idx int64 0 165k | question stringlengths 73 4.15k | target stringlengths 5 918 | len_question int64 21 890 | len_target int64 3 255 |
|---|---|---|---|---|
17,100 | 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 ) ; } | Scale an envelope to have a given width . | 96 | 9 |
17,101 | 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" ) ; } | Get the Day of the year in WATER SOLAR or CALENDAR year . | 196 | 17 |
17,102 | 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 ) { return increments / 60 ; } else if ( calUnit == Calendar . SECOND ) { return increments / 3600 ; } return - 1 ; } | This used to be deltim in MMS . | 89 | 10 |
17,103 | protected ValidationMessage < Origin > reportError ( Origin origin , String messageKey , Object ... params ) { return reportMessage ( Severity . ERROR , origin , messageKey , params ) ; } | Creates an error validation message for the feature and adds it to the validation result . | 40 | 17 |
17,104 | 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 ; } | Creates an error validation message for the feature and adds it to the validation result . If there are locus_tag or gene qualifiers the values of these will be added to the message as a curator comment . | 70 | 42 |
17,105 | 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 ( ) ) ; } } } | If a feature had locus_tag or gene qualifiers - appends the value of these to the message as a curator comment . Useful for some submitters who want more of a handle on the origin than just a line number . | 223 | 46 |
17,106 | protected ValidationMessage < Origin > reportWarning ( Origin origin , String messageKey , Object ... params ) { return reportMessage ( Severity . WARNING , origin , messageKey , params ) ; } | Creates a warning validation message for the feature and adds it to the validation result . | 40 | 17 |
17,107 | 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 ; } | Creates a validation message for the feature and adds it to the validation result . | 85 | 16 |
17,108 | 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 ; } | Checks if the given geometry is connected to any other line . | 309 | 13 |
17,109 | 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 ) ; } | An utility method to use the module with default values and shapefiles . | 184 | 14 |
17,110 | @ 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 ; } | space point operations | 68 | 3 |
17,111 | public static byte [ ] generateSecretKey ( ) { final byte [ ] k = new byte [ KEY_LEN ] ; final SecureRandom random = new SecureRandom ( ) ; random . nextBytes ( k ) ; return k ; } | Generates a 32 - byte secret key . | 49 | 9 |
17,112 | 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 ; } | Calculates a CRC value for a byte to be used by CRC calculation functions . | 92 | 17 |
17,113 | 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 ) & 0x00FFFFFF L ; long tmp2 = values [ ( int ) ( ( crc ^ Character . toUpperCase ( ( char ) buffer [ i ] ) ) & 0xff ) ] ; crc = tmp1 ^ tmp2 ; // System.out.println("CRC: "+crc); } return crc ; } | Calculates the CRC - 32 of a block of data all at once | 133 | 15 |
17,114 | 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 ; } | get the URL class loader for all the resources ( just for jar files | 506 | 14 |
17,115 | 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." ) ; } } | Calculates the GeodesicLength between to points . | 189 | 12 |
17,116 | 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 ; } | Moves the flowDirColRow variable to the next trigger point . | 278 | 14 |
17,117 | public static void memclr ( byte [ ] array , int offset , int length ) { for ( int i = 0 ; i < length ; ++ i , ++ offset ) array [ offset ] = 0 ; } | Fill the given array with zeros . | 44 | 8 |
17,118 | 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 ; } | Return a new array equal to original except zero - padded to an integral mulitple of blocks . If the original is already an integral multiple of blocks just return it . | 112 | 34 |
17,119 | public static boolean isSupportedVectorExtension ( String name ) { for ( String ext : supportedVectors ) { if ( name . toLowerCase ( ) . endsWith ( ext ) ) { return true ; } } return false ; } | Checks a given name of a file if it is a supported vector extension . | 50 | 16 |
