idx int64 0 41.2k | question stringlengths 74 4.21k | target stringlengths 5 888 |
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7,500 | public void registerClass ( Class < ? > clazz ) { registeredClasses . add ( clazz ) ; for ( Field field : clazz . getFields ( ) ) { if ( field . isAnnotationPresent ( Opt . class ) ) { int mod = field . getModifiers ( ) ; if ( ! Modifier . isPublic ( mod ) ) { throw new IllegalStateException ( "@" + Opt . class . getName ( ) + " on non-public field: " + field ) ; } if ( Modifier . isFinal ( mod ) ) { throw new IllegalStateException ( "@" + Opt . class . getName ( ) + " on final field: " + field ) ; } if ( Modifier . isAbstract ( mod ) ) { throw new IllegalStateException ( "@" + Opt . class . getName ( ) + " on abstract field: " + field ) ; } Opt opt = field . getAnnotation ( Opt . class ) ; String name = getName ( opt , field ) ; if ( ! names . add ( name ) ) { throw new RuntimeException ( "Multiple options have the same name: --" + name ) ; } String shortName = null ; if ( createShortNames ) { shortName = getAndAddUniqueShortName ( name ) ; } Option apacheOpt = new Option ( shortName , name , opt . hasArg ( ) , opt . description ( ) ) ; apacheOpt . setRequired ( opt . required ( ) ) ; options . addOption ( apacheOpt ) ; optionFieldMap . put ( apacheOpt , field ) ; if ( ! field . getType ( ) . equals ( Boolean . TYPE ) && ! opt . hasArg ( ) ) { throw new RuntimeException ( "Only booleans can not have arguments." ) ; } } } } | Registers all the |
7,501 | private static String getName ( Opt option , Field field ) { if ( option . name ( ) . equals ( Opt . DEFAULT_STRING ) ) { return field . getName ( ) ; } else { return option . name ( ) ; } } | Gets the name specified in |
7,502 | public void printUsage ( ) { String name = mainClass == null ? "<MainClass>" : mainClass . getName ( ) ; String usage = "java " + name + " [OPTIONS]" ; final HelpFormatter formatter = new HelpFormatter ( ) ; formatter . setWidth ( 120 ) ; formatter . printHelp ( usage , options , true ) ; } | Prints the usage of the main class for this ArgParser . |
7,503 | public static int safeStrToInt ( String str ) { if ( sciInt . matcher ( str ) . find ( ) ) { return SafeCast . safeDoubleToInt ( Double . parseDouble ( str . toUpperCase ( ) ) ) ; } else { return Integer . parseInt ( str ) ; } } | Correctly casts 1e + 06 to 1000000 . |
7,504 | @ SuppressWarnings ( { "unchecked" , "rawtypes" } ) public List serialize ( ClassUnwrapper unwrapper , Object agent ) { List variables = new ArrayList < > ( ) ; List < GetterMethodCover > methods = unwrapper . getMethods ( ) ; for ( GetterMethodCover method : methods ) { Object value = method . invoke ( agent ) ; if ( value == null ) continue ; variables . add ( newVariable ( method . getKey ( ) , getValue ( method , value ) , method . isHidden ( ) ) ) ; } return variables ; } | Serialize java object |
7,505 | @ SuppressWarnings ( "rawtypes" ) protected Object getValue ( GetterMethodCover method , Object value ) { if ( method . isByte ( ) ) { value = ( ( Byte ) value ) . intValue ( ) ; } else if ( method . isChar ( ) ) { value = ( int ) ( ( Character ) value ) . charValue ( ) ; } else if ( method . isFloat ( ) ) { value = ( ( Float ) value ) . doubleValue ( ) ; } else if ( method . isLong ( ) ) { value = ( ( Long ) value ) . doubleValue ( ) ; } else if ( method . isShort ( ) ) { value = ( ( Short ) value ) . intValue ( ) ; } else if ( method . isObject ( ) ) { value = parseObject ( method , value ) ; } else if ( method . isObjectArray ( ) ) { value = parseArray ( method , value ) ; } else if ( method . isArrayObjectCollection ( ) ) { return parseArrayObjectCollection ( method , ( Collection ) value ) ; } else if ( method . isObjectCollection ( ) ) { return parseObjectCollection ( method , ( Collection ) value ) ; } else if ( method . isArrayCollection ( ) ) { return parseArrayCollection ( method , ( Collection ) value ) ; } else if ( method . isArray ( ) || method . isColection ( ) ) { return transformSimpleValue ( value ) ; } return value ; } | Call getter method and get value |
7,506 | private void updateBuddyProperties ( BuddyProperties buddyProperties , ApiBuddyProperties apiBuddyProperties ) { apiBuddyProperties . setInited ( buddyProperties . isInited ( ) ) ; apiBuddyProperties . setNickName ( buddyProperties . getNickName ( ) ) ; apiBuddyProperties . setOnline ( buddyProperties . isOnline ( ) ) ; apiBuddyProperties . setState ( buddyProperties . getState ( ) ) ; } | Update buddy properties of user |
7,507 | void apply ( final LambdaUnaryOpDouble lambda ) { params . apply ( new FnIntDoubleToDouble ( ) { public double call ( int idx , double val ) { return lambda . call ( val ) ; } } ) ; } | ONLY FOR TESTING . |
7,508 | ImmutableCell < V > validateCounts ( int rowCount , int columnCount ) { if ( row >= rowCount || column >= columnCount ) { throw new IndexOutOfBoundsException ( "Invalid row-column: " + row + "," + column + " for grid " + rowCount + "x" + columnCount ) ; } return this ; } | Validates this cell against the specified counts . |
7,509 | public static double approxSumPaths ( WeightedIntDiGraph g , RealVector startWeights , RealVector endWeights , Iterator < DiEdge > seq , DoubleConsumer c ) { DefaultDict < DiEdge , Double > prefixWeightsEndingAt = new DefaultDict < DiEdge , Double > ( Void -> 0.0 ) ; RealVector currentSums = startWeights . copy ( ) ; double currentTotal = currentSums . dotProduct ( endWeights ) ; if ( c != null ) { c . accept ( currentTotal ) ; } for ( DiEdge e : ScheduleUtils . iterable ( seq ) ) { int s = e . get1 ( ) ; int t = e . get2 ( ) ; double oldTargetSum = currentSums . getEntry ( t ) ; double oldEdgeSum = prefixWeightsEndingAt . get ( e ) ; double newEdgeSum = currentSums . getEntry ( s ) * g . getWeight ( e ) ; double newTargetSum = oldTargetSum + ( newEdgeSum - oldEdgeSum ) ; double newTotal = currentTotal + ( newTargetSum - oldTargetSum ) * endWeights . getEntry ( t ) ; prefixWeightsEndingAt . put ( e , newEdgeSum ) ; currentSums . setEntry ( t , newTargetSum ) ; currentTotal = newTotal ; if ( c != null ) { c . accept ( currentTotal ) ; } } return currentTotal ; } | Computes the approximate sum of paths through the graph where the weight of each path is the product of edge weights along the path ; |
7,510 | public static int hash32 ( final long data , int seed ) { final int m = 0x5bd1e995 ; final int r = 24 ; final int length = 8 ; int h = seed ^ length ; for ( int i = 0 ; i < 2 ; i ++ ) { int k = ( i == 0 ) ? ( int ) ( data & 0xffffffffL ) : ( int ) ( ( data >>> 32 ) & 0xffffffffL ) ; k *= m ; k ^= k >>> r ; k *= m ; h *= m ; h ^= k ; } h ^= h >>> 13 ; h *= m ; h ^= h >>> 15 ; return h ; } | My conversion of MurmurHash to take a long as input . |
