Home
last modified time | relevance | path

Searched refs:salp (Results 1 – 25 of 278) sorted by relevance

12345678910>>...12

/dports/biology/ncbi-toolkit/ncbi/api/
H A Dsalpacc.c54 if(salp==NULL) in SeqIdPtrFromSeqAlign()
131 if (salp!=NULL) { in SeqAlignId()
147 for (salp = salphead; salp!= NULL; salp=salp->next) in SeqAlignFindSeqId()
167 return salp; in SeqAlignIdReplace()
209 return salp; in SeqAlignIdReplace()
263 if (salp==NULL) in SeqAlignLengthForId()
595 if (salp==NULL) in SeqAlignMolType()
653 if (salp==NULL) in SeqAnnotForSeqAlign()
847 if(salp) { in SeqAlignWrite()
1054 salp=salp->next; in SeqAlignStartStop()
[all …]
H A Dalignval.c362 if (salp->segtype == SAS_DENDIAG && salp->segs != NULL) { in BioseqForAlignmentWork()
747 if(salp) in ValidateSeqIdInSeqAlign()
788 else if(salp->segtype==2||salp->segtype==4) in ValidateSeqIdInSeqAlign()
1007 if(salp) in ValidateStrandinSeqAlign()
1015 ValidateStrandInDenseSeg(salp->segs, salp->segtype, salp); in ValidateStrandinSeqAlign()
1456 if (salp) in ValidateSeqlengthinSeqAlign()
1481 if(salp) in ValidateDimSeqIds()
1507 else if(salp->segtype==2||salp->segtype==4) in ValidateDimSeqIds()
1672 if(salp->type!=1&&salp->type!=3) in Is_Fasta_Seqalign()
1769 if(salp) in Segment_Gap_In_SeqAlign()
[all …]
H A Dsalsap.h77 NLM_EXTERN SeqIdPtr LIBCALL SeqAlignIDList (SeqAlignPtr salp);
101 NLM_EXTERN Boolean LIBCALL is_dim1seqalign (SeqAlignPtr salp);
103 NLM_EXTERN Boolean LIBCALL is_dim2seqalign (SeqAlignPtr salp);
114 NLM_EXTERN ValNodePtr LIBCALL SeqLocListFromSeqAlign (SeqAlignPtr salp);
123 NLM_EXTERN Int4 LIBCALL SeqAlignBestScore (SeqAlignPtr salp);
131 NLM_EXTERN Boolean LIBCALL is_fasta_seqalign (SeqAlignPtr salp);
152 NLM_EXTERN SeqAlignPtr LIBCALL SortSeqAlign (SeqAlignPtr PNTR salp);
203 SeqAlignPtr salp);
208 NLM_EXTERN SeqAlignPtr LIBCALL CompSeqAlignFree (SeqAlignPtr salp);
214 NLM_EXTERN void LIBCALL CompSeqAlignPrint (SeqAlignPtr salp);
[all …]
H A Dviewmgr.c364 pInfo = ViewMgr_GetInfo(salp); in ViewMgr_AddTransform()
551 pInfo = ViewMgr_GetInfo(salp); in ViewMgr_GetTarget()
568 pInfo = ViewMgr_GetInfo(salp); in ViewMgr_GetBegin()
586 pInfo = ViewMgr_GetInfo(salp); in ViewMgr_SetBegin()
607 pInfo = ViewMgr_GetInfo(salp); in ViewMgr_GetBeginIndexed()
633 pInfo = ViewMgr_GetInfo(salp); in ViewMgr_IsNeat()
651 pInfo = ViewMgr_GetInfo(salp); in ViewMgr_IsIBM()
817 if(salp == NULL) in ViewMgr_MakeMultiple()
830 return ViewMgr_Update(salp); in ViewMgr_MakeMultiple()
890 pInfo->pView = salp; in ViewMgr_Attach()
[all …]
H A Dsalpacc.h54 NLM_EXTERN SeqIdPtr LIBCALL SeqIdPtrFromSeqAlign(SeqAlignPtr salp);
55 NLM_EXTERN SeqIdPtr LIBCALL SeqAlignId (SeqAlignPtr salp, Int2 index);
61 NLM_EXTERN Int4 LIBCALL SeqAlignLength (SeqAlignPtr salp);
70 NLM_EXTERN Int4 LIBCALL SeqAlignStart (SeqAlignPtr salp, Int2 index);
72 NLM_EXTERN Int4 LIBCALL SeqAlignStop (SeqAlignPtr salp, Int2 index);
74 NLM_EXTERN Uint1 LIBCALL SeqAlignMolType (SeqAlignPtr salp);
