#include <psl.h>
Collaboration diagram for psl:
Data Fields | |
| psl * | next |
| unsigned | match |
| unsigned | misMatch |
| unsigned | repMatch |
| unsigned | nCount |
| unsigned | qNumInsert |
| int | qBaseInsert |
| unsigned | tNumInsert |
| int | tBaseInsert |
| char | strand [3] |
| char * | qName |
| unsigned | qSize |
| int | qStart |
| int | qEnd |
| char * | tName |
| unsigned | tSize |
| int | tStart |
| int | tEnd |
| unsigned | blockCount |
| unsigned * | blockSizes |
| unsigned * | qStarts |
| unsigned * | tStarts |
| char ** | qSequence |
| char ** | tSequence |
Definition at line 42 of file psl.h.
| unsigned psl::match |
Definition at line 46 of file psl.h.
Referenced by accumCounts(), fillInMatchEtc(), pslCalcMilliBad(), pslCmpMatch(), pslLoad(), pslOutFormat(), pslOutput(), pslOutputShort(), and pslScore().
| unsigned psl::misMatch |
Definition at line 47 of file psl.h.
Referenced by accumCounts(), fillInMatchEtc(), pslCalcMilliBad(), pslLoad(), pslOutFormat(), pslOutput(), pslOutputShort(), and pslScore().
| unsigned psl::repMatch |
Definition at line 48 of file psl.h.
Referenced by accumCounts(), fillInMatchEtc(), pslCalcMilliBad(), pslLoad(), pslOutFormat(), pslOutput(), pslOutputShort(), and pslScore().
| unsigned psl::nCount |
Definition at line 49 of file psl.h.
Referenced by accumCounts(), fillInMatchEtc(), pslLoad(), pslOutFormat(), and pslOutput().
| unsigned psl::qNumInsert |
Definition at line 50 of file psl.h.
Referenced by accumCounts(), chainToPsl(), pslCalcMilliBad(), pslLoad(), pslOutput(), pslOutputShort(), pslScore(), and pslSwap().
| int psl::qBaseInsert |
Definition at line 51 of file psl.h.
Referenced by accumCounts(), chainToPsl(), pslLoad(), pslOutput(), pslOutputShort(), and pslSwap().
| unsigned psl::tNumInsert |
Definition at line 52 of file psl.h.
Referenced by accumCounts(), chainToPsl(), pslCalcMilliBad(), pslLoad(), pslOutput(), pslOutputShort(), pslScore(), and pslSwap().
| int psl::tBaseInsert |
Definition at line 53 of file psl.h.
Referenced by accumCounts(), chainToPsl(), pslLoad(), pslOutput(), pslOutputShort(), and pslSwap().
| char psl::strand[3] |
Definition at line 54 of file psl.h.
Referenced by adjustOrientation(), chainToPsl(), createMappedPsl(), printPslDesc(), pslCheck(), pslCmpTargetAndStrand(), pslDump(), pslFromFakeFfAli(), pslGenoShowAlignment(), pslHasIntron(), pslIsProtein(), pslLoad(), pslNew(), pslOrientation(), pslOutFormat(), pslOutput(), pslOutputShort(), pslRangeTreeOverlap(), pslRc(), pslRecalcBounds(), pslShowAlignment(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslSwap(), pslTrimToQueryRange(), pslTrimToTargetRange(), and pslWeightedIntronOrientation().
| char* psl::qName |
Definition at line 55 of file psl.h.
Referenced by chainToPsl(), createMappedPsl(), doDetailLine(), loadPsl(), printPslDesc(), pslCheck(), pslCmpQuery(), pslCmpQueryScore(), pslDump(), pslFree(), pslFromFakeFfAli(), pslLoad(), pslNew(), pslOutFormat(), pslOutput(), pslOutputShort(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslSwap(), pslTransMap(), pslTrimToQueryRange(), and pslTrimToTargetRange().
| unsigned psl::qSize |
Definition at line 56 of file psl.h.
Referenced by chainToPsl(), createMappedPsl(), pslCheck(), pslFromAlign(), pslFromFakeFfAli(), pslLoad(), pslNAToProt(), pslNew(), pslOutFormat(), pslOutput(), pslProtToNA(), pslRc(), pslRcBoth(), pslRecalcBounds(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslSwap(), pslTailSizes(), pslTransMap(), pslTrimToQueryRange(), pslTrimToTargetRange(), setPslBounds(), and swapRCBlocks().
| int psl::qStart |
Definition at line 57 of file psl.h.
Referenced by chainToPsl(), printPslDesc(), pslCalcMilliBad(), pslCheck(), pslCmpQuery(), pslDump(), pslFromAlign(), pslFromFakeFfAli(), pslLoad(), pslNAToProt(), pslNew(), pslOutFormat(), pslOutput(), pslOutputShort(), pslProtToNA(), pslRecalcBounds(), pslSwap(), pslTailSizes(), pslTrimToQueryRange(), setPslBounds(), and trimAlignment().
| int psl::qEnd |
Definition at line 58 of file psl.h.
Referenced by chainToPsl(), printPslDesc(), pslCalcMilliBad(), pslCheck(), pslDump(), pslFromAlign(), pslFromFakeFfAli(), pslLoad(), pslNAToProt(), pslNew(), pslOutFormat(), pslOutput(), pslOutputShort(), pslProtToNA(), pslRecalcBounds(), pslSwap(), pslTailSizes(), pslTrimToQueryRange(), setPslBounds(), and trimAlignment().
| char* psl::tName |
Definition at line 59 of file psl.h.
