--- /dev/null
+Command line: [exonerate --model protein2genome Input_Sequences63/dcsA.fas NewSequencedGenome/A_Ellipt_clc_pe_contigs.fa --bestn 1 --showtargetgff]
+Hostname: [ningal.cluster.lifesci.dundee.ac.uk]
+
+C4 Alignment:
+------------
+ Query: DDB_G0269124
+ Target: contig_1146 [revcomp]
+ Model: protein2genome:local
+ Raw score: 3652
+ Query range: 142 -> 1059
+ Target range: 11269 -> 8533
+
+ 143 : SerProSerSerGluTyrGlyThrThrSerGlyGlyGlnArgPheAspThrLeuValAsp : 162
+ ||||||!:!! !||| !.! ! ! !!.! !! !!.!|||!!:||||||:!!|||
+ SerProAsnMetGluLeuAlaArgAspLeuAlaGlnProHisPheGluThrLeuIleAsp
+ 11269 : TCGCCCAACATGGAGCTGGCGCGCGACCTCGCCCAGCCGCACTTTGAGACGCTGATCGAC : 11212
+
+ 163 : ProAspIleSerLeuAlaGluMetGluGluLysMetArgGlnHisLysValTyrGlnGlu : 182
+ ||||||!!:!!!! !!.!|||!!:||||||||||||||||||||||||!.!:!!! |||
+ ProAspMetThrProGlyGluIleGluGluLysMetArgGlnHisLysAlaHisLeuGlu
+ 11211 : CCCGACATGACGCCCGGCGAGATCGAGGAGAAGATGCGCCAGCACAAGGCGCACCTCGAG : 11152
+
+ 183 : GlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnLysGlnLysAspLysGluLeuSer : 202
+ ..!|||:!!.....!..!:!!! |||:!!|||..!:!! !! ! !
+ ------------MetGlnLysSerSerSerGluLeuLysLysLysSerGlnMetGlnLeu
+ 11151 : ------------ATGCAAAAGTCCTCGTCGGAACTCAAGAAGAAGTCCCAAATGCAACTC : 11104
+
+ 203 : SerGlnLysLysLysProSerSerMetGlnLeuSerLysLysLysHisValAlaLysGlu : 222
+ !.!||| ! :!!:!! !..!..!:!: !!.!||| ::: :!! !:!!!!:
+ LysGlnAspGlnGlnLysGlnGlnValValAlaLysLysProArgSerIleLeuGlnAsp
+ 11103 : AAGCAGGATCAGCAGAAACAACAAGTCGTCGCAAAGAAGCCCCGTTCGATCCTCCAGGAC : 11044
+
+ 223 : AspSerGluThrLeuGluThrIleIleGlyGluGluLysLysGluValValPheGluVal : 242
+ |||! !||||||! !||||||:!!.!!!.!||||||:::|||||||||||||||||||||
+ AspMetGluThrSerGluThrLeuPheAlaGluGluArgLysGluValValPheGluVal
+ 11043 : GACATGGAGACGTCGGAGACCCTTTTCGCCGAGGAACGCAAGGAGGTCGTCTTTGAGGTG : 10984
+
+ 243 : LysProTyrPheSerHisAlaIleLeuGlnAlaThrMetAlaValPheLeuIleTrpAsn : 262
+ :::|||||||||||||||:!!|||||||||||||||||||||||||||||||||||||||
+ ArgProTyrPheSerHisSerIleLeuGlnAlaThrMetAlaValPheLeuIleTrpAsn
+ 10983 : CGTCCCTACTTCTCGCACTCTATCCTCCAGGCGACGATGGCCGTCTTCCTCATCTGGAAC : 10924
+
+ 263 : IlePheTyrPheAlaTyrArgAlaGlyTrpThrMetAsnArgThrAspTyrIle<->Thr : 281
+ ||||||||||||||||||||| !|||||||||||||||! ! !:!! !:!! ..!
+ IlePheTyrPheAlaTyrArgMetGlyTrpThrMetAsnThrGlnAsnGlyValTyrVal
+ 10923 : ATCTTTTACTTTGCCTACCGTATGGGCTGGACCATGAACACCCAGAACGGCGTCTACGTG : 10864
+
+ 282 : PheSerTyrSerIleLeuPheIleIleValGluPheIleSerPheLeuGlySerAlaLeu : 301
+ .!!!!!||||||:!:||||||:!!||||||||||||||||||||||||||||||||||||
+ LeuCysTyrSerValLeuPheLeuIleValGluPheIleSerPheLeuGlySerAlaLeu
+ 10863 : CTCTGCTACTCGGTGCTCTTCCTCATCGTCGAGTTCATCTCTTTCCTCGGCTCCGCGCTC : 10804
+
+ 302 : HisLeuAsnAsnPheThrAsnProCysThrPheValLeuValValThrLeuGluGlnIle : 321
+ |||||||||||||||||||||||||||||||||:!!||||||||||||||||||||||||
+ HisLeuAsnAsnPheThrAsnProCysThrPheIleLeuValValThrLeuGluGlnIle
+ 10803 : CATCTCAACAACTTTACCAATCCGTGCACCTTTATCCTGGTGGTCACGCTGGAGCAGATC : 10744
+
+ 322 : LeuAlaLysArgArgLysLysHisProThrValMetMetTyrValCysThrTyrLysGlu : 341
+ ||||||:::||||||||| !||||||||||||||||||:!!|||||||||||||||
+ LeuAlaArgArgArgLysProPheProThrValMetMetTyrIleCysThrTyrLysGlu
+ 10743 : CTCGCGCGCCGTCGCAAGCCCTTCCCCACCGTCATGATGTACATCTGTACCTACAAGGAG : 10684
+
+ 342 : ProProSerIleValSerArgThrPheArgThrAlaIleSerMetAspTyrProSerGlu : 361
+ |||||||||||||||||||||||||||||||||||||||:!!||||||||||||:!!|||
+ ProProSerIleValSerArgThrPheArgThrAlaIleAlaMetAspTyrProAlaGlu
+ 10683 : CCGCCCTCGATCGTCTCGCGCACGTTCCGCACCGCCATCGCCATGGACTACCCCGCCGAG : 10624
+
+ 362 : AsnLeuTrpIleGlyLeuLeuAspAspSerValAsnTyrArgGluSerArgGlyTrpAla : 381
+ ||||||||||||||||||||||||||||||:!!|||!:!||||||||||||||||||:!!
+ AsnLeuTrpIleGlyLeuLeuAspAspSerIleAsnPheArgGluSerArgGlyTrpSer
+ 10623 : AACCTCTGGATCGGCCTGCTCGACGACTCGATCAACTTCCGCGAGTCGCGCGGCTGGTCG : 10564
+
+ 382 : HisLeuGlnSerValGluLysAsnPheLeuTyrValLeuLeuGlnLysAlaValTyrSer : 401
+ ||||||||||||||||||||||||||||||!:! !|||||||||::::!!||||||:!!
+ HisLeuGlnSerValGluLysAsnPheLeuPheGlnLeuLeuGlnArgSerValTyrAla
+ 10563 : CACCTCCAATCGGTCGAGAAGAACTTCCTCTTCCAGCTGCTCCAGCGCTCCGTGTACGCC : 10504
+
+ 402 : ValHisAsnIleArgProProValThrSerGlnHisGluAspProHisGlyIleLeuAsn : 421
+ |||||||||||| !|||||||||.!!..!||| !|||||||||:!!|||||||||..!
+ ValHisAsnIleAlaProProValAlaGlnGlnAlaGluAspProTyrGlyIleLeuGly
+ 10503 : GTGCACAACATCGCGCCGCCCGTCGCGCAGCAGGCCGAGGACCCGTACGGCATCCTCGGC : 10444
+
+ 422 : GluThrSerSerLysIleGluSerSerThrLysGluValIleGluAlaGluValGlnTrp : 441
+ |||||||||..!:::||||||!.!!!!||||||||||||:!!||||||||||||||||||
+ GluThrSerGluArgIleGluLysThrThrLysGluValValGluAlaGluValGlnTrp
+ 10443 : GAGACGTCCGAGCGCATCGAAAAGACCACGAAAGAGGTCGTCGAGGCCGAGGTGCAGTGG : 10384
+
+ 442 : PheIleGluTyrPheLeuLeuAsnSerTrpPheGlyValGlyGlnGluIleProArgAsp : 461
+ ||||||||||||||||||||||||||||||||||||:!!! !!::||| ! !! !!!:
+ PheIleGluTyrPheLeuLeuAsnSerTrpPheGlyIleAspArgGluProGluIleGlu
+ 10383 : TTCATCGAGTACTTCCTCCTGAACAGCTGGTTCGGCATCGACCGCGAGCCCGAGATCGAG : 10324
+
+ 462 : AlaAspAspAlaGluArgAlaLeuIleAlaLysLeuArgAspAspAsnPheSerProTyr : 481
+ !!..!|||||||||||| !!!!|||:!!! !||||||!!:|||||||||||| !!|||
+ ProSerAspAlaGluArgAsnPheIleSerMetLeuArgGluAspAsnPheSerAlaTyr
+ 10323 : CCCTCCGACGCCGAACGCAACTTTATCTCGATGCTGCGCGAGGACAACTTCTCGGCGTAC : 10264
+
+ 482 : ArgThrPheThrLysSerGluSerGluLysIleSerAsnPheThrIleAspSerLeuGln : 501
+ ||||||.!!||| ! ..!||| !!||| |||! !!..|||:!!! !|||:!!||||||
+ ArgThrIleThrAspGlnGluArgGluLeuIleTyrThrPheSerSerAspAlaLeuGln
+ 10263 : CGCACCATCACCGACCAGGAGCGCGAGCTCATCTACACGTTCTCGAGCGACGCGCTCCAG : 10204
+
+ 502 : SerLeuTrpHisGlySerAlaPhePheArgProLeuIleArgSerIleLeuLeuLysLys : 521
+ |||:!!|||||||||||| !!.!.!:!|||||||||:!:|||!:! !|||!!!:!!:::
+ SerIleTrpHisGlySerProMetTyrArgProLeuValArgAsnAlaLeuPheGlnArg
+ 10203 : TCGATCTGGCACGGCTCGCCCATGTACCGCCCGCTGGTGCGCAACGCCCTGTTCCAGCGC : 10144
+
+ 522 : AspTyrValArgAsnPheValSerGluLeuAsnAsnGlnHisArgLeuArgPheLeuAsn : 541
+ !||||||!:!:!!|||:!!:!!|||! !||| ..!|||||||||||||||||||||
+ ArgTyrValLysAspPheIleAlaGluHisAsnAlaSerHisArgLeuArgPheLeuAsn
+ 10143 : CGCTACGTCAAGGACTTTATCGCCGAGCACAACGCGTCGCACCGTCTGCGCTTCCTCAAC : 10084
+
+ 542 : ThrGluAlaLeuAlaMetAlaGlnTyrGlnValLeuMetMetGlyArgGlnGluLeuPro : 561
+ ..!!!:|||:!! !||||||||||||:!!|||! !||||||||||||||||||:!!|||
+ ValAspAlaIleAsnMetAlaGlnTyrLysValHisMetMetGlyArgGlnGluValPro
+ 10083 : GTCGACGCGATCAACATGGCGCAGTACAAGGTGCACATGATGGGCCGCCAGGAGGTGCCC : 10024
+
+ 562 : TrpAspGluIleSerSerGlyAsnValArgIleAspPheAspThrCysAspGlyProIle : 581
+ !::|||!!::!:|||:!!|||||||||||||||||||||||| !! !||| !!:!!
+ PheAspAspValSerAlaGlyAsnValArgIleAspPheAspPro---ThrGlySerVal
+ 10023 : TTCGACGACGTGTCCGCGGGCAACGTGCGCATCGACTTTGACCCG---ACCGGCTCGGTC : 9967
+
+ 582 : ValSerProLysCysThrTyrLeuArgArgArgLysProProIleProHisAsnLysAla : 601
+ |||!!!|||:::||||||||||||||||||||||||||||||||||||||||||||||||
+ ValThrProArgCysThrTyrLeuArgArgArgLysProProIleProHisAsnLysAla
+ 9966 : GTCACGCCGCGCTGCACCTACCTGCGCCGCCGCAAGCCGCCCATCCCGCACAACAAGGCC : 9907
+
+ 602 : GlyAsnIleAsnAsnAlaLeuPheAsnGluSerThrLysAlaAspTyrGluPheLeuGly : 621
+ |||||||||||||||!.!|||||||||||||||! ! ! |||||||||||||||:!!|||
+ GlyAsnIleAsnAsnGlyLeuPheAsnGluSerIleHisAlaAspTyrGluPheMetGly
+ 9906 : GGCAACATCAACAACGGCCTCTTCAACGAGTCGATCCACGCCGACTACGAGTTCATGGGC : 9847
+
+ 622 : LeuLeuAspAlaAspGlnGlnProHisProAspPheLeuLysArgValLeuProTyrPhe : 641
+ ||||||||||||||||||||||||||||||||||||||||||||||||:!!|||||||||
+ LeuLeuAspAlaAspGlnGlnProHisProAspPheLeuLysArgValMetProTyrPhe
+ 9846 : CTGCTCGATGCCGACCAGCAGCCGCACCCCGACTTCCTCAAGCGCGTCATGCCCTACTTC : 9787
+
+ 642 : TyrSerAspGluGlyGlnAspLeuAlaPheValGlnThrProGlnPhePheSerAsnIle : 661
+ !:!||||||!!:|||!!.!!::!!||||||||||||||||||||||||||||||||||||
+ PheSerAspAspGlyHisGluValAlaPheValGlnThrProGlnPhePheSerAsnIle
+ 9786 : TTCAGCGACGACGGCCACGAGGTCGCCTTTGTCCAGACGCCGCAGTTCTTCTCCAACATC : 9727
+
+ 662 : TyrProValAspAspProLeuGlyHisArgAsnMetGluPheTyrGlyProValMetGlu : 681
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ TyrProValAspAspProLeuGlyHisArgAsnMetGluPheTyrGlyProValMetGlu
+ 9726 : TACCCCGTCGACGACCCGCTCGGCCACAGAAACATGGAGTTCTACGGTCCCGTAATGGAG : 9667
+
+ 682 : GlyArgSerAlaAsnAsnAlaCysProPheValGlyThrAsnAlaIlePheArgArgGln : 701
+ |||||||||.!!|||..!|||||||||||||||||||||||||||||||||||||||:!!
