#include <gnSequence.h>
Inheritance diagram for gnSequence:
Public Member Functions | |
virtual uint32 | addFeature (gnBaseFeature *feature) |
Adds the specified feature to the feature list. | |
virtual void | addHeader (const uint32 contigI, gnBaseHeader *header, const uint32 headerI) |
Adds header information to a specified contig. | |
virtual void | append (const gnSequence &seq) |
Appends the bases in "seq" to this sequence. | |
virtual void | assign (gnSequence &seq) |
Assigns the sequence "seq" to this sequence. | |
gnSequence * | Clone () const |
virtual int | compare (const string &str) const |
virtual int | compare (const gnSequence &seq) const |
Compares the bases in "seq" to this sequence. | |
gnSequence | contig (const uint32 contigI) const |
Returns a gnSequence containing the specified fragment. | |
gnSequence | contigByBase (const gnSeqI baseI) const |
Returns a gnSequence containing only the fragment which contains the specified base. | |
virtual gnSequence | contigByName (string &contigName) const |
Returns a gnSequence containing only the named contig. | |
uint32 | contigIndexByBase (const gnSeqI baseI) const |
Returns the index of the contig which contains the specified base. | |
virtual uint32 | contigIndexByName (string &contigName) const |
Returns the index of the contig with the given name. | |
virtual gnSeqI | contigLength (const uint32 contigI) const |
Returns the length in base pairs of the specified contig in this sequence. | |
gnSeqI | contigListLength () const |
Returns the number of sequence fragments in this sequence. | |
gnSeqI | contigListSize () const |
Returns the number of sequence fragments in this sequence. | |
virtual string | contigName (const uint32 contigI) const |
Returns the name of the specified contig. | |
virtual gnSeqI | contigStart (const uint32 contigI) const |
Returns the index of the base pair where the specified contig starts in this sequence. | |
virtual void | erase (const gnSeqI offset=0, const gnSeqI length=GNSEQI_END) |
Deletes the "len" bases starting at "offset". | |
virtual gnSeqI | find (const gnSequence &search, const gnSeqI offset=0) const |
Find looks for the search sequence within this gnSequence and returns the position of the first match if any exists. | |
virtual void | getBrokenFeatures (const gnLocation <, vector< gnBaseFeature * > &feature_vector) const |
Creates a list of features which may have been broken by an edit. | |
virtual void | getContainedFeatures (const gnLocation <, vector< gnBaseFeature * > &feature_vector, vector< uint32 > &index_vector) const |
Creates a list of all features which are contained by coordinates specified. | |
virtual gnBaseFeature * | getFeature (const uint32 featureI) const |
Returns the feature specified by featureI. | |
virtual uint32 | getFeatureListLength () const |
Returns the size of the feature list for the specified contig. | |
virtual list< const gnBaseFilter * > | getFilterList () const |
Returns the list of filters currently being used. | |
virtual gnBaseHeader * | getHeader (const uint32 contigI, const uint32 headerI) const |
Returns the feature specified by featureI. | |
virtual uint32 | getHeaderListLength (const uint32 contigI) const |
Returns the size of the header list for the specified contig. | |
virtual void | getIntersectingFeatures (const gnLocation <, vector< gnBaseFeature * > &feature_vector, vector< uint32 > &index_vector) const |
Creates a list of all features which intersect the coordinates specified. | |
virtual gnSeqC | GetSeqC (const gnSeqI offset) const |
Returns the base at "offset". | |
virtual gnGenomeSpec * | GetSpec () const |
Get the spec (annotated sequence) which this sequence represents. | |
virtual void | globalToLocal (uint32 &contigI, gnSeqI &baseI) const |
Converts the global sequence coordinate baseI to a contig local coordinate. | |
virtual void | globalToSource (uint32 &contigI, gnSeqI &baseI) const |
Converts the global sequence coordinate baseI to a local coordinate in the original data source. | |
gnSequence (const gnSequence &seq) | |
Copies the gnSequence "seq". | |
gnSequence (gnSeqC *bases, const gnSeqI length) | |
Creates a gnSequence with a single fragment containing the bases in "bases". | |
gnSequence (const gnContigSpec &gncs) | |
Creates a gnSequence with the contig stored in the gnContigSpec "gncs". | |
gnSequence (const gnFragmentSpec &gnfs) | |