7,511 | private void ensureVarTensor ( ) { if ( vt == null ) { log . warn ( "Generating VarTensor for a GlobalFactor. This should only ever be done during testing." ) ; vt = BruteForceInferencer . safeNewVarTensor ( s , f ) ; if ( fillVal != null ) { vt . fill ( fillVal ) ; } } } | Ensures that the VarTensor is loaded . |
7,512 | protected Object checkUserAgent ( ServerUserHandlerClass handler , ApiUser userAgent ) { if ( handler . getUserClass ( ) . isAssignableFrom ( userAgent . getClass ( ) ) ) return userAgent ; return UserAgentUtil . getGameUser ( userAgent , handler . getUserClass ( ) ) ; } | Check whether context of user agent is application or game |
7,513 | public String getLabel ( ) { if ( label == null ) { StringBuilder label = new StringBuilder ( ) ; label . append ( headNode . getLabel ( ) ) ; label . append ( "<--" ) ; for ( Hypernode tailNode : tailNodes ) { label . append ( tailNode . getLabel ( ) ) ; label . append ( "," ) ; } if ( tailNodes . length > 0 ) { label . deleteCharAt ( label . length ( ) - 1 ) ; } return label . toString ( ) ; } return label ; } | Gets a name for this edge . |
7,514 | public static ApiUser getUserAgent ( User sfsUser ) { Object userAgent = sfsUser . getProperty ( APIKey . USER ) ; if ( userAgent == null ) throw new RuntimeException ( "Can not get user agent" ) ; return ( ApiUser ) userAgent ; } | Get user agent object mapped to smartfox user object |
7,515 | public static ApiRoom getRoomAgent ( Room sfsRoom ) { Object roomAgent = sfsRoom . getProperty ( APIKey . ROOM ) ; if ( roomAgent == null ) throw new RuntimeException ( "Can not get user agent" ) ; return ( ApiRoom ) roomAgent ; } | Get room agent object mapped to smartfox room object |
7,516 | public static < X , Y > Map < X , Y > zip ( List < X > keys , List < Y > values ) { if ( keys . size ( ) != values . size ( ) ) { throw new IllegalArgumentException ( "Lengths are not equal" ) ; } Map < X , Y > map = new HashMap < > ( keys . size ( ) ) ; for ( int i = 0 ; i < keys . size ( ) ; i ++ ) { map . put ( keys . get ( i ) , values . get ( i ) ) ; } return map ; } | Like Python s zip this creates a map by zipping together the key and values lists . |
7,517 | private void extractAllFeats ( FgExampleList data , FactorTemplateList templates ) { IFgModel counts = new IFgModel ( ) { public void addAfterScaling ( FeatureVector fv , double multiplier ) { } public void add ( int feat , double addend ) { } } ; for ( int i = 0 ; i < data . size ( ) ; i ++ ) { if ( i % 1000 == 0 ) { log . debug ( "Processing example: " + i ) ; } LFgExample ex = data . get ( i ) ; FactorGraph fgLat = MarginalLogLikelihood . getFgLat ( ex . getFactorGraph ( ) , ex . getGoldConfig ( ) ) ; NoOpInferencer inferencer = new NoOpInferencer ( ex . getFactorGraph ( ) ) ; for ( int a = 0 ; a < ex . getFactorGraph ( ) . getNumFactors ( ) ; a ++ ) { Factor f = fgLat . getFactor ( a ) ; if ( f instanceof ObsFeatureCarrier && f instanceof TemplateFactor ) { int t = templates . getTemplateId ( ( TemplateFactor ) f ) ; if ( t != - 1 ) { ( ( ObsFeatureCarrier ) f ) . getObsFeatures ( ) ; } } else { f = ex . getFactorGraph ( ) . getFactor ( a ) ; if ( f instanceof GlobalFactor ) { ( ( GlobalFactor ) f ) . addExpectedPartials ( counts , 0 , inferencer , a ) ; } else { VarTensor marg = inferencer . getMarginalsForFactorId ( a ) ; f . addExpectedPartials ( counts , marg , 0 ) ; } } } } } | Loops through all examples to create the features thereby ensuring that the FTS are initialized . |
7,518 | private IntIntDenseVector [ ] [ ] countFeatures ( FgExampleList data , FactorTemplateList templates ) { IntIntDenseVector [ ] [ ] counts = new IntIntDenseVector [ numTemplates ] [ ] ; for ( int t = 0 ; t < numTemplates ; t ++ ) { FactorTemplate template = templates . get ( t ) ; int numConfigs = template . getNumConfigs ( ) ; int numFeats = template . getAlphabet ( ) . size ( ) ; counts [ t ] = new IntIntDenseVector [ numConfigs ] ; for ( int c = 0 ; c < numConfigs ; c ++ ) { counts [ t ] [ c ] = new IntIntDenseVector ( numFeats ) ; } } for ( int i = 0 ; i < data . size ( ) ; i ++ ) { LFgExample ex = data . get ( i ) ; FactorGraph fg = ex . getFactorGraph ( ) ; for ( int a = 0 ; a < ex . getFactorGraph ( ) . getNumFactors ( ) ; a ++ ) { Factor f = fg . getFactor ( a ) ; if ( f instanceof ObsFeatureCarrier && f instanceof TemplateFactor ) { int t = templates . getTemplateId ( ( TemplateFactor ) f ) ; if ( t != - 1 ) { FeatureVector fv = ( ( ObsFeatureCarrier ) f ) . getObsFeatures ( ) ; VarConfig predVc = ex . getGoldConfigPred ( a ) ; IntIter iter = IndexForVc . getConfigIter ( ex . getFactorGraph ( ) . getFactor ( a ) . getVars ( ) , predVc ) ; while ( iter . hasNext ( ) ) { int config = iter . next ( ) ; for ( IntDoubleEntry entry : fv ) { counts [ t ] [ config ] . add ( entry . index ( ) , 1 ) ; } } } } } } return counts ; } | Counts the number of times each feature appears in the gold training data . |
7,519 | protected void notifyToHandler ( ServerHandlerClass handler , ApiZone zone , ApiBuddyImpl buddy ) { ReflectMethodUtil . invokeHandleMethod ( handler . getHandleMethod ( ) , handler . newInstance ( ) , context , zone , buddy ) ; } | Notify event to handler |
7,520 | private void checkIndices ( int ... indices ) { if ( indices . length != dims . length ) { throw new IllegalArgumentException ( String . format ( "Indices array is not the correct length. expected=%d actual=%d" , indices . length , dims . length ) ) ; } for ( int i = 0 ; i < indices . length ; i ++ ) { if ( indices [ i ] < 0 || dims [ i ] <= indices [ i ] ) { throw new IllegalArgumentException ( String . format ( "Indices array contains an index that is out of bounds: i=%d index=%d" , i , indices [ i ] ) ) ; } } } | Checks that the indices are valid . |
7,521 | public double [ ] getValuesAsNativeArray ( ) { double [ ] vs = new double [ this . size ( ) ] ; for ( int c = 0 ; c < vs . length ; c ++ ) { vs [ c ] = getValue ( c ) ; } return vs ; } | Gets a copy of the internal values as a native array . |
7,522 | public static VTensor combine ( VTensor t1 , VTensor t2 ) { checkSameDims ( t1 , t2 ) ; checkSameAlgebra ( t1 , t2 ) ; int [ ] dims3 = IntArrays . insertEntry ( t1 . getDims ( ) , 0 , 2 ) ; VTensor y = new VTensor ( t1 . s , dims3 ) ; y . addTensor ( t1 , 0 , 0 ) ; y . addTensor ( t2 , 0 , 1 ) ; return y ; } | Combines two identically sized tensors by adding an initial dimension of size 2 . |
7,523 | static int guessNumWords ( Beliefs b ) { int n = - 1 ; for ( int v = 0 ; v < b . varBeliefs . length ; v ++ ) { Var var = b . varBeliefs [ v ] . getVars ( ) . get ( 0 ) ; if ( var instanceof LinkVar ) { LinkVar link = ( LinkVar ) var ; int p = link . getParent ( ) ; int c = link . getChild ( ) ; n = Math . max ( n , Math . max ( p , c ) ) ; } } return n + 1 ; } | Gets the maximum index of a parent or child in a LinkVar plus one . |