17,120 | public static boolean isSupportedRasterExtension ( String name ) { for ( String ext : supportedRasters ) { if ( name . toLowerCase ( ) . endsWith ( ext ) ) { return true ; } } return false ; } | Checks a given name of a file if it is a supported raster extension . | 50 | 17 |
17,121 | public static GridCoverage2D readRaster ( String path ) throws Exception { OmsRasterReader reader = new OmsRasterReader ( ) ; reader . file = path ; reader . process ( ) ; GridCoverage2D geodata = reader . outRaster ; return geodata ; } | Utility method to quickly read a grid in default mode . | 66 | 12 |
17,122 | private void swap ( int i , int j ) { double [ ] temp = data [ i ] ; data [ i ] = data [ j ] ; data [ j ] = temp ; } | swap rows i and j | 39 | 6 |
17,123 | 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 ; } | create and return the transpose of the invoking matrix | 72 | 10 |
17,124 | 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 ; } | return x = A^ - 1 b assuming A is square and has full rank | 488 | 16 |
17,125 | 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 ( ) ; } } | print matrix to standard output | 69 | 5 |
17,126 | 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 ( ) ; } } | Create the mbtiles tables in the db . | 115 | 10 |
17,127 | 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 ) ; } | Populate the metadata table . | 310 | 6 |
17,128 | 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 "" ; } } ) ; } | Add a single tile . | 123 | 5 |
17,129 | 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 ) ; } } ) ; } | Add a list of tiles in batch mode . | 187 | 9 |
17,130 | 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 ; } ) ; } | Get a Tile s image bytes from the database . | 203 | 10 |
17,131 | 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 ) ; } | Get the db envelope . | 121 | 5 |
17,132 | 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 ; } ) ; } | Get the bounds of a zoomlevel in tile indexes . | 189 | 11 |
17,133 | public void out2in ( Object from , String from_out , Object ... tos ) { for ( Object co : tos ) { out2in ( from , from_out , co , from_out ) ; } } | Connects field1 of cmd1 with the same named fields in cmds | 48 | 15 |
17,134 | public void in2in ( String in , Object to , String to_in ) { controller . mapIn ( in , to , to_in ) ; } | Maps a Compound Input field to a internal simple input field . | 33 | 13 |
17,135 | public void in2in ( String in , Object ... to ) { for ( Object cmd : to ) { in2in ( in , cmd , in ) ; } } | Maps a compound input to an internal simple input field . Both fields have the same name . | 35 | 18 |
17,136 | public void field2in ( Object o , String field , Object to , String to_in ) { controller . mapInField ( o , field , to , to_in ) ; } | Maps a object s field to an In field | 39 | 9 |
17,137 | 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 ) ; } } | Maps an object s field to a component s In field with the same name | 100 | 15 |
17,138 | public void out2field ( Object from , String from_out , Object o , String field ) { controller . mapOutField ( from , from_out , o , field ) ; } | Maps a component s Out field to an object field . | 39 | 11 |
17,139 | public void out2field ( Object from , String from_out , Object o ) { out2field ( from , from_out , o , from_out ) ; } | Maps a component Out field to an object s field . Both field have the same name . | 36 | 18 |
17,140 | public void out2out ( String out , Object to , String to_out ) { controller . mapOut ( out , to , to_out ) ; } | Maps a Compound Output field to a internal simple output field . | 33 | 13 |
17,141 | @ Deprecated public void connect ( Object from , String from_out , Object to , String to_in ) { controller . connect ( from , from_out , to , to_in ) ; } | deprecated methods starting here . | 42 | 6 |
17,142 | protected void reportError ( ValidationResult result , String messageKey , Object ... params ) { reportMessage ( result , Severity . ERROR , messageKey , params ) ; } | Creates an error validation message for the sequence and adds it to the validation result . | 36 | 17 |
17,143 | protected void reportWarning ( ValidationResult result , String messageKey , Object ... params ) { reportMessage ( result , Severity . WARNING , messageKey , params ) ; } | Creates a warning validation message for the sequence and adds it to the validation result . | 36 | 17 |
