0;
double sum = 0;
double del = 0;
int it = 0;
int j = 0;
if (n == 1) {
strapezoid = 0.5f * (upperlimit - lowerlimit)
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/utils/MercatorUtils.java | MercatorUtils.tileLatLonBounds | public static double[] tileLatLonBounds( int tx, int ty, int zoom, int tileSize ) {
double[] bounds = tileBounds3857(tx, ty, zoom, tileSize);
double[] mins = metersToLatLon(bounds[0], bounds[1]);
double[] maxs = metersToLatLon(bounds[2], bounds[3]);
return new double[]{mins[1], maxs[0], ... | java | public static double[] tileLatLonBounds( int tx, int ty, int zoom, int tileSize ) {
double[] bounds = tileBounds3857(tx, ty, zoom, tileSize);
double[] mins = metersToLatLon(bounds[0], bounds[1]);
double[] maxs = metersToLatLon(bounds[2], bounds[3]);
return new double[]{mins[1], maxs[0], ... | [
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/utils/MercatorUtils.java | MercatorUtils.metersYToLatitude | public static double metersYToLatitude( double y ) {
return Math.toDegrees(Math.atan(Math.sinh(y / EQUATORIALRADIUS)));
} | java | public static double metersYToLatitude( double y ) {
return Math.toDegrees(Math.atan(Math.sinh(y / EQUATORIALRADIUS)));
} | [
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/postgis/PostgisDb.java | PostgisDb.addGeometryXYColumnAndIndex | public void addGeometryXYColumnAndIndex( String tableName, String geomColName, String geomType, String epsg,
boolean avoidIndex ) throws Exception {
String epsgStr = "4326";
if (epsg != null) {
epsgStr = epsg;
}
String geomTypeStr = "LINESTRING";
if (geomT... | java | public void addGeometryXYColumnAndIndex( String tableName, String geomColName, String geomType, String epsg,
boolean avoidIndex ) throws Exception {
String epsgStr = "4326";
if (epsg != null) {
epsgStr = epsg;
}
String geomTypeStr = "LINESTRING";
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/r/tmsgenerator/MBTilesHelper.java | MBTilesHelper.getTile | public BufferedImage getTile( int x, int y, int z ) throws Exception {
try (PreparedStatement statement = connection.prepareStatement(SELECTQUERY)) {
statement.setInt(1, z);
statement.setInt(2, x);
statement.setInt(3, y);
ResultSet resultSet = statement.executeQue... | java | public BufferedImage getTile( int x, int y, int z ) throws Exception {
try (PreparedStatement statement = connection.prepareStatement(SELECTQUERY)) {
statement.setInt(1, z);
statement.setInt(2, x);
statement.setInt(3, y);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/r/tmsgenerator/MBTilesHelper.java | MBTilesHelper.readGridcoverageImageForTile | public static BufferedImage readGridcoverageImageForTile( AbstractGridCoverage2DReader reader, int x, int y, int zoom,
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double north = tile2lat(y, zoom);
double south = tile2lat(y + 1, zoom);
double west = tile2lon(x, zoom);... | java | public static BufferedImage readGridcoverageImageForTile( AbstractGridCoverage2DReader reader, int x, int y, int zoom,
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/utils/BinaryFast.java | BinaryFast.convertToArray | public int[] convertToArray() {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/utils/BinaryFast.java | BinaryFast.generatePixels | public void generatePixels( HashSet<Point> pix ) {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/utils/BinaryFast.java | BinaryFast.convertToPixels | public void convertToPixels( HashSet<Point> pix ) {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/utils/BinaryFast.java | BinaryFast.generateForegroundEdge | public void generateForegroundEdge() {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/utils/BinaryFast.java | BinaryFast.generateBackgroundEdgeFromForegroundEdge | public void generateBackgroundEdgeFromForegroundEdge() {
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backgroundEdgePixels.clear();
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/CSVParser.java | CSVParser.nextValue | public String nextValue() throws IOException {
Token tkn = nextToken();
String ret = null;
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String ret = null;
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/CSVParser.java | CSVParser.getLine | public String[] getLine() throws IOException {
String[] ret = EMPTY_STRING_ARRAY;
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/CSVParser.java | CSVParser.nextToken | Token nextToken(Token tkn) throws IOException {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/CSVParser.java | CSVParser.simpleTokenLexer | private Token simpleTokenLexer(Token tkn, int c) throws IOException {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/CSVParser.java | CSVParser.encapsulatedTokenLexer | private Token encapsulatedTokenLexer(Token tkn, int c) throws IOException {