7,524 | public Map getSingleInfoServiceByRep ( String sql , Map requestParamMap ) throws Exception { List placeList = new ArrayList ( ) ; sqlTemplateService ( sql , requestParamMap , placeList ) ; String realSql = sqlTemplateService ( sql , requestParamMap , placeList ) ; ; Map retMap = getInnerDao ( ) . querySingleObjJoinByCondition ( realSql , placeList . toArray ( ) ) ; CheckModelTypeUtil . addMetaCols ( retMap ) ; CheckModelTypeUtil . changeNoStrCols ( retMap ) ; return retMap ; } | add 20190430 by ning |
7,525 | private void setOutMsgs ( VarTensor outMsg , SpanVar span , double outMsgTrue , double outMsgFalse ) { Algebra s = outMsg . getAlgebra ( ) ; outMsg . setValue ( SpanVar . FALSE , s . fromLogProb ( outMsgFalse ) ) ; outMsg . setValue ( SpanVar . TRUE , s . fromLogProb ( outMsgTrue ) ) ; if ( log . isTraceEnabled ( ) ) { log . trace ( String . format ( "outMsgTrue: %s = %.2f" , span . getName ( ) , outMsg . getValue ( LinkVar . TRUE ) ) ) ; log . trace ( String . format ( "outMsgFalse: %s = %.2f" , span . getName ( ) , outMsg . getValue ( LinkVar . FALSE ) ) ) ; } assert ! outMsg . containsBadValues ( ) : "message = " + outMsg ; } | Sets the outgoing messages . |
7,526 | private static boolean [ ] [ ] getChart ( int n , VarConfig vc ) { boolean [ ] [ ] chart = new boolean [ n ] [ n + 1 ] ; int count = 0 ; for ( Var v : vc . getVars ( ) ) { SpanVar span = ( SpanVar ) v ; chart [ span . getStart ( ) ] [ span . getEnd ( ) ] = ( vc . getState ( span ) == SpanVar . TRUE ) ; count ++ ; } if ( count != ( n * ( n + 1 ) / 2 ) ) { return null ; } return chart ; } | Creates a boolean chart representing the set of spans which are on or null if the number of span variables in the assignment is invalid . |
7,527 | private static boolean isTree ( int n , boolean [ ] [ ] chart ) { if ( ! chart [ 0 ] [ n ] ) { return false ; } for ( int width = 1 ; width <= n ; width ++ ) { for ( int start = 0 ; start <= n - width ; start ++ ) { int end = start + width ; if ( width == 1 ) { if ( ! chart [ start ] [ end ] ) { return false ; } } else { if ( chart [ start ] [ end ] ) { int childPairCount = 0 ; for ( int mid = start + 1 ; mid <= end - 1 ; mid ++ ) { if ( chart [ start ] [ mid ] && chart [ mid ] [ end ] ) { childPairCount ++ ; } } if ( childPairCount != 1 ) { return false ; } } } } } return true ; } | Returns true if the boolean chart represents a set of spans that form a valid constituency tree false otherwise . |
7,528 | public static IndexForVc getConfigIter ( VarSet indexVars , VarConfig config ) { int fixedConfigContrib = getConfigIndex ( indexVars , config ) ; VarSet forVars = new VarSet ( indexVars ) ; forVars . removeAll ( config . getVars ( ) ) ; return new IndexForVc ( indexVars , forVars , fixedConfigContrib ) ; } | Iterates over all the configurations of indexVars where the subset of variables in config have been clamped to their given values . The iterator returns the configuration index of variables in indexVars . |
7,529 | public static int [ ] getConfigArr ( VarSet vars , VarConfig config ) { IntArrayList a = new IntArrayList ( config . getVars ( ) . calcNumConfigs ( ) ) ; IntIter iter = getConfigIter ( vars , config ) ; while ( iter . hasNext ( ) ) { a . add ( iter . next ( ) ) ; } return a . toNativeArray ( ) ; } | Gets an array version of the configuration iterator . |
7,530 | public static int getConfigIndex ( VarSet vars , VarConfig config ) { int configIndex = 0 ; int numStatesProd = 1 ; for ( int v = vars . size ( ) - 1 ; v >= 0 ; v -- ) { Var var = vars . get ( v ) ; int state = config . getState ( var , 0 ) ; configIndex += state * numStatesProd ; numStatesProd *= var . getNumStates ( ) ; } return configIndex ; } | Gets the index of the configuration of the variables where all those in config have the specified value and all other variables in vars have the zero state . |
7,531 | public static int configIdToLibDaiIx ( int configId , VarSet vs ) { int [ ] indices = vs . getVarConfigAsArray ( configId ) ; int [ ] dims = vs . getDims ( ) ; return Tensor . ravelIndexMatlab ( indices , dims ) ; } | converts the internal pacaya index of a config on the varset into the libdai index corresponding to the same configuration |
7,532 | public PrivateKey get ( KeyStoreChooser keyStoreChooser , PrivateKeyChooserByAlias privateKeyChooserByAlias ) { CacheKey cacheKey = new CacheKey ( keyStoreChooser . getKeyStoreName ( ) , privateKeyChooserByAlias . getAlias ( ) ) ; PrivateKey retrievedPrivateKey = cache . get ( cacheKey ) ; if ( retrievedPrivateKey != null ) { return retrievedPrivateKey ; } KeyStore keyStore = keyStoreRegistry . get ( keyStoreChooser ) ; if ( keyStore != null ) { PrivateKeyFactoryBean factory = new PrivateKeyFactoryBean ( ) ; factory . setKeystore ( keyStore ) ; factory . setAlias ( privateKeyChooserByAlias . getAlias ( ) ) ; factory . setPassword ( privateKeyChooserByAlias . getPassword ( ) ) ; try { factory . afterPropertiesSet ( ) ; PrivateKey privateKey = ( PrivateKey ) factory . getObject ( ) ; if ( privateKey != null ) { cache . put ( cacheKey , privateKey ) ; } return privateKey ; } catch ( Exception e ) { throw new PrivateKeyException ( "error initializing private key factory bean" , e ) ; } } return null ; } | Returns the selected private key or null if not found . |
7,533 | public static int [ ] unravelIndex ( int configIx , int ... dims ) { int numConfigs = IntArrays . prod ( dims ) ; assert configIx < numConfigs ; int [ ] strides = getStrides ( dims ) ; return unravelIndexFromStrides ( configIx , strides ) ; } | Returns an integer array of the same length as dims that matches the configIx th configuration if enumerated configurations in order such that the leftmost dimension changes slowest |
7,534 | public static int [ ] unravelIndexMatlab ( int configIx , int ... dims ) { dims = dims . clone ( ) ; ArrayUtils . reverse ( dims ) ; int [ ] config = unravelIndex ( configIx , dims ) ; ArrayUtils . reverse ( config ) ; return config ; } | Returns an integer array of the same length as dims that matches the configIx th configuration if enumerated configurations in order such that the rightmost dimension is fastest |
7,535 | public static int [ ] unravelIndexFromStrides ( int configIx , int ... strides ) { int offset = 0 ; int [ ] config = new int [ strides . length ] ; for ( int i = 0 ; i < strides . length ; i ++ ) { int ix = ( configIx - offset ) / strides [ i ] ; config [ i ] = ix ; offset += ix * strides [ i ] ; } return config ; } | strides are given in order from left to right slowest to fastest |
7,536 | public double setValue ( int idx , double val ) { double prev = values [ idx ] ; values [ idx ] = val ; return prev ; } | Sets the value of the idx th entry . |
7,537 | public void add ( double addend ) { for ( int c = 0 ; c < this . values . length ; c ++ ) { addValue ( c , addend ) ; } } | Add the addend to each value . |
7,538 | public void multiply ( double val ) { for ( int c = 0 ; c < this . values . length ; c ++ ) { multiplyValue ( c , val ) ; } } | Scale each value by lambda . |