+ GlyArgSerThrAsnGlyAlaCysProPheValGlyThrAsnAlaIlePheArgArgLys
+ 9666 : GGTCGCTCCACCAACGGCGCCTGCCCCTTCGTCGGAACCAACGCCATCTTCCGTCGCAAG : 9607
+
+ 702 : ProLeuTyrAspIleGlyGlyIleMetTyrAsnSerValThrGluAspMetTyrThrGly : 721
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ ProLeuTyrAspIleGlyGlyIleMetTyrAsnSerValThrGluAspMetTyrThrGly
+ 9606 : CCCCTCTACGACATTGGCGGCATCATGTACAACTCTGTCACTGAGGATATGTACACGGGA : 9547
+
+ 722 : MetLysLeuGlnValSerGlyTyrLysSerTrpTyrHisAsnGluValLeuValValGly : 741
+ |||||||||||||||||||||!:!||||||||||||||||||||||||||||||||||||
+ MetLysLeuGlnValSerGlyPheLysSerTrpTyrHisAsnGluValLeuValValGly
+ 9546 : ATGAAGCTCCAGGTCTCGGGATTCAAGTCGTGGTACCACAACGAGGTGCTCGTCGTCGGT : 9487
+
+ 742 : ThrAlaProValAspLeuLysGluThrLeuGluGlnArgLysArgTrpAlaGlnGlyAla : 761
+ |||||||||||||||:!!||||||||||||||||||||||||||||||||||||||||||
+ ThrAlaProValAspIleLysGluThrLeuGluGlnArgLysArgTrpAlaGlnGlyAla
+ 9486 : ACCGCGCCCGTCGATATCAAGGAAACGCTCGAGCAGAGAAAGCGTTGGGCGCAGGGCGCC : 9427
+
+ 762 : ValGluIlePheSerLeuThrProTrpGlyTyrIleArgGlyLysLeuGlyTrpArgLys : 781
+ ||||||||||||||||||||||||||||||||||||||| !||||||||||||||||||
+ ValGluIlePheSerLeuThrProTrpGlyTyrIleArgLysLysLeuGlyTrpArgLys
+ 9426 : GTCGAAATCTTCTCGCTCACGCCGTGGGGCTACATCCGCAAGAAGCTCGGCTGGAGAAAG : 9367
+
+ 782 : MetLeuTyrAsnLeuAspSerCysIleTyrProPheLeuSerProThrAlaPhePheTyr : 801
+ |||||||||||||||||||||||||||||||||||||||||||||||||||.!!||||||
+ MetLeuTyrAsnLeuAspSerCysIleTyrProPheLeuSerProThrAlaIlePheTyr
+ 9366 : ATGCTCTACAACCTCGACTCGTGCATCTACCCGTTCCTCTCGCCGACTGCCATCTTCTAC : 9307
+
+ 802 : GlyAlaSerProLeuIleMetSerIleTrpThrValProIleValValLysAspProIle : 821
+ ||| !:!!||||||||||||!!!:!:|||||||||||||||||||||! :!!||||||
+ GlyLeuAlaProLeuIleMetCysLeuTrpThrValProIleValValThrAsnProIle
+ 9306 : GGTCTGGCGCCGCTGATCATGTGTCTGTGGACCGTGCCCATCGTCGTCACCAACCCCATC : 9247
+
+ 822 : IlePheIleLeuValGlyMetIleProValMetValLeuProArgValIleGlnTyrMet : 841
+ |||||||||||||||||||||||||||||||||:!!||||||||||||!!:|||||||||
+ IlePheIleLeuValGlyMetIleProValMetIleLeuProArgValMetGlnTyrMet
+ 9246 : ATCTTCATCCTCGTCGGTATGATCCCCGTCATGATCCTGCCGCGTGTCATGCAGTACATG : 9187
+
+ 842 : IleLeuArgAlaLysArgProTyrGluAlaGlyLysSerGlyProSerLeuTrpValGlu : 861
+ ||||||||||||! !||||||!:!||||||||||||||||||||||||||||||||||||
+ IleLeuArgAlaThrArgProPheGluAlaGlyLysSerGlyProSerLeuTrpValGlu
+ 9186 : ATCCTCCGCGCCACGCGTCCCTTCGAGGCCGGAAAGTCCGGCCCCTCGCTCTGGGTCGAA : 9127
+
+ 862 : AlaThrAspLeuTrpArgAlaGluGlnThrPhePheGlyPheAlaGlyThrTyrIleSer : 881
+ ||||||||||||||||||||||||||||||||||||!.!|||||||||||||||||||||
+ AlaThrAspLeuTrpArgAlaGluGlnThrPhePheAlaPheAlaGlyThrTyrIleSer
+ 9126 : GCCACCGATCTCTGGCGTGCCGAACAGACCTTCTTTGCGTTCGCCGGAACCTACATCTCT : 9067
+
+ 882 : SerTrpArgGluGlySerAlaSerIleValLysLeuLeuLysAlaArgLysIleSerArg : 901
+ :!!|||!:!! ||||||||||||:!!|||:::|||:!!|||||||||||||||||||||
+ AlaTrpLysAlaGlySerAlaSerValValArgLeuIleLysAlaArgLysIleSerArg
+ 9066 : GCGTGGAAGGCCGGCTCCGCGTCGGTCGTCCGTCTCATCAAGGCGCGCAAGATCTCGCGT : 9007
+
+ 902 : HisLysLeuAlaMetTrpAsnTrpLysArgAspPheValLysLysProValValCysGlu : 921
+ ||||||||||||||||||||||||||||||!!:|||!.!||||||||||||:!! !|||
+ HisLysLeuAlaMetTrpAsnTrpLysArgGluPheAlaLysLysProValIleValGlu
+ 9006 : CACAAACTCGCCATGTGGAACTGGAAGCGTGAGTTTGCCAAGAAGCCCGTCATCGTCGAG : 8947
+
+ 922 : ValPheArgGlnThrLysLeuValAsnGluAsnAspAsnAlaGlnGluSerSerGlyLys : 941
+ !!:!||||||:!!|||||||||:!!.!. !!!: .!!:!!||| !!.!||| !
+ ArgTyrArgGlnSerLysLeuValHisHisAlaGlu---ThrGluGluHisLysGlyPro
+ 8946 : CGCTACCGCCAGTCGAAGCTGGTGCACCACGCCGAG---ACCGAGGAGCACAAGGGCCCG : 8890
+
+ 942 : HisLysAlaGluGlnSerPheArgThrSerAsnLysGluSerAspThrIleLysAsnSer : 961
+ !.!|||||||||||||||||||||:!!|||||||||||||||||||||||||||||||||
+ ArgLysAlaGluGlnSerPheArgSerSerAsnLysGluSerAspThrIleLysAsnSer
+ 8889 : CGCAAGGCCGAGCAGTCGTTCCGTTCCTCCAACAAGGAGTCCGACACCATCAAGAACTCG : 8830
+
+ 962 : ArgLeuPheLeuProAsnIleIleLeuPheValValAsnIleLeuAlaMetMetSerAla : 981
+ ||||||||| !||||||:!!|||:!!|||! !!.!||||||||||||!!::!! !.!!
+ ArgLeuPheAlaProAsnLeuIleMetPheGlyAlaAsnIleLeuAlaIleLeuLeuThr
+ 8829 : CGTCTCTTTGCGCCGAATCTCATCATGTTTGGCGCCAACATCCTCGCCATCCTGCTGACC : 8770
+
+ 982 : ValLeuArgPheAsnCysPheGlnAsnAspMetTrpLeuLeuValValValAlaGlyPhe : 1001
+ :!!||| !||||||||||||! |||||||||||||||:!!:!!|||||||||||||||
+ LeuLeuSerPheAsnCysPheLeuAsnAspMetTrpLeuMetIleValValAlaGlyPhe
+ 8769 : CTGCTCTCGTTCAACTGCTTCCTCAACGACATGTGGCTGATGATTGTCGTCGCCGGTTTC : 8710
+
+ 1002 : SerPheSerThrLeuTrpHisLeuTrpSerPheIleProMetAlaLeuArgGlnSerGlu : 1021
+ :!!|||||||||! !|||||||||||||||||||||||||||||||||||||||||||||
+ AlaPheSerThrCysTrpHisLeuTrpSerPheIleProMetAlaLeuArgGlnSerGlu
+ 8709 : GCCTTCTCCACGTGCTGGCATCTCTGGTCGTTCATCCCTATGGCCCTCAGACAGTCCGAG : 8650
+
+ 1022 : LysGlnTrpProTyrAlaSerSerTyrHisAlaHisAsnIleValLeuPheLeuValLeu : 1041
+ ||||||||||||||||||||||||||||||||||||||||||:!!:!!||||||:!!|||
+ LysGlnTrpProTyrAlaSerSerTyrHisAlaHisAsnIleLeuIlePheLeuIleLeu
+ 8649 : AAGCAGTGGCCCTACGCCTCCTCGTACCACGCGCACAACATTCTCATCTTTCTCATTCTC : 8590
+
+ 1042 : GlyPheLeuValLeuLeuPheValAspValLysValCysIleProArgValGly : 1059
+ |||||||||||||||||||||..! ! ||| |||||||||||||||||||||
+ GlyPheLeuValLeuLeuPheThrLysValAlaValCysIleProArgValGly
+ 8589 : GGTTTCCTGGTGCTCCTGTTCACCAAGGTCGCTGTCTGTATTCCTCGTGTCGGA : 8534
+
+vulgar: DDB_G0269124 142 1059 . contig_1146 11269 8533 - 3652 M 40 120 G 4 0 M 94 282 G 0 3 M 296 888 G 1 0 M 356 1068 G 1 0 M 125 375
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:protein2genome:local 2.2.0
+##date 2015-01-16
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+contig_1146 exonerate:protein2genome:local gene 8534 11269 3652 - . gene_id 0 ; sequence DDB_G0269124 ; gene_orientation .
+contig_1146 exonerate:protein2genome:local cds 8534 11269 . - .
+contig_1146 exonerate:protein2genome:local exon 8534 11269 . - . insertions 3 ; deletions 6
+contig_1146 exonerate:protein2genome:local similarity 8534 11269 3652 - . alignment_id 0 ; Query DDB_G0269124 ; Align 11270 143 120 ; Align 11150 187 282 ; Align 10865 281 888 ; Align 9977 578 1068 ; Align 8909 935 375
+# --- END OF GFF DUMP ---
+#
+-- completed exonerate analysis
--- /dev/null
+##gff-version 2
+##source-version exonerate:protein2genome:local 2.2.0
+##date 2015-01-16
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+contig_1146 exonerate:protein2genome:local gene 8534 11269 3652 - . gene_id 0 ; sequence DDB_G0269124 ; gene_orientation .
+contig_1146 exonerate:protein2genome:local cds 8534 11269 . - .