17,144 | protected void reportMessage ( ValidationResult result , Severity severity , String messageKey , Object ... params ) { result . append ( EntryValidations . createMessage ( origin , severity , messageKey , params ) ) ; } | Creates a validation message for the sequence and adds it to the validation result . | 46 | 16 |
17,145 | 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 ; } } | Evaluate the radiation . | 436 | 6 |
17,146 | 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 ; } | Checks if a crs is valid i . e . if it is not a wildcard default one . | 107 | 22 |
17,147 | @ 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 ( ) ) ; } } | Fill the prj file with the actual map projection . | 211 | 11 |
17,148 | 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 ) ; } } | Reproject a set of geometries | 93 | 9 |
17,149 | 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 ) ; } } | Reproject a set of coordinates . | 87 | 8 |
17,150 | 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 ; } | Converts meters to degrees based on a given coordinate in 90 degrees direction . | 123 | 15 |
17,151 | 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 ) ; } } } | Convert Values in Hough Space to an 8 - Bit Image Space . | 174 | 15 |
17,152 | 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 ; } } } | Draw the circles found in the original image . | 765 | 9 |
17,153 | public String getSequence ( Long beginPosition , Long endPosition ) { byte [ ] sequenceByte = getSequenceByte ( beginPosition , endPosition ) ; if ( sequenceByte != null ) return new String ( sequenceByte ) ; return null ; } | Returns a subsequence string or null if the location is not valid . | 52 | 14 |
17,154 | private void set ( Matrix m ) { this . nRows = this . nCols = Math . min ( m . nRows , m . nCols ) ; this . values = m . values ; } | Set this square matrix from another matrix . Note that this matrix will reference the values of the argument matrix . If the values are not square only the upper left square is used . | 46 | 35 |
17,155 | protected void set ( double values [ ] [ ] ) { super . set ( values ) ; nRows = nCols = Math . min ( nRows , nCols ) ; } | Set this square matrix from a 2 - d array of values . If the values are not square only the upper left square is used . | 41 | 27 |
17,156 | 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 ( ) ; } } | Print data from a matrix . | 94 | 6 |
17,157 | public static String envelope2WKT ( org . locationtech . jts . geom . Envelope env ) { GeometryFactory gf = GeometryUtilities . gf ( ) ; Geometry geometry = gf . toGeometry ( env ) ; return geometry . toText ( ) ; } | Print the envelope as WKT . | 64 | 7 |
17,158 | 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 * position after the end of stream, for example, after invalid * `setStartOffset()` call followed by `rewind()`. * This situation is not handled currently. */ if ( fOffset == fEndOffset ) { return - 1 ; } /* * Ok, we should actually read data from underlying stream, but * first it will be good to check if buffer array should be * expanded. Each time buffer size is doubled. */ 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 ; } | Reads next byte from this stream . This byte is either being read from underlying InputStream or taken from the internal buffer in case it was already read at some point before . | 287 | 35 |
17,159 | public void close ( ) throws IOException { if ( fInputStream != null ) { fInputStream . close ( ) ; fInputStream = null ; fData = null ; } } | Closes underlying byte stream . | 39 | 6 |
17,160 | public String getTranslation ( ) { if ( codons == null ) { return "" ; } StringBuilder translation = new StringBuilder ( ) ; for ( Codon codon : codons ) { translation . append ( codon . getAminoAcid ( ) ) ; } return translation . toString ( ) ; } | Returns the translation including stop codons and trailing bases . | 67 | 11 |
17,161 | 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 ( ) ; } | Returns the translation excluding stop codons and trailing bases . | 90 | 11 |
17,162 | 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 ; } | Smooth an array of values with a gaussian blur . | 264 | 12 |
17,163 | 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 ; } | Smooth an array of values with an averaging moving window . | 205 | 12 |
17,164 | public Coordinate wgs84ToEnu ( Coordinate cLL ) { checkZ ( cLL ) ; Coordinate cEcef = wgs84ToEcef ( cLL ) ; Coordinate enu = ecefToEnu ( cEcef ) ; return enu ; } | Converts the wgs84 coordinate to ENU . | 65 | 11 |