7,539 | public void divide ( double val ) { for ( int c = 0 ; c < this . values . length ; c ++ ) { divideValue ( c , val ) ; } } | Divide each value by lambda . |
7,540 | public Tensor select ( int dim , int idx ) { int [ ] yDims = IntArrays . removeEntry ( this . getDims ( ) , dim ) ; Tensor y = new Tensor ( s , yDims ) ; DimIter yIter = new DimIter ( y . getDims ( ) ) ; while ( yIter . hasNext ( ) ) { int [ ] yIdx = yIter . next ( ) ; int [ ] xIdx = IntArrays . insertEntry ( yIdx , dim , idx ) ; y . set ( yIdx , this . get ( xIdx ) ) ; } return y ; } | Selects a sub - tensor from this one . This can be though of as fixing a particular dimension to a given index . |
7,541 | public void addTensor ( Tensor addend , int dim , int idx ) { checkSameAlgebra ( this , addend ) ; DimIter yIter = new DimIter ( addend . getDims ( ) ) ; while ( yIter . hasNext ( ) ) { int [ ] yIdx = yIter . next ( ) ; int [ ] xIdx = IntArrays . insertEntry ( yIdx , dim , idx ) ; this . add ( xIdx , addend . get ( yIdx ) ) ; } } | Adds a smaller tensor to this one inserting it at a specified dimension and index . This can be thought of as selecting the sub - tensor of this tensor adding the smaller tensor to it . |
7,542 | public VarConfig getVarConfig ( int configIndex ) { int i ; int [ ] states = getVarConfigAsArray ( configIndex ) ; VarConfig config = new VarConfig ( ) ; i = 0 ; for ( Var var : this ) { config . put ( var , states [ i ++ ] ) ; } return config ; } | Gets the variable configuration corresponding to the given configuration index . |
7,543 | public void getVarConfigAsArray ( int configIndex , int [ ] putInto ) { if ( putInto . length != this . size ( ) ) throw new IllegalArgumentException ( ) ; int i = putInto . length - 1 ; for ( int v = this . size ( ) - 1 ; v >= 0 ; v -- ) { Var var = this . get ( v ) ; putInto [ i -- ] = configIndex % var . getNumStates ( ) ; configIndex /= var . getNumStates ( ) ; } } | this is the no - allocation version of the non - void method of the same name . |
7,544 | public int [ ] getDims ( ) { int [ ] dims = new int [ size ( ) ] ; for ( int i = 0 ; i < size ( ) ; i ++ ) { dims [ i ] = get ( i ) . getNumStates ( ) ; } return dims ; } | Returns an array holding the number of values the corresponding variables can take on |
7,545 | public static void runCommand ( String [ ] cmdArray , File logFile , File dir ) { Process proc = System . runProcess ( cmdArray , logFile , dir ) ; if ( proc . exitValue ( ) != 0 ) { throw new RuntimeException ( "Command failed with exit code " + proc . exitValue ( ) + ": " + System . cmdToString ( cmdArray ) + "\n" + QFiles . tail ( logFile ) ) ; } } | Checks the exit code and throws an Exception if the process failed . |
7,546 | public static Process runProcess ( String [ ] cmdArray , File logFile , File dir ) { try { ProcessBuilder pb = new ProcessBuilder ( cmdArray ) ; pb . redirectErrorStream ( true ) ; pb . directory ( dir ) ; Process proc = pb . start ( ) ; if ( logFile != null ) { InputStream inputStream = new BufferedInputStream ( proc . getInputStream ( ) ) ; BufferedOutputStream out = new BufferedOutputStream ( new FileOutputStream ( logFile ) ) ; int read = 0 ; byte [ ] bytes = new byte [ 1024 ] ; while ( ( read = inputStream . read ( bytes ) ) != - 1 ) { out . write ( bytes , 0 , read ) ; } inputStream . close ( ) ; out . flush ( ) ; out . close ( ) ; } proc . waitFor ( ) ; return proc ; } catch ( Exception e ) { String tail = "" ; try { tail = QFiles . tail ( logFile ) ; } catch ( Throwable t ) { } throw new RuntimeException ( "Exception thrown while trying to exec command " + System . cmdToString ( cmdArray ) + "\n" + tail , e ) ; } } | Returns the Process which contains the exit code . |
7,547 | private void forwardSendMessage ( int edge , int iter ) { double oldResidual = residuals [ edge ] ; residuals [ edge ] = smartResidual ( msgs [ edge ] , newMsgs [ edge ] , edge ) ; if ( oldResidual > prm . convergenceThreshold && residuals [ edge ] <= prm . convergenceThreshold ) { numConverged ++ ; } if ( oldResidual <= prm . convergenceThreshold && residuals [ edge ] > prm . convergenceThreshold ) { numConverged -- ; } if ( log . isTraceEnabled ( ) && iter > 0 ) { if ( msgs [ edge ] . getArgmaxConfigId ( ) != newMsgs [ edge ] . getArgmaxConfigId ( ) ) { oscillationCount . incrementAndGet ( ) ; } sendCount . incrementAndGet ( ) ; log . trace ( "Residual: {} {}" , fg . edgeToString ( edge ) , residuals [ edge ] ) ; } int child = bg . childE ( edge ) ; if ( ! bg . isT1T2 ( edge ) && bg . numNbsT1 ( child ) >= prm . minVarNbsForCache ) { varBeliefs [ child ] . elemDivBP ( msgs [ edge ] ) ; varBeliefs [ child ] . elemMultiply ( newMsgs [ edge ] ) ; assert ! varBeliefs [ child ] . containsBadValues ( ) : "varBeliefs[child] = " + varBeliefs [ child ] ; } else if ( bg . isT1T2 ( edge ) && bg . numNbsT2 ( child ) >= prm . minFacNbsForCache ) { Factor f = bg . t2E ( edge ) ; if ( ! ( f instanceof GlobalFactor ) ) { facBeliefs [ child ] . divBP ( msgs [ edge ] ) ; facBeliefs [ child ] . prod ( newMsgs [ edge ] ) ; assert ! facBeliefs [ child ] . containsBadValues ( ) : "facBeliefs[child] = " + facBeliefs [ child ] ; } } VarTensor oldMessage = msgs [ edge ] ; msgs [ edge ] = newMsgs [ edge ] ; newMsgs [ edge ] = oldMessage ; assert ! msgs [ edge ] . containsBadValues ( ) : "msgs[edge] = " + msgs [ edge ] ; if ( log . isTraceEnabled ( ) ) { log . trace ( "Message sent: {} {}" , fg . edgeToString ( edge ) , msgs [ edge ] ) ; } } | Sends the message that is currently pending for this edge . This just copies the message in the pending slot to the message slot for this edge . |
7,548 | private double smartResidual ( VarTensor message , VarTensor newMessage , int edge ) { return CachingBpSchedule . isConstantMsg ( edge , fg ) ? 0.0 : getResidual ( message , newMessage ) ; } | Returns the converged residual for constant messages and the actual residual otherwise . |
7,549 | private double getResidual ( VarTensor t1 , VarTensor t2 ) { assert s == t1 . getAlgebra ( ) && s == t2 . getAlgebra ( ) ; Tensor . checkEqualSize ( t1 , t2 ) ; Tensor . checkSameAlgebra ( t1 , t2 ) ; double residual = Double . NEGATIVE_INFINITY ; for ( int c = 0 ; c < t1 . size ( ) ; c ++ ) { double abs = Math . abs ( s . toLogProb ( t1 . get ( c ) ) - s . toLogProb ( t2 . get ( c ) ) ) ; if ( abs > residual ) { residual = abs ; } } return residual ; } | Gets the residual for a new message as the maximum error over all assignments . |
7,550 | private void calcProductAtVar ( int v , VarTensor prod , int excl1 , int excl2 ) { for ( int nb = 0 ; nb < bg . numNbsT1 ( v ) ; nb ++ ) { if ( nb == excl1 || nb == excl2 ) { continue ; } VarTensor nbMsg = msgs [ bg . opposingT1 ( v , nb ) ] ; prod . elemMultiply ( nbMsg ) ; } } | Computes the product of all messages being sent to a node optionally excluding messages sent from another node or two . |
