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| Packages that use AlignParams | |
| gata.aligner | For aligning and post processing DNA sequences using BLAST for subsequent import into GATAPlotter. |
| gata.main | Main app, utility, and params for GATAPlotter. |
| gata.plotter | GATAPlotter primary panel, sliders, tools, and conservation panels. |
| Uses of AlignParams in gata.aligner |
| Fields in gata.aligner declared as AlignParams | |
AlignParams |
Blast.ap
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| Methods in gata.aligner that return AlignParams | |
AlignParams |
LocalAlignment.getAP()
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| Constructors in gata.aligner with parameters of type AlignParams | |
Seqs(AlignParams ap,
MultiFastaParser ref,
MultiFastaParser comp,
int index)
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LocalAlignment(java.lang.String seq_1,
int startSeq_1,
int stopSeq_1,
java.lang.String seq_2,
int startSeq_2,
int stopSeq_2,
int ori_,
AlignParams ap_,
int score_)
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Blast(AlignParams AP)
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Alignment(java.lang.String s1,
int start1,
int stop1,
java.lang.String s2,
int start2,
int stop2,
int aScore,
int ori,
AlignParams ap,
LocalAlignment la)
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| Uses of AlignParams in gata.main |
| Methods in gata.main that return AlignParams | |
AlignParams |
GATAParams.getAlignParams()
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| Methods in gata.main with parameters of type AlignParams | |
void |
GATAParams.setAlignParams(AlignParams ap)
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| Uses of AlignParams in gata.plotter |
| Methods in gata.plotter with parameters of type AlignParams | |
static boolean |
MultiAlignPanel.checkAlignParams(AlignParams[] alignParams)
Checks to see if the same params were used used in making the alignments, note score cut off is not checked |
static int |
MultiAlignPanel.fetchMinScore(AlignParams[] alignParams)
Finds lowest minScore in an array of AlignParams. |
| Constructors in gata.plotter with parameters of type AlignParams | |
Sliders(AlignParams ap,
GATAParams params)
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