// save current line
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/CSVParser.java | CSVParser.unicodeEscapeLexer | protected int unicodeEscapeLexer(int c) throws IOException {
int ret = 0;
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/CSVParser.java | CSVParser.isEndOfLine | private boolean isEndOfLine(int c) throws IOException {
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return (c == '\n');
} | java | private boolean isEndOfLine(int c) throws IOException {
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/skyview/OmsSkyview.java | OmsSkyview.skyviewfactor | private WritableRaster skyviewfactor( WritableRaster pitWR, double res ) {
/*
* evalutating the normal vector (in the center of the square compound
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*/
normalVectorWR = normalVector(pitWR, res);
WritableRaster skyviewFactorWR = CoverageUtilities.createW... | java | private WritableRaster skyviewfactor( WritableRaster pitWR, double res ) {
/*
* evalutating the normal vector (in the center of the square compound
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normalVectorWR = normalVector(pitWR, res);
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/skyview/OmsSkyview.java | OmsSkyview.shadow | protected WritableRaster shadow( int x, int y, WritableRaster tmpWR, WritableRaster pitWR, double res,
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double zcompare = -Double.MAX_VALUE;
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double dy ... | java | protected WritableRaster shadow( int x, int y, WritableRaster tmpWR, WritableRaster pitWR, double res,
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/adige/core/MonitoringPoint.java | MonitoringPoint.connectIfPossible | public boolean connectIfPossible( MonitoringPoint monitoringPoint ) {
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/adige/core/MonitoringPoint.java | MonitoringPoint.getRelatedMonitoringPoint | public MonitoringPoint getRelatedMonitoringPoint( String pfafStetter ) {
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/adige/core/MonitoringPoint.java | MonitoringPoint.toFeatureCollection | public SimpleFeatureCollection toFeatureCollection(
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TheHortonMachine/hortonmachine | dbs/src/main/java/jsqlite/Blob.java | BlobR.skip | public long skip(long n) throws IOException {
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ret = 0;
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TheHortonMachine/hortonmachine | dbs/src/main/java/jsqlite/Blob.java | BlobR.read | public int read() throws IOException {
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TheHortonMachine/hortonmachine | dbs/src/main/java/jsqlite/Blob.java | BlobR.read | public int read(byte b[], int off, int len) throws IOException {
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/dbs/rasterlite/Rasterlite2Db.java | Rasterlite2Db.getRasterCoverages | public List<Rasterlite2Coverage> getRasterCoverages( boolean doOrder ) throws Exception {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/io/dxfdwg/libs/dwg/objects/DwgEndblk.java | DwgEndblk.readDwgEndblkV15 | public void readDwgEndblkV15(int[] data, int offset) throws Exception {
int bitPos = offset;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/features/FilterUtilities.java | FilterUtilities.getBboxFilter | public static Filter getBboxFilter( String attribute, BoundingBox bbox ) throws CQLException {
double w = bbox.getMinX();
double e = bbox.getMaxX();
double s = bbox.getMinY();
double n = bbox.getMaxY();
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double w = bbox.getMinX();
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/features/FilterUtilities.java | FilterUtilities.getBboxFilter | public static Filter getBboxFilter( String attribute, double west, double east, double south, double north )
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/features/FilterUtilities.java | FilterUtilities.getIntersectsGeometryFilter | public static Filter getIntersectsGeometryFilter( String geomName, Geometry geometry ) throws CQLException {
Filter result = CQL.toFilter("INTERSECTS(" + geomName + ", " + geometry.toText() + " )");
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/ngmf/util/cosu/DDS.java | DDS.neigh_value | private double neigh_value(double x_cur, double x_min, double x_max, double r) {