+contig_1146 exonerate:protein2genome:local exon 8534 11269 . - . insertions 3 ; deletions 6
+contig_1146 exonerate:protein2genome:local similarity 8534 11269 3652 - . alignment_id 0 ; Query DDB_G0269124 ; Align 11270 143 120 ; Align 11150 187 282 ; Align 10865 281 888 ; Align 9977 578 1068 ; Align 8909 935 375
+# --- END OF GFF DUMP ---
--- /dev/null
+>DDB_G0280897
+MTDKINNLINQWLKWDKNEITRKEIEQLKENNNEKELLVRLEERIQFGTAGLRGAMRAGF
+SCMNDLTVTQASQGLCEYVIETIEQSKSKGIVIGYDGRHNSYIFAKITAATFKSKGFKVY
+LFSHIVPTPYVSFAVPNLKAAIGVMITASHNPKNDNGYKVYWETGCQINTPHDKGISKKI
+DENLEPWSNVDATSDIKYGNGDDGESMIDPLSVITELYNKNIKEYSVGSKIELANEPIVY
+TAMHGVGGVYAKKAFETFQLKPFIPVAQQIEPDAEFPTVTYPNPEEGKGALKLSIETAEA
+NNSRLILANDPDADRLAVAEKLADGSWKVFNGNEIGVLLADWAWTNRSTLTKGGSTLENN
+KYFMINTAVSSAMLKTMSEKEGFIHQECLTGFKWIGNAAYNAINNNDGTTFLFGYEEAIG
+FQYGDVSFDKDGVRAAAIFAEFALSLYKKGSSVQDHLESMYKRYGYHISKNRYFFCYEPS
+KMVSIFNKIRNDGKYLTKLGDDDDEQFTITRIRDLTTGYDNGYPDCKARLPVSSSTQMIT
+FYFKNGGIATLRGSGTEPKLKYYVEMIGEVKSNVESTLTKAVELVINQLLKPIENQLEPP
+KDD
+>PPL_06716
+MSNIKELAESWLKWDKNAETRKEIQSLLESDNQSELKSRLEQRIAFGTAGLRGPMKAGFS
+CMNDLTVIQASQGLCIYVEQTLSNSKNSGIVVGYDGRHHSKEFARLTAATFASRGFKVYL
+FSKIVPTPYVVILYLISNYMDCYVHQAFAVPELKASVGVMITASHNPKDDNGYKVYWDNG
+CQINTPHDIRIAMQIDLNLEPWNIDVNELLNGSLVSDPLDTITKSYFGKIAKYSVKNEVK
+LATSEKIVYTAMHGVGGEYAKMAFETFGLPAFIPVDQQIQPDPEFPTVAFPNPEEGKGAL
+KLSIETAERNNSRLILANDPDADRLAVAERQPDGQWKVFNGNEIGVLFADWAWQNARRAD
+STTPAERFCMINTAVSSSMLKTMANKDGYRHEECLTGFKWVGNKARELMDKGYNFLFAYE
+EAIGFMYGDVSLDKDGVRCAPIFAELALTCYQAGKSCQDHLEELYKRYGYHISKNRYFFC
+YDPKKMVAIFDKIRNYGQFPTNCGDFYITRVRDLTVGYDSGYPDHKARLPVSSSTQMITF
+YFENGGIATLRGSGTEPKLKYYVEMIGSDRQLVESTLSQLVEQVINQFLRPVENELTPPK
+DD
+>DFA_03821
+MTDINQLAQNWLKWDRNPKTHKEIEQLVEAKDENELRARLENRIAFGTAGIVSTTIVQSH
+MNIGPMKAGFANMNDLTVIQASQGLSIYVQETISQAQSKGVVVGYDGRYNSEVFAKLTAA
+TFASKGFKVYLFSKIVPTPFVAFAVPELGASVGVMVTASHNPKDDNGYKVYWDNGCQINT
+PHDKGIAKQIDLNLEPWTINIDKLLSSELVNDPLETISNAYFSKIYSYSVKNRSTPLELA
+NEKVVYTAMHGVGGDYVKKAFETFKLPPYVEVAQQIKPDPAFPTVAFPNPEEGKGALKLS
+IETAESVNSRLILANDPDADRLAVAEKLKDGSWKVFNGNEIGILLADWAWTNAKINHPDV
+PAEKFFMINTAVSSAMLKTMAKKEGYICEETLTGFKWVGNKAKEMIDQGYKFLFAYEEAI
+GFMYGDVSLDKDGVRCAPIFAEYALNLYANGSSCQDHLDHLMQRYGYHISKNRYFFCYEP
+SKMVRIFNDIRKSNNGQFPDKCGPYEIIRIRDLTVDYDTAYPDNKARLPVSTSTQMITFY
+FKNGAIATLRGSGTEPKLKYYVEMIGDNKQEVESTLQQVVQQVIDNFLQPVVNQLTPPKD
+D
+>DLA_10096
+MDIYTLANKWLEWDKNEKNRKEIQHFVDEKNEQELRERLENRIQFGTAGLRGPMKAGFAN
+MNDLTVIQASQGLALYVKETIDSALTKGVVVGYDGRHNSQTFARLTAATFLSKGFKVYLF
+SKLVPTPFVAFAVPELGASCGVMITASHNPKDDNGYKVYWDNGCQINTPHDKGISKLIDE
+NLVPWTMNLDDLNKSDLVSDPLERVSKSYFTKISKYSVVKSGATIKQEKVVYTPMHGVGG
+DYAAEAFKVFDLHPFIPVELQIKPDAEFPTVAFPNPEEGKGALKLAIETAESNQSRLILA
+NDPDADRLAVAEKQSSDGSWKVFNGNEIGVLFADWAWRKERALFSEGYNCKPSEYTMIST
+AVSSAMLSTMAKKEGFQHEEVLTGFKWVGNAAKQAMDRGQKFLFAYEEAIGFMYGDVSLD
+KDGVRGASIFAELAFDLYQQGSSCQEHLESLYKKYGYHISNNRYFFCYDPKKMVRIFNEI
+RGNNREYVKELGEFKVERIRDLTTGYDTAFPPEFKAQLPTSSSTQMITFYFTNGSIATLR
+GSGTEPKLKYYVESIGSDKLQVQQTLTKLVSLVIEKLLRPKENELTPPKESVGSERLLAL
+LSEVMSTSMKIQVKYNESITEYNIIKGVKLLTQIDVLCQIFKVDANPDRFVLNYRESNLI
+LSEDNLSKLFSNEISSCSSQSQNGSNGELSSLYSSFGENSSNNNNNSTLKFELILAPIYQ
+VDSVLEHLNNSNLIKKRII
+>DPU1265769
+MSMIRSISGVRGVIGQSWTPTLVSNHIIGFTQLLESEKYYNQKQKKIVVGRDSRVSGPWI
+EMIVNGSLISMGYQVIHIDIAATPTVQYMVEKTKSSGGIVITSSHNPVEWNGLKFVGPDG
+LFIAPVECEVLFSLADNPSSFKFPNYDKLGSVVCNTTANKEHIEAIFKLPFISVDKIKEK
+KFKVCLDSVNGAGGPIMSYLLTELGCEVIGINLEPTGLFAHTPEPVPANLGQLCELVKTH
+KADFGIAVDPDVDRCVFIDDKGVPLGEEYTLAMAVELLLGDCGRRGNVCKNLSSSRAIDD
+ICKKYDSQVICAPVGEIQVAKKMQQVNAVIGGEGNGGVMLPDIHIGRDAPVAATLALQLL
+ANRNAASISEFKRTTLPTYEIVKLKAGIEGLDPDAILAEYTKQYENKEGVVINQEDGLKI
+DSADWWVHLRKSNTEHIIRVISEAKNTKEATDIATKFINEIESKRK
+>440792448
+MASRVSGRMRKISDETQQMVNAWLSVDWDPESREHVKGLVAAGKEEELVAHLGRRISFGT
+AGLRGKMKWGFAFMNAVTVTQASQGLCAYLRTVHPCLTDLRERGVIVGHDGRYNSRMFAR
+LTAAVFLSRKIKVHLFRDDVPTPLVAFGVRHLKCAAGVMVTASHNPKEDNGYKVYWANSA
+QITAPHDAQIARAIEANFSIWDRMPDDKAIDEHPLCLDPTTDVCAAYLAAARHWSFRTPQ
+QNAAAQLRVVYTAMHGVGGQSVERIFDAFGLPPVIAVREQHDPDPDFTTVEFPNPEEANG
+CSLRLAMSTADREGAPLILANDPDADRLAVAERQRDSGEWRILDGNEIALLLADWLWRNY
+TERHPEVDRAKIVMLNSTVSSKALAAMAAKEGFHYRETLTGFKWLGNLADELVRAGYTFL
+FAYEVEIGFMIGDMSLDTDGVRAAPVFVEMANHLYERGLTLSDHLDNLYHKYGYYKMAVG
+YYFCHDPRLMDQIFNEIRNDGLYISTCGDHKVQYVRDLTTGFDNSQPHNRAVLPVSSAAH
+MITFTFENECVATFRGSGTEPKLKYYIEVANASNEQLATDLLDSMKQEIIDRFLQPSQNG
+LRPPAAAEDAHNSPHNSGNSPEQMAPARIARDVIHKEIQALQNLEATLGRDFEKVVEIIE
+SRGSGRVIFTGVGKSGIIAQKISASFSSLGISSFFVHATEAAHGDLGVITAEDVIIAISN
+SGNTPELIFIIPSLRVLAGKIIGITSNKDSLLARYSDASIITGKIMEADQHKIAPTASTI
+VCLAIGDALAVTLSARMKFTLPEFGLRHPGGVLGEKVLGKVFQEFAMKGQGRFLRFWKRM
+TNEERDKLRRDFERIDLAELSRIYLQCRSKAEKGAIDPHSLEPLPSHTWVKLHESDPAAV
+AAWRDAGLRALREGKIGVVLMAGGQATRLGMTMPKGFLDLNLPSHKSLYQLHAEKLLRLQ
+DEVRQTFGGGGGDEEVQQQQQQIQIPFYVMTSPEALQQTHQFFIKHQFFGLCPKQVFFFK
+QRSLPCVAPSGEIIMDTKCSVVFSPDGHGGLFVALKDAKAYEDMKRRGVEYVFAFGVDNP
+LCEVADPAYMGYCIQRNVKMGYKVVDRRDPQETAGVVCVRDGVINCVEYSELPESVAELR
+DEQSGELVYNAANMLNLFFTLRFMRKIADNPSLMEYHLAKKRIPFVNDNGVRTEPLVPNG
+WKFEKYLVDCTPYANNSVAVMFVKREEEFAPIKNGWNSEVDSPRSARRLLAAHYRRRIER
+AGGKLAADDPDKMVEVSPLVTDRKLAQLLQDKHLVTGPAVLQ
+>ENY64621.1
+MALNNYIKKTEMDYLYEQAALWLKWDKTPETRKEIEDLVASKNEEELKKRFCKRIEFGTA
+GLRGKMCAGFNCMNNLIVQQASQGLALAVEELVQNAHEKGVVIGYDGRYHSKEFAAITAK
+VFISKGFKTYLFSTLCPTPWTAFAVGYLKTACGVMVTASHNPKADNGYKVYWENGCQIIE
+PIDANIASKIHSNLEPWDLSNVDISKVIDPLADVSAEYYKQMMLTIPHFECPEQPKVKYV
+YTAMHGVGSKYVQDAFKTAKLPQPILVPLQNEPDPEFPTVPFPNPEEGKGALKCSIEVAE
+ANGATVIIANDPDADRLSVAVKSGNGWRQFTGNEMANLIADWTYNKYIVSGDKTPAFMVR
+STVSSSFISKMGEVEGFDTYETLTGFKWIGNKAKEIVDTQHKKLLMAYEEAIGFVIGNMS
+YDKDGVRAAVCFAAMALEYAEQGFNLEDRLNMLYEKYGYFASNNKYYFCYDPKLMEKIFN
+KMRNNGQYYWKFGKYAVKSIRDLTVGIDTAQPDKKPLLPVSASTQMITYTFENGCKATLR
+GSGTEPKLKYYIELPGKKGVKAEDVIAELMDLSHELLQASLEPEKNGLIPPKAE
+>Ppo014092.000
+MSISPSVQELVGKWLQWDKNPQNIKEIKDLVAANNEAELKNRLATRIAFGTAGLRGPMRA
+GFSCMNDLTVIQASQGLCKYLQQMVSDIKTRGIVVGYDGRHHSKEFAEWTAATFLSQGIT
+VYLFTRLVPTPFVSYATPLLRCAAGIMITASHNPKDDNGYKVYWDNGCQINVPHDKGISD
+CIEQNLTPWDINKAELLKSELVKDPTETVASAYLKEIKAKCCFHHDENSQKIPVTYTAMH
+GVGSEWVARAFEVFGLAPYVPVAPQISADPEFPTVAFPNPEEGKGALKLSMEAADKAGST
+LILATDPDADRLAVAEKLPSGSWKIFTGNEIGALLAYWAWLKYKERNPKVDPSKCVVINS
+TVSSKLLKALADKEGLKYDETLTGFKWIGGQAAIRIKEGYTFIFGFEEAIGFLFGDVNLD
+KDGVRAAAVFAEMNIQLHKQGITVVQQLEKIYKLYGYFITRNRYFFCYDPAKMERIFNAI
+RNYNNSGTYPTSCGPFKIKNTRDLTTGYDDSQTDKKAILPVSKSTQMITFFFENGGVVTL
+RGSGTEPKLKYYTELSGSDPEKVKSTLDEMVQAIIDTCLKPVENQLQPPSDE
+>ADB0001102_3
+MSTTTSINKLAQDWLKWDKNPKTRAEIQELVEQNDVKELTARLENRIAFGTAGLRGPMKA
+GFSCMNDLTVIQASQGLCLYVIDTIPNAIKSGVVIGYDGRYNSKEFAKYTAATFLSKGYK
+VYLFSKVVPTPYVAFAVTDLKASIGVMITASHNPKDDNGYKVYWENGCQINTPHDKGIAK
+LIDLNLEPWEINVDQLLSGPLVEDPLDRIVSSYNTKIAQYSVASHVKFANEKIIYTAMHG
+VGGEYTKMAFEAFKLPPFIPVAQQYQPDPAFPTVTFPNPEEGKGALKLSIETAEANGSRL
+ILANDPDADRLAVAERLKDGTWKVFNGNEIGVLLADWAWQNARRSHPDTPAEKFFMINTA
+VSSAMLKTMAKKDGYRCEETLTGFKWVGNRAREVMDAEGLHFLFAYEEAIGFLYGDVSLD
+KDGVRCAAIFAELALSYYANGSSCEDHLESLYKRYGYHISRNRYFFCYEPPKMVAIFNKI
+RNNRNFPTKCGRFEIERVRDLTIDYDDGFPDKKARLPVSTSTQMITFYFKNGAIATLRGS
+GTEPKLKYYVEMIGQDKAHVQQELAELVQCIINEFLRPVENELTPPKDD
+>Carpum
+MTQSTCITSMVINNYLSIYIFIYTINDYLKRSLFVLCLVAKMSHHKVAITHPISSYNSII
+NELAQNWLRWDKNKETRKEIEQLVEQKNEKELYDCLAKRIAFGTADNEIMMLLTHTLHTG
+LRGQMKAGFSNMNDLTVIQASQGLCKYVKETIPEAQKKGVVVGYDCRHHSETFARLTAAT
+FASQGFTVYLYSKMVPTPFVAFGVTDLKACVGVMVTASHNPKEDNGYKVYWENGCQINSP
+HDKGISQQIELNLEPWTIDVNSLLEKVDDPLERVTKSYMDQISKYSVRGSVDMATENVVY
+TAMHGVGGVFVKDAFAAFGLAPYIPVPAQVGPDAEFPTVTLPNPEEGKGALKLSIETAEA
+NNSRLIVANDPDADRLAAAEKLKDGSWKVFNGNEIGVLFADWAWQNARRQHGGDSINPSE
+YFMVTTAVSSSMLRTMATKEGYGYDETLTGFKWVGNKARDLIDQGKKFLFAYEESIGYMY
+GEVSLDKDGVRGAAVFTEMALSCYARGTSCQEHLESLYVKYGYHLSKNRYYFCYDPSKMV
+SIFNRIRNNGEFPKTCGPFEITRIRDLTVDYDNGYEDKKARLPVSSSTQMITFYFKNGAI
+ATLRGSGTEPKLKYYVEMIGDDKEQVKATLDQVHDQVIQQFLRPTENQLSPPSDE
+>Cephalum
+MTTDIYQIAQNWLRWDRNPKTHKEISQLVQDKNESELKARLESRIAFGTAGLRGPMKAGF
+SCMNDLTVIQASQGLCMYVKQTLAPDAERKGIVVGYDGRYNSEVFAKLTAATFVSQGFKV
+HLFSRLVPTPFVAFAVPFLKACVGVMITASHNPKDDNGYKVYWDNGCQINTPHDKGIAKQ
+IELNLEPWNVFYKEYFDRIERYTVRHNKQMAREKIVYSAMHGVGGEYTKRAFEVFALDPF
+IAVKEQFHPDPAFPTVTFPNPEEGKGALKLSIETAEANNNWAWKNGKPYYEKGLGSFPND
+QYFMINTAVSSAMLKTMAMKEGFTYEEVLTGFKWVGNAAQNLIEKGKHLLFAYEEAIGFM
+YGDVSLDKDGVRCAPIFAELAQHLYSKGSSCQDHLEELYKRYGYHISKNRYFFCYDPLKM
+EKIFNRIRNGGQYPTKCGDFEITRIRDLTTGYDTGYPPENKAQLPTSTSTQMITFYFKNG
+GIATLRGSGTEPKLKYYVEMIGDDKENVELILQSMVDQVINQFLRPIENELIPPKD
+>Violaceum
+MVINPFYPYYLYFCYSPGISYQGVKINKTKLEQSTLTTINQWLNGNYDEQTKKNIQNLLD
+QESYTELTDAFYRNLEFGTGGLRGIMGAGSNRINKYTIGTATQGLSNYLLKKYPGEKIKV
+AIAHDSRNNSDQFAKITADVFSANGIYVYFFKELRPTPELSFAIRELGCRSGVMLTASHN
+PKEYNGYKAYGADGGQFTAPDDRLVMDEVAKITSIDEVKFTRIDANIELIGEEIDQLYLD
+KITALSVSPEAISRQKDLKIVYSPIHGTGITLVPKALAQFGFDNVTIVEEQSKPDGNFPT
+VVYPNPEEKEAMTLALKKAQEIDADLVLATDPDADRVGIAVKNNNNEWILLNGNQTGSLL
+VHYVLTAWEEKGKIDGNQYIVKTVVTSNLIEAIAKAKKVDCYNTLTGFKWIGQLITSLQG
+KKTFVVGGEESYGYSVGELVRDKDAVISCAFIAEMTAYYKDKGSSLYNALIDMYVTHGLY
+KEELVSLTKKGKTGAEEIKAMMEKFRNNPPASLGGSKVSTLKDYELGTETDLNTGKISKL
+SLPKSDVLQFVTEDGSIVSARPSGTEPKIKFYCSVNATLSQASEFDKTDEKLGLKINALM
+EDLQK
+>Deminut
+MTDIYQIAQNWLKWDRNPKTHKEISTLVEKKDEAELRARLETRIAFGTAGLRGPMKAGFS
+CMNDLTVIQASQGLSLYVKKTLAGSESKGAVVGYDGRYNSEVFAKLTAATFASQGFKVYL
+FSKVVPTPYVAFAVPELGASVGVMVTASHNPKDDNGYKVYWDNGCQINTPHDKHISELIE
+SNLEPWNVCIYITLQINIDKLLSGVIDPLQVVTSSYMSKIEKYSVKHLPQPLKLATEQKI
+VYTAMHGVGAEYAKLAFEAFSLPPFIPVTQQVTPDPAFPTVAFPNPEEGKGALKLAIETA
+EANKSRIILANDPDADRLAVAEKQPEYVFLFYLISNNGTWKVFNGNEIGILFADWAWQNC
+RRVYPDVPADQFFMINTAVSSAMLKSMAKKDGYIHEETLTGFKWVGNKARELLDQNKRFL
+FAYEEAIGFMYGDVSLDKDGVRCAAIFAELALYQYANGSSCQRHLDSLYERYGYHISKNR
+YFFCYEPPKMVAIFNAIRNNKNYPTKCGEFEIERIRDLTDDYDNGYPDNKARLPISKSTQ
+MITFFFKNGAIATLRGSGTEPKLKYYVEMIGDNKSEVEAILAKVVTAVIDNFLRPVENQL
+TPPKDD
+>Ellipt
+MADLDKLVEDWMRWDKNTKTRDEVQKMVAQGDKKALAAALQNRIAFGTAGLRGPMKAGFA
+NMNDLTVIQASQGLCIYVSATIADAAKKGVVVGYDGRHNSLQFARLTAATFRSKGFKVYL
+FSTVVPTPYVAFSVPELGACVGVMVTASHNPKDDNGYKIDVEKLLKEDGVEDPLEKITAS
+YMSKVADYSIKSHPATKDIVMSDDKIVYTAMHGVGGEYTRRSFKAFSLPEFIPVVQQFHP
+DPEFPTVTFPNPEEGKGALKLAIETAEKNNSRLILANDPDADRLAVAERQPDGTWKVFNG
+NEIGVLFADWAWKNARARDPTTPASEFFMVNTAVSSAMLKTMAKTEGYTYEETLTGFKWV
+GNKAKEAIDKGGRFLFAYEEAIGFMYGDVSLDKDGVRTAPIFAQMALSLYAKGLSCVDHL
+EQLMKTYGYHISRNRYFFCYEPPKMVAIFDKIRNNGNFPKHCGPFEIVRVRDLTVDYDDA
+YEDKKARLPVSTSTQMITFYFKNGAIATLRGSGTEPKLKYYVEMIGDKSAKKEDVEKTLA
+EVVKQVIDNFLRPVENELTPPKDD
+>Lepto
+MASSERLQQLIQDWLKWDKNPTTLSEIQELVKKNDEKELRARLENRIAFGTAGMFLLGPM
+KAGFSCMNDLTVIQASQGLCIYVSDTIPNALNSGVVVGYDGRYNSKEFAKYTAATFLSKG
+YKVYLFSKVVPTPYVAFAVTELKAAIGVMITASHNPKDDNGYKVYWDNGCQINTPHDKGI
+AKQIQLNLEPWNVCAFFLDINANELLSGSSVVDPLDTIVNSYNSKITSYSVGNSGVKLAN
+EKIVYTAMHGVGGEYTKLAFEAFKLPPFVPVPQQYTPDPAFPTVAFPNPEEGKGALKLSI
+ETAEANGSRLILANDPDADRLAVAERNTNGTWKVFNGNEIGVLLADWAWQNARRAHPDTP
+ANRYFMINTAVSSAMLKTMAKHEGYRCDETLTGFKWVGNQARKVIDEEKLNFLFAYEEAI
+GFMYGDVSLDKDGVRCAPIFAEMALSYYAQGHSCEDHLETLYKRYGYHISRNRYFFCYEP
+PKMVAIFDRIRNGRNFPTKCGRFEIERVRDLTVDYDDAYPDKKARLPVSTSTQMITFWFK
+NGGIATLRGSGTEPKLKYYVEMIGQDKQVVEKELAELVDAVIQQFLRPVENELTPPKDD
--- /dev/null
+<?xml version="1.0"?>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<!DOCTYPE rnaml SYSTEM "rnaml.dtd">
+
+<rnaml version="1.0">
+
+ <molecule id="1">
+ <sequence>
+ <numbering-system id="1" used-in-file="false">
+ <numbering-range>
+ <start>1</start>
+ <end>249</end>
+ </numbering-range>
+ </numbering-system>
+ <seq-data>
+ gaggaaaguc cggacUUCGC AGAAAAAGGU GCCAGUGAAA AACUGGGGGC CGUAAGGCUA
+ CGGAAAGUGU AACAGAAAAC AAACCGCUAA UUCUACCUAG GUAAGAUUAG ACAGGAUGAA
+ AAUGUCGAGC UUAUGGCUCG ACCUCUUUGU GGAAACACAA GGACGCUGCA AACCCCACCU
+ GAAGCAAGAA AGAGUUCGUU UCAGUUUUUC GCUCAGGAAC UCUUAGAGUC GCUCGAGGAU
+ UUUGGUGAC
+ </seq-data>
+ </sequence>
+ <structure>
+ <model id="?">