7,551 | private VarTensor calcVarBeliefs ( Var var ) { VarTensor prod = new VarTensor ( s , new VarSet ( var ) , s . one ( ) ) ; calcProductAtVar ( var . getId ( ) , prod , - 1 , - 1 ) ; return prod ; } | Gets the unnormalized variable beleifs . |
7,552 | private VarTensor calcFactorBeliefs ( Factor factor ) { if ( factor instanceof GlobalFactor ) { log . warn ( "Getting marginals of a global factor is not supported." + " This will require exponential space to store the resulting factor." + " This should only be used for testing." ) ; } VarTensor prod = safeNewVarTensor ( factor ) ; calcProductAtFactor ( factor . getId ( ) , prod , - 1 , - 1 ) ; return prod ; } | Gets the unnormalized factor beleifs . |
7,553 | private static File getTempPath ( String prefix , File parentDir ) throws IOException { final int maxI = ( int ) Math . pow ( 10 , NUM_DIGITS ) ; String formatStr = "%s_%0" + NUM_DIGITS + "d" ; File path ; int i ; for ( i = 0 ; i < maxI ; i ++ ) { path = new File ( parentDir , String . format ( formatStr , prefix , i ) ) ; if ( ! path . exists ( ) ) { return path ; } } path = File . createTempFile ( prefix , "" , parentDir ) ; if ( ! path . delete ( ) ) { throw new RuntimeException ( "Could not delete temp file as expected: " + path ) ; } return path ; } | Creates a file object of a currently available path but does not create the file . This method is not thread safe . |
7,554 | public static void readUntil ( BufferedReader reader , String breakpoint ) throws IOException { String line ; while ( ( line = reader . readLine ( ) ) != null ) { if ( line . equals ( breakpoint ) ) { return ; } } } | Read until the current line equals the breakpoint string . |
7,555 | public static void runOutsideAlgorithm ( final int [ ] sent , final CnfGrammar grammar , final LoopOrder loopOrder , final Chart inChart , final Chart outChart , final Scorer scorer ) { ChartCell outRootCell = outChart . getCell ( 0 , sent . length ) ; outRootCell . updateCell ( grammar . getRootSymbol ( ) , 0 , - 1 , null ) ; for ( int width = sent . length ; width >= 1 ; width -- ) { for ( int start = 0 ; start <= sent . length - width ; start ++ ) { int end = start + width ; ChartCell outCell = outChart . getCell ( start , end ) ; ScoresSnapshot scoresSnapshot = outCell . getScoresSnapshot ( ) ; int [ ] nts = outCell . getNts ( ) ; for ( final int parentNt : nts ) { for ( final Rule r : grammar . getUnaryRulesWithParent ( parentNt ) ) { double score = scorer . score ( r , start , end , end ) + scoresSnapshot . getScore ( parentNt ) ; outCell . updateCell ( r . getLeftChild ( ) , score , end , r ) ; } } if ( loopOrder == LoopOrder . CARTESIAN_PRODUCT ) { processCellCartesianProduct ( grammar , inChart , outChart , start , end , outCell , scorer ) ; } else if ( loopOrder == LoopOrder . LEFT_CHILD ) { processCellLeftChild ( grammar , inChart , outChart , start , end , outCell , scorer ) ; } else if ( loopOrder == LoopOrder . RIGHT_CHILD ) { processCellRightChild ( grammar , inChart , outChart , start , end , outCell , scorer ) ; } else { throw new RuntimeException ( "Not implemented: " + loopOrder ) ; } } } for ( int i = 0 ; i <= sent . length - 1 ; i ++ ) { ChartCell outCell = outChart . getCell ( i , i + 1 ) ; ScoresSnapshot scoresSnapshot = outCell . getScoresSnapshot ( ) ; for ( final Rule r : grammar . getLexicalRulesWithChild ( sent [ i ] ) ) { double score = scorer . score ( r , i , i + 1 , i + 1 ) + scoresSnapshot . getScore ( r . getParent ( ) ) ; outCell . updateCell ( r . getLeftChild ( ) , score , i + 1 , r ) ; } } } | Runs the outside algorithm given an inside chart . |
7,556 | public static IntDoubleVector estimateGradientFd ( Function fn , IntDoubleVector x , double epsilon ) { int numParams = fn . getNumDimensions ( ) ; IntDoubleVector gradFd = new IntDoubleDenseVector ( numParams ) ; for ( int j = 0 ; j < numParams ; j ++ ) { IntDoubleVector d = new IntDoubleDenseVector ( numParams ) ; d . set ( j , 1 ) ; double dotFd = getGradDotDirApprox ( fn , x , d , epsilon ) ; if ( Double . isNaN ( dotFd ) ) { log . warn ( "Hit NaN" ) ; } gradFd . set ( j , dotFd ) ; } return gradFd ; } | Estimates a gradient of a function by an independent finite - difference computation along each dimension of the domain of the function . |
7,557 | public void reset ( Sentence sentence ) { this . sentence = sentence ; if ( sentence . size ( ) > chart . length ) { chart = getNewChart ( sentence , grammar , cellType , parseType , constraint ) ; } else { for ( int i = 0 ; i < sentence . size ( ) ; i ++ ) { for ( int j = i + 1 ; j < sentence . size ( ) + 1 ; j ++ ) { chart [ i ] [ j ] . reset ( sentence ) ; } } } } | Resets the chart for the input sentence . |
7,558 | private static ChartCell [ ] [ ] getNewChart ( Sentence sentence , CnfGrammar grammar , ChartCellType cellType , ParseType parseType , ChartCellConstraint constraint ) { ChartCell [ ] [ ] chart = new ChartCell [ sentence . size ( ) ] [ sentence . size ( ) + 1 ] ; for ( int i = 0 ; i < chart . length ; i ++ ) { for ( int j = i + 1 ; j < chart [ i ] . length ; j ++ ) { if ( parseType == ParseType . INSIDE && cellType != ChartCellType . FULL ) { throw new RuntimeException ( "Inside algorithm not implemented for cell type: " + cellType ) ; } ChartCell cell ; switch ( cellType ) { case SINGLE_HASH : chart [ i ] [ j ] = new SingleHashChartCell ( grammar , false ) ; break ; case SINGLE_HASH_BREAK_TIES : chart [ i ] [ j ] = new SingleHashChartCell ( grammar , true ) ; break ; case CONSTRAINED_SINGLE : cell = new SingleHashChartCell ( grammar , true ) ; chart [ i ] [ j ] = new ConstrainedChartCell ( i , j , cell , constraint , sentence ) ; break ; case DOUBLE_HASH : chart [ i ] [ j ] = new DoubleHashChartCell ( grammar ) ; break ; case FULL : chart [ i ] [ j ] = new FullChartCell ( i , j , grammar , parseType ) ; break ; case FULL_BREAK_TIES : chart [ i ] [ j ] = new FullTieBreakerChartCell ( grammar , true ) ; break ; case CONSTRAINED_FULL : cell = new FullTieBreakerChartCell ( grammar , true ) ; chart [ i ] [ j ] = new ConstrainedChartCell ( i , j , cell , constraint , sentence ) ; break ; default : throw new RuntimeException ( "not implemented for " + cellType ) ; } } } return chart ; } | Gets a new chart of the appropriate size for the sentence specific to this grammar and with cells of the specified type . |
7,559 | public void setInitializationVector ( String initializationVector ) { try { this . initializationVectorSpec = new IvParameterSpec ( Base64 . decodeBase64 ( initializationVector . getBytes ( "UTF-8" ) ) ) ; } catch ( UnsupportedEncodingException e ) { throw new SymmetricEncryptionException ( "UTF-8 is an unsupported encoding on this platform" , e ) ; } } | A base64 encoded representation of the raw byte array containing the initialization vector . |