17,165 | public Coordinate enuToWgs84 ( Coordinate enu ) { checkZ ( enu ) ; Coordinate cEcef = enuToEcef ( enu ) ; Coordinate wgs84 = ecefToWgs84 ( cEcef ) ; return wgs84 ; } | Converts the ENU coordinate to wgs84 . | 67 | 11 |
17,166 | 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 ; } } | Converts a geometry from ENU to WGS . | 114 | 11 |
17,167 | 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 ; } } | Converts a geometry from WGS to ENU . | 109 | 11 |
17,168 | public Envelope convertEnvelopeFromWgsToEnu ( Envelope envelopeWgs ) { Polygon polygonEnu = GeometryUtilities . createPolygonFromEnvelope ( envelopeWgs ) ; convertGeometryFromWgsToEnu ( polygonEnu ) ; Envelope envelopeEnu = polygonEnu . getEnvelopeInternal ( ) ; return envelopeEnu ; } | Converts an envelope from WGS to ENU . | 90 | 11 |
17,169 | 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 ; } | Move to a given location . | 314 | 6 |
17,170 | public void goTo ( Sector sector , boolean animate ) { View view = getWwd ( ) . getView ( ) ; view . stopAnimations ( ) ; view . stopMovement ( ) ; if ( sector == null ) { return ; } // Create a bounding box for the specified sector in order to estimate // its size in model coordinates. Box extent = Sector . computeBoundingBox ( getWwd ( ) . getModel ( ) . getGlobe ( ) , getWwd ( ) . getSceneController ( ) . getVerticalExaggeration ( ) , sector ) ; // Estimate the distance between the center position and the eye // position that is necessary to cause the sector to // fill a viewport with the specified field of view. Note that we change // the distance between the center and eye // position here, and leave the field of view constant. Angle fov = view . getFieldOfView ( ) ; double zoom = extent . getRadius ( ) / fov . cosHalfAngle ( ) / fov . tanHalfAngle ( ) ; // Configure OrbitView to look at the center of the sector from our // estimated distance. This causes OrbitView to // animate to the specified position over several seconds. To affect // this change immediately use the following: if ( animate ) { view . goTo ( new Position ( sector . getCentroid ( ) , 0d ) , zoom ) ; } else { ( ( OrbitView ) wwd . getView ( ) ) . setCenterPosition ( new Position ( sector . getCentroid ( ) , 0d ) ) ; ( ( OrbitView ) wwd . getView ( ) ) . setZoom ( zoom ) ; } } | Move to see a given sector . | 358 | 7 |
17,171 | public void setFlatGlobe ( boolean doMercator ) { EarthFlat globe = new EarthFlat ( ) ; globe . setElevationModel ( new ZeroElevationModel ( ) ) ; wwd . getModel ( ) . setGlobe ( globe ) ; wwd . getView ( ) . stopMovement ( ) ; GeographicProjection projection ; if ( doMercator ) { projection = new ProjectionMercator ( ) ; } else { projection = new ProjectionEquirectangular ( ) ; } globe . setProjection ( projection ) ; wwd . redraw ( ) ; } | Set the globe as flat . | 128 | 6 |
17,172 | public void setSphereGlobe ( ) { Earth globe = new Earth ( ) ; wwd . getModel ( ) . setGlobe ( globe ) ; wwd . getView ( ) . stopMovement ( ) ; wwd . redraw ( ) ; } | Set the globe as sphere . | 55 | 6 |
17,173 | public void setFlatSphereGlobe ( ) { Earth globe = new Earth ( ) ; globe . setElevationModel ( new ZeroElevationModel ( ) ) ; wwd . getModel ( ) . setGlobe ( globe ) ; wwd . getView ( ) . stopMovement ( ) ; wwd . redraw ( ) ; } | Set the globe as flat sphere . | 75 | 7 |
17,174 | public List < Message > getFilteredList ( EMessageType messageType , Long fromTsMillis , Long toTsMillis , long limit ) throws Exception { String tableName = TABLE_MESSAGES ; String sql = "select " + getQueryFieldsString ( ) + " from " + tableName ; List < String > wheresList = new ArrayList <> ( ) ; if ( messageType != null && messageType != EMessageType . ALL ) { String where = type_NAME + "=" + messageType . getCode ( ) ; wheresList . add ( where ) ; } if ( fromTsMillis != null ) { String where = TimeStamp_NAME + ">" + fromTsMillis ; wheresList . add ( where ) ; } if ( toTsMillis != null ) { String where = TimeStamp_NAME + "<" + toTsMillis ; wheresList . add ( where ) ; } if ( wheresList . size ( ) > 0 ) { sql += " WHERE " ; for ( int i = 0 ; i < wheresList . size ( ) ; i ++ ) { if ( i > 0 ) { sql += " AND " ; } sql += wheresList . get ( i ) ; } } sql += " order by " + ID_NAME + " desc" ; if ( limit > 0 ) { sql += " limit " + limit ; } String _sql = sql ; List < Message > messages = new ArrayList < Message > ( ) ; logDb . execOnConnection ( connection -> { try ( IHMStatement stmt = connection . createStatement ( ) ; IHMResultSet rs = stmt . executeQuery ( _sql ) ; ) { while ( rs . next ( ) ) { Message event = resultSetToItem ( rs ) ; messages . add ( event ) ; } } return null ; } ) ; return messages ; } | Get the list of messages filtered . | 403 | 7 |
