| /dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
| H A D | ajfeat.h | 100 AjPFeature ajFeatNewFeat(const AjPFeature orig);
101 void ajFeatDel(AjPFeature *pthis);
146 AjPFeature ajFeatNew(AjPFeattable thys,
180 AjPFeature ajFeatNewSub(AjPFeattable thys, AjPFeature parent,
184 AjPFeature ajFeatNewIISub(AjPFeattable thys, AjPFeature parent,
186 AjPFeature ajFeatNewIIRevSub(AjPFeattable thys, AjPFeature parent,
188 AjPFeature ajFeatNewNucSub(AjPFeattable thys, AjPFeature parent,
195 AjPFeature ajFeatNewNucFlagsSub(AjPFeattable thys, AjPFeature parent,
203 AjPFeature ajFeatNewProtSub(AjPFeattable thys, AjPFeature parent,
207 AjPFeature ajFeatNewProtFlagsSub(AjPFeattable thys, AjPFeature parent,
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| H A D | ajfeat.c | 790 AjPFeature ajFeatNewIIRevSub(AjPFeattable thys, AjPFeature parent, in ajFeatNewIIRevSub()
867 AjPFeature ajFeatNewProtSub(AjPFeattable thys, AjPFeature parent, in ajFeatNewProtSub()
1074 const AjPFeature gfa; in ajFeatCompByStart()
1075 const AjPFeature gfb; in ajFeatCompByStart()
1113 const AjPFeature gfa; in ajFeatCompByEnd()
1932 AjPFeature featsrc; in ajFeattableMerge()
8480 AjPFeature ajFeatNewFeat(const AjPFeature orig) in ajFeatNewFeat()
8482 AjPFeature ret; in ajFeatNewFeat()
8483 AjPFeature subfeat; in ajFeatNewFeat()
10063 AjPFeature ret; in featFeatureNew()
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| H A D | ajfeatwrite.c | 99 const AjPFeature gftop);
1069 AjPFeature gf = NULL; in ajFeattableWriteGff2()
1130 AjPFeature gf = NULL; in ajFeattableWriteGff3()
1203 AjPFeature gf = NULL; in ajFeattableWriteBed()
2128 AjPFeature gf = NULL; in ajFeattableWriteSwiss()
2129 AjPFeature gfsub = NULL; in ajFeattableWriteSwiss()
2305 AjPFeature gf = NULL; in ajFeattableWriteDasgff()
3825 AjPFeature copy = NULL; in featDumpPir()
4091 AjPFeature gf = NULL; in featDumpBed()
4487 static void featDumpGff3(const AjPFeature thys, const AjPFeature parent, in featDumpGff3()
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| H A D | ajreport.c | 515 AjPFeature feature = NULL; in reportWriteDbMotif()
671 AjPFeature feature = NULL; in reportWriteDiffseq()
874 AjPFeature feature = NULL; in reportWriteDraw()
965 AjPFeature feature = NULL; in reportWriteRestrict()
1124 AjPFeature feature = NULL; in reportWriteExcel()
1248 AjPFeature feature = NULL; in reportWriteFeatTable()
1351 AjPFeature feature = NULL; in reportWriteListFile()
1456 AjPFeature feature = NULL; in reportWriteMotif()
1686 AjPFeature feature = NULL; in reportWriteNameTable()
1839 AjPFeature feature = NULL; in reportWriteRegions()
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| H A D | ajfeatread.c | 1950 AjPFeature feature = NULL; in featReadDasgff()
3409 AjPFeature ret; in featSwissProcess()
3687 AjPFeature ret = NULL; in featEmblProcess()
3688 AjPFeature gf = NULL; in featEmblProcess()
4782 AjPFeature gf = NULL; in featGff2FromLine()
4911 AjPFeature gf = NULL; in featGff3FromLine()
4912 AjPFeature gftop = NULL; in featGff3FromLine()
5470 AjPFeature gf = NULL; in featGff3Matchtable()
5471 AjPFeature gfid = NULL; in featGff3Matchtable()
5751 AjPFeature ret = NULL; in featRefseqpProcess()
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| H A D | ajfeatdata.h | 423 #define AjPFeature AjOFeature* macro
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| /dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