+ <str-annotation>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>15</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>184</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>16</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>183</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>17</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>182</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>18</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>181</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>22</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>210</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>23</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>209</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>24</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>208</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>25</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>207</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>27</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>180</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>28</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>179</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>29</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>178</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>30</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>177</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>31</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>176</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>32</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>46</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>33</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>45</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>34</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>44</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>35</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>43</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>36</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>42</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>47</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>61</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>48</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>59</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>49</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>58</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>50</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>57</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>51</position></base-id>
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+ <base-id-5p>
+ <base-id><position>50</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>57</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>51</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>56</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>62</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>171</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>63</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>170</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>67</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>169</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>68</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>168</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>69</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>165</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>70</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>164</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>71</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>163</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>83</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>110</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>84</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>109</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>85</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>106</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>86</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>105</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>87</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>104</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>91</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>102</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>92</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>101</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>93</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>100</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>94</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>99</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>118</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>136</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>119</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>135</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>120</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>134</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>121</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>133</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>122</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>132</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>123</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>131</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>137</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>160</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>138</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>158</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>139</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>157</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>140</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>156</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>141</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>155</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>142</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>154</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>143</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>152</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>144</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>151</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>145</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>150</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>184</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>232</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>185</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>231</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>186</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>230</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>187</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>229</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>194</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>223</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>195</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>222</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>196</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>221</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>197</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>220</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>198</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>219</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>199</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>218</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>203</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>217</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>204</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>216</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>205</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>215</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>206</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>214</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>207</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>213</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>239</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>258</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>240</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>257</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>241</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>256</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>242</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>255</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>243</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>254</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>244</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>253</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>245</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>252</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ <base-pair comment="?">
+ <base-id-5p>
+ <base-id><position>246</position></base-id>
+ </base-id-5p>
+ <base-id-3p>
+ <base-id><position>251</position></base-id>
+ </base-id-3p>
+ </base-pair>
+ </str-annotation>
+ </model>
+ </structure>
+ </molecule>
+</rnaml>
--- /dev/null
+##gff-version 2
+##source-version exonerate:protein2genome:local 2.2.0
+##date 2015-01-16
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+seq1 exonerate:protein2genome:local gene 8 11 3652 - . gene_id 0 ; sequence seq2 ; gene_orientation .
+seq1 exonerate:protein2genome:local cds 9 11 . - .
+seq1 exonerate:protein2genome:local exon 9 11 . - . insertions 3 ; deletions 6
+seq1 exonerate:protein2genome:local similarity 8 11 3652 - . alignment_id 0 ; Query seq2 ; Align 11 1 3
+##FASTA
+>seq1
+ACTACGACACGACGACGACGACG
+>seq2
+CDEQEATGTQDAQEQAQC
+
+
*/
package MCview;
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.AlignSeq;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.io.FileParse;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
public class PDBfile extends jalview.io.AlignFile
{
private static String CALC_ID_PREFIX = "JalviewPDB";
"getSeqsAsArray", new Class[]
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]
- { Alignment.class }).invoke(jmf, al);
+ { AlignmentI.class }).invoke(jmf, al);
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
import java.util.Vector;
/**
*/
public class SequenceIdMatcher
{
- private Hashtable names;
+ private HashMap<SeqIdName, SequenceI> names;
- public SequenceIdMatcher(SequenceI[] seqs)
+ public SequenceIdMatcher(List<SequenceI> seqs)
{
- names = new Hashtable();
- for (int i = 0; i < seqs.length; i++)
+ names = new HashMap<SeqIdName, SequenceI>();
+ addAll(seqs);
+ }
+
+ /**
+ * add more sequences to this matcher - also used by the constructor
+ *
+ * @param seqs
+ */
+ public void addAll(List<SequenceI> seqs)
+ {
+ for (SequenceI seq : seqs)
{
// TODO: deal with ID collisions - SequenceI should be appended to list
// associated with this key.
- names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
- SequenceI dbseq = seqs[i];
+ names.put(new SeqIdName(seq.getDisplayId(true)), seq);
+ SequenceI dbseq = seq;
while (dbseq.getDatasetSequence()!=null)
{
dbseq = dbseq.getDatasetSequence();
for (int r = 0; r < dbr.length; r++)
{
sid = new SeqIdName(dbr[r].getAccessionId());
- if (!names.contains(sid))
+ if (!names.containsKey(sid))
{
- names.put(sid, seqs[i]);
+ names.put(sid, seq);
}
}
}
}
/**
+ * convenience method to make a matcher from concrete array
+ *
+ * @param sequences
+ */
+ public SequenceIdMatcher(SequenceI[] sequences)
+ {
+ this(Arrays.asList(sequences));
+ }
+
+ /**
* returns the closest SequenceI in matches to SeqIdName and returns all the
* matches to the names hash.
*
* @param candName
* SeqIdName
* @param matches
- * Vector of SequenceI objects
+ * List of SequenceI objects
* @return SequenceI closest SequenceI to SeqIdName
*/
- private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
+ private SequenceI pickbestMatch(SeqIdName candName,
+ List<SequenceI> matches)
{
- SequenceI[] st = pickbestMatches(candName, matches);
- return st == null || st.length == 0 ? null : st[0];
+ List<SequenceI> st = pickbestMatches(candName, matches);
+ return st == null || st.size() == 0 ? null : st.get(0);
}
/**
* @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[]
* ties }
*/
- private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
+ private List<SequenceI> pickbestMatches(SeqIdName candName,
+ List<SequenceI> matches)
{
- ArrayList best = new ArrayList();
- SequenceI match = null;
+ ArrayList<SequenceI> best = new ArrayList<SequenceI>();
if (candName == null || matches == null || matches.size() == 0)
{
return null;
}
- match = (SequenceI) matches.elementAt(0);
- matches.removeElementAt(0);
+ SequenceI match = matches.remove(0);
best.add(match);
names.put(new SeqIdName(match.getName()), match);
int matchlen = match.getName().length();
while (matches.size() > 0)
{
// look through for a better one.
- SequenceI cand = (SequenceI) matches.elementAt(0);
- matches.remove(0);
+ SequenceI cand = matches.remove(0);
names.put(new SeqIdName(cand.getName()), cand);
int q, w, candlen = cand.getName().length();
// keep the one with an id 'closer' to the given seqnam string
return null;
}
;
- return (SequenceI[]) best.toArray(new SequenceI[0]);
+ return best;
}
/**
*
* @param seqnam
* string to query Matcher with.