17,175 | @ Override public boolean accept ( File file ) { String name = file . getName ( ) ; if ( FilenameUtils . wildcardMatch ( name , wildcards , caseSensitivity ) ) { return true ; } return false ; } | Checks to see if the filename matches one of the wildcards . | 51 | 14 |
17,176 | public SimpleFeature convertDwgAttribute ( String typeName , String layerName , DwgAttrib attribute , int id ) { Point2D pto = attribute . getInsertionPoint ( ) ; Coordinate coord = new Coordinate ( pto . getX ( ) , pto . getY ( ) , attribute . getElevation ( ) ) ; String textString = attribute . getText ( ) ; return createPointTextFeature ( typeName , layerName , id , coord , textString ) ; } | Builds a point feature from a dwg attribute . | 108 | 11 |
17,177 | public SimpleFeature convertDwgPolyline2D ( String typeName , String layerName , DwgPolyline2D polyline2d , int id ) { Point2D [ ] ptos = polyline2d . getPts ( ) ; CoordinateList coordList = new CoordinateList ( ) ; if ( ptos != null ) { for ( int j = 0 ; j < ptos . length ; j ++ ) { Coordinate coord = new Coordinate ( ptos [ j ] . getX ( ) , ptos [ j ] . getY ( ) , 0.0 ) ; coordList . add ( coord ) ; } SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder ( ) ; b . setName ( typeName ) ; b . setCRS ( crs ) ; b . add ( THE_GEOM , LineString . class ) ; b . add ( LAYER , String . class ) ; SimpleFeatureType type = b . buildFeatureType ( ) ; SimpleFeatureBuilder builder = new SimpleFeatureBuilder ( type ) ; Geometry lineString = gF . createLineString ( coordList . toCoordinateArray ( ) ) ; Object [ ] values = new Object [ ] { lineString , layerName } ; builder . addAll ( values ) ; return builder . buildFeature ( typeName + "." + id ) ; } return null ; } | Builds a line feature from a dwg polyline 2D . | 292 | 14 |
17,178 | public SimpleFeature convertDwgPoint ( String typeName , String layerName , DwgPoint point , int id ) { double [ ] p = point . getPoint ( ) ; Point2D pto = new Point2D . Double ( p [ 0 ] , p [ 1 ] ) ; CoordinateList coordList = new CoordinateList ( ) ; Coordinate coord = new Coordinate ( pto . getX ( ) , pto . getY ( ) , 0.0 ) ; coordList . add ( coord ) ; SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder ( ) ; b . setName ( typeName ) ; b . setCRS ( crs ) ; b . add ( THE_GEOM , MultiPoint . class ) ; b . add ( LAYER , String . class ) ; SimpleFeatureType type = b . buildFeatureType ( ) ; SimpleFeatureBuilder builder = new SimpleFeatureBuilder ( type ) ; Geometry points = gF . createMultiPoint ( coordList . toCoordinateArray ( ) ) ; Object [ ] values = new Object [ ] { points , layerName } ; builder . addAll ( values ) ; return builder . buildFeature ( typeName + "." + id ) ; } | Builds a point feature from a dwg point . | 261 | 11 |
17,179 | public SimpleFeature convertDwgLine ( String typeName , String layerName , DwgLine line , int id ) { double [ ] p1 = line . getP1 ( ) ; double [ ] p2 = line . getP2 ( ) ; Point2D [ ] ptos = new Point2D [ ] { new Point2D . Double ( p1 [ 0 ] , p1 [ 1 ] ) , new Point2D . Double ( p2 [ 0 ] , p2 [ 1 ] ) } ; CoordinateList coordList = new CoordinateList ( ) ; for ( int j = 0 ; j < ptos . length ; j ++ ) { Coordinate coord = new Coordinate ( ptos [ j ] . getX ( ) , ptos [ j ] . getY ( ) , 0.0 ) ; coordList . add ( coord ) ; } SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder ( ) ; b . setName ( typeName ) ; b . setCRS ( crs ) ; b . add ( THE_GEOM , LineString . class ) ; b . add ( LAYER , String . class ) ; SimpleFeatureType type = b . buildFeatureType ( ) ; SimpleFeatureBuilder builder = new SimpleFeatureBuilder ( type ) ; Geometry lineString = gF . createLineString ( coordList . toCoordinateArray ( ) ) ; Object [ ] values = new Object [ ] { lineString , layerName } ; builder . addAll ( values ) ; return builder . buildFeature ( typeName + "." + id ) ; } | Builds a line feature from a dwg line . | 336 | 11 |