| H A D | showpep.c | 36 static AjBool showpep_MatchFeature(const AjPFeature gf,
37 AjPFeature newgf,
45 AjPFeature newgf,
56 static AjPFeature showpep_FeatCopy(const AjPFeature orig);
360 AjPFeature gf = NULL; in showpep_FeatureFilter()
361 AjPFeature newgf = NULL; in showpep_FeatureFilter()
372 gf = (AjPFeature)ajListIterGet(iter); in showpep_FeatureFilter()
416 static AjBool showpep_MatchFeature(const AjPFeature gf, AjPFeature newgf, in showpep_MatchFeature()
495 AjPFeature newgf, in showpep_MatchPatternTags()
582 static AjPFeature showpep_FeatCopy(const AjPFeature orig) in showpep_FeatCopy()
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| H A D | splitsource.c | 31 static void splitsource_AddSubSeqFeat(AjPFeattable ftable, const AjPFeature gf,
34 const AjPFeature gf,
38 const AjPFeature gf);
60 AjPFeature gf = NULL; in main()
153 const AjPFeature gf) in splitsource_MakeSubSeqName()
193 const AjPFeature gf, const AjPStr name, in splitsource_ProcessChunk()
256 const AjPFeature gfsrc, in splitsource_AddSubSeqFeat()
271 AjPFeature gf = ajListIterGet(iter); in splitsource_AddSubSeqFeat()
273 AjPFeature copy = NULL; in splitsource_AddSubSeqFeat()
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| H A D | showfeat.c | 269 AjPFeature gf = NULL ; in showfeat_ShowFeatSeq()
270 AjPFeature gfsub = NULL ; in showfeat_ShowFeatSeq()
787 const AjPFeature c; in showfeat_CompareFeatSource()
788 const AjPFeature d; in showfeat_CompareFeatSource()
791 c = *(AjPFeature const *)a; in showfeat_CompareFeatSource()
792 d = *(AjPFeature const *)b; in showfeat_CompareFeatSource()
839 const AjPFeature c; in showfeat_CompareFeatType()
840 const AjPFeature d; in showfeat_CompareFeatType()
842 c = *(AjPFeature const *)a; in showfeat_CompareFeatType()
887 const AjPFeature c; in showfeat_CompareFeatPos()
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| H A D | showseq.c | 42 static AjBool showseq_MatchFeature(const AjPFeature gf,
43 AjPFeature newgf,
52 AjPFeature newgf,
64 static AjPFeature showseq_FeatCopy(const AjPFeature orig);
641 AjPFeature gf = NULL; in showseq_FeatureFilter()
642 AjPFeature newgf = NULL; in showseq_FeatureFilter()
653 gf = (AjPFeature)ajListIterGet(iter); in showseq_FeatureFilter()
699 static AjBool showseq_MatchFeature(const AjPFeature gf, AjPFeature newgf, in showseq_MatchFeature()
781 AjPFeature newgf, in showseq_MatchPatternTags()
868 static AjPFeature showseq_FeatCopy(const AjPFeature orig) in showseq_FeatCopy()
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| H A D | twofeat.c | 44 AjPFeature gfA;
45 AjPFeature gfB;
63 static AjBool twofeat_check_match(AjPFeature gfA, AjPFeature gfB,
74 static AjBool twofeat_MatchFeature(const AjPFeature gf,
359 AjPFeature gfA = NULL; in twofeat_rippledown()
362 AjPFeature gfB = NULL; in twofeat_rippledown()
440 AjPFeature feature; in twofeat_report_hits()
540 AjPFeature gf = NULL; in twofeat_find_features()
541 AjPFeature gfcopy = NULL; in twofeat_find_features()
607 static AjBool twofeat_MatchFeature(const AjPFeature gf, in twofeat_MatchFeature()
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| H A D | union.c | 31 const AjPFeature source_feature);
60 AjPFeature source_feature = NULL; in main()
225 const AjPFeature source_feature) in union_CopyFeatures()
228 AjPFeature gf = NULL; in union_CopyFeatures()
230 AjPFeature copy = NULL; in union_CopyFeatures()
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| H A D | extractfeat.c | 59 static AjBool extractfeat_MatchFeature(const AjPFeature gf,