76 NLM_EXTERN SeqAnnotPtr LIBCALL SeqAnnotForSeqAlign (SeqAlignPtr salp);
112 NLM_EXTERN ScorePtr LIBCALL SeqAlignScorePtrGet(SeqAlignPtr salp);
121 NLM_EXTERN void LIBCALL SeqAlignWrite(SeqAlignPtr salp,CharPtr file);
137 NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignListFree (SeqAlignPtr salp);
[all …]
H A Dsalsap.c83 if (salp->dim == 2 && salp->next != NULL) { in is_dim2seqalign()
176 for (salp = salphead; salp!= NULL; salp=salp->next) in SeqAlignSeqLocComp()
549 salp = salp->next; in SeqAlignBoolSegCpy()
678 salp = salp->next; in SeqAnnotDenseSegToBoolSeg()
790 salp = salp->next; in SeqAnnotBoolSegToDenseSeg()
1938 for (salp = salphead; salp!= NULL; salp=salp->next) in SeqAlignIDCache()
1963 for (salp = salphead; salp!= NULL; salp=salp->next) in SeqAlignIDUncache()
1982 for (salp = salphead; salp!= NULL; salp=salp->next) in SeqAlignIDUncacheAll()
2873 if ( ( salp = salp->next) != NULL ) in DeleteRegion()
2877 salp = salp->next; in DeleteRegion()
[all …]
H A Dviewmgr.h177 NLM_EXTERN Int4 ViewMgr_VRow2TRow(SeqAlign *salp, Int4 VRow);
191 NLM_EXTERN Int4 ViewMgr_TRow2VRow (SeqAlign *salp, Int4 TRow);
205 NLM_EXTERN Int4 ViewMgr_MakeMultiple(SeqAlign *salp);
214 NLM_EXTERN SeqAlign * ViewMgr_GetTarget(SeqAlign *salp);
223 NLM_EXTERN SeqAlign * ViewMgr_GetBegin(SeqAlign *salp);
243 NLM_EXTERN SeqAlign * ViewMgr_GetBeginIndexed(SeqAlign *salp);
252 NLM_EXTERN Boolean ViewMgr_IsNeat(SeqAlign *salp);
261 NLM_EXTERN Boolean ViewMgr_IsIBM(SeqAlign *salp);
319 NLM_EXTERN Int4 ViewMgr_RemoveSA(SeqAlign *salp);
349 NLM_EXTERN Int4 ViewMgr_Attach(SeqAlign *salp, Boolean Neat,
[all …]
H A Dsalpedit.h31 NLM_EXTERN SeqAlignPtr SeqAlignSort(SeqAlignPtr salp,SeqAlignSortCB sort_fn);
33 NLM_EXTERN SeqAlignPtr SeqAlignSortByLength(SeqAlignPtr salp);
34 NLM_EXTERN SeqAlignPtr SeqAlignSortByScore(SeqAlignPtr salp);
36 NLM_EXTERN SeqAlignPtr SeqAlignSortByEvalue(SeqAlignPtr salp);
38 NLM_EXTERN SeqAlignPtr SeqAlignSortByStart(SeqAlignPtr salp,Int2 order);
39 NLM_EXTERN SeqAlignPtr SeqAlignSortByRegion(SeqAlignPtr salp,Int2 order);
44 NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignListReverseStrand (SeqAlignPtr salp);
45 NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignDup (SeqAlignPtr salp);
46 NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignListDup (SeqAlignPtr salp);
H A Dalignmgr.c806 salp = salp->next; in AMFreeAllIndexes()
1001 salp = salp->next; in AlnMgrIndexSeqAlign()
1652 salp = salp->next; in AlnMgrIndexParentSA()
1709 salp = salp->next; in AlnMgrPropagateUpSeqIdPtrs()
1855 salp = salp->next; in AlnMgrRemoveInconsistentFromPairwiseSetEx()
5380 salp = salp->next; in AlnMgrNeatlyIndex()
5398 salp = salp->next; in AlnMgrNeatlyIndex()
5515 salp = salp->next; in AlnMgrTossNeatRows()
5572 salp = salp->next; in AlnMgrMakeMultByIntersectOnMaster()
5679 salp = salp->next; in am_guess_numrows()
[all …]
H A Dsalpstat.c471 salp=salp->next; in SeqAlignSimpleStats()
956 if (salp == NULL) in SelectLongestSeqAlign()