double ranval, zvalue, new_value;
double work3, work2 = 0, work1 = 0;
double x_range = x_max - x_min;
// ------------ generate a standard normal random variate (zvalue) -------------------
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double ranval, zvalue, new_value;
double work3, work2 = 0, work1 = 0;
double x_range = x_max - x_min;
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/hydrogeomorphology/hillshade/OmsHillshade.java | OmsHillshade.calchillshade | private void calchillshade( WritableRaster pitWR, WritableRaster hillshadeWR, WritableRaster gradientWR, double dx ) {
pAzimuth = Math.toRadians(pAzimuth);
pElev = Math.toRadians(pElev);
double[] sunVector = calcSunVector();
double[] normalSunVector = calcNormalSunVector(sunVector);
... | java | private void calchillshade( WritableRaster pitWR, WritableRaster hillshadeWR, WritableRaster gradientWR, double dx ) {
pAzimuth = Math.toRadians(pAzimuth);
pElev = Math.toRadians(pElev);
double[] sunVector = calcSunVector();
double[] normalSunVector = calcNormalSunVector(sunVector);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/coverage/ProfilePoint.java | ProfilePoint.getMeanSlope | public static double getMeanSlope( List<ProfilePoint> points ) {
double meanSlope = 0;
int num = 0;
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double dx = p2.progressive - p1.progressi... | java | public static double getMeanSlope( List<ProfilePoint> points ) {
double meanSlope = 0;
int num = 0;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/coverage/ProfilePoint.java | ProfilePoint.getLastVisiblePointData | public static double[] getLastVisiblePointData( List<ProfilePoint> profile ) {
if (profile.size() < 2) {
throw new IllegalArgumentException("A profile needs to have at least 2 points.");
}
ProfilePoint first = profile.get(0);
double baseElev = first.getElevation();
Co... | java | public static double[] getLastVisiblePointData( List<ProfilePoint> profile ) {
if (profile.size() < 2) {
throw new IllegalArgumentException("A profile needs to have at least 2 points.");
}
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double baseElev = first.getElevation();
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/validation/check/sourcefeature/SourceFeatureQualifierCheck.java | SourceFeatureQualifierCheck.checkMetagenomeSource | private void checkMetagenomeSource(Origin origin, SourceFeature source) {
List<Qualifier> metagenomeSourceQual = source.getQualifiers(Qualifier.METAGENOME_SOURCE_QUALIFIER_NAME);
if(metagenomeSourceQual != null && !metagenomeSourceQual.isEmpty()) {
Qualifier envSample = source.getSingleQualifier(Qualifier.ENVIR... | java | private void checkMetagenomeSource(Origin origin, SourceFeature source) {
List<Qualifier> metagenomeSourceQual = source.getQualifiers(Qualifier.METAGENOME_SOURCE_QUALIFIER_NAME);
if(metagenomeSourceQual != null && !metagenomeSourceQual.isEmpty()) {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/images/ImageGenerator.java | ImageGenerator.addFeaturePath | public void addFeaturePath( String featurePath, String filter ) {
if (!featurePaths.contains(featurePath)) {
featurePaths.add(featurePath);
if (filter == null) {
filter = "";
}
featureFilter.add(filter);
}
} | java | public void addFeaturePath( String featurePath, String filter ) {
if (!featurePaths.contains(featurePath)) {
featurePaths.add(featurePath);
if (filter == null) {
filter = "";
}
featureFilter.add(filter);
}
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/images/ImageGenerator.java | ImageGenerator.drawImageWithNewMapContent | public BufferedImage drawImageWithNewMapContent( ReferencedEnvelope ref, int imageWidth, int imageHeight, double buffer ) {
MapContent content = new MapContent();
content.setTitle("dump");
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content.getViewport().setCoordinateReferenceSystem(forceCrs);
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content.setTitle("dump");
if (forceCrs != null) {
content.getViewport().setCoordinateReferenceSystem(forceCrs);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/images/ImageGenerator.java | ImageGenerator.dumpPngImage | public void dumpPngImage( String imagePath, ReferencedEnvelope bounds, int imageWidth, int imageHeight, double buffer,
int[] rgbCheck ) throws IOException {
BufferedImage dumpImage = drawImageWithNewMapContent(bounds, imageWidth, imageHeight, buffer);
boolean dumpIt = true;
if (rgbCh... | java | public void dumpPngImage( String imagePath, ReferencedEnvelope bounds, int imageWidth, int imageHeight, double buffer,