7,560 | public double getValue ( int idx ) { int vSize = MVecArray . count ( varBeliefs ) ; if ( idx < vSize ) { return MVecArray . getValue ( idx , varBeliefs ) ; } else { return MVecArray . getValue ( idx - vSize , facBeliefs ) ; } } | Gets a particular value by treating this object as a vector . |
7,561 | public double setValue ( int idx , double val ) { int vSize = MVecArray . count ( varBeliefs ) ; if ( idx < vSize ) { return MVecArray . setValue ( idx , val , varBeliefs ) ; } else { return MVecArray . setValue ( idx - vSize , val , facBeliefs ) ; } } | Sets a particular value by treating this object as a vector . |
7,562 | public FactorGraph readBnAsFg ( File networkFile , File cpdFile ) throws IOException { return readBnAsFg ( new FileInputStream ( networkFile ) , new FileInputStream ( cpdFile ) ) ; } | Reads a Bayesian Network from a network file and a CPD file and returns a factor graph representation of it . |
7,563 | public FactorGraph readBnAsFg ( InputStream networkIs , InputStream cpdIs ) throws IOException { BufferedReader networkReader = new BufferedReader ( new InputStreamReader ( networkIs ) ) ; int numVars = Integer . parseInt ( networkReader . readLine ( ) . trim ( ) ) ; varMap = new HashMap < String , Var > ( ) ; VarSet allVars = new VarSet ( ) ; for ( int i = 0 ; i < numVars ; i ++ ) { Var var = parseVar ( networkReader . readLine ( ) ) ; allVars . add ( var ) ; varMap . put ( var . getName ( ) , var ) ; } assert ( allVars . size ( ) == numVars ) ; networkReader . close ( ) ; BufferedReader cpdReader = new BufferedReader ( new InputStreamReader ( cpdIs ) ) ; factorMap = new LinkedHashMap < VarSet , ExplicitFactor > ( ) ; String line ; while ( ( line = cpdReader . readLine ( ) ) != null ) { VarConfig config = new VarConfig ( ) ; String [ ] assns = whitespaceOrComma . split ( line ) ; for ( int i = 0 ; i < assns . length - 1 ; i ++ ) { String assn = assns [ i ] ; String [ ] va = equals . split ( assn ) ; assert ( va . length == 2 ) ; String varName = va [ 0 ] ; String stateName = va [ 1 ] ; config . put ( varMap . get ( varName ) , stateName ) ; } double value = Double . parseDouble ( assns [ assns . length - 1 ] ) ; value = FastMath . log ( value ) ; VarSet vars = config . getVars ( ) ; ExplicitFactor f = factorMap . get ( vars ) ; if ( f == null ) { f = new ExplicitFactor ( vars ) ; } f . setValue ( config . getConfigIndex ( ) , value ) ; factorMap . put ( vars , f ) ; } cpdReader . close ( ) ; FactorGraph fg = new FactorGraph ( ) ; for ( ExplicitFactor f : factorMap . values ( ) ) { fg . addFactor ( f ) ; } return fg ; } | Reads a Bayesian Network from a network InputStream and a CPD InputStream and returns a factor graph representation of it . |
7,564 | private static Var parseVar ( String varLine ) { String [ ] ws = whitespace . split ( varLine ) ; String name = ws [ 0 ] ; List < String > stateNames = Arrays . asList ( comma . split ( ws [ 1 ] ) ) ; int numStates = stateNames . size ( ) ; return new Var ( VarType . PREDICTED , numStates , name , stateNames ) ; } | Reads a variable from a line containing the variable name a space then a comma - separated list of the values it can take . |
7,565 | public boolean add ( T e ) { if ( elements . add ( e ) ) { ordered . add ( e ) ; return true ; } else { return false ; } } | maintain the set so that it is easy to test membership the list so that there is a fixed order |
7,566 | public boolean remove ( Object o ) { if ( elements . remove ( o ) ) { ordered . remove ( o ) ; return true ; } else { return false ; } } | remove will be slow |
7,567 | public String digest ( String message ) { final byte [ ] messageAsByteArray ; try { messageAsByteArray = message . getBytes ( charsetName ) ; } catch ( UnsupportedEncodingException e ) { throw new DigestException ( "error converting message to byte array: charsetName=" + charsetName , e ) ; } final byte [ ] digest = digest ( messageAsByteArray ) ; switch ( outputMode ) { case BASE64 : return Base64 . encodeBase64String ( digest ) ; case HEX : return Hex . encodeHexString ( digest ) ; default : return null ; } } | Returns the message digest . The representation of the message digest depends on the outputMode property . |
7,568 | public void addEdge ( DiEdge e ) { if ( ! getEdges ( ) . contains ( e ) ) { super . addEdge ( e ) ; weights . put ( e , makeDefaultWeight . apply ( e ) ) ; } } | Attempts to adds the edge to the graph with default weight if not already present ; If the edge is already present does nothing . |
7,569 | public void addEdge ( DiEdge e , double w ) { if ( ! getEdges ( ) . contains ( e ) ) { super . addEdge ( e ) ; weights . put ( e , w ) ; } } | Adds the edge with the given weight |
7,570 | public void setWeight ( int s , int t , double w ) { DiEdge e = edge ( s , t ) ; assertEdge ( e ) ; weights . put ( e , w ) ; } | Sets the weight of the edge s - > t to be w if the edge is present otherwise an IndexOutOfBoundsException is thrown |
7,571 | public static < X > ArrayList < X > sublist ( List < X > list , int start , int end ) { ArrayList < X > sublist = new ArrayList < X > ( ) ; for ( int i = start ; i < end ; i ++ ) { sublist . add ( list . get ( i ) ) ; } return sublist ; } | Creates a new list containing a slice of the original list . |
7,572 | public static ArrayList < String > getInternedList ( List < String > oldList ) { ArrayList < String > newList = new ArrayList < String > ( oldList . size ( ) ) ; for ( String elem : oldList ) { newList . add ( elem . intern ( ) ) ; } return newList ; } | Gets a new list of Strings that have been interned . |
7,573 | public static void intern ( List < String > list ) { if ( list == null ) { return ; } for ( int i = 0 ; i < list . size ( ) ; i ++ ) { String interned = list . get ( i ) ; if ( interned != null ) { interned = interned . intern ( ) ; } list . set ( i , interned ) ; } } | Interns a list of strings in place . |
7,574 | public static < T > Collection < T > collect ( Iterable < T > stream ) { LinkedList < T > collection = new LinkedList < > ( ) ; for ( T e : stream ) { collection . add ( e ) ; } return collection ; } | Returns a Collections that contains all of the objects from the underlying stream in order |
7,575 | public static < T > Iterable < Indexed < T > > enumerate ( Iterable < T > stream ) { return new Iterable < Indexed < T > > ( ) { public Iterator < Indexed < T > > iterator ( ) { Iterator < T > itr = stream . iterator ( ) ; return new Iterator < Indexed < T > > ( ) { private int i = 0 ; public boolean hasNext ( ) { return itr . hasNext ( ) ; } public Indexed < T > next ( ) { Indexed < T > nextPair = new Indexed < T > ( itr . next ( ) , i ) ; i ++ ; return nextPair ; } } ; } } ; } | Returns an iterable over Index objects that each hold one of the original objects of the stream as well its index in the stream |