+ * @return a new array or (possibly) null
*/
public SequenceI[] findAllIdMatches(String seqnam)
{
SeqIdName nam = new SeqIdName(seqnam);
- return findAllIdMatches(nam);
+ List<SequenceI> m = findAllIdMatches(nam);
+ if (m!=null)
+ {
+ return m.toArray(new SequenceI[m.size()]);
+ }
+ return null;
}
/**
* SeqIdName
* @return SequenceI[]
*/
- private SequenceI[] findAllIdMatches(
+ private List<SequenceI> findAllIdMatches(
jalview.analysis.SequenceIdMatcher.SeqIdName nam)
{
- Vector matches = new Vector();
+ ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
while (names.containsKey(nam))
{
- matches.addElement(names.remove(nam));
+ matches.add(names.remove(nam));
}
- SequenceI[] r = pickbestMatches(nam, matches);
+ List<SequenceI> r = pickbestMatches(nam, matches);
return r;
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.api;
+
+/**
+ * Abstract interface implemented by Alignment Export dialog to retrieve user
+ * configurations
+ *
+ * @author tcnofoegbu
+ *
+ */
+public interface AlignExportSettingI
+{
+ /**
+ * Checks if hidden sequences should be exported
+ *
+ * @return
+ */
+ public boolean isExportHiddenSequences();
+
+ /**
+ * Checks if hidden columns shoulb be exported
+ *
+ * @return
+ */
+ public boolean isExportHiddenColumns();
+
+ /**
+ * Checks if Annotations should be exported, note this is available for
+ * complex flat file exports like JSON, HTML, GFF
+ *
+ * @return
+ */
+ public boolean isExportAnnotations();
+
+ /**
+ * Checks if SequenceFeatures should be exported, note this is available for
+ * complex flat file exports like JSON, HTML, GFF
+ *
+ * @return
+ */
+ public boolean isExportFeatures();
+
+ /**
+ * Checks if SequenceGroups should be exported, note this is available for
+ * complex flat file exports like JSON, HTML, GFF
+ *
+ * @return
+ */
+ public boolean isExportGroups();
+
+ /**
+ * Checks if settings/export process is cancelled
+ *
+ * @return
+ */
+ public boolean isCancelled();
+}
package jalview.api;
import jalview.commands.CommandI;
+import jalview.schemes.ColourSchemeI;
/**
* Interface implemented by gui implementations managing a Jalview Alignment
void addHistoryItem(CommandI command);
+ void setShowSeqFeatures(boolean show);
+
+ void setMenusForViewport();
+
+ void changeColour(ColourSchemeI cs);
+
+ /**
+ * trigger an update of the UI in response to a model data change, and if
+ * necessary enable the display of sequence feature annotation on the view.
+ *
+ * @param enableIfNecessary
+ */
+ void refreshFeatureUI(boolean enableIfNecessary);
+
+ /**
+ * get the Feature Settings control panel for the alignment view if one exists
+ *
+ * @return
+ */
+ FeatureSettingsControllerI getFeatureSettingsUI();
}
*/
void sortAlignmentByFeatureDensity(String[] typ);
+ /**
+ * add a features file of some kind to the current view
+ *
+ * @param file
+ * @param protocol
+ * @param relaxedIdMatching
+ * if true, try harder to match up IDs with local sequence data
+ * @return true if parsing resulted in something being imported to the view or
+ * dataset
+ */
+ public boolean parseFeaturesFile(String file, String protocol,
+ boolean relaxedIdMatching);
+
}
*/
package jalview.api;
-import java.awt.Color;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
/**
* @author jimp
*
* Set whether view should scroll to show the highlighted region of a sequence
*/
void setFollowHighlight(boolean b);
-
- public FeatureRenderer getFeatureRenderer();
-
- public void setFeatureRenderer(FeatureRenderer featureRenderer);
-
- public boolean isIncludeHiddenRegion();
-
}
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
public interface FeatureRenderer
{
+ /**
+ * compute the perceived colour for a given column position in sequenceI,
+ * taking transparency and feature visibility into account.
+ *
+ * @param col
+ * - background colour (due to alignment/group shading schemes, etc).
+ * @param sequenceI
+ * - sequence providing features
+ * @param r
+ * - column position
+ * @return
+ */
Color findFeatureColour(Color col, SequenceI sequenceI, int r);
+ /**
+ * trigger the feature discovery process for a newly created feature renderer.
+ */
void featuresAdded();
+ /**
+ *
+ * @param ft
+ * @return display style for a feature
+ */
Object getFeatureStyle(String ft);
+ /**
+ * update the feature style for a particular feature
+ *
+ * @param ft
+ * @param ggc
+ * - currently allows java.awt.Color and
+ * jalview.schemes.GraduatedColor
+ */
void setColour(String ft, Object ggc);
AlignViewportI getViewport();
+ /**
+ *
+ * @return container managing list of feature types and their visibility
+ */
FeaturesDisplayedI getFeaturesDisplayed();
+ /**
+ * get display style for all features types - visible or invisible
+ *
+ * @return
+ */
Map<String,Object> getFeatureColours();
+ /**
+ * query the alignment view to find all features
+ *
+ * @param newMadeVisible
+ * - when true, automatically make newly discovered types visible
+ */
void findAllFeatures(boolean newMadeVisible);
+ /**
+ * get display style for all features types currently visible
+ *
+ * @return
+ */
Map<String,Object> getDisplayedFeatureCols();
+ /**
+ * get all registered groups
+ *
+ * @return
+ */
List<String> getFeatureGroups();
+ /**
+ * get groups that are visible/invisible
+ *
+ * @param visible
+ * @return
+ */
List<String> getGroups(boolean visible);
+ /**
+ * change visibility for a range of groups
+ *
+ * @param toset
+ * @param visible
+ */
void setGroupVisibility(List<String> toset, boolean visible);
+ /**
+ * change visibiilty of given group
+ *
+ * @param group
+ * @param visible
+ */
void setGroupVisibility(String group, boolean visible);
+ /**
+ * locate features at a particular position on the given sequence
+ *
+ * @param sequence
+ * @param res
+ * @return
+ */
List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
+ /**
+ *
+ * @return true if the rendering platform supports transparency
+ */
boolean isTransparencyAvailable();
+ /**
+ * get current displayed types
+ *
+ * @return
+ */
+
String[] getDisplayedFeatureTypes();
+ /**
+ * get current displayed groups
+ *
+ * @return
+ */
String[] getDisplayedFeatureGroups();
+ /**
+ * display all features of these types
+ *
+ * @param featureTypes
+ */
void setAllVisible(List<String> featureTypes);
+ /**
+ * display featureType
+ *
+ * @param featureType
+ */
void setVisible(String featureType);
}
public interface FeatureSettingsControllerI
{
+
+ void discoverAllFeatureData();
}
*/
package jalview.appletgui;
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
{
// TODO consider using getSequenceSelection instead here
cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
- e.getActionCommand(), ap.av.getShowJVSuffix(), ap.av, true));
+ e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
}
{
if (seq.getPDBId() != null)
{
- PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
+ PDBEntry entry = seq.getPDBId().firstElement();
if (ap.av.applet.jmolAvailable)
{
*/
package jalview.appletgui;
-import java.awt.BorderLayout;
-import java.awt.Canvas;
-import java.awt.CheckboxMenuItem;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Label;
-import java.awt.Menu;
-import java.awt.MenuBar;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.IOException;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
{
if (hiddenSeqs != null && hiddenSeqs.length > 0)
{
viewport.hideSequence(hiddenSeqs);
- viewport.setHasHiddenRows(true);
}
if (columnSelection != null)
{
{ e.getActionCommand() }), 600, 500);
FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
- viewport.setFeatureRenderer(fr);
- viewport.setIncludeHiddenRegion(false);
- cap.setText(new AppletFormatAdapter(viewport).formatSequences(
+ cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
e.getActionCommand(), viewport.getAlignment(),
viewport.getShowJVSuffix()));
}
{
this.splitFrame = sf;
}
+
+ // may not need this
+ @Override
+ public void setShowSeqFeatures(boolean b)
+ {
+ // showSeqFeatures.setSelected(b);
+ viewport.setShowSequenceFeatures(b);
+
+ }
+
+ @Override
+ public void setMenusForViewport()
+ {
+ // setMenusFromViewport(viewport);
+
+ }
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ if (enableIfNecessary)
+ {
+ sequenceFeatures.setState(true);
+ alignPanel.av.setShowSequenceFeatures(true);
+ }
+ }
+
+ @Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return alignPanel.av.featureSettings;
+ }
+
}
*/
package jalview.appletgui;
-import java.awt.Font;
-
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
import jalview.structure.VamsasSource;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.Font;
+
public class AlignViewport extends AlignmentViewport implements
SelectionSource, VamsasSource, CommandListener
{
private AnnotationColumnChooser annotationColumnSelectionState;
- private FeatureRenderer featureRenderer;
-
- private boolean includeHiddenRegion = true;
-
public void finalize()
{
applet = null;
}
}
- @Override
- public FeatureRenderer getFeatureRenderer()
- {
- return featureRenderer;
- }
-
- @Override
- public void setFeatureRenderer(FeatureRenderer featureRenderer)
- {
- this.featureRenderer = featureRenderer;
-
- }
-
- public boolean isIncludeHiddenRegion()
- {
- return includeHiddenRegion;
- }
-
- public void setIncludeHiddenRegion(boolean includeHiddenRegion)
- {
- this.includeHiddenRegion = includeHiddenRegion;
- }
}
*/
package jalview.appletgui;
-import java.awt.BorderLayout;
-import java.awt.Button;
-import java.awt.Dialog;
-import java.awt.Font;
-import java.awt.Frame;
-import java.awt.Label;
-import java.awt.Panel;
-import java.awt.TextArea;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-
import jalview.analysis.AlignmentUtils;
import jalview.api.ComplexAlignFile;
import jalview.bin.JalviewLite;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Dialog;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.TextArea;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
public class CutAndPasteTransfer extends Panel implements ActionListener,
MouseListener
{
protected void loadAlignment(String text, boolean newWindow,
AlignViewport viewport)
{
- Alignment al = null;
+ AlignmentI al = null;
String format = new IdentifyFile().Identify(text,
AppletFormatAdapter.PASTE);
- AppletFormatAdapter afa = new AppletFormatAdapter(viewport);
+ AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
try
{
al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
* @param al
* @return
*/
- protected boolean openSplitFrame(Alignment al, String format)
+ protected boolean openSplitFrame(AlignmentI al, String format)
{
final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
if (thisAlignment.isNucleotide() == al.isNucleotide())
*/
package jalview.appletgui;
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.AlignmentSorter;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Image;
+import java.awt.Label;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.ScrollPane;
+import java.awt.Scrollbar;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener
+ AdjustmentListener, FeatureSettingsControllerI
{
FeatureRenderer fr;
fr.findAllFeatures(true); // was default - now true to make all visible
}
- setTableData();
+ discoverAllFeatureData();
this.setLayout(new BorderLayout());
scrollPane = new ScrollPane();
men.show(this.featurePanel, x, y);
}
- public void setTableData()
+ @Override
+ public void discoverAllFeatureData()
{
if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
{
}
// TODO: JAL-964 - smoothly incorporate new group entries if panel already
// displayed and new groups present
- for (String group:(List<String>)fr.getFeatureGroups())
+ for (String group:fr.getFeatureGroups())
{
boolean vis = fr.checkGroupVisibility(group, false);
Checkbox check = new MyCheckbox(group, vis,
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
ap.seqPanel.seqCanvas.repaint();
}
PaintRefresher.Register(this, av.getSequenceSetId());
}
- public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
+ public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
+ int i, int starty,
int ypos)
{
int charHeight = av.getCharHeight();
((i - starty) * charHeight) + ypos + charHeight
- (charHeight / 5));
- if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+ if (hiddenRows)
{
drawMarker(i, starty, ypos);
}
Color currentColor = Color.white;
Color currentTextColor = Color.black;
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows()
+ && av.getShowHiddenMarkers();
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
int cHeight = alheight * avcharHeight + hgap + annotationHeight;
int rowSize = av.getEndRes() - av.getStartRes();
-
// Draw the rest of the panels
for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
&& (row < maxwidth); ypos += cHeight, row += rowSize)
SequenceI s = av.getAlignment().getSequenceAt(i);
gg.setFont(italic);
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+ if (doHiddenCheck)
{
setHiddenFont(s);
}
- drawIdString(gg, s, i, 0, ypos);
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
}
if (labels != null)
}
gg.setFont(italic);
// boolean isrep=false;
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+ if (doHiddenCheck)
{
// isrep =
setHiddenFont(seq);
(((i - starty) * avcharHeight) + avcharHeight)
- (avcharHeight / 5));
- if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+ if (hiddenRows)
{
drawMarker(i, starty, 0);
}
import jalview.datamodel.AlignmentI;
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
public class OverviewPanel extends Panel implements Runnable,
MouseMotionListener, MouseListener
Color color = Color.yellow;
int row, col, sameRow = 0, sameCol = 0;
jalview.datamodel.SequenceI seq;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
boolean hiddenRow = false;
AlignmentI alignment = av.getAlignment();
for (row = 0; row <= sequencesHeight; row++)
}
hiddenRow = false;
- if (av.hasHiddenRows())
+ if (hasHiddenRows)
{
seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
if (seq == null)
}
if (hiddenRow
- || (av.hasHiddenColumns() && !av.getColumnSelection()
+ || (hasHiddenCols && !av.getColumnSelection()
.isVisible(lastcol)))
{
color = color.darker().darker();
*/
package jalview.bin;
-import java.applet.Applet;
-import java.awt.Button;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.EventQueue;
-import java.awt.Font;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.event.ActionEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.URL;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import netscape.javascript.JSException;
-import netscape.javascript.JSObject;
-
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.AlignViewport;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import java.applet.Applet;
+import java.awt.Button;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.EventQueue;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import netscape.javascript.JSException;
+import netscape.javascript.JSObject;
+
/**
* Jalview Applet. Runs in Java 1.18 runtime
*
*/
public AlignFrame loadAlignment(String text, String title)
{
- Alignment al = null;
+ AlignmentI al = null;
String format = new IdentifyFile().Identify(text,
AppletFormatAdapter.PASTE);
*/
package jalview.bin;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
{
System.out.println("User specified Format is " + format);
}
- Alignment al = null;
+ AlignmentI al = null;
try
{
al = new AppletFormatAdapter().readFile(file, protocol, format);
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
import jalview.util.MessageManager;
import java.awt.Color;
{
sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
}
+
+ @Override
+ public boolean parseFeaturesFile(String file, String protocol,
+ boolean relaxedIdMatching)
+ {
+ boolean featuresFile = false;
+ try
+ {
+ featuresFile = new FeaturesFile(file, protocol).parse(viewport
+ .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
+ .getFeatureColours(), false, relaxedIdMatching);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (featuresFile)
+ {
+ avcg.refreshFeatureUI(true);
+ if (alignPanel.getFeatureRenderer() != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.getFeatureRenderer().findAllFeatures(true);
+ }
+ if (avcg.getFeatureSettingsUI() != null)
+ {
+ avcg.getFeatureSettingsUI().discoverAllFeatureData();
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ return featuresFile;
+
+ }
}
import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsModelI;
-public class FeatureSettingsController implements jalview.api.FeatureSettingsControllerI
+public class FeatureSettingsController // implements
+ // jalview.api.FeatureSettingsControllerI
{
FeatureSettingsControllerGuiI settingUI;
FeatureRenderer fr;
--- /dev/null
+/**
+ *
+ */
+package jalview.datamodel;
+
+/**
+ * Metadata for a sequence that may or may not be physically present in Jalview
+ * at the moment
+ *
+ * @author jprocter
+ *
+ */
+public class ASequence implements ASequenceI
+{
+
+}
--- /dev/null
+package jalview.datamodel;
+
+/**
+ * interfaces to access the basic metadata for a concrete or virtual sequence
+ *
+ * @author jprocter
+ *
+ */
+public interface ASequenceI
+{
+
+}
*
* Example: in "G-AT-C-GA" the aligned codons are (0, 2, 3) and (5, 7, 8).