int[] rgbCheck ) throws IOException {
BufferedImage dumpImage = drawImageWithNewMapContent(bounds, imageWidth, imageHeight, buffer);
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/images/ImageGenerator.java | ImageGenerator.dumpPngImageForScaleAndPaper | public void dumpPngImageForScaleAndPaper( String imagePath, ReferencedEnvelope bounds, double scale, EPaperFormat paperFormat,
Double dpi, BufferedImage legend, int legendX, int legendY, String scalePrefix, float scaleSize, int scaleX,
int scaleY ) throws Exception {
if (dpi == null) {
... | java | public void dumpPngImageForScaleAndPaper( String imagePath, ReferencedEnvelope bounds, double scale, EPaperFormat paperFormat,
Double dpi, BufferedImage legend, int legendX, int legendY, String scalePrefix, float scaleSize, int scaleX,
int scaleY ) throws Exception {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/clustering/GvmSpace.java | GvmSpace.distance | public double distance(Object pt1, Object pt2) {
Object p = newCopy(pt1);
subtract(p, pt2);
return magnitude(p);
} | java | public double distance(Object pt1, Object pt2) {
Object p = newCopy(pt1);
subtract(p, pt2);
return magnitude(p);
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/demmanipulation/pitfiller/OmsDePitter.java | OmsDePitter.makeCellsFlowReady | private void makeCellsFlowReady( int iteration, GridNode pitfillExitNode, List<GridNode> cellsToMakeFlowReady,
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iteration++;
double exitElevation = pitfillExitNode.elevation;
List<GridNode> connected = new ArrayL... | java | private void makeCellsFlowReady( int iteration, GridNode pitfillExitNode, List<GridNode> cellsToMakeFlowReady,
BitMatrix allPitsPositions, WritableRandomIter pitIter, float delta ) {
iteration++;
double exitElevation = pitfillExitNode.elevation;
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TheHortonMachine/hortonmachine | lesto/src/main/java/org/hortonmachine/lesto/modules/raster/adaptivetinfilter/TinHandler.java | TinHandler.setStartCoordinates | public void setStartCoordinates( List<Coordinate> coordinateList ) {
generateTin(coordinateList);
for( int i = 0; i < tinGeometries.length; i++ ) {
Coordinate[] coordinates = tinGeometries[i].getCoordinates();
if (!tinCoordinateList.contains(coordinates[0])) {
tin... | java | public void setStartCoordinates( List<Coordinate> coordinateList ) {
generateTin(coordinateList);
for( int i = 0; i < tinGeometries.length; i++ ) {
Coordinate[] coordinates = tinGeometries[i].getCoordinates();
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tin... | [
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TheHortonMachine/hortonmachine | lesto/src/main/java/org/hortonmachine/lesto/modules/raster/adaptivetinfilter/TinHandler.java | TinHandler.filterOnAllData | public void filterOnAllData( final ALasDataManager lasHandler ) throws Exception {
final ConcurrentSkipListSet<Double> angleSet = new ConcurrentSkipListSet<Double>();
final ConcurrentSkipListSet<Double> distanceSet = new ConcurrentSkipListSet<Double>();
if (isFirstStatsCalculation) {
... | java | public void filterOnAllData( final ALasDataManager lasHandler ) throws Exception {
final ConcurrentSkipListSet<Double> angleSet = new ConcurrentSkipListSet<Double>();
final ConcurrentSkipListSet<Double> distanceSet = new ConcurrentSkipListSet<Double>();
if (isFirstStatsCalculation) {
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TheHortonMachine/hortonmachine | lesto/src/main/java/org/hortonmachine/lesto/modules/raster/adaptivetinfilter/TinHandler.java | TinHandler.generateTin | private void generateTin( List<Coordinate> coordinateList ) {
pm.beginTask("Generate tin...", -1);
DelaunayTriangulationBuilder b = new DelaunayTriangulationBuilder();
b.setSites(coordinateList);
Geometry tinTriangles = b.getTriangles(gf);
tinGeometries = new Geometry[tinTriangle... | java | private void generateTin( List<Coordinate> coordinateList ) {
pm.beginTask("Generate tin...", -1);
DelaunayTriangulationBuilder b = new DelaunayTriangulationBuilder();
b.setSites(coordinateList);
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TheHortonMachine/hortonmachine | lesto/src/main/java/org/hortonmachine/lesto/modules/raster/adaptivetinfilter/TinHandler.java | TinHandler.generateTinIndex | public STRtree generateTinIndex( Double maxEdgeLength ) {
double maxEdge = maxEdgeLength != null ? maxEdgeLength : 0.0;
pm.beginTask("Creating tin indexes...", tinGeometries.length);
final STRtree tinTree = new STRtree(tinGeometries.length);