7,576 | public int find ( int element ) { if ( trees [ element ] != element ) trees [ element ] = find ( trees [ element ] ) ; return trees [ element ] ; } | Return the set where the given element is . This implementation compresses the followed path . |
7,577 | public Certificate get ( KeyStoreChooser keyStoreChooser , CertificateChooserByAlias certificateChooserByAlias ) { CacheCert cacheCert = new CacheCert ( keyStoreChooser . getKeyStoreName ( ) , certificateChooserByAlias . getAlias ( ) ) ; Certificate retrievedCertificate = cache . get ( cacheCert ) ; if ( retrievedCertificate != null ) { return retrievedCertificate ; } KeyStore keyStore = keyStoreRegistry . get ( keyStoreChooser ) ; if ( keyStore != null ) { CertificateFactoryBean factory = new CertificateFactoryBean ( ) ; factory . setKeystore ( keyStore ) ; factory . setAlias ( certificateChooserByAlias . getAlias ( ) ) ; try { factory . afterPropertiesSet ( ) ; Certificate certificate = ( Certificate ) factory . getObject ( ) ; if ( certificate != null ) { cache . put ( cacheCert , certificate ) ; } return certificate ; } catch ( Exception e ) { throw new CertificateException ( "error initializing the certificate factory bean" , e ) ; } } return null ; } | Returns the selected certificate or null if not found . |
7,578 | protected boolean checkHandler ( RoomHandlerClass handler , ApiRoom roomAgent , Object user ) { return ( handler . getRoomClass ( ) . isAssignableFrom ( roomAgent . getClass ( ) ) ) && ( roomAgent . getName ( ) . startsWith ( handler . getRoomName ( ) ) ) ; } | Validate the handler |
7,579 | private void callHandleMethod ( Method method , Object instance , Object roomAgent , Object userAgent ) { ReflectMethodUtil . invokeHandleMethod ( method , instance , context , roomAgent , userAgent ) ; } | Invoke handle method |
7,580 | @ SuppressWarnings ( "unchecked" ) public ApiRoom execute ( ) { Room sfsRoom = CommandUtil . getSfsRoom ( agent , extension ) ; User sfsUser = CommandUtil . getSfsUser ( user , api ) ; if ( sfsRoom == null ) return null ; AgentClassUnwrapper unwrapper = context . getRoomAgentClass ( agent . getClass ( ) ) . getUnwrapper ( ) ; List < RoomVariable > variables = new RoomAgentSerializer ( ) . serialize ( unwrapper , agent ) ; List < RoomVariable > answer = variables ; if ( includedVars . size ( ) > 0 ) answer = getVariables ( variables , includedVars ) ; answer . removeAll ( getVariables ( answer , excludedVars ) ) ; if ( toClient ) api . setRoomVariables ( sfsUser , sfsRoom , answer ) ; else sfsRoom . setVariables ( answer ) ; return agent ; } | Execute update room variables |
7,581 | public static EdgeScores getEdgeMarginalsRealSemiring ( O2AllGraDpHypergraph graph , Scores sc ) { Algebra s = graph . getAlgebra ( ) ; int nplus = graph . getNumTokens ( ) + 1 ; Hypernode [ ] [ ] [ ] [ ] c = graph . getChart ( ) ; EdgeScores marg = new EdgeScores ( graph . getNumTokens ( ) , 0.0 ) ; for ( int width = 1 ; width < nplus ; width ++ ) { for ( int i = 0 ; i < nplus - width ; i ++ ) { int j = i + width ; for ( int g = 0 ; g < nplus ; g ++ ) { if ( i <= g && g <= j && ! ( i == 0 && g == O2AllGraDpHypergraph . NIL ) ) { continue ; } if ( j > 0 ) { marg . incrScore ( i - 1 , j - 1 , s . toReal ( sc . marginal [ c [ i ] [ j ] [ g ] [ O2AllGraDpHypergraph . INCOMPLETE ] . getId ( ) ] ) ) ; } if ( i > 0 ) { marg . incrScore ( j - 1 , i - 1 , s . toReal ( sc . marginal [ c [ j ] [ i ] [ g ] [ O2AllGraDpHypergraph . INCOMPLETE ] . getId ( ) ] ) ) ; } } } } return marg ; } | Gets the edge marginals in the real semiring from an all - grandparents hypergraph and its marginals in scores . |
7,582 | public static boolean hasOneParentPerToken ( int n , VarConfig vc ) { int [ ] parents = new int [ n ] ; Arrays . fill ( parents , - 2 ) ; for ( Var v : vc . getVars ( ) ) { if ( v instanceof LinkVar ) { LinkVar link = ( LinkVar ) v ; if ( vc . getState ( v ) == LinkVar . TRUE ) { if ( parents [ link . getChild ( ) ] != - 2 ) { return false ; } parents [ link . getChild ( ) ] = link . getParent ( ) ; } } } return ! ArrayUtils . contains ( parents , - 2 ) ; } | Returns whether this variable assignment specifies one parent per token . |
7,583 | public static int [ ] getParents ( int n , VarConfig vc ) { int [ ] parents = new int [ n ] ; Arrays . fill ( parents , - 2 ) ; for ( Var v : vc . getVars ( ) ) { if ( v instanceof LinkVar ) { LinkVar link = ( LinkVar ) v ; if ( vc . getState ( v ) == LinkVar . TRUE ) { if ( parents [ link . getChild ( ) ] != - 2 ) { throw new IllegalStateException ( "Multiple parents defined for the same child. Is this VarConfig for only one example?" ) ; } parents [ link . getChild ( ) ] = link . getParent ( ) ; } } } return parents ; } | Extracts the parents as defined by a variable assignment for a single sentence . |
7,584 | private static VarTensor getProductOfAllFactors ( FactorGraph fg , Algebra s ) { VarTensor joint = new VarTensor ( s , new VarSet ( ) , s . one ( ) ) ; for ( int a = 0 ; a < fg . getNumFactors ( ) ; a ++ ) { Factor f = fg . getFactor ( a ) ; VarTensor factor = safeNewVarTensor ( s , f ) ; assert ! factor . containsBadValues ( ) : factor ; joint . prod ( factor ) ; } return joint ; } | Gets the product of all the factors in the factor graph . If working in the log - domain this will do factor addition . |
7,585 | protected boolean checkHandler ( ZoneHandlerClass handler , ApiZone apiZone ) { return apiZone . getName ( ) . startsWith ( handler . getZoneName ( ) ) ; } | Check zone name |
7,586 | private void callHandleMethod ( Method method , Object instance , ApiZone apiZone , Object userAgent ) { ReflectMethodUtil . invokeHandleMethod ( method , instance , context , apiZone , userAgent ) ; } | Call handle method |
7,587 | public static double probabilityTruncZero ( double a , double b , double mu , double sigma ) { a = Math . max ( a , 0.0 ) ; b = Math . max ( b , 0.0 ) ; final double denom = sigma * SQRT2 ; final double scaledSDA = ( a - mu ) / denom ; final double scaledSDB = ( b - mu ) / denom ; final double probNormTimes2 = Erf . erf ( scaledSDA , scaledSDB ) ; final double scaledSD0 = - mu / denom ; final double reZTimes2 = Erf . erfc ( scaledSD0 ) ; return probNormTimes2 / reZTimes2 ; } | returns the probability of x falling within the range of a to b under a normal distribution with mean mu and standard deviation sigma if the distribution is truncated below 0 and renormalized |
7,588 | public static double meanTruncLower ( double mu , double sigma , double lowerBound ) { double alpha = ( lowerBound - mu ) / sigma ; double phiAlpha = densityNonTrunc ( alpha , 0 , 1.0 ) ; double cPhiAlpha = cumulativeNonTrunc ( alpha , 0 , 1.0 ) ; return mu + sigma * phiAlpha / ( 1.0 - cPhiAlpha ) ; } | Returns the mean of the normal distribution truncated to 0 for values of x < lowerBound |