17,180 | public SimpleFeature convertDwgCircle ( String typeName , String layerName , DwgCircle circle , int id ) { double [ ] center = circle . getCenter ( ) ; double radius = circle . getRadius ( ) ; Point2D [ ] ptos = GisModelCurveCalculator . calculateGisModelCircle ( new Point2D . Double ( center [ 0 ] , center [ 1 ] ) , radius ) ; CoordinateList coordList = new CoordinateList ( ) ; for ( int j = 0 ; j < ptos . length ; j ++ ) { Coordinate coord = new Coordinate ( ptos [ j ] . getX ( ) , ptos [ j ] . getY ( ) , 0.0 ) ; coordList . add ( coord ) ; } // close to create a polygon if ( ( ptos [ ptos . length - 1 ] . getX ( ) != ptos [ 0 ] . getX ( ) ) || ( ptos [ ptos . length - 1 ] . getY ( ) != ptos [ 0 ] . getY ( ) ) ) { Coordinate coord = new Coordinate ( ptos [ 0 ] . getX ( ) , ptos [ 0 ] . getY ( ) , 0.0 ) ; coordList . add ( coord ) ; } SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder ( ) ; b . setName ( typeName ) ; b . setCRS ( crs ) ; b . add ( THE_GEOM , Polygon . class ) ; b . add ( LAYER , String . class ) ; SimpleFeatureType type = b . buildFeatureType ( ) ; SimpleFeatureBuilder builder = new SimpleFeatureBuilder ( type ) ; LinearRing linearRing = gF . createLinearRing ( coordList . toCoordinateArray ( ) ) ; Geometry polygon = gF . createPolygon ( linearRing , null ) ; Object [ ] values = new Object [ ] { polygon , layerName } ; builder . addAll ( values ) ; return builder . buildFeature ( typeName + "." + id ) ; } | Builds a polygon feature from a dwg circle . | 453 | 12 |
17,181 | public SimpleFeature convertDwgSolid ( String typeName , String layerName , DwgSolid solid , int id ) { double [ ] p1 = solid . getCorner1 ( ) ; double [ ] p2 = solid . getCorner2 ( ) ; double [ ] p3 = solid . getCorner3 ( ) ; double [ ] p4 = solid . getCorner4 ( ) ; Point2D [ ] ptos = new Point2D [ ] { new Point2D . Double ( p1 [ 0 ] , p1 [ 1 ] ) , new Point2D . Double ( p2 [ 0 ] , p2 [ 1 ] ) , new Point2D . Double ( p3 [ 0 ] , p3 [ 1 ] ) , new Point2D . Double ( p4 [ 0 ] , p4 [ 1 ] ) } ; CoordinateList coordList = new CoordinateList ( ) ; for ( int j = 0 ; j < ptos . length ; j ++ ) { Coordinate coord = new Coordinate ( ptos [ j ] . getX ( ) , ptos [ j ] . getY ( ) ) ; coordList . add ( coord ) ; } coordList . closeRing ( ) ; SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder ( ) ; b . setName ( typeName ) ; b . setCRS ( crs ) ; b . add ( THE_GEOM , Polygon . class ) ; b . add ( LAYER , String . class ) ; SimpleFeatureType type = b . buildFeatureType ( ) ; SimpleFeatureBuilder builder = new SimpleFeatureBuilder ( type ) ; LinearRing linearRing = gF . createLinearRing ( coordList . toCoordinateArray ( ) ) ; Geometry polygon = gF . createPolygon ( linearRing , null ) ; Object [ ] values = new Object [ ] { polygon , layerName } ; builder . addAll ( values ) ; return builder . buildFeature ( typeName + "." + id ) ; } | Builds a polygon feature from a dwg solid . | 431 | 12 |
17,182 | public SimpleFeature convertDwgArc ( String typeName , String layerName , DwgArc arc , int id ) { double [ ] c = arc . getCenter ( ) ; Point2D center = new Point2D . Double ( c [ 0 ] , c [ 1 ] ) ; double radius = ( arc ) . getRadius ( ) ; double initAngle = Math . toDegrees ( ( arc ) . getInitAngle ( ) ) ; double endAngle = Math . toDegrees ( ( arc ) . getEndAngle ( ) ) ; Point2D [ ] ptos = GisModelCurveCalculator . calculateGisModelArc ( center , radius , initAngle , endAngle ) ; CoordinateList coordList = new CoordinateList ( ) ; for ( int j = 0 ; j < ptos . length ; j ++ ) { Coordinate coord = new Coordinate ( ptos [ j ] . getX ( ) , ptos [ j ] . getY ( ) , 0.0 ) ; coordList . add ( coord ) ; } SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder ( ) ; b . setName ( typeName ) ; b . setCRS ( crs ) ; b . add ( THE_GEOM , LineString . class ) ; b . add ( LAYER , String . class ) ; SimpleFeatureType type = b . buildFeatureType ( ) ; SimpleFeatureBuilder builder = new SimpleFeatureBuilder ( type ) ; Geometry lineString = gF . createLineString ( coordList . toCoordinateArray ( ) ) ; Object [ ] values = new Object [ ] { lineString , layerName } ; builder . addAll ( values ) ; return builder . buildFeature ( typeName + "." + id ) ; } | Builds a line feature from a dwg arc . | 384 | 11 |
17,183 | public static double norm_vec ( double x , double y , double z ) { return Math . sqrt ( x * x + y * y + z * z ) ; } | Normalized Vector . | 37 | 4 |
17,184 | public static double lag1 ( double [ ] vals ) { double mean = mean ( vals ) ; int size = vals . length ; double r1 ; double q = 0 ; double v = ( vals [ 0 ] - mean ) * ( vals [ 0 ] - mean ) ; for ( int i = 1 ; i < size ; i ++ ) { double delta0 = ( vals [ i - 1 ] - mean ) ; double delta1 = ( vals [ i ] - mean ) ; q += ( delta0 * delta1 - q ) / ( i + 1 ) ; v += ( delta1 * delta1 - v ) / ( i + 1 ) ; } r1 = q / v ; return r1 ; } | Returns the lag - 1 autocorrelation of a dataset ; | 156 | 13 |