66 static AjBool extractfeat_MatchPatternTags(const AjPFeature feat,
70 static AjBool extractfeat_MatchPatternDescribe(const AjPFeature feat,
196 AjPFeature gf = NULL; in extractfeat_FeatSeqExtract()
197 AjPFeature gftop = NULL; in extractfeat_FeatSeqExtract()
709 AjPFeature gf = NULL; in extractfeat_FeatureFilter()
727 gf = (AjPFeature)ajListIterGet(iter); in extractfeat_FeatureFilter()
764 static AjBool extractfeat_MatchFeature(const AjPFeature gf, in extractfeat_MatchFeature()
864 static AjBool extractfeat_MatchPatternTags(const AjPFeature feat, in extractfeat_MatchPatternTags()
938 static AjBool extractfeat_MatchPatternDescribe(const AjPFeature feat, in extractfeat_MatchPatternDescribe()
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| H A D | diffseq.c | 113 static void diffseq_Features(const char* typefeat, AjPFeature rf,
117 static void diffseq_AddTags(AjPStr* strval, const AjPFeature feat,
299 AjPFeature gf = NULL; in diffseq_Diff()
496 AjPFeature feature = NULL; in diffseq_WordMatchListConvDiffToFeat()
658 static void diffseq_Features(const char* typefeat, AjPFeature rf, in diffseq_Features()
663 AjPFeature gf = NULL; in diffseq_Features()
719 const AjPFeature feat, AjBool values) in diffseq_AddTags()
992 AjPFeature gf = NULL; in diffseq_FeatSetCDSFrame()
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| H A D | fuzztran.c | 217 AjPFeature protfeature = NULL; in fuzztran_SourceFeature()
218 AjPFeature sourcefeature = NULL; in fuzztran_SourceFeature()
249 protfeature = (AjPFeature)ajListIterGet(iter); in fuzztran_SourceFeature()
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| H A D | splitter.c | 262 AjPFeature gf = ajListIterGet(iter); in splitter_AddSubSeqFeat()
264 AjPFeature copy = NULL; in splitter_AddSubSeqFeat()
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| H A D | psiphi.c | 65 static AjPFeature psiphi_write_psi_phi(AjPFeattable angletab,
898 static AjPFeature psiphi_write_psi_phi (AjPFeattable angletab, in psiphi_write_psi_phi()
903 AjPFeature angleft; in psiphi_write_psi_phi()
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| H A D | maskfeat.c | 102 AjPFeature gf = NULL ; in maskfeat_FeatSeqMask()
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| H A D | sirna.c | 428 AjPFeature gf = NULL; in sirna_begin()
615 AjPFeature gf; in sirna_output()
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| H A D | antigenic.c | 69 AjPFeature gf = NULL; in main()
515 AjPFeature feature; in antigenic_dumptoFeat()
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| H A D | equicktandem.c | 248 AjPFeature gf; in equicktandem_report()
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| H A D | patmatmotifs.c | 69 AjPFeature gf; in main()
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| H A D | checktrans.c | 265 AjPFeature feature; in checktrans_dumptofeat()
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| H A D | cpgreport.c | 164 AjPFeature feature; in cpgreport_cpgsearch()
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| /dports/biology/emboss/EMBOSS-6.6.0/nucleus/ |
| H A D | embpatlist.c | 264 AjPFeature sf = NULL; in embPatternRegexSearch()
394 AjPFeature sf = NULL; in embPatternRegexSearchAll()
537 AjPFeature sf = NULL; in embPatternSeqSearch()
683 AjPFeature sf = NULL; in embPatternSeqSearchAll()
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