Creates a gnSequence with the sequence fragment stored in the gnFragmentSpec "gnfs". | |
gnSequence (const gnGenomeSpec &gngs) | |
Creates a gnSequence with the genome stored in the gnGenomeSpec "gngs". | |
gnSequence (const string &str) | |
Creates a gnSequence with a single fragment containing the bases in "str". | |
gnSequence (const gnSeqC *seq) | |
Creates a gnSequence with a single fragment containing the bases in "seq". | |
gnSequence () | |
Empty Constructor, creates an empty gnSequence. | |
virtual void | insert (const gnSeqI offset, const gnGenomeSpec &gnbs) |
Inserts the annotated sequence in "gnbs" into this sequence.at "offset". | |
virtual void | insert (const gnSeqI offset, const gnSequence &seq) |
Inserts the annotated sequence in "seq" into this sequence.at "offset". | |
virtual void | insert (const gnSeqI offset, const gnSeqC *bases, const gnSeqI length) |
Inserts the first "len" bases in "bases" into this sequence.at "offset". | |
virtual boolean | isCircular () const |
Returns true if this sequence is circular. | |
virtual boolean | isReverseComplement (const uint32 contigI=ALL_CONTIGS) |
Returns true if a specified contig, or the entire sequence is reverse complement. | |
virtual gnSeqI | length () const |
Returns the length of this sequence. | |
virtual bool | LoadSource (const string sourcename) |
Loads the sequence located at the URL in "sourcename". | |
virtual void | localToGlobal (const uint32 contigI, gnSeqI &baseI) const |
Converts the local contig coordinate baseI to a global sequence coordinate. | |
virtual void | localToSource (uint32 &contigI, gnSeqI &baseI) const |
Converts the contig local sequence coordinate baseI in contig contigI to a local coordinate in the original data source. | |
virtual void | merge (const gnSeqI startI, const gnSeqI endI) |
Merges the bases starting at base index "startI" and ending at "endI" into one contig, splitting existing contigs. | |
virtual void | mergeContigs (const uint32 startC, const uint32 endC) |
Merges the contigs starting at the contig index "startC" and ending at "endC" into one contig. | |
boolean | operator!= (const gnSequence &seq) const |
gnSequence const | operator+ (const gnSequence &seq) const |
Concatenates this sequence with the annotated sequence in "seq". | |
gnSequence & | operator+= (const gnSequence &seq) |
Appends the bases in "seq" to this sequence. | |
boolean | operator< (const gnSequence &seq) const |
boolean | operator<= (const gnSequence &seq) const |
void | operator= (gnSequence &seq) |
Assigns the sequence "seq" to this sequence. | |
gnSequence & | operator= (const gnSequence &seq) |
Copies the gnSequence. | |
boolean | operator== (const gnSequence &seq) const |
boolean | operator> (const gnSequence &seq) const |
boolean | operator>= (const gnSequence &seq) const |
gnSeqC | operator[] (const gnSeqI offset) const |
Returns the base at the specified index. | |
virtual void | removeFeature (const uint32 featureI) |
Removes the specified feature. | |
virtual void | removeHeader (const uint32 contigI, const uint32 headerI) |
Removes header information from a specified contig. | |
virtual void | setCircular (const boolean value) |
Sets whether this sequence should be read circular. | |
virtual void | setContigName (const uint32 contigI, const string &contig_name) |
virtual void | setFilter (const gnBaseFilter *filt) |
Assigns a filter which all sequence data must pass through when read from the object. | |
virtual void | setFilterList (list< const gnBaseFilter * > &filt_list) |
Assigns a list of filters which all sequence data passes through in order when read from the object. | |
virtual void | setReverseComplement (const boolean revComp, const uint32 contigI=ALL_CONTIGS) |
Reverse complements a specified contig, or the entire sequence if ALL_CONTIGS is specified. | |
virtual void | SetSpec (gnGenomeSpec *s) |
Set the spec (annotated sequence) which this sequence represents. | |
virtual gnSeqI | size () const |
Returns the length of this sequence. | |
virtual void | splitContig (const gnSeqI splitI, const uint32 contigI=ALL_CONTIGS) |
Splits the specified contig after splitI. | |
gnSequence | subseq (const gnSeqI offset, const gnSeqI length) const |
Creates a sequence containing the "length" bases starting at "offset". | |
virtual boolean | ToArray (gnSeqC *pSeqC, gnSeqI length, const gnSeqI offset=1) const |