17,185 | public static double round ( double val , int places ) { long factor = ( long ) Math . pow ( 10 , places ) ; // Shift the decimal the correct number of places // to the right. val = val * factor ; // Round to the nearest integer. long tmp = Math . round ( val ) ; // Shift the decimal the correct number of places // back to the left. return ( double ) tmp / factor ; } | Round a double value to a specified number of decimal places . | 88 | 12 |
17,186 | public static double random ( double min , double max ) { assert max > min ; return min + Math . random ( ) * ( max - min ) ; } | Generate a random number in a range . | 33 | 9 |
17,187 | private boolean checkStructure ( ) { File ds ; ds = new File ( mapsetPath + File . separator + GrassLegacyConstans . CATS + File . separator ) ; if ( ! ds . exists ( ) ) if ( ! ds . mkdir ( ) ) return false ; ds = new File ( mapsetPath + File . separator + GrassLegacyConstans . CELL + File . separator ) ; if ( ! ds . exists ( ) ) if ( ! ds . mkdir ( ) ) return false ; ds = new File ( mapsetPath + File . separator + GrassLegacyConstans . CELL_MISC + File . separator ) ; if ( ! ds . exists ( ) ) if ( ! ds . mkdir ( ) ) return false ; ds = new File ( mapsetPath + File . separator + GrassLegacyConstans . CELL_MISC + File . separator + name ) ; if ( ! ds . exists ( ) ) if ( ! ds . mkdir ( ) ) return false ; ds = new File ( mapsetPath + File . separator + GrassLegacyConstans . FCELL + File . separator ) ; if ( ! ds . exists ( ) ) if ( ! ds . mkdir ( ) ) return false ; ds = new File ( mapsetPath + File . separator + GrassLegacyConstans . CELLHD + File . separator ) ; if ( ! ds . exists ( ) ) if ( ! ds . mkdir ( ) ) return false ; ds = new File ( mapsetPath + File . separator + GrassLegacyConstans . COLR + File . separator ) ; if ( ! ds . exists ( ) ) if ( ! ds . mkdir ( ) ) return false ; ds = new File ( mapsetPath + File . separator + GrassLegacyConstans . HIST + File . separator ) ; if ( ! ds . exists ( ) ) if ( ! ds . mkdir ( ) ) return false ; return true ; } | check if the needed folders are there ( they could be missing if the mapset has just been created and this is the first file that gets into it | 458 | 30 |
17,188 | private boolean createEmptyHeader ( String filePath , int rows ) { try { RandomAccessFile theCreatedFile = new RandomAccessFile ( filePath , "rw" ) ; rowaddresses = new long [ rows + 1 ] ; // the size of a long theCreatedFile . write ( 4 ) ; // write the addresses of the row begins. Since we don't know how // much // they will be compressed, they will be filled after the // compression for ( int i = 0 ; i < rows + 1 ; i ++ ) { theCreatedFile . writeInt ( 0 ) ; } pointerInFilePosition = theCreatedFile . getFilePointer ( ) ; rowaddresses [ 0 ] = pointerInFilePosition ; theCreatedFile . close ( ) ; } catch ( Exception e ) { e . printStackTrace ( ) ; return false ; } return true ; } | creates the space for the header of the rasterfile filling the spaces with zeroes . After the compression the values will be rewritten | 182 | 28 |
17,189 | private void createCellhd ( int chproj , int chzone , double chn , double chs , double che , double chw , int chcols , int chrows , double chnsres , double chewres , int chformat , int chcompressed ) throws Exception { StringBuffer data = new StringBuffer ( 512 ) ; data . append ( "proj: " + chproj + "\n" ) . append ( "zone: " + chzone + "\n" ) . append ( "north: " + chn + "\n" ) . append ( "south: " + chs + "\n" ) . append ( "east: " + che + "\n" ) . append ( "west: " + chw + "\n" ) . append ( "cols: " + chcols + "\n" ) . append ( "rows: " + chrows + "\n" ) . append ( "n-s resol: " + chnsres + "\n" ) . append ( "e-w resol: " + chewres + "\n" ) . append ( "format: " + chformat + "\n" ) . append ( "compressed: " + chcompressed ) ; File ds = new File ( mapsetPath + File . separator + GrassLegacyConstans . CELLHD + File . separator + name ) ; OutputStreamWriter windFile = new OutputStreamWriter ( new FileOutputStream ( ds ) ) ; windFile . write ( data . toString ( ) ) ; windFile . close ( ) ; } | changes the cellhd file inserting the new values obtained from the environment | 339 | 13 |