7,589 | void set ( int row , int column , V value ) { this . row = row ; this . column = column ; this . value = value ; } | Sets the content of the cell . |
7,590 | public DeviceEnvelope getDevice ( String deviceId ) throws ApiException { ApiResponse < DeviceEnvelope > resp = getDeviceWithHttpInfo ( deviceId ) ; return resp . getData ( ) ; } | Get Device Retrieves a device |
7,591 | public SubscriptionEnvelope deleteSubscription ( String subId ) throws ApiException { ApiResponse < SubscriptionEnvelope > resp = deleteSubscriptionWithHttpInfo ( subId ) ; return resp . getData ( ) ; } | Delete Subscription Delete Subscription |
7,592 | private void init ( DelaunayTriangulation delaunay , int xCellCount , int yCellCount , BoundingBox region ) { indexDelaunay = delaunay ; indexRegion = region ; x_size = region . getWidth ( ) / yCellCount ; y_size = region . getHeight ( ) / xCellCount ; grid = new Triangle [ xCellCount ] [ yCellCount ] ; Triangle colStartTriangle = indexDelaunay . find ( middleOfCell ( 0 , 0 ) ) ; updateCellValues ( 0 , 0 , xCellCount - 1 , yCellCount - 1 , colStartTriangle ) ; } | Initialize the grid index |
7,593 | public Triangle findCellTriangleOf ( Point3D point ) { int x_index = ( int ) ( ( point . x - indexRegion . minX ( ) ) / x_size ) ; int y_index = ( int ) ( ( point . y - indexRegion . minY ( ) ) / y_size ) ; return grid [ x_index ] [ y_index ] ; } | Finds a triangle near the given point |
7,594 | public void updateIndex ( Iterator < Triangle > updatedTriangles ) { BoundingBox updatedRegion = new BoundingBox ( ) ; while ( updatedTriangles . hasNext ( ) ) { updatedRegion = updatedRegion . unionWith ( updatedTriangles . next ( ) . getBoundingBox ( ) ) ; } if ( updatedRegion . isNull ( ) ) return ; if ( ! indexRegion . contains ( updatedRegion ) ) { init ( indexDelaunay , ( int ) ( indexRegion . getWidth ( ) / x_size ) , ( int ) ( indexRegion . getHeight ( ) / y_size ) , indexRegion . unionWith ( updatedRegion ) ) ; } else { Vector2i minInvalidCell = getCellOf ( updatedRegion . getMinPoint ( ) ) ; Vector2i maxInvalidCell = getCellOf ( updatedRegion . getMaxPoint ( ) ) ; Triangle adjacentValidTriangle = findValidTriangle ( minInvalidCell ) ; updateCellValues ( minInvalidCell . getX ( ) , minInvalidCell . getY ( ) , maxInvalidCell . getX ( ) , maxInvalidCell . getY ( ) , adjacentValidTriangle ) ; } } | Updates the grid index to reflect changes to the triangulation . Note that added triangles outside the indexed region will force to recompute the whole index with the enlarged region . |
7,595 | private Vector2i getCellOf ( Point3D coordinate ) { int xCell = ( int ) ( ( coordinate . x - indexRegion . minX ( ) ) / x_size ) ; int yCell = ( int ) ( ( coordinate . y - indexRegion . minY ( ) ) / y_size ) ; return new Vector2i ( xCell , yCell ) ; } | Locates the grid cell point covering the given coordinate |
7,596 | private Vector3 middleOfCell ( int x_index , int y_index ) { float middleXCell = ( float ) ( indexRegion . minX ( ) + x_index * x_size + x_size / 2 ) ; float middleYCell = ( float ) ( indexRegion . minY ( ) + y_index * y_size + y_size / 2 ) ; return new Vector3 ( middleXCell , middleYCell , 0 ) ; } | Create a point at the center of a cell |
7,597 | public static double Function ( double x ) { double [ ] P = { 1.60119522476751861407E-4 , 1.19135147006586384913E-3 , 1.04213797561761569935E-2 , 4.76367800457137231464E-2 , 2.07448227648435975150E-1 , 4.94214826801497100753E-1 , 9.99999999999999996796E-1 } ; double [ ] Q = { - 2.31581873324120129819E-5 , 5.39605580493303397842E-4 , - 4.45641913851797240494E-3 , 1.18139785222060435552E-2 , 3.58236398605498653373E-2 , - 2.34591795718243348568E-1 , 7.14304917030273074085E-2 , 1.00000000000000000320E0 } ; double p , z ; double q = Math . abs ( x ) ; if ( q > 33.0 ) { if ( x < 0.0 ) { p = Math . floor ( q ) ; if ( p == q ) { try { throw new ArithmeticException ( "Overflow" ) ; } catch ( Exception e ) { e . printStackTrace ( ) ; } } z = q - p ; if ( z > 0.5 ) { p += 1.0 ; z = q - p ; } z = q * Math . sin ( Math . PI * z ) ; if ( z == 0.0 ) { try { throw new ArithmeticException ( "Overflow" ) ; } catch ( Exception e ) { e . printStackTrace ( ) ; } } z = Math . abs ( z ) ; z = Math . PI / ( z * Stirling ( q ) ) ; return - z ; } else { return Stirling ( x ) ; } } z = 1.0 ; while ( x >= 3.0 ) { x -= 1.0 ; z *= x ; } while ( x < 0.0 ) { if ( x == 0.0 ) { throw new ArithmeticException ( ) ; } else if ( x > - 1.0E-9 ) { return ( z / ( ( 1.0 + 0.5772156649015329 * x ) * x ) ) ; } z /= x ; x += 1.0 ; } while ( x < 2.0 ) { if ( x == 0.0 ) { throw new ArithmeticException ( ) ; } else if ( x < 1.0E-9 ) { return ( z / ( ( 1.0 + 0.5772156649015329 * x ) * x ) ) ; } z /= x ; x += 1.0 ; } if ( ( x == 2.0 ) || ( x == 3.0 ) ) return z ; x -= 2.0 ; p = Special . Polevl ( x , P , 6 ) ; q = Special . Polevl ( x , Q , 7 ) ; return z * p / q ; } | Gamma function of the specified value . |
7,598 | public static double Stirling ( double x ) { double [ ] STIR = { 7.87311395793093628397E-4 , - 2.29549961613378126380E-4 , - 2.68132617805781232825E-3 , 3.47222221605458667310E-3 , 8.33333333333482257126E-2 , } ; double MAXSTIR = 143.01608 ; double w = 1.0 / x ; double y = Math . exp ( x ) ; w = 1.0 + w * Special . Polevl ( w , STIR , 4 ) ; if ( x > MAXSTIR ) { double v = Math . pow ( x , 0.5 * x - 0.25 ) ; y = v * ( v / y ) ; } else { y = Math . pow ( x , x - 0.5 ) / y ; } y = 2.50662827463100050242E0 * y * w ; return y ; } | Gamma function as computed by Stirling s formula . |
7,599 | public static double Digamma ( double x ) { double s = 0 ; double w = 0 ; double y = 0 ; double z = 0 ; double nz = 0 ; boolean negative = false ; if ( x <= 0.0 ) { negative = true ; double q = x ; double p = ( int ) Math . floor ( q ) ; if ( p == q ) { try { throw new ArithmeticException ( "Function computation resulted in arithmetic overflow." ) ; } catch ( Exception e ) { e . printStackTrace ( ) ; } } nz = q - p ; if ( nz != 0.5 ) { if ( nz > 0.5 ) { p = p + 1.0 ; nz = q - p ; } nz = Math . PI / Math . tan ( Math . PI * nz ) ; } else { nz = 0.0 ; } x = 1.0 - x ; } if ( x <= 10.0 && x == Math . floor ( x ) ) { y = 0.0 ; int n = ( int ) Math . floor ( x ) ; for ( int i = 1 ; i <= n - 1 ; i ++ ) { w = i ; y = y + 1.0 / w ; } y = y - 0.57721566490153286061 ; } else { s = x ; w = 0.0 ; while ( s < 10.0 ) { w = w + 1.0 / s ; s = s + 1.0 ; } if ( s < 1.0E17 ) { z = 1.0 / ( s * s ) ; double polv = 8.33333333333333333333E-2 ; polv = polv * z - 2.10927960927960927961E-2 ; polv = polv * z + 7.57575757575757575758E-3 ; polv = polv * z - 4.16666666666666666667E-3 ; polv = polv * z + 3.96825396825396825397E-3 ; polv = polv * z - 8.33333333333333333333E-3 ; polv = polv * z + 8.33333333333333333333E-2 ; y = z * polv ; } else { y = 0.0 ; } y = Math . log ( s ) - 0.5 / s - y - w ; } if ( negative == true ) { y = y - nz ; } return y ; } | Digamma function . |
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