961 return salp; in SelectLongestSeqAlign()
967 select = salp; in SelectLongestSeqAlign()
968 salptmp= salp; in SelectLongestSeqAlign()
1395 return salp; in SeqAlignNonRedundant()
2231 if(!salp) in SeqAlignSameIdMerge()
2424 salp=SeqAlignSetFree(salp); in SeqAlignStats()
2444 salp=salp_in; in SeqAlignListGlobalStats()
2458 salp=SeqAlignSetFree(salp); in SeqAlignListGlobalStats()
[all …]
H A Dsalpedit.c38 SeqAlignPtr salp, in SeqAlignBioseqDeleteById() local
46 salp = salphead; in SeqAlignBioseqDeleteById()
53 if (salp->segtype == 1 || salp->dim == 2) in SeqAlignBioseqDeleteById()
60 salp = SeqAlignFree (salp); in SeqAlignBioseqDeleteById()
3605 if(salp==NULL || salp->next==NULL) in SeqAlignSort()
3627 return salp; in SeqAlignSort()
3638 if(salp==NULL || salp->next==NULL) in SeqAlignSortByLength()
3670 if(salp==NULL || salp->next==NULL) in SeqAlignSortByScore()
3708 if(salp==NULL || salp->next==NULL) in SeqAlignSortByEvalue()
3746 if(salp==NULL || salp->next==NULL) in SeqAlignSortByStart()
[all …]
H A Dalignval.h109 NLM_EXTERN Boolean ValidateSeqAlign (SeqAlignPtr salp, Uint2 entityID, Boolean message,
118 extern Uint2 AlignmentPercentIdentity (SeqAlignPtr salp, Boolean internal_gaps);
122 (SeqAlignPtr salp,
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dsalign.c526 return salp; in SeqAlignList2PosStrand()
713 salp = SeqAlignMerge (salp, salp2, FALSE); in AlignExtreme5()
738 salp = SeqAlignMerge (salp, salp2, FALSE); in AlignExtreme5()
741 return salp; in AlignExtreme5()
772 salp = SeqAlignMerge (salp, salp2, TRUE); in AlignExtreme3()
797 salp = SeqAlignMerge (salp, salp2, TRUE); in AlignExtreme3()
800 return salp; in AlignExtreme3()
1102 headnode->salp = salp; in CreateGraph()
1204 salp=nodetmp->salp; in link_solution()
1253 salp=nodetmp->salp; in find_maxsolution()
[all …]
H A Dsalptool.c1541 if (salp == NULL in TruncateAlignment()
1712 if (salp == NULL || salp->segtype != 2 || salp->segs == NULL || seq_num < 1) in CutAlignmentAtGaps()
1731 salp->next = NULL; in CutAlignmentAtGaps()
1878 salp = SeqAlignFree (salp); in RemoveSequencesInGapFromAlignments()
1889 salp = SeqAlignBioseqDeleteById (salp, sip); in RemoveSequencesInGapFromAlignments()
1896 salp->next = RemoveSequencesInGapFromAlignments (salp->next); in RemoveSequencesInGapFromAlignments()
1899 return salp; in RemoveSequencesInGapFromAlignments()
1907 if (salp == NULL || salp->segtype != 2 || salp->segs == NULL) in MakeDiscontiguousAlignments()
1909 return salp; in MakeDiscontiguousAlignments()
1917 salp = RemoveSequencesInGapFromAlignments (salp); in MakeDiscontiguousAlignments()
[all …]
H A Dspidey.c603 salp = SeqAlignListReverseStrand(salp); in SPI_AlnSinglemRNAToGen()
607 salp = salp->next; in SPI_AlnSinglemRNAToGen()
1459 SeqAlignPtr salp; in SPI_RemoveOutsideBounds() local
2621 salp->dim = 2; in SPI_CreateContinuousAln()
2624 return salp; in SPI_CreateContinuousAln()
2896 salp = salp->next; in SPI_AlnSinglemRNAToPieces()