17,190 | public boolean compressAndWriteObj ( RandomAccessFile theCreatedFile , RandomAccessFile theCreatedNullFile , Object dataObject ) throws RasterWritingFailureException { if ( dataObject instanceof double [ ] [ ] ) { compressAndWrite ( theCreatedFile , theCreatedNullFile , ( double [ ] [ ] ) dataObject ) ; } else { throw new RasterWritingFailureException ( "Raster type not supported." ) ; } | Passing the object after defining the type of data that will be written | 91 | 14 |
17,191 | public String getStyle ( StyleType type , Color color , String colorName , String layerName ) { throw new UnsupportedOperationException ( ) ; } | Generates a style from a template using the provided substitutions . | 31 | 13 |
17,192 | protected Reader toReader ( Object input ) throws IOException { if ( input instanceof Reader ) { return ( Reader ) input ; } if ( input instanceof InputStream ) { return new InputStreamReader ( ( InputStream ) input ) ; } if ( input instanceof String ) { return new StringReader ( ( String ) input ) ; } if ( input instanceof URL ) { return new InputStreamReader ( ( ( URL ) input ) . openStream ( ) ) ; } if ( input instanceof File ) { return new FileReader ( ( File ) input ) ; } throw new IllegalArgumentException ( "Unable to turn " + input + " into reader" ) ; } | Turns input into a Reader . | 141 | 7 |
17,193 | public static boolean supportsNative ( ) { if ( ! testedLibLoading ) { LiblasJNALibrary wrapper = LiblasWrapper . getWrapper ( ) ; if ( wrapper != null ) { isNativeLibAvailable = true ; } testedLibLoading = true ; } return isNativeLibAvailable ; } | Checks of nativ libs are available . | 64 | 10 |
17,194 | public static ALasReader getReader ( File lasFile , CoordinateReferenceSystem crs ) throws Exception { if ( supportsNative ( ) ) { return new LiblasReader ( lasFile , crs ) ; } else { return new LasReaderBuffered ( lasFile , crs ) ; } } | Get a las reader . | 62 | 5 |
17,195 | public static ALasWriter getWriter ( File lasFile , CoordinateReferenceSystem crs ) throws Exception { if ( supportsNative ( ) ) { return new LiblasWriter ( lasFile , crs ) ; } else { return new LasWriterBuffered ( lasFile , crs ) ; } } | Get a las writer . | 62 | 5 |
17,196 | public void setRoot ( DbLevel v ) { DbLevel oldRoot = v ; root = v ; fireTreeStructureChanged ( oldRoot ) ; } | Sets the root to a given variable . | 34 | 9 |
17,197 | public void onError ( Exception e ) { e . printStackTrace ( ) ; String localizedMessage = e . getLocalizedMessage ( ) ; if ( localizedMessage == null ) { localizedMessage = e . getMessage ( ) ; } if ( localizedMessage == null || localizedMessage . trim ( ) . length ( ) == 0 ) { localizedMessage = "An undefined error was thrown. Please send the below trace to your technical contact:\n" ; localizedMessage += ExceptionUtils . getStackTrace ( e ) ; } String _localizedMessage = localizedMessage ; SwingUtilities . invokeLater ( new Runnable ( ) { public void run ( ) { JOptionPane . showMessageDialog ( parent , _localizedMessage , "ERROR" , JOptionPane . ERROR_MESSAGE ) ; } } ) ; } | Called if an error occurrs . Can be overridden . SHows dialog by default . | 177 | 19 |
17,198 | public static boolean tcaMax ( FlowNode flowNode , RandomIter tcaIter , RandomIter hacklengthIter , double maxTca , double maxDistance ) { List < FlowNode > enteringNodes = flowNode . getEnteringNodes ( ) ; for ( Node node : enteringNodes ) { double tca = node . getValueFromMap ( tcaIter ) ; if ( tca >= maxTca ) { if ( NumericsUtilities . dEq ( tca , maxTca ) ) { if ( node . getValueFromMap ( hacklengthIter ) > maxDistance ) return false ; } else return false ; } } return true ; } | Compare two value of tca and distance . | 142 | 9 |
17,199 | public static boolean isCircularBoundary ( CompoundLocation < Location > location , long sequenceLength ) { if ( location . getLocations ( ) . size ( ) == 1 ) { return false ; // cant be if there is only 1 location element } boolean lastLocation = false ; List < Location > locationList = location . getLocations ( ) ; for ( int i = 0 ; i < locationList . size ( ) ; i ++ ) { if ( i == locationList . size ( ) - 1 ) { lastLocation = true ; } Long position = location . getLocations ( ) . get ( i ) . getEndPosition ( ) ; if ( position == sequenceLength && ! lastLocation ) { return true ; } } return false ; } | Checks to see if a feature s location spans a circular boundary - assumes the genome the feature is coming from is circular . | 157 | 25 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.