for( Geometry geometry : tinGeometries ) {
... | java | public STRtree generateTinIndex( Double maxEdgeLength ) {
double maxEdge = maxEdgeLength != null ? maxEdgeLength : 0.0;
pm.beginTask("Creating tin indexes...", tinGeometries.length);
final STRtree tinTree = new STRtree(tinGeometries.length);
for( Geometry geometry : tinGeometries ) {
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TheHortonMachine/hortonmachine | lesto/src/main/java/org/hortonmachine/lesto/modules/raster/adaptivetinfilter/TinHandler.java | TinHandler.getOrderedNodes | private Coordinate[] getOrderedNodes( Coordinate c, Coordinate coordinate1, Coordinate coordinate2, Coordinate coordinate3 ) {
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Coordinate nearest = coordinate1;
Coordinate c2 = coordinate2;
Coordinate c3 = coordinate3;
double d2 = dis... | java | private Coordinate[] getOrderedNodes( Coordinate c, Coordinate coordinate1, Coordinate coordinate2, Coordinate coordinate3 ) {
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/flatfile/reader/BufferedFileLineReader.java | BufferedFileLineReader.seek | public void seek(long pos) throws IOException {
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/flatfile/reader/BufferedFileLineReader.java | BufferedFileLineReader.readLine | @Override
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/StringUtilities.java | StringUtilities.checkSameName | public static String checkSameName( List<String> strings, String string ) {
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throw new RuntimeException();
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/StringUtilities.java | StringUtilities.splitString | public static List<String> splitString( String string, int limit ) {
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int start = 0;
int end = start;
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/StringUtilities.java | StringUtilities.streamToScanner | @SuppressWarnings("resource")
public static Scanner streamToScanner( InputStream stream, String delimiter ) {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/utils/StringUtilities.java | StringUtilities.stringToDoubleArray | public static double[] stringToDoubleArray( String string, String separator ) {
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separator = ",";
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enasequence/sequencetools | src/main/java/uk/ac/ebi/embl/api/entry/feature/Feature.java | Feature.getTextDescription | public String getTextDescription() {
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codahale/xsalsa20poly1305 | src/main/java/com/codahale/xsalsa20poly1305/SimpleBox.java | SimpleBox.seal | public byte[] seal(byte[] plaintext) {
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codahale/xsalsa20poly1305 | src/main/java/com/codahale/xsalsa20poly1305/SimpleBox.java | SimpleBox.open | public Optional<byte[]> open(byte[] ciphertext) {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/io/dxfdwg/libs/dwg/objects/DwgVertex3D.java | DwgVertex3D.readDwgVertex3DV15 | public void readDwgVertex3DV15(int[] data, int offset) throws Exception {
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/modules/utils/fileiterator/OmsFileIterator.java | OmsFileIterator.addPrj | public static void addPrj( String folder, String epsg ) throws Exception {
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fiter.pCode = epsg;
fiter.process();
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TheHortonMachine/hortonmachine | hmachine/src/main/java/org/hortonmachine/hmachine/modules/geomorphology/draindir/OmsDrainDir.java | OmsDrainDir.process | @Execute
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TheHortonMachine/hortonmachine | gears/src/main/java/org/hortonmachine/gears/io/geopaparazzi/geopap4/DaoMetadata.java | DaoMetadata.fillProjectMetadata | public static void fillProjectMetadata(Connection connection, String name, String description, String notes, String creationUser) throws Exception {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.sliceByTime | public static int[] sliceByTime(CSTable table, int timeCol, Date start, Date end) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.getProperties | public static AbstractTableModel getProperties(final CSProperties p) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.toArrayString | public static String toArrayString(String[] arr) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.getDate | public static Date getDate(CSProperties p, String key) throws ParseException {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.getInt | public static int getInt(CSProperties p, String key) throws ParseException {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.print | public static void print(CSProperties props, PrintWriter out) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.print | public static void print(CSTable table, PrintWriter out) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.save | public static void save(CSTable table, File file) throws IOException {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.properties | public static CSProperties properties(Reader r, String name) throws IOException {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.properties | public static CSProperties properties(Reader[] r, String name) throws IOException {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.properties | public static Properties properties(CSProperties p) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.table | public static CSTable table(File file, String name) throws IOException {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.table | public static CSTable table(String s, String name) throws IOException {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.columnExist | public static boolean columnExist(CSTable table, String name) {
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TheHortonMachine/hortonmachine | gears/src/main/java/oms3/io/DataIO.java | DataIO.columnIndex | public static int columnIndex(CSTable table, String name) {
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TheHortonMachine/hortonmachine | gui/src/main/java/org/hortonmachine/gui/spatialtoolbox/core/ModuleDescription.java | ModuleDescription.addOutput | public void addOutput( String fieldName, String type, String description, String defaultValue, String uiHint ) {
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/ssh/SshUtilities.java | SshUtilities.getPreference | public static String getPreference( String preferenceKey, String defaultValue ) {
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/ssh/SshUtilities.java | SshUtilities.getProcessPid | public static String getProcessPid( Session session, String userName, String grep1, String grep2 )
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/ssh/SshUtilities.java | SshUtilities.killProcessByPid | public static void killProcessByPid( Session session, int pid ) throws Exception {
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/ssh/SshUtilities.java | SshUtilities.getRunningDockerContainerId | public static String getRunningDockerContainerId( Session session, String containerName ) throws JSchException, IOException {
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/ssh/SshUtilities.java | SshUtilities.launchACommand | private static String launchACommand( Session session, String command ) throws JSchException, IOException {
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/ssh/SshUtilities.java | SshUtilities.runShellCommand | public static String runShellCommand( Session session, String command ) throws JSchException, IOException {
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/ssh/SshUtilities.java | SshUtilities.runDemonShellCommand | public static String runDemonShellCommand( Session session, String command ) throws JSchException, IOException {
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TheHortonMachine/hortonmachine | dbs/src/main/java/org/hortonmachine/ssh/SshUtilities.java | SshUtilities.downloadFile | public static void downloadFile( Session session, String remoteFilePath, String localFilePath ) throws Exception {
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... | java | public static void downloadFile( Session session, String remoteFilePath, String localFilePath ) throws Exception {
// exec 'scp -f rfile' remotely
String command = "scp -f " + remoteFilePath;
Channel channel = session.openChannel("exec");
((ChannelExec) channel).setCommand(command);
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... | Download a remote file via scp.
@param session the session to use.
@param remoteFilePath the remote file path.
@param localFilePath the local file path to copy into.
@throws Exception | [
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] | d2b436bbdf951dc1fda56096a42dbc0eae4d35a5 | https://github.com/TheHortonMachine/hortonmachine/blob/d2b436bbdf951dc1fda56096a42dbc0eae4d35a5/dbs/src/main/java/org/hortonmachine/ssh/SshUtilities.java#L307-L392 | train |
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