Converts the "length" bases starting at "offset" into the character array "pSeqC".. | |
virtual boolean | ToString (string &str, const gnSeqI length=GNSEQI_END, const gnSeqI offset=1) const |
Converts the "length" bases starting at "offset" into the string "str". | |
virtual string | ToString (const gnSeqI length=GNSEQI_END, const gnSeqI offset=1) const |
Returns the "length" bases starting at "offset" as a string. | |
~gnSequence () | |
Destructor, frees the memory used by this sequence. | |
Private Attributes | |
const gnCompare * | comparator |
list< const gnBaseFilter * > | filter_list |
gnGenomeSpec * | spec |
Friends | |
std::ostream & | operator<< (std::ostream &os, const gnSequence &gns) |
Writes the bases in this sequence to the specified output stream (e.g. | |
std::istream & | operator>> (std::istream &is, gnSequence &gns) |
Reads bases from the specified input stream (e.g. |
It provides a simple and general way to manipulate genetic sequences, regardless of what kind of database, web site, or file they are stored in. Sequence data can be manipulated like a c++ string by using subseq() and erase(). gnSequence updates annotated sequences with each change, breaking features if necessary.
Definition at line 35 of file gnSequence.h.
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Empty Constructor, creates an empty gnSequence. Definition at line 22 of file gnSequence.cpp. References comparator, gnCompare::DNASeqCompare(), and spec. Referenced by Clone(), contig(), contigByBase(), contigByName(), and subseq(). |
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Creates a gnSequence with a single fragment containing the bases in "seq".
References gnMultiSpec< SubSpec >::AddSpec(), comparator, gnCompare::DNASeqCompare(), gnSeqC, and spec. |
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Creates a gnSequence with a single fragment containing the bases in "str".
References gnMultiSpec< SubSpec >::AddSpec(), comparator, gnCompare::DNASeqCompare(), and spec. |
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Creates a gnSequence with the genome stored in the gnGenomeSpec "gngs".
References gnGenomeSpec::Clone(), comparator, gnCompare::DNASeqCompare(), and spec. |
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Creates a gnSequence with the sequence fragment stored in the gnFragmentSpec "gnfs".
References gnMultiSpec< SubSpec >::AddSpec(), gnFragmentSpec::Clone(), comparator, gnCompare::DNASeqCompare(), and spec. |
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Creates a gnSequence with the contig stored in the gnContigSpec "gncs". Usually gncs will be a gnStringSpec or a gnSourceSpec.
References gnMultiSpec< SubSpec >::AddSpec(), gnContigSpec::Clone(), comparator, gnCompare::DNASeqCompare(), and spec. |
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Creates a gnSequence with a single fragment containing the bases in "bases".
References gnMultiSpec< SubSpec >::AddSpec(), comparator, gnCompare::DNASeqCompare(), gnSeqC, gnSeqI, and spec. |
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Copies the gnSequence "seq".
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Destructor, frees the memory used by this sequence. Definition at line 75 of file gnSequence.cpp. References spec. |
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Adds the specified feature to the feature list.
References gnGenomeSpec::AddFeature(), spec, and uint32. |
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Adds header information to a specified contig.
References gnMultiSpec< SubSpec >::AddHeader(), gnMultiSpec< SubSpec >::GetSpec(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Appends the bases in "seq" to this sequence.
References GNSEQI_END, insert(), and spec. Referenced by main(), and operator>>(). |
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Assigns the sequence "seq" to this sequence.
References gnGenomeSpec::Clone(), and spec. |
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Implements gnClone. Definition at line 89 of file gnSequence.cpp. References gnSequence(). |
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Definition at line 94 of file gnSequence.cpp. References comparator, gnSeqI, length(), gnCompare::LessThan(), STACK_TRACE_END, STACK_TRACE_START, and ToString(). |
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Compares the bases in "seq" to this sequence.