*
+ * JBPComment: Is this useful anywhere other than jalview.analysis.Dna ?
+ *
* @author gmcarstairs
*
*/
public class AlignedCodonFrame
{
- /*
+ /**
* tied array of na Sequence objects.
*/
private SequenceI[] dnaSeqs = null;
- /*
+ /**
* tied array of Mappings to protein sequence Objects and SequenceI[]
* aaSeqs=null; MapLists where each maps from the corresponding dnaSeqs
* element to corresponding aaSeqs element
* profileseq marked as hidden.
*/
public static ColumnSelection propagateInsertions(SequenceI profileseq,
- Alignment al, AlignmentView input)
+ AlignmentI al, AlignmentView input)
{
int profsqpos = 0;
* @author $author$
* @version $Revision$
*/
-public class Sequence implements SequenceI
+public class Sequence extends ASequence implements SequenceI
{
SequenceI datasetSequence;
*/
public Sequence(String name, String sequence, int start, int end)
{
- this.name = name;
- this.sequence = sequence.toCharArray();
- this.start = start;
- this.end = end;
- parseId();
- checkValidRange();
+ initSeqAndName(name, sequence.toCharArray(), start, end);
}
public Sequence(String name, char[] sequence, int start, int end)
{
- this.name = name;
- this.sequence = sequence;
- this.start = start;
- this.end = end;
+ initSeqAndName(name, sequence, start, end);
+ }
+
+ /**
+ * Stage 1 constructor - assign name, sequence, and set start and end fields.
+ * start and end are updated values from name2 if it ends with /start-end
+ *
+ * @param name2
+ * @param sequence2
+ * @param start2
+ * @param end2
+ */
+ protected void initSeqAndName(String name2, char[] sequence2, int start2,
+ int end2)
+ {
+ this.name = name2;
+ this.sequence = sequence2;
+ this.start = start2;
+ this.end = end2;
parseId();
checkValidRange();
}
*/
public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
{
- this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+ initSeqFrom(seq, alAnnotation);
+
+ }
+
+ protected void initSeqFrom(SequenceI seq,
+ AlignmentAnnotation[] alAnnotation)
+ {
+ initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
+ seq.getEnd());
description = seq.getDescription();
if (seq.getSequenceFeatures() != null)
{
--- /dev/null
+package jalview.datamodel;
+
+public class SequenceDummy extends Sequence implements SequenceI
+{
+ public SequenceDummy(String sequenceId)
+ {
+ super(sequenceId, "THISAPLACEHOLDER");
+ }
+
+ private boolean dummy = true;
+ /**
+ * become a proxy for mseq, merging any existing annotation on this sequence
+ *
+ * @param mseq
+ */
+ public void become(SequenceI mseq)
+ {
+ initSeqFrom(mseq, null);
+ dummy=false;
+ }
+
+ /**
+ * Test if the SequenceDummy has been promoted to a real sequence via
+ * SequenceDummy.become
+ *
+ * @return true if this is a placeholder and contains no actual sequence data
+ */
+ public boolean isDummy()
+ {
+ return dummy;
+ }
+}
return begin;
}
+ public int getStrand()
+ {
+ String str;
+ if (otherDetails == null
+ || (str = otherDetails.get("STRAND").toString()) == null)
+ {
+ return 0;
+ }
+ if (str.equals("-"))
+ {
+ return -1;
+ }
+ if (str.equals("+"))
+ {
+ return 1;
+ }
+ return 0;
+ }
+
}
import fr.orsay.lri.varna.models.rna.RNA;
/**
- * DOCUMENT ME!
+ * Methods for manipulating a sequence, its metadata and related annotation in
+ * an alignment or dataset.
*
* @author $author$
* @version $Revision$
*/
-public interface SequenceI
+public interface SequenceI extends ASequenceI
{
/**
* Set the display name for the sequence
--- /dev/null
+package jalview.gui;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JDialog;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
+import jalview.api.AlignExportSettingI;
+import jalview.jbgui.GAlignExportSettings;
+
+@SuppressWarnings("serial")
+public class AlignExportSettings extends GAlignExportSettings implements
+ AlignExportSettingI
+{
+ protected JInternalFrame frame;
+
+ boolean cancelled = false;
+
+ private int width = 450;
+
+ private int height = 200;
+
+ JDialog dialog;
+
+ public AlignExportSettings(boolean hasHiddenSeq, boolean hasHiddenCols,
+ String alignFileFormat)
+ {
+ super(hasHiddenSeq, hasHiddenCols, alignFileFormat);
+
+ // frame = new JInternalFrame();
+ // frame.setContentPane(this);
+ // frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ // Desktop.addInternalFrame(frame, "Export Settings", width, height);
+
+ JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
+ JOptionPane.DEFAULT_OPTION, null, new Object[]
+ { this });
+ dialog = pane.createDialog(Desktop.desktop, "Export Settings");
+
+ // dialog = new JDialog(Desktop.instance, true);
+ // dialog.setTitle("Export Settings");
+
+ dialog.pack();
+ dialog.setVisible(true);
+
+ dialog.setContentPane(this);
+ dialog.validate();
+
+ }
+
+ // public static void main(String[] args)
+ // {
+ // new AlignExportSettings(false, false, false);
+ // }
+
+ // public void cancel_actionPerformed(ActionEvent e)
+ // {
+ // try
+ // {
+ // frame.setClosed(true);
+ // } catch (Exception ex)
+ // {
+ // }
+ // }
+
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ cancelled = false;
+ dialog.setVisible(false);
+ }
+
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ cancelled = true;
+ dialog.setVisible(false);
+ }
+
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return chkHiddenSeqs.isSelected();
+ }
+
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return chkHiddenCols.isSelected();
+ }
+
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return chkExportAnnots.isSelected();
+ }
+
+ @Override
+ public boolean isExportFeatures()
+ {
+ return chkExportFeats.isSelected();
+ }
+
+ @Override
+ public boolean isExportGroups()
+ {
+ return chkExportGrps.isSelected();
+ }
+
+ @Override
+ public boolean isCancelled()
+ {
+ return cancelled;
+ }
+
+}
*/
package jalview.gui;
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Dna;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
-import jalview.io.FeaturesFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.seqfetcher.DbSourceProxy;
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
/**
* DOCUMENT ME!
*
if (hiddenSeqs != null && hiddenSeqs.length > 0)
{
viewport.hideSequence(hiddenSeqs);
- viewport.setHasHiddenRows(true);
}
alignPanel = new AlignmentPanel(this, viewport);
addAlignmentPanel(alignPanel, true);
return false;
}
- ExportData exportData = getAlignmentForExport();
- FormatAdapter f = new FormatAdapter(viewport);
+ ExportData exportData = getAlignmentForExport(format);
+ FormatAdapter f = new FormatAdapter(alignPanel);
String output = f.formatSequences(format,
exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
protected void outputText_actionPerformed(ActionEvent e)
{
- ExportData exportData = getAlignmentForExport();
+ ExportData exportData = getAlignmentForExport(e.getActionCommand());
+ if (exportData.getSettings().isCancelled())
+ {
+ return;
+ }
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
-
try
{
- cap.setText(new FormatAdapter(viewport).formatSequences(
+ cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
+ .formatSequences(
e.getActionCommand(),
exportData.getAlignment(),
exportData.getOmitHidden(), exportData.getStartEndPostions(),
}
- public ExportData getAlignmentForExport()
+ public ExportData getAlignmentForExport(String exportFomat)
{
AlignmentI alignmentToExport = null;
String[] omitHidden = null;
int[] alignmentStartEnd = new int[2];
- FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
- viewport.setFeatureRenderer(fr);
+
HiddenSequences hiddenSeqs = viewport.getAlignment()
.getHiddenSequences();
alignmentStartEnd = new int[]
{ 0, alignmentToExport.getWidth() - 1 };
- if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
- {
- int reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.alignment_contains_hidden_columns"),
- MessageManager
- .getString("action.save_omit_hidden_columns"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+ AlignExportSettingI settings = new AlignExportSettings(hasHiddenSeqs,
+ viewport.hasHiddenColumns(), exportFomat);
+ settings.isExportAnnotations();
- if (reply == JOptionPane.YES_OPTION)
- {
- // export only visible region
- omitHidden = viewport.getViewAsString(false);
- alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
- .getColumnSelection().getHiddenColumns());
- viewport.setIncludeHiddenRegion(false);
- }
- else
- {
- // export all region including visible
- alignmentToExport = hiddenSeqs.getFullAlignment();
- viewport.setIncludeHiddenRegion(true);
- }
+ if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+ {
+ omitHidden = viewport.getViewAsString(false);
}
- return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd);
+ if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ {
+ alignmentToExport = hiddenSeqs.getFullAlignment();
+ }
+ else
+ {
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+ .getColumnSelection().getHiddenColumns());
+ }
+ return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd,
+ settings);
}
private static int[] getStartEnd(int[] aligmentStartEnd,
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- // new HTMLOutput(alignPanel,
- // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
- // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
new HtmlSvgOutput(null, alignPanel);
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel,
- alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
public void createImageMap(File file, String image)
public FeatureSettings featureSettings;
@Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return featureSettings;
+ }
+
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
* contents or path to retrieve file
* @param type
* access mode of file (see jalview.io.AlignFile)
- * @return true if features file was parsed corectly.
+ * @return true if features file was parsed correctly.
*/
public boolean parseFeaturesFile(String file, String type)
{
- boolean featuresFile = false;
- try
- {
- featuresFile = new FeaturesFile(file, type).parse(viewport
- .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer().getFeatureColours(), false,
- jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ return avc.parseFeaturesFile(file, type,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+
+ }
- if (featuresFile)
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ // note - currently this is only still here rather than in the controller
+ // because of the featureSettings hard reference that is yet to be
+ // abstracted
+ if (enableIfNecessary)
{
viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
- if (alignPanel.getSeqPanel().seqCanvas.fr != null)
- {
- // update the min/max ranges where necessary
- alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
- }
- if (featureSettings != null)
- {
- featureSettings.setTableData();
- }
- alignPanel.paintAlignment(true);
}
- return featuresFile;
- }
+ }
@Override
public void dragEnter(DropTargetDragEvent evt)
{
private int[] startEnd;
- public ExportData(AlignmentI align, String[] ommit, int[] startEnd)
+ private AlignExportSettingI settings;
+
+ public ExportData(AlignmentI align, String[] ommit, int[] startEnd,
+ AlignExportSettingI settings)
{
this.alignment = align;
this.omitHidden = ommit;
this.startEnd = startEnd;
+ this.settings = settings;
}
public AlignmentI getAlignment()
{
this.startEnd = startEnd;
}
+
+ public AlignExportSettingI getSettings()
+ {
+ return settings;
+ }
+
+ public void setSettings(AlignExportSettingI settings)
+ {
+ this.settings = settings;
+ }
}
}
*/
package jalview.gui;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
/**
* DOCUMENT ME!
*
private Rectangle explodedGeometry;
- private FeatureRenderer featureRenderer;
-
- private boolean includeHiddenRegion = true;
String viewName;
/*
}
}
- @Override
- public FeatureRenderer getFeatureRenderer()
- {
- return featureRenderer;
- }
-
- @Override
- public void setFeatureRenderer(FeatureRenderer featureRenderer)
- {
- this.featureRenderer = featureRenderer;
- }
-
- public boolean isIncludeHiddenRegion()
- {
- return includeHiddenRegion;
- }
-
- public void setIncludeHiddenRegion(boolean includeHiddenRegion)
- {
- this.includeHiddenRegion = includeHiddenRegion;
- }
}
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.ComplexAlignFile;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.DataFlavor;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
-import jalview.api.ComplexAlignFile;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GCutAndPasteTransfer;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
/**
* Cut'n'paste files into the desktop See JAL-1105
*
public class CutAndPasteTransfer extends GCutAndPasteTransfer
{
- AlignViewport viewport;
+ AlignmentViewPanel alignpanel;
+
+ AlignViewportI viewport;
FileParse source = null;
public CutAndPasteTransfer()
/**
* DOCUMENT ME!
