* @ brief Base class for all exception classes in the project. * * @author Emmanouil Stafilarakis */

* @brief a class for converting sequence into integer replacing Base4Int * * @author Mario Stanke */

Without above two lines we get a compiler warning since C++14. * Reason found on http://en.cppreference.com/w/cpp/language/namespace: * "Nam

* @brief Exception class for the GenBank classes. * * @author Emmanouil Stafilarakis */

* @brief This class implements a double object with a very large * range. * @details It is designed to handle very small (or high) floating

* @author Mario Stanke */

* @brief Hints on the gene structure * * @author Mario Stanke */

* @author Oliver Keller * @author Mario Stanke */

* @brief Necessary for the throwing of Error's and catching them with try and catch. */

* @brief The base exception class for Properties * * @author Emmanouil Stafilarakis */

* @author Emmanouil Stafilarakis * @author Mario Stanke */

* @author Mario Stanke * @author Emmanouil Stafilarakis */

* A data structure representing an integer interval */

type to label the hint lists with their IDs (see RefNameByID)

! @brief exception indicating access out of the defined range This exception is thrown in case a library function is called on an input parameter tha

* * @author Mario Stanke */

* @author Mario Stanke */

* @author Emmanouil Stafilarakis */

* MsaInsertion, specifies a string to be inserted into a StringAlignment */

* @author Emmanouil Stafilarakis */

* @author Emmanouil Stafilarakis * @author Mario Stanke */

* @brief intron profile for a block and the inter-block section before the block * @author: Lars Gabriel */

Implements polymorphic matchers MatchesRegex(regex) and ContainsRegex(regex), which can be used as a Matcher<T> as long as T can be converted to a str

* @brief exceptions thrown by Viterbi * * @author Oliver Keller * @author Mario Stanke */

* @author Mario Stanke */

* @brief Range of prediction and a set of HintGroups turned off * * @author Mario Stanke */

this type represents the results for a particular part of the input sequence when translated and aligned to a block - how many residues of the transla

sorting operator, with respect to a given species index

* @author Mario Stanke */

! Input adapter for a (caching) istream. Ignores a UFT Byte Order Mark at beginning of input. Does not support changing the underlying std::streambuf

! @brief exception indicating a parse error This exception is thrown by the library when a parse error occurs. Parse errors can occur during the dese

* @brief Predecessor in the state transition Graph * * @author Emmanouil Stafilarakis * @author Mario Stanke */

* @author Mario Stanke */

* @author Emmanouil Stafilarakis * @author Mario Stanke */

* @author Mario Stanke */

* @brief holds all type-specific extrinsic feature information * * @author Mario Stanke */

* @brief HintGroup * @details Hints that are known to belong to the same gene, * for example, because they come from the same mRNA, form a group.

sorting operator, with respect to a given species index, index version for sorting a vector or list of indices to another vector that holds the Alignm

This class generates an JSON output file.

* @author Emmanouil Stafilarakis */

* @author Mario Stanke */

Allows a controller thread to pause execution of newly created threads until notified. Instances of this class must be created and destroyed in the c

* @brief Options lists are used for sampling; items also in backtracking * * @author Oliver Keller * @author Mario Stanke */

* Exception class thrown from PP:: classes */

forward declarations

* @author Oliver Keller * @author Mario Stanke */

The friend relationship of some of these classes is cyclic. If we don't forward declare them the compiler might confuse the classes in friendship clau

A copyable object representing a user specified test property which can be output as a key/value string pair. Don't inherit from TestProperty as its

A predicate that checks the key of a TestProperty against a known key. TestPropertyKeyIs is copyable.

A predicate that checks the name of a TestSuite against a known value. This is used for implementation of the UnitTest class only. We put it in the

* @brief one entry in the viterbi matrix, including the index for the substate map * * @author Oliver Keller * @author Mario Stanke */

* @author Oliver Keller * @author Mario Stanke */

This class generates an XML output file.

! Input adapter for stdio file access. This adapter read only 1 byte and do not use any buffer. This adapter is a very low level adapter. */

* @brief gapless alignment fragment * * @author Mario Stanke */

! @brief exception indicating errors with iterators This exception is thrown if iterators passed to a library function do not match the expected sema

! @brief exception indicating other library errors This exception is thrown in case of errors that cannot be classified with the other exception type

@brief an iterator for primitive JSON types This class models an iterator for primitive JSON types (boolean, number, string). It's only purpose is to