References comparator, gnSeqI, length(), gnCompare::LessThan(), STACK_TRACE_END, STACK_TRACE_START, and ToString(). Referenced by operator!=(), operator<(), operator<=(), operator==(), operator>(), and operator>=(). |
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Returns a gnSequence containing the specified fragment.
References gnMultiSpec< SubSpec >::GetSpec(), gnSequence(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. Referenced by isReverseComplement(), main(), and setReverseComplement(). |
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Returns a gnSequence containing only the fragment which contains the specified base.
References gnMultiSpec< SubSpec >::GetSpecByBase(), gnSeqI, gnSequence(), spec, STACK_TRACE_END, and STACK_TRACE_START. |
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Returns a gnSequence containing only the named contig. If two contigs have the same name, contigByName() will return the first.
References gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecIndexByName(), gnSequence(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Returns the index of the contig which contains the specified base.
References gnMultiSpec< SubSpec >::GetSpecIndexByBase(), gnSeqI, spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. Referenced by globalToLocal(). |
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Returns the index of the contig with the given name. If two contigs have the same name, contigIndexByName() will return the first.
References gnMultiSpec< SubSpec >::GetSpecIndexByName(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Returns the length in base pairs of the specified contig in this sequence.
References gnMultiSpec< SubSpec >::GetLength(), gnMultiSpec< SubSpec >::GetSpec(), gnSeqI, spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. Referenced by localToGlobal(), gnGBKSource::Write(), and gnFASSource::Write(). |
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Returns the number of sequence fragments in this sequence.
References gnMultiSpec< SubSpec >::GetSpecListLength(), gnSeqI, spec, STACK_TRACE_END, and STACK_TRACE_START. Referenced by main(), and gnFASSource::Write(). |
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Returns the number of sequence fragments in this sequence.
References gnMultiSpec< SubSpec >::GetSpecListLength(), gnSeqI, spec, STACK_TRACE_END, and STACK_TRACE_START. Referenced by main(). |
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Returns the name of the specified contig.
References gnBaseSpec::GetName(), gnMultiSpec< SubSpec >::GetSpec(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. Referenced by main(), and gnFASSource::Write(). |
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Returns the index of the base pair where the specified contig starts in this sequence.
References gnMultiSpec< SubSpec >::GetSpecStartBase(), gnSeqI, int64, spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. Referenced by globalToLocal(), localToGlobal(), and gnGBKSource::Write(). |
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Deletes the "len" bases starting at "offset".
References gnGenomeSpec::CloneRange(), gnMultiSpec< SubSpec >::CropEnd(), gnMultiSpec< SubSpec >::GetLength(), gnSeqI, GNSEQI_END, insert(), length(), spec, STACK_TRACE_END, STACK_TRACE_START, Throw_gnEx, and uint32. |
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Find looks for the search sequence within this gnSequence and returns the position of the first match if any exists.
References gnSeqI, GNSEQI_ERROR, STACK_TRACE_END, and STACK_TRACE_START. |
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Creates a list of features which may have been broken by an edit.
References gnGenomeSpec::GetBrokenFeatures(), and spec. |
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Creates a list of all features which are contained by coordinates specified.
References gnGenomeSpec::GetContainedFeatures(), and spec. |
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Returns the feature specified by featureI.
References gnGenomeSpec::GetFeature(), spec, and uint32. Referenced by main(). |
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Returns the size of the feature list for the specified contig.
References gnGenomeSpec::GetFeatureListLength(), spec, and uint32. Referenced by main(). |
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Returns the list of filters currently being used.
References filter_list. |
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Returns the feature specified by featureI.
References gnMultiSpec< SubSpec >::GetHeader(), gnMultiSpec< SubSpec >::GetSpec(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Returns the size of the header list for the specified contig.
References gnMultiSpec< SubSpec >::GetHeaderListLength(), gnMultiSpec< SubSpec >::GetSpec(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Creates a list of all features which intersect the coordinates specified.
References gnGenomeSpec::GetIntersectingFeatures(), and spec. Referenced by main(). |
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Returns the base at "offset".