*/
- public void setForInput(AlignViewport viewport)
+ public void setForInput(AlignmentViewPanel viewpanel)
{
- this.viewport = viewport;
+ this.alignpanel = viewpanel;
+ if (alignpanel != null)
+ {
+
+ }
+ this.viewport = alignpanel.getAlignViewport();
if (viewport != null)
{
ok.setText(MessageManager.getString("action.add"));
{
String format = new IdentifyFile().Identify(getText(), "Paste");
// TODO: identify feature, annotation or tree file and parse appropriately.
- Alignment al = null;
+ AlignmentI al = null;
if (FormatAdapter.isValidFormat(format))
{
try
{
- FormatAdapter fa = new FormatAdapter(viewport);
+ FormatAdapter fa = new FormatAdapter(alignpanel);
al = fa.readFile(getText(), "Paste", format);
source = fa.getAlignFile();
{ format });
if (viewport != null)
{
- viewport.addAlignment(al, title);
+ ((AlignViewport) viewport).addAlignment(al, title);
}
else
{
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.ParamManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GSplitFrame;
-import jalview.jbgui.GStructureViewer;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-
/**
* Jalview Desktop
*
public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(viewport);
+ cap.setForInput(viewport.getAlignPanel());
Desktop.addInternalFrame(cap,
MessageManager.getString("label.cut_paste_alignmen_file"),
true, 600, 500);
*/
package jalview.gui;
+import jalview.api.FeatureSettingsControllerI;
import jalview.bin.Cache;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
-public class FeatureSettings extends JPanel
+public class FeatureSettings extends JPanel implements
+ FeatureSettingsControllerI
{
DasSourceBrowser dassourceBrowser;
fr.findAllFeatures(true); // display everything!
}
- setTableData();
+ discoverAllFeatureData();
final PropertyChangeListener change;
final FeatureSettings fs = this;
fr.addPropertyChangeListener(change = new PropertyChangeListener()
*/
Hashtable typeWidth = null;
- synchronized public void setTableData()
+ @Override
+ synchronized public void discoverAllFeatureData()
{
Vector allFeatures = new Vector();
Vector allGroups = new Vector();
*
* @param gg
* DOCUMENT ME!
+ * @param hiddenRows
+ * true - check and display hidden row marker if need be
* @param s
* DOCUMENT ME!
* @param i
* @param ypos
* DOCUMENT ME!
*/
- public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
+ public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+ int i, int starty,
int ypos)
{
int xPos = 0;
gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
- if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+ if (hiddenRows)
{
drawMarker(i, starty, ypos);
}
Color currentColor = Color.white;
Color currentTextColor = Color.black;
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows();
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
for (int i = starty; i < alheight; i++)
{
SequenceI s = av.getAlignment().getSequenceAt(i);
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+ if (doHiddenCheck)
{
setHiddenFont(s);
}
gg.setFont(getIdfont());
}
- drawIdString(gg, s, i, 0, ypos);
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
}
if (labels != null && av.isShowAnnotation())
continue;
}
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
+ if (doHiddenCheck)
{
setHiddenFont(sequence);
}
(((i - starty) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
- if (av.hasHiddenRows() && av.getShowHiddenMarkers())
+ if (hiddenRows)
{
drawMarker(i, starty, 0);
}
int color = Color.white.getRGB();
int row, col;
jalview.datamodel.SequenceI seq;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
boolean hiddenRow = false;
for (row = 0; row < sequencesHeight; row++)
{
lastrow = (int) (row * sampleRow);
hiddenRow = false;
- if (av.hasHiddenRows())
+ if (hasHiddenRows)
{
seq = av.getAlignment().getHiddenSequences()
.getHiddenSequence(lastrow);
}
if (hiddenRow
- || (av.hasHiddenColumns() && !av.getColumnSelection()
+ || (hasHiddenCols && !av.getColumnSelection()
.isVisible(lastcol)))
{
color = new Color(color).darker().darker().getRGB();
// wysiwig behaviour
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- ap.av, true));
+ ap, true));
}
public void pdbFromFile_actionPerformed()
*/
package jalview.gui;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
import java.awt.BorderLayout;
import java.awt.Font;
import java.awt.event.ActionEvent;
import com.stevesoft.pat.Regex;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.util.DBRefUtils;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
public class SequenceFetcher extends JPanel implements Runnable
{
JLabel dbeg = new JLabel();
AlignmentI parseResult(String result, String title)
{
String format = new IdentifyFile().Identify(result, "Paste");
- Alignment sequences = null;
+ AlignmentI sequences = null;
if (FormatAdapter.isValidFormat(format))
{
sequences = null;
*/
package jalview.io;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
/**
* DOCUMENT ME!
*
*
* @param al
*/
- public void addAnnotations(Alignment al)
+ public void addAnnotations(AlignmentI al)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
}
+ /**
+ * register sequence groups on the alignment for **output**
+ *
+ * @param al
+ */
public void addSeqGroups(AlignmentI al)
{
this.seqGroups = al.getGroups();
* @note implicitly called by addAnnotations()
* @param al
*/
- public void addProperties(Alignment al)
+ public void addProperties(AlignmentI al)
{
if (properties != null && properties.size() > 0)
{
return newickStrings == null ? 0 : newickStrings.size();
}
+ public void addGroups(AlignmentI al)
+ {
+
+ for (SequenceGroup sg : getSeqGroups())
+ {
+ al.addGroup(sg);
+ }
+ }
+
}
*/
package jalview.io;
-import java.io.File;
-import java.io.InputStream;
-import java.util.List;
-
-import jalview.api.AlignViewportI;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SequenceGroup;
+import jalview.gui.AlignmentPanel;
import jalview.util.MessageManager;
+import java.io.File;
+import java.io.InputStream;
+import java.util.List;
+
/**
* A low level class for alignment and feature IO with alignment formatting
* methods used by both applet and application for generating flat alignment
*/
public class AppletFormatAdapter
{
- private AlignViewportI viewport;
+ private AlignmentViewPanel viewpanel;
public static String FILE = "File";
*/
protected String newline = System.getProperty("line.separator");
+ private AlignExportSettingI exportSettings;
+
/**
* List of valid format strings used in the isValidFormat method
*/
public static final String[] READABLE_FORMATS = new String[]
{ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
+ "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
"HTML" };
/**
public static final String[] READABLE_EXTENSIONS = new String[]
{ "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
"sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
+ ".gff2,gff3",
"jar,jvp", HtmlFile.FILE_EXT };
/**
*/
public static final String[] READABLE_FNAMES = new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
- "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview",
+ "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview",
HtmlFile.FILE_DESC };
/**
{
}
- public AppletFormatAdapter(AlignViewportI viewport)
+ public AppletFormatAdapter(AlignmentViewPanel viewpanel)
+ {
+ this.viewpanel = viewpanel;
+ }
+
+ public AppletFormatAdapter(AlignmentPanel alignPanel,
+ AlignExportSettingI settings)
{
- this.viewport = viewport;
+ viewpanel = alignPanel;
+ exportSettings = settings;
}
/**
*
* @return DOCUMENT ME!
*/
- public Alignment readFile(String inFile, String type, String format)
+ public AlignmentI readFile(String inFile, String type, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
this.inFile = inFile;
try
{
- Alignment al;
if (format.equals("FASTA"))
{
alignFile = new FastaFile(inFile, type);
else if (format.equals(JSONFile.FILE_DESC))
{
alignFile = new JSONFile(inFile, type);
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- ((JSONFile) alignFile).setViewport(viewport);
- for (SequenceGroup sg : alignFile.getSeqGroups())
- {
- al.addGroup(sg);
- }
-
- return al;
}
else if (format.equals(HtmlFile.FILE_DESC))
{
alignFile = new HtmlFile(inFile, type);
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- for (SequenceGroup sg : alignFile.getSeqGroups())
- {
- al.addGroup(sg);
- }
- return al;
}
else if (format.equals("RNAML"))
{
alignFile = new RnamlFile(inFile, type);
}
-
- al = new Alignment(alignFile.getSeqsAsArray());
-
- alignFile.addAnnotations(al);
-
- return al;
+ else if (format.equals(IdentifyFile.GFF3File))
+ {
+ alignFile = new Gff3File(inFile, type);
+ }
+ return buildAlignmentFrom(alignFile);
} catch (Exception e)
{
e.printStackTrace();
{
// Possible sequence is just residues with no label
alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- Alignment al = new Alignment(alignFile.getSeqsAsArray());
-
- alignFile.addSeqGroups(al);
- alignFile.addAnnotations(al);
- return al;
+ return buildAlignmentFrom(alignFile);
} catch (Exception ex)
{
String type = source.type;
try
{
- Alignment al;
if (format.equals("FASTA"))
{
alignFile = new FastaFile(source);
{
alignFile = new PhylipFile(source);
}
+ else if (format.equals(IdentifyFile.GFF3File))
+ {
+ alignFile = new Gff3File(inFile, type);
+ }
else if (format.equals(JSONFile.FILE_DESC))
{
alignFile = new JSONFile(source);
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- alignFile.addSeqGroups(al);
- return al;
}
else if (format.equals(HtmlFile.FILE_DESC))
{
alignFile = new HtmlFile(source);
}
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- return al;
+ return buildAlignmentFrom(alignFile);
+
} catch (Exception e)
{
e.printStackTrace();
{
// Possible sequence is just residues with no label
alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- Alignment al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- alignFile.addSeqGroups(al);
- return al;
+ return buildAlignmentFrom(alignFile);
} catch (Exception ex)
{
/**
+ * boilerplate method to handle data from an AlignFile and construct a new
+ * alignment or import to an existing alignment
+ *
+ * @param alignFile2
+ * @return AlignmentI instance ready to pass to a UI constructor
+ */
+ private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
+ {
+ // Standard boilerplate for creating alignment from parser
+ alignFile.configureForView(viewpanel);
+
+ AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
+
+ alignFile.addAnnotations(al);
+
+ alignFile.addGroups(al);
+
+ return al;
+ }
+
+ /**
* create an alignment flatfile from a Jalview alignment view
* @param format
* @param jvsuffix
* @return flatfile in a string
*/
public String formatSequences(String format, boolean jvsuffix,
- AlignViewportI av, boolean selectedOnly)
+ AlignmentViewPanel ap, boolean selectedOnly)
{
- AlignmentView selvew = av.getAlignmentView(selectedOnly, false);
- AlignmentI aselview = selvew.getVisibleAlignment(av
+ AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
+ selectedOnly, false);
+ AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
.getGapCharacter());
- List<AlignmentAnnotation> ala = (av
+ List<AlignmentAnnotation> ala = (ap.getAlignViewport()
.getVisibleAlignmentAnnotation(selectedOnly));
if (ala != null)
{
else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
{
afile = new JSONFile();
- afile.setViewport(viewport);
- // Add groups to AlignFile
- afile.seqGroups = alignment.getGroups();
-
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : alignment.getAlignmentAnnotation())
- {
- if (annot != null && !annot.autoCalculated)
- {
- if (annot.label.equals("PDB.CATempFactor"))
- {
- continue;
- }
- afile.annotations.add(annot);
- }
- }
}
else if (format.equalsIgnoreCase("RNAML"))
{
afile.setNewlineString(newline);
afile.addJVSuffix(jvsuffix);
- afile.setSeqs(alignment.getSequencesArray());
+ afile.setExportSettings(exportSettings);
+ afile.configureForView(viewpanel);
+
+ // check whether we were given a specific alignment to export, rather than
+ // the one in the viewpanel
+ if (viewpanel == null || viewpanel.getAlignment() == null
+ || viewpanel.getAlignment() != alignment)
+ {
+ afile.setSeqs(alignment.getSequencesArray());
+ }
+ else
+ {
+ afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
+ }
String afileresp = afile.print();
if (afile.hasWarningMessage())
System.gc();
long memf = -r.totalMemory() + r.freeMemory();
long t1 = -System.currentTimeMillis();
- Alignment al = afa.readFile(args[i], FILE,
+ AlignmentI al = afa.readFile(args[i], FILE,
new IdentifyFile().Identify(args[i], FILE));
t1 += System.currentTimeMillis();
System.gc();
package jalview.io;
+import jalview.api.AlignmentViewPanel;
import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
import jalview.json.binding.v1.BioJSReleasePojo;
import jalview.json.binding.v1.BioJSRepositoryPojo;
import jalview.util.MessageManager;
public class BioJsHTMLOutput
{
- private AlignViewport av;
+ private AlignmentViewPanel ap;
private static File currentBJSTemplateFile;
"biojs_template_git_repo",
"https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
- public BioJsHTMLOutput(AlignmentPanel ap, FeatureRenderer fr1)
+ public BioJsHTMLOutput(AlignmentViewPanel ap)
{
if (ap != null)
{
- this.av = ap.av;
- av.setFeatureRenderer(new FeatureRenderer(ap));
+ this.ap = ap;
}
}
try
{
String outputFile = getOutputFile();
- String jalviewAlignmentJson = JSONFile.getJSONData(av);
+ String jalviewAlignmentJson = JSONFile.getJSONData(ap);
String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
.replaceAll(
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
-
import jalview.analysis.SequenceIdMatcher;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.UserColourScheme;
import jalview.util.Format;
+import jalview.util.MapList;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* Parse and create Jalview Features files Detects GFF format features files and
*/
private boolean doGffSource = true;
+ private int gffversion;
+
/**
* Creates a new FeaturesFile object.
*/
}
/**
- * Creates a new FeaturesFile object.
- *
* @param inFile
- * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
- *
* @throws IOException
- * DOCUMENT ME!
