#include <Gmapres.h>
Public Member Functions | |
| Gmapres () | |
| Gmapres (const string &id, int np) | |
| ~Gmapres () | |
| void | addPath (Gmapath &gp) |
| void | addPath (Gmapath *gp) |
| void | addAlignment (vector< Gmapalnseg * > &aln, int idx) |
| void | storeChain (map< string, set< Noschain > > &chainstore, float idencut) |
| void | storeChain (map< string, map< Alnchain, int > > &chainstore) |
| void | storeChain (map< string, set< Alnchainid > > &chainstore) |
| void | storeChain (map< string, set< Alnchainid *, lessChainPtr > > &chainstore) |
| int | strandByESTName () const |
| void | guessDirection () |
| const string & | ESTId () const |
Static Public Member Functions | |
| static void | setMaximumIntron (int maxil) |
| static void | setMinimumIntron (int minil) |
| static void | setDangleExon (const pair< int, int > &dang) |
Private Attributes | |
| int | numpath |
| vector< Gmapath * > | paths |
| string | cid |
Static Private Attributes | |
| static int | maxintron = 5000 |
| static int | minintron = 19 |
| static int | dangleinlen = 900 |
| static int | danglexlen = 21 |
Friends | |
| ostream & | operator<< (ostream &ous, const Gmapres &res) |
>MXL006g03_r Paths (1): Path 1: query 1--446 (446 bp) => chr chromosome_1:1,436,005--1,436,726 (722 bp) cDNA direction: sense Genomic pos: Chlre4:1,436,005--1,436,726 (+ strand) Accessions: chromosome_1:1,436,005--1,436,726 (out of 9982135 bp) Number of exons: 2 Coverage: 98.2 (query length: 454 bp) Trimmed coverage: 98.2 (trimmed length: 454 bp, trimmed region: 1..454) Percent identity: 95.5 (426 matches, 19 mismatches, 1 indels, 0 unknowns) Non-intron gaps: 1 openings, 1 bases in cdna; 0 openings, 0 bases in genome Translation: 174..447 (91 aa) Amino acid changes: A42T [296], Y54F [332], Q61K [353], L64F [362], V66G [368], V67R [371], E73D [389], A76W [398]
Alignments: Alignment for path 1:
+chromosome_1:1436005-1436373 (1-369) 98% -> ...277... +chromosome_1:1436651-1436726 (370-446) 80% <== to be discarded with CUTOFF (around 90%) Container for individual paths Most (>92%) 454 EST has only one path (footprint)
This class records the number of paths. and store the path objects in a vector.
This class should store direction information about the cDNA, sense or antisense.
| Gmapres::Gmapres | ( | ) | [inline] |
| Gmapres::Gmapres | ( | const string & | id, | |
| int | np | |||
| ) | [inline] |
| Gmapres::~Gmapres | ( | ) |
References paths.
| void Gmapres::addPath | ( | Gmapath & | gp | ) | [inline] |
| void Gmapres::addAlignment | ( | vector< Gmapalnseg * > & | aln, | |
| int | idx | |||
| ) |
add alignment to the idx path. This is bacuase the output format of gmap split the two parts of the information
References paths.
Referenced by readandstoreGmap().
| void Gmapres::storeChain | ( | map< string, set< Noschain > > & | chainstore, | |
| float | idencut | |||
| ) |
this function will store away all the chains from this result into a common map indexed by genomic id in string format. In the process, redundant paths will be discarded; only unique paths will be left. Lost counting. If need counting, I can simply switch set to map. Or implement another function that will have the counting information.
References Range::length(), maxintron, Noschain::maxIntron(), paths, and strandByESTName().
Referenced by readandstoreGmap().
| void Gmapres::storeChain | ( | map< string, map< Alnchain, int > > & | chainstore | ) |
this is the production version, all parameters are set through static members.
| chainstore | is a map for genomieid => { Alnchain => count } Each alignment chain has a count associated with it so that we can use it to count the number of ESTs in each alignment. There are very few alignment have counts over 1. 1 out of 50000. This indicate the small chance that two alignments having the exact bounds. |
References Range::length(), maxintron, Noschain::maxIntron(), minintron, Noschain::minIntron(), Noschain::numberOfRanges(), paths, and strandByESTName().
| void Gmapres::storeChain | ( | map< string, set< Alnchainid > > & | chainstore | ) |
newest production version
References Alnchainid::absorbESTIds(), cid, dangleinlen, danglexlen, Noschain::isDangle(), Range::length(), maxintron, Noschain::maxIntron(), minintron, Noschain::minIntron(), Noschain::numberOfRanges(), paths, and strandByESTName().
| void Gmapres::storeChain | ( | map< string, set< Alnchainid *, lessChainPtr > > & | chainstore | ) |
pointer version for efficiency. This reduced the need for copying large objects.
References Alnchainid::absorbESTIds(), cid, dangleinlen, danglexlen, Alnchain::identity(), Noschain::isDangle(), Range::length(), maxintron, Noschain::maxIntron(), minintron, Noschain::minIntron(), Noschain::numberOfRanges(), paths, and strandByESTName().
| int Gmapres::strandByESTName | ( | ) | const |
| void Gmapres::guessDirection | ( | ) |
References paths, and strandByESTName().
| const string& Gmapres::ESTId | ( | ) | const [inline] |
| static void Gmapres::setMaximumIntron | ( | int | maxil | ) | [inline, static] |
| void Gmapres::setMinimumIntron | ( | int | minil | ) | [static] |
also set Gmapath trimShortIntronlen
References minintron, and Gmapath::setTrimShortIntronlen().
Referenced by main().
| static void Gmapres::setDangleExon | ( | const pair< int, int > & | dang | ) | [inline, static] |
| ostream& operator<< | ( | ostream & | ous, | |
| const Gmapres & | res | |||
| ) | [friend] |
<cDNA id>=""> TAB <number of="" paths>=""> Gmappath objects ....
int Gmapres::numpath [private] |
total number of paths, the result may have fewer shown. So the paths.size() may actually < numpath
Referenced by operator<<().
vector<Gmapath*> Gmapres::paths [private] |
contain the actual paths shown by the gmap program
Referenced by addAlignment(), addPath(), guessDirection(), operator<<(), storeChain(), and ~Gmapres().
string Gmapres::cid [private] |
Referenced by ESTId(), operator<<(), storeChain(), and strandByESTName().
int Gmapres::maxintron = 5000 [static, private] |
the cutoff value to discard path if sum exon length < this value
Referenced by setMaximumIntron(), and storeChain().
int Gmapres::minintron = 19 [static, private] |
This is to apply to models with one or more introns. Default value is 1. Means no filtering on intron length. Now allowing user to set this one. My study shows that minimal intron length for Aspca3 is 41 nt. Only a few have 40 nt introns, one or two of them may be true. All the otehr introns occur at very low frequencies. There are introns that are only one nt long. Not sure what it means.
Referenced by setMinimumIntron(), and storeChain().
int Gmapres::dangleinlen = 900 [static, private] |
Referenced by setDangleExon(), and storeChain().
int Gmapres::danglexlen = 21 [static, private] |
Referenced by setDangleExon(), and storeChain().
1.5.6