4032 salp = 0; in SPI_CheckForPolyAExon()
4036 salp = salp->next; in SPI_CheckForPolyAExon()
4577 salp = salp->next; in SPI_GetNthSeqLenInSASet()
4622 salp = salp->next; in SPI_GetNthSeqRangeInSASet()
[all …]
/dports/biology/ncbi-toolkit/ncbi/desktop/
H A Dsalsa.c3459 salp = SeqAlignList2PosStrand(salp); in SetupAlignDataSap()
4204 salp = salp->next; in DoReplaceBtn()
4439 salp = salp->next; in DoMergeBtn()
4521 salp = salp->next; in DoCopyFeatBtn()
4544 salp = SeqAlignBoolSegToDenseSeg (salp); in LaunchAlignEdit()
4581 salp = salp->next; in SkipThisWindowProc()
5152 salp = salp->next; in OldAlignmentEditor()
5199 salp = DenseSegToDenseDiag (salp); in AnnotAlgEditFunc()
5216 salp = salp->next; in AnnotAlgEditFunc()
6090 p->salp = SeqAlignFree (p->salp); in FarPointerFree()
[all …]
H A Dseqpanel.h37 (SeqAlignPtr salp,
43 (SeqAlignPtr salp,
49 (SeqAlignPtr salp,
58 extern ForM CreateAlnEditorWindow (Int2 left, Int2 top, CharPtr windowname, SeqAlignPtr salp, Uint2…
61 (Int2 left, Int2 top, CharPtr windowname, SeqAlignPtr salp, Uint2 entityID,
66 NLM_EXTERN CharPtr FeatureLocationAlignment (SeqFeatPtr sfp, SeqAlignPtr salp, Int4 begin, Int4 fin…
67 extern void FlipAlignment (SeqAlignPtr salp);
H A Dsaledit.h184 …ignDataPtr EditAlignDataRepopulateFromSeqAlign (PaneL pnl, EditAlignDataPtr adp, SeqAlignPtr salp);
191 extern void repopulate_panel (WindoW w, EditAlignDataPtr adp, SeqAlignPtr salp);
200 extern void LaunchAlignEditor (SeqAlignPtr salp);
201 extern void LaunchAlignViewer (SeqAlignPtr salp);
202 extern void OpenNewAlignmentEditor (SeqAlignPtr salp, Uint2 input_entityID);
220 NLM_EXTERN Boolean ValidateSeqAlignandACC (SeqAlignPtr salp, Uint2 entityID,
233 NLM_EXTERN Boolean CheckAlignmentSequenceLengths (SeqAlignPtr salp);
235 NLM_EXTERN Boolean UpdateOneSeqAlignFarPointer (SeqAlignPtr salp, Int4 pos);
H A Ddotvibrant.c2494 hit_stop=ABS(salp->q_stop-salp->q_start); in DOT_SVDisplaySequence()
2501 buf_len=ABS(salp->q_stop-salp->q_start)+1; in DOT_SVDisplaySequence()
2683 salp=vdp2->sv->salp; in DOT_SVPopulateSequenceViewer()
2738 salp->q_stop = salp->q_start - len; in DOT_SVFindHit()
2749 return salp; in DOT_SVFindHit()
2846 vdp2->sv->salp=salp; in DOT_SVClickProc()
3881 salp = vdp2->sv->salp; in DOT_GotoProc()
5367 while (salp) in DOT_GetAlign()
5405 salp=salp->next; in DOT_GetAlign()
5585 salp=sap; in DOT_FillAlignInfoPointer()
[all …]
H A Dseqpanel.c523 if (salp == NULL) in GetAlignmentBioseqLists()
581 salp = salp->next; in FreeAlignmentBioseqLists()
1026 bvp->salp = SeqAlignFree (bvp->salp); in PopulateAlnView()
2681 bvp->salp = SeqAlignFree (bvp->salp); in UpdateSeqViewPanel()
8614 (SeqAlignPtr salp, in WriteAlignmentInterleaveToFileEx() argument
8683 (SeqAlignPtr salp, in WriteAlignmentInterleaveToFile() argument
8692 (SeqAlignPtr salp, in WriteAlignmentContiguousToFile() argument
9283 if (salp == NULL) in IsAlignmentOnSet()
9477 sefp->bfp->bvd.salp = salp; in CreateAlnEditorWindowEx()