References filter_list, gnSeqC, GNSEQC_NULL, gnSeqI, gnMultiSpec< SubSpec >::SeqRead(), spec, STACK_TRACE_END, and STACK_TRACE_START. Referenced by operator[](). |
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Get the spec (annotated sequence) which this sequence represents.
References spec. Referenced by main(), gnGBKSource::Write(), gnFASSource::Write(), gnSEQSource::Write(), and gnDNXSource::Write(). |
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Converts the global sequence coordinate baseI to a contig local coordinate.
References contigIndexByBase(), contigStart(), gnSeqI, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Converts the global sequence coordinate baseI to a local coordinate in the original data source. globalToSource() will overwrite any values passed to it!
References gnContigSpec::GetSourceContigIndex(), gnContigSpec::GetSourceLength(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecIndexByBase(), gnMultiSpec< SubSpec >::GetSpecStartBase(), gnContigSpec::GetStart(), gnSeqI, gnBaseSpec::IsReverseComplement(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. Referenced by localToSource(). |
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Inserts the annotated sequence in "gnbs" into this sequence.at "offset". insert() will update the locations of all affected features.
References gnMultiSpec< SubSpec >::AddSpec(), gnGenomeSpec::Clone(), gnFragmentSpec::Clone(), gnMultiSpec< SubSpec >::CropEnd(), gnMultiSpec< SubSpec >::CropStart(), gnMultiSpec< SubSpec >::GetLength(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecListLength(), gnSeqI, GNSEQI_END, insert(), spec, STACK_TRACE_END, STACK_TRACE_START, Throw_gnEx, and uint32. |
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Inserts the annotated sequence in "seq" into this sequence.at "offset". insert() will update the locations of all affected features.
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Inserts the first "len" bases in "bases" into this sequence.at "offset". insert() will update the locations of all affected features.
References gnSeqC, gnSeqI, STACK_TRACE_END, and STACK_TRACE_START. Referenced by append(), erase(), insert(), operator+=(), and splitContig(). |
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Returns true if this sequence is circular.
References gnBaseSpec::IsCircular(), and spec. |
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Returns true if a specified contig, or the entire sequence is reverse complement.
References contig(), gnMultiSpec< SubSpec >::GetSpec(), gnBaseSpec::IsReverseComplement(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Returns the length of this sequence.
References gnMultiSpec< SubSpec >::GetLength(), gnSeqI, and spec. Referenced by compare(), erase(), main(), splitContig(), ToString(), and gnRAWSource::Write(). |
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Loads the sequence located at the URL in "sourcename". Possible URLs currently include only "file:///" URLs. If no URL prefix is found then LoadSource assumes that "sourcename" contains the name of a local file.
References gnSourceFactory::GetSourceFactory(), gnBaseSource::GetSpec(), spec, STACK_TRACE_END, and STACK_TRACE_START. Referenced by main(). |
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Converts the local contig coordinate baseI to a global sequence coordinate.
References contigLength(), contigStart(), gnSeqI, STACK_TRACE_END, STACK_TRACE_START, Throw_gnEx, and uint32. Referenced by localToSource(), and splitContig(). |
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Converts the contig local sequence coordinate baseI in contig contigI to a local coordinate in the original data source. localToSource() will overwrite any values passed to it!
References globalToSource(), gnSeqI, localToGlobal(), STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Merges the bases starting at base index "startI" and ending at "endI" into one contig, splitting existing contigs.
References gnSeqI, STACK_TRACE_END, and STACK_TRACE_START. |
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Merges the contigs starting at the contig index "startC" and ending at "endC" into one contig.