Referenced by chainToPsl(), createMappedPsl(), doDetailLine(), printPslDesc(), pslCheck(), pslCmpTarget(), pslCmpTargetAndStrand(), pslCmpTargetScore(), pslCmpTargetStart(), pslDump(), pslFree(), pslFromFakeFfAli(), pslLoad(), pslNew(), pslOutFormat(), pslOutput(), pslOutputShort(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslSwap(), pslTransMap(), pslTrimToQueryRange(), pslTrimToTargetRange(), and readPslToBinKeeper().
| unsigned psl::tSize |
Definition at line 60 of file psl.h.
Referenced by chainToPsl(), createMappedPsl(), doDetailLine(), pslCheck(), pslFromAlign(), pslFromFakeFfAli(), pslHasIntron(), pslIsProtein(), pslLoad(), pslNew(), pslOutput(), pslRangeTreeOverlap(), pslRc(), pslRcBoth(), pslRecalcBounds(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslSwap(), pslTailSizes(), pslTransMap(), pslTrimToQueryRange(), pslTrimToTargetRange(), setPslBounds(), and swapRCBlocks().
| int psl::tStart |
Definition at line 61 of file psl.h.
Referenced by chainToPsl(), doDetailLine(), printPslDesc(), pslCalcMilliBad(), pslCheck(), pslCmpTarget(), pslCmpTargetAndStrand(), pslCmpTargetStart(), pslDump(), pslFromAlign(), pslFromFakeFfAli(), pslIsProtein(), pslLoad(), pslNew(), pslOutFormat(), pslOutput(), pslOutputShort(), pslRcBoth(), pslRecalcBounds(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslSwap(), pslTailSizes(), pslTargetOffset(), pslTrimToTargetRange(), readPslToBinKeeper(), setPslBounds(), and trimAlignment().
| int psl::tEnd |
Definition at line 62 of file psl.h.
Referenced by chainToPsl(), doDetailLine(), printPslDesc(), pslCalcMilliBad(), pslCheck(), pslDump(), pslFromAlign(), pslFromFakeFfAli(), pslIsProtein(), pslLoad(), pslNew(), pslOutFormat(), pslOutput(), pslOutputShort(), pslRcBoth(), pslRecalcBounds(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslSwap(), pslTailSizes(), pslTargetOffset(), pslTrimToTargetRange(), readPslToBinKeeper(), setPslBounds(), and trimAlignment().
| unsigned psl::blockCount |
Definition at line 63 of file psl.h.
Referenced by addBlock(), addPslBlock(), chainToPsl(), getBlockMapping(), pslCheck(), pslDump(), pslFromFakeFfAli(), pslGenoShowAlignment(), pslHasIntron(), pslIsProtein(), pslLoad(), pslNAToProt(), pslOutput(), pslOutputShort(), pslProtToNA(), pslRangeTreeOverlap(), pslRc(), pslRcBoth(), pslRecalcBounds(), pslShowAlignment(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslTargetOffset(), pslToFakeFfAli(), pslToFfAli(), pslTransMap(), pslTrimToQueryRange(), pslTrimToTargetRange(), pslWeightedIntronOrientation(), pslxLoadLm(), setPslBounds(), swapBlocks(), and swapRCBlocks().
| unsigned* psl::blockSizes |
Definition at line 64 of file psl.h.
Referenced by chainToPsl(), getBlockMapping(), pslCheck(), pslDump(), pslFree(), pslFromFakeFfAli(), pslGrow(), pslHasIntron(), pslIsProtein(), pslLoad(), pslNAToProt(), pslNew(), pslOutput(), pslProtToNA(), pslRangeTreeOverlap(), pslRc(), pslRcBoth(), pslRecalcBounds(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslToFakeFfAli(), pslToFfAli(), pslTrimToQueryRange(), pslTrimToTargetRange(), pslWeightedIntronOrientation(), setPslBounds(), and swapRCBlocks().
| unsigned* psl::qStarts |
Definition at line 65 of file psl.h.
Referenced by chainToPsl(), getBlockMapping(), pslCheck(), pslDump(), pslFree(), pslFromFakeFfAli(), pslGrow(), pslHasIntron(), pslLoad(), pslNAToProt(), pslNew(), pslOutput(), pslProtToNA(), pslRc(), pslRcBoth(), pslRecalcBounds(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslToFakeFfAli(), pslToFfAli(), pslTrimToQueryRange(), pslTrimToTargetRange(), pslWeightedIntronOrientation(), setPslBounds(), swapBlocks(), and swapRCBlocks().
| unsigned* psl::tStarts |
Definition at line 66 of file psl.h.
Referenced by chainToPsl(), getBlockMapping(), pslCheck(), pslDump(), pslFree(), pslFromFakeFfAli(), pslGrow(), pslHasIntron(), pslIsProtein(), pslLoad(), pslNew(), pslOutput(), pslRangeTreeOverlap(), pslRc(), pslRcBoth(), pslRecalcBounds(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslTargetOffset(), pslToFakeFfAli(), pslToFfAli(), pslTrimToQueryRange(), pslTrimToTargetRange(), pslWeightedIntronOrientation(), setPslBounds(), swapBlocks(), and swapRCBlocks().
| char** psl::qSequence |
Definition at line 68 of file psl.h.
Referenced by pslFree(), pslGrow(), pslNew(), pslOutput(), pslRc(), pslxLoad(), pslxLoadLm(), swapBlocks(), and swapRCBlocks().
| char** psl::tSequence |
Definition at line 69 of file psl.h.
Referenced by pslFree(), pslGrow(), pslNew(), pslOutput(), pslRc(), pslxLoad(), pslxLoadLm(), swapBlocks(), and swapRCBlocks().
1.5.2