Field Detail

• public static final java.lang.String QBIC_ENTITY_SAMPLE_CODE_SCHEMA

• public static final java.lang.String QBIC_SAMPLE_BARCODE_SCHEMA

• @java.lang.Deprecated public static final java.lang.String QBIC_SAMPLE_ID_SCHEMA

  deprecated:

  this is deprecated since 2.4.0 please use QBIC_SAMPLE_BARCODE_SCHEMA instead

• private static final org.apache.logging.log4j.Logger logger

• public static java.util.Map<SampleType, ExperimentType> sampleTypesToExpTypes

Constructor Detail

• SampleCodeFunctions()

Method Detail

• public static char checksum(java.lang.String s)

  Computes a checksum digit for a given String. This checksum is weighted position-specific, meaning it will also most likely fail a check if there is a typo of the String resulting in a swapping of two numbers.

  Parameters:

  s - String for which a checksum should be computed.

  Returns:

  Character representing the checksum of the input String.

• public static int compareSampleCodes(java.lang.String c1, java.lang.String c2)

• public static java.lang.String createCountString(int id, int length)

  Creates a string with leading zeroes from a number

  Parameters:

  id - number

  length - of the final string

  Returns:

  the completed String with leading zeroes

• public static java.util.List<java.lang.String> findAllQbicSampleCodes(java.lang.String text)

  Finds all QBiC sample codes in a String object. Only works for the codes with check digit, not for the entity codes.

  Parameters:

  text - The text to search

  Returns:

  A list of found codes. Is empty if no code was found.

• public static java.lang.String getBarcodeRange(java.util.List<java.lang.String> ids)

  Returns a String denoting the range of a list of barcodes as used in QBiC

  Parameters:

  ids - List of code strings

  Returns:

  String denoting a range of the barcodes

• public static float getPercentageStep(int max)

• public static java.lang.String getProjectPrefix(java.lang.String sample)

  Returns the 5 character project prefix used for samples in openBIS.

  Parameters:

  sample - sample ID starting with a standard project prefix.

  Returns:

  Project prefix of the sample id

• public static java.lang.String incrementSampleCode(java.lang.String code)

  Increments to the next sample string in the order, meaning the project code stays the same and the 3 letter number is incremented, except if it's 999, then the following letter is incremented and the number starts with 001 again.

  Parameters:

  code - a 10 digit sample code

  Returns:

  a new sample code

• public static char incrementUppercase(char c)

  Increments the value of an upper case char. When at "Z" restarts with "A".

  Parameters:

  c - the char to be incremented

  Returns:

  the next letter in the alphabet relative to the input char

• public static boolean isInteger(java.lang.String s)

  Checks if a String can be parsed to an Integer

  Parameters:

  s - a String

  Returns:

  true, if the String can be parsed to an Integer successfully, false otherwise

• public static boolean isMeasurementOfBarcode(java.lang.String code, java.lang.String type)

• public static boolean isQbicBarcode(java.lang.String code)

  Checks if a String fits the QBiC barcode pattern and has a correct checksum

  Parameters:

  code - A String that may be a barcode

  Returns:

  true if String is a QBiC barcode with matching checksum, false if not

• public static boolean isQbicEntityCode(java.lang.String code)

  Checks if a String fits the QBiC entity code pattern, as used for the species level

  Parameters:

  code - A String that may be a qbic entity code

  Returns:

  true if String is a QBiC entity code, false if not

• public static char mapToChar(int i)

  Maps an integer to a char representation. This can be used for computing the checksum.

  Parameters:

  i - number to be mapped

  Returns:

  char representing the input number

• public static java.lang.String max(java.lang.String a, java.lang.String b)

  Checks which of two Strings can be parsed to a larger Integer and returns it.

  Parameters:

  a - a String

  b - another String

  Returns:

  the String that represents the larger number.

• public static java.util.List<java.lang.Integer> strArrToInt(java.util.List<java.lang.String> strings)

  Parses a whole String list to integers and returns them in another list.

  Parameters:

  strings - List of Strings

  Returns:

  list of integer representations of the input list