References gnGenomeSpec::MergeFragments(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Definition at line 527 of file gnSequence.h. References compare(). |
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Concatenates this sequence with the annotated sequence in "seq". Definition at line 179 of file gnSequence.cpp. References STACK_TRACE_END, and STACK_TRACE_START. |
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Appends the bases in "seq" to this sequence. Definition at line 548 of file gnSequence.h. References GNSEQI_END, insert(), and spec. |
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Definition at line 531 of file gnSequence.h. References compare(). |
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Definition at line 535 of file gnSequence.h. References compare(). |
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Assigns the sequence "seq" to this sequence. Definition at line 515 of file gnSequence.h. References gnGenomeSpec::Clone(), and spec. |
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Copies the gnSequence. Definition at line 81 of file gnSequence.cpp. References gnGenomeSpec::Clone(), comparator, filter_list, and spec. |
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Definition at line 523 of file gnSequence.h. References compare(). |
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Definition at line 539 of file gnSequence.h. References compare(). |
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Definition at line 543 of file gnSequence.h. References compare(). |
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Returns the base at the specified index.
References GetSeqC(), gnSeqC, gnSeqI, STACK_TRACE_END, and STACK_TRACE_START. |
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Removes the specified feature.
References gnGenomeSpec::RemoveFeature(), spec, and uint32. |
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Removes header information from a specified contig.
References gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::RemoveHeader(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Sets whether this sequence should be read circular. If circular is set, reads beyond the end of the sequence will pick up at the beginning.
References gnBaseSpec::SetCircular(), and spec. |
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Definition at line 438 of file gnSequence.cpp. References gnMultiSpec< SubSpec >::GetSpec(), gnBaseSpec::SetName(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. |
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Assigns a filter which all sequence data must pass through when read from the object.
References filter_list. Referenced by main(), and runTests(). |
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Assigns a list of filters which all sequence data passes through in order when read from the object. There may not be any NULL pointers in the list.
References filter_list. Referenced by runTests(). |
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Reverse complements a specified contig, or the entire sequence if ALL_CONTIGS is specified.
References contig(), gnMultiSpec< SubSpec >::GetSpec(), gnFragmentSpec::SetReverseComplement(), gnGenomeSpec::SetReverseComplement(), spec, STACK_TRACE_END, STACK_TRACE_START, and uint32. Referenced by runTests(). |
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Set the spec (annotated sequence) which this sequence represents.
References spec. |
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Returns the length of this sequence.
References gnMultiSpec< SubSpec >::GetLength(), gnSeqI, and spec. |
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Splits the specified contig after splitI.
References gnGenomeSpec::Clone(), gnMultiSpec< SubSpec >::CropEnd(), gnMultiSpec< SubSpec >::CropStart(), gnSeqI, GNSEQI_END, insert(), length(), localToGlobal(), spec, STACK_TRACE_END, STACK_TRACE_START, Throw_gnEx, and uint32. |
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Creates a sequence containing the "length" bases starting at "offset".
References gnGenomeSpec::CloneRange(), gnSeqI, gnSequence(), spec, STACK_TRACE_END, STACK_TRACE_START, and Throw_gnEx. Referenced by main(). |
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Converts the "length" bases starting at "offset" into the character array "pSeqC".. After converting, "length" will be set to the actual length of the sequence. Be sure to null terminate the character array if you are going to print it!
References filter_list, gnSeqC, gnSeqI, GNSEQI_END, gnMultiSpec< SubSpec >::SeqRead(), spec, STACK_TRACE_END, and STACK_TRACE_START. Referenced by main(), gnRAWSource::Write(), gnGBKSource::Write(), and gnFASSource::Write(). |
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Converts the "length" bases starting at "offset" into the string "str".
References filter_list, gnSeqI, length(), gnMultiSpec< SubSpec >::SeqRead(), spec, STACK_TRACE_END, and STACK_TRACE_START. |
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Returns the "length" bases starting at "offset" as a string.
References gnSeqI, STACK_TRACE_END, and STACK_TRACE_START. Referenced by compare(), main(), operator<<(), and WriteData(). |
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Writes the bases in this sequence to the specified output stream (e.g. cout). |
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Reads bases from the specified input stream (e.g. cin). |
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Reimplemented in gnDNASequence, gnProteinSequence, and gnRNASequence. Definition at line 504 of file gnSequence.h. Referenced by compare(), gnSequence(), and operator=(). |
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Reimplemented in gnDNASequence, gnProteinSequence, and gnRNASequence. Definition at line 503 of file gnSequence.h. Referenced by getFilterList(), GetSeqC(), operator=(), setFilter(), setFilterList(), ToArray(), and ToString(). |
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