9916 return salp; in GetSeqAlignEx()
[all …]
/dports/biology/ncbi-toolkit/ncbi/biostruc/cdd/
H A Dcddutil.h450 Int4Ptr LIBCALL GetAlignmentSize(SeqAlignPtr salp);
456 Boolean LIBCALL SeqAlignHasConsensus(SeqAlignPtr salp);
488 SeqAlignPtr LIBCALL CddMSLMixedToMSLDenDiag(SeqAlignPtr salp);
489 SeqAlignPtr LIBCALL CddMSLDenDiagToMSLDenSeg(SeqAlignPtr salp);
490 SeqAlignPtr LIBCALL CddMSLDenSegToMSLDenDiag(SeqAlignPtr salp);
596 SeqAlignPtr salp,
608 SeqAlignPtr LIBCALL CddCopyMSLDenDiag(SeqAlignPtr salp);
638 SeqAnnotPtr LIBCALL CddSeqAnnotForSeqAlign (SeqAlignPtr salp);
639 SeqAlignPtr LIBCALL CddSeqAlignDup (SeqAlignPtr salp);
640 SeqAlignPtr LIBCALL SeqAlignSetDup(SeqAlignPtr salp);
[all …]
H A Dcddutil.c771 salp = salp->next; in CddGetAlignmentLength()
916 salp = salp->next; in CddCount3DAlignments()
1561 salp = salp->next; in CddMSLMixedToMSLDenDiag()
1648 salp = salp->next; in CddMSLDenSegToMSLDenDiag()
1702 salp = salp->next; in CddMSLDenDiagToMSLDenSeg()
1901 salp = salp->next; in SeqAlignConservation()
2012 salp = salp->next; in SeqAlignInform()
2107 salp = salp->next; in CddCountResTypes()
3179 if (!salp->segs) salp = SeqAlignFree(salp); in CddExpAlignToSeqAlign()
5499 for(salp=head; salp; salp=salp->next) { in CddTrimSeqAligns()
[all …]
/dports/biology/ncbi-toolkit/ncbi/biostruc/cblast/
H A Dcblastutil.c339 salp = salp->next; in MultiHSP()
375 salp = salp->next; in ReplaceSeqIdForSeqAnnot()
461 salp = salp->next; in CblastAlgTruncate()
498 salp = salp->next; in CblastAlgTruncateAndExtend()
567 salp = salp->next; in GetAlgForSubjectPairPerHSP()
598 salp = salp->next; in GetAlgForSubjectPair()
1159 salp = salp->next; in FillCdInfo()
1195 salp = salp->next; in FillCdInfo()
1339 salp = salp->next; in FillCdInfo()
1383 salp = salp->next; in BlastPDBNbInfoBuild()
[all …]
/dports/biology/ncbi-toolkit/ncbi/cn3d/
H A Dcn3dmsg.c413 SeqAlign *salp; in Cn3D_LaunchSeqAnnot() local
422 salp = sap->data; in Cn3D_LaunchSeqAnnot()
458 NLM_EXTERN Int4 Cn3D_CountRows(SeqAlign *salp) in Cn3D_CountRows() argument
463 if(salp == NULL) return 0; in Cn3D_CountRows()
465 salptmp = SeqAlignListDup(salp); in Cn3D_CountRows()
488 SeqAlign *salp; in Cn3D_RegisterSeqAnnot() local
495 salp = sap->data; in Cn3D_RegisterSeqAnnot()
499 SAM_MakeViewerFree((void *) salp); in Cn3D_RegisterSeqAnnot()
511 ViewMgr_Attach(salp, Neat, IBM, 0, 0); in Cn3D_RegisterSeqAnnot()
529 SeqAlign *salp; in Cn3D_SendUpdate() local
[all …]
H A Dcn3dopen.c513 SeqAlign *salp; in Cn3D_ShredCBlast() local
527 if (salp) { in Cn3D_ShredCBlast()
568 if (salp) { in Cn3D_MarkStrucSeqs()
584 while (salp) { in Cn3D_MarkStrucSeqs()
612 salp = salp->next; in Cn3D_MarkStrucSeqs()
877 salp = sanp->data; in Cn3D_StoreAlignRowNumsInMMDs()
880 if (!salp) return; in Cn3D_StoreAlignRowNumsInMMDs()
1471 annot->data = salp; in Cn3D_ImportSAEnd()
1484 ViewMgr_Update(salp); in Cn3D_ImportSAEnd()
1573 salp->next = NULL; in Cn3D_ImportCBSE()
[all …]

12345678910>>...12