*/
public FeaturesFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
+ /**
+ * @param source
+ * @throws IOException
+ */
public FeaturesFile(FileParse source) throws IOException
{
super(source);
}
/**
+ * @param parseImmediately
+ * @param source
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, FileParse source)
+ throws IOException
+ {
+ super(parseImmediately, source);
+ }
+
+ /**
+ * @param parseImmediately
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, String inFile, String type)
+ throws IOException
+ {
+ super(parseImmediately, inFile, type);
+ }
+
+ /**
* Parse GFF or sequence features file using case-independent matching,
* discarding URLs
*
return parse(align, colours, featureLink, removeHTML, false);
}
+ @Override
+ public void addAnnotations(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addAnnotations(al);
+ }
+
+ @Override
+ public void addProperties(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addProperties(al);
+ }
+
+ @Override
+ public void addSeqGroups(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addSeqGroups(al);
+ }
+
/**
* Parse GFF or sequence features file
*
try
{
SequenceI seq = null;
+ /**
+ * keep track of any sequences we try to create from the data if it is a GFF3 file
+ */
+ ArrayList<SequenceI> newseqs = new ArrayList<SequenceI>();
String type, desc, token = null;
int index, start, end;
* when true, assume GFF style features rather than Jalview style.
*/
boolean GFFFile = true;
+ Map<String, String> gffProps = new HashMap<String, String>();
while ((line = nextLine()) != null)
{
+ // skip comments/process pragmas
if (line.startsWith("#"))
{
+ if (line.startsWith("##"))
+ {
+ // possibly GFF2/3 version and metadata header
+ processGffPragma(line, gffProps, align, newseqs);
+ line = "";
+ }
continue;
}
// Still possible this is an old Jalview file,
// which does not have type colours at the beginning
seqId = token = st.nextToken();
- seq = findName(align, seqId, relaxedIdmatching);
+ seq = findName(align, seqId, relaxedIdmatching, newseqs);
if (seq != null)
{
desc = st.nextToken();
if (st.hasMoreTokens())
{
StringBuffer attributes = new StringBuffer();
+ boolean sep = false;
while (st.hasMoreTokens())
{
- attributes.append("\t" + st.nextElement());
+ attributes.append((sep ? "\t" : "") + st.nextElement());
+ sep = true;
}
// TODO validate and split GFF2 attributes field ? parse out
// ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as
sf.setValue("ATTRIBUTES", attributes.toString());
}
- seq.addSequenceFeature(sf);
- while ((seq = align.findName(seq, seqId, true)) != null)
+ if (processOrAddSeqFeature(align, newseqs, seq, sf, GFFFile,
+ relaxedIdmatching))
{
- seq.addSequenceFeature(new SequenceFeature(sf));
+ // check whether we should add the sequence feature to any other
+ // sequences in the alignment with the same or similar
+ while ((seq = align.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
}
break;
}
if (!token.equals("ID_NOT_SPECIFIED"))
{
- seq = findName(align, seqId = token, relaxedIdmatching);
+ seq = findName(align, seqId = token, relaxedIdmatching, null);
st.nextToken();
}
else
resetMatcher();
} catch (Exception ex)
{
+ // should report somewhere useful for UI if necessary
+ warningMessage = ((warningMessage == null) ? "" : warningMessage)
+ + "Parsing error at\n" + line;
System.out.println("Error parsing feature file: " + ex + "\n" + line);
ex.printStackTrace(System.err);
resetMatcher();
return true;
}
+ private enum GffPragmas
+ {
+ gff_version, sequence_region, feature_ontology, attribute_ontology, source_ontology, species_build, fasta, hash
+ };
+
+ private static Map<String, GffPragmas> GFFPRAGMA;
+ static
+ {
+ GFFPRAGMA = new HashMap<String, GffPragmas>();
+ GFFPRAGMA.put("sequence-region", GffPragmas.sequence_region);
+ GFFPRAGMA.put("feature-ontology", GffPragmas.feature_ontology);
+ GFFPRAGMA.put("#", GffPragmas.hash);
+ GFFPRAGMA.put("fasta", GffPragmas.fasta);
+ GFFPRAGMA.put("species-build", GffPragmas.species_build);
+ GFFPRAGMA.put("source-ontology", GffPragmas.source_ontology);
+ GFFPRAGMA.put("attribute-ontology", GffPragmas.attribute_ontology);
+ }
+
+ private void processGffPragma(String line, Map<String, String> gffProps,
+ AlignmentI align, ArrayList<SequenceI> newseqs)
+ throws IOException
+ {
+ // line starts with ##
+ int spacepos = line.indexOf(' ');
+ String pragma = spacepos == -1 ? line.substring(2).trim() : line
+ .substring(2, spacepos);
+ GffPragmas gffpragma = GFFPRAGMA.get(pragma.toLowerCase());
+ if (gffpragma == null)
+ {
+ return;
+ }
+ switch (gffpragma)
+ {
+ case gff_version:
+ try
+ {
+ gffversion = Integer.parseInt(line.substring(spacepos + 1));
+ } finally
+ {
+
+ }
+ break;
+ case feature_ontology:
+ // resolve against specific feature ontology
+ break;
+ case attribute_ontology:
+ // resolve against specific attribute ontology
+ break;
+ case source_ontology:
+ // resolve against specific source ontology
+ break;
+ case species_build:
+ // resolve against specific NCBI taxon version
+ break;
+ case hash:
+ // close off any open feature hierarchies
+ break;
+ case fasta:
+ // process the rest of the file as a fasta file and replace any dummy
+ // sequence IDs
+ process_as_fasta(align, newseqs);
+ break;
+ default:
+ // we do nothing ?
+ System.err.println("Ignoring unknown pragma:\n" + line);
+ }
+ }
+
+ private void process_as_fasta(AlignmentI align, List<SequenceI> newseqs)
+ throws IOException
+ {
+ try
+ {
+ mark();
+ } catch (IOException q)
+ {
+ }
+ FastaFile parser = new FastaFile(this);
+ List<SequenceI> includedseqs = parser.getSeqs();
+ SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);
+ // iterate over includedseqs, and replacing matching ones with newseqs
+ // sequences. Generic iterator not used here because we modify includedseqs
+ // as we go
+ for (int p = 0, pSize = includedseqs.size(); p < pSize; p++)
+ {
+ // search for any dummy seqs that this sequence can be used to update
+ SequenceI dummyseq = smatcher.findIdMatch(includedseqs.get(p));
+ if (dummyseq != null)
+ {
+ // dummyseq was created so it could be annotated and referred to in
+ // alignments/codon mappings
+
+ SequenceI mseq = includedseqs.get(p);
+ // mseq is the 'template' imported from the FASTA file which we'll use
+ // to coomplete dummyseq
+ if (dummyseq instanceof SequenceDummy)
+ {
+ // probably have the pattern wrong
+ // idea is that a flyweight proxy for a sequence ID can be created for
+ // 1. stable reference creation
+ // 2. addition of annotation
+ // 3. future replacement by a real sequence
+ // current pattern is to create SequenceDummy objects - a convenience
+ // constructor for a Sequence.
+ // problem is that when promoted to a real sequence, all references
+ // need
+ // to be updated somehow.
+ ((SequenceDummy) dummyseq).become(mseq);
+ includedseqs.set(p, dummyseq); // template is no longer needed
+ }
+ }
+ }
+ // finally add sequences to the dataset
+ for (SequenceI seq : includedseqs)
+ {
+ align.addSequence(seq);
+ }
+ }
+
+ /**
+ * take a sequence feature and examine its attributes to decide how it should
+ * be added to a sequence
+ *
+ * @param seq
+ * - the destination sequence constructed or discovered in the
+ * current context
+ * @param sf
+ * - the base feature with ATTRIBUTES property containing any
+ * additional attributes
+ * @param gFFFile
+ * - true if we are processing a GFF annotation file
+ * @return true if sf was actually added to the sequence, false if it was
+ * processed in another way
+ */
+ public boolean processOrAddSeqFeature(AlignmentI align, List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
+ boolean gFFFile, boolean relaxedIdMatching)
+ {
+ String attr = (String) sf.getValue("ATTRIBUTES");
+ boolean add = true;
+ if (gFFFile && attr != null)
+ {
+ int nattr=8;
+
+ for (String attset : attr.split("\t"))
+ {
+ if (attset==null || attset.trim().length()==0)
+ {
+ continue;
+ }
+ nattr++;
+ Map<String, List<String>> set = new HashMap<String, List<String>>();
+ // normally, only expect one column - 9 - in this field
+ // the attributes (Gff3) or groups (gff2) field
+ for (String pair : attset.trim().split(";"))
+ {
+ pair = pair.trim();
+ if (pair.length() == 0)
+ {
+ continue;
+ }
+
+ // expect either space seperated (gff2) or '=' separated (gff3)
+ // key/value pairs here
+
+ int eqpos = pair.indexOf('='),sppos = pair.indexOf(' ');
+ String key = null, value = null;
+
+ if (sppos > -1 && (eqpos == -1 || sppos < eqpos))
+ {
+ key = pair.substring(0, sppos);
+ value = pair.substring(sppos + 1);
+ } else {
+ if (eqpos > -1 && (sppos == -1 || eqpos < sppos))
+ {
+ key = pair.substring(0, eqpos);
+ value = pair.substring(eqpos + 1);
+ } else
+ {
+ key = pair;
+ }
+ }
+ if (key != null)
+ {
+ List<String> vals = set.get(key);
+ if (vals == null)
+ {
+ vals = new ArrayList<String>();
+ set.put(key, vals);
+ }
+ if (value != null)
+ {
+ vals.add(value.trim());
+ }
+ }
+ }
+ try
+ {
+ add &= processGffKey(set, nattr, seq, sf, align, newseqs,
+ relaxedIdMatching); // process decides if
+ // feature is actually
+ // added
+ } catch (InvalidGFF3FieldException ivfe)
+ {
+ System.err.println(ivfe);
+ }
+ }
+ }
+ if (add)
+ {
+ seq.addSequenceFeature(sf);
+ }
+ return add;
+ }
+
+ public class InvalidGFF3FieldException extends Exception
+ {
+ String field, value;
+
+ public InvalidGFF3FieldException(String field,
+ Map<String, List<String>> set, String message)
+ {
+ super(message + " (Field was " + field + " and value was "
+ + set.get(field).toString());
+ this.field = field;
+ this.value = set.get(field).toString();
+ }
+
+ }
+
+ /**
+ * take a set of keys for a feature and interpret them
+ *
+ * @param set
+ * @param nattr
+ * @param seq
+ * @param sf
+ * @return
+ */
+ public boolean processGffKey(Map<String, List<String>> set, int nattr,
+ SequenceI seq, SequenceFeature sf, AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching)
+ throws InvalidGFF3FieldException
+ {
+ String attr;
+ // decide how to interpret according to type
+ if (sf.getType().equals("similarity"))
+ {
+ int strand = sf.getStrand();
+ // exonerate cdna/protein map
+ // look for fields
+ List<SequenceI> querySeq = findNames(align, newseqs,
+ relaxedIdMatching, set.get(attr="Query"));
+ if (querySeq==null || querySeq.size()!=1)
+ {
+ throw new InvalidGFF3FieldException( attr, set,
+ "Expecting exactly one sequence in Query field (got "
+ + set.get(attr) + ")");
+ }
+ if (set.containsKey(attr="Align"))
+ {
+ // process the align maps and create cdna/protein maps
+ // ideally, the query sequences are in the alignment, but maybe not...
+
+ AlignedCodonFrame alco = new AlignedCodonFrame();
+ MapList codonmapping = constructCodonMappingFromAlign(set, attr,
+ strand);
+
+ // add codon mapping, and hope!
+ alco.addMap(seq, querySeq.get(0), codonmapping);
+ align.addCodonFrame(alco);
+ // everything that's needed to be done is done
+ // no features to create here !
+ return false;
+ }
+
+ }
+ return true;
+ }
+
+ private MapList constructCodonMappingFromAlign(
+ Map<String, List<String>> set,
+ String attr, int strand) throws InvalidGFF3FieldException
+ {
+ if (strand == 0)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid strand for a codon mapping (cannot be 0)");
+ }
+ List<Integer> fromrange = new ArrayList<Integer>(), torange = new ArrayList<Integer>();
+ int lastppos = 0, lastpframe = 0;
+ for (String range : set.get(attr))
+ {
+ List<Integer> ints = new ArrayList<Integer>();
+ StringTokenizer st = new StringTokenizer(range, " ");
+ while (st.hasMoreTokens())
+ {
+ String num = st.nextToken();
+ try
+ {
+ ints.add(new Integer(num));
+ } catch (NumberFormatException nfe)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid number in field " + num);
+ }
+ }
+ // Align positionInRef positionInQuery LengthInRef
+ // contig_1146 exonerate:protein2genome:local similarity 8534 11269
+ // 3652 - . alignment_id 0 ;
+ // Query DDB_G0269124
+ // Align 11270 143 120
+ // corresponds to : 120 bases align at pos 143 in protein to 11270 on
+ // dna in strand direction
+ // Align 11150 187 282
+ // corresponds to : 282 bases align at pos 187 in protein to 11150 on
+ // dna in strand direction
+ //
+ // Align 10865 281 888
+ // Align 9977 578 1068
+ // Align 8909 935 375
+ //
+ if (ints.size() != 3)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid number of fields for this attribute ("
+ + ints.size() + ")");
+ }
+ fromrange.add(new Integer(ints.get(0).intValue()));
+ fromrange.add(new Integer(ints.get(0).intValue() + strand
+ * ints.get(2).intValue()));
+ // how are intron/exon boundaries that do not align in codons
+ // represented
+ if (ints.get(1).equals(lastppos) && lastpframe > 0)
+ {
+ // extend existing to map
+ lastppos += ints.get(2) / 3;
+ lastpframe = ints.get(2) % 3;
+ torange.set(torange.size() - 1, new Integer(lastppos));
+ }
+ else
+ {
+ // new to map range
+ torange.add(ints.get(1));
+ lastppos = ints.get(1) + ints.get(2) / 3;
+ lastpframe = ints.get(2) % 3;
+ torange.add(new Integer(lastppos));
+ }
+ }
+ // from and to ranges must end up being a series of start/end intervals
+ if (fromrange.size() % 2 == 1)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Couldn't parse the DNA alignment range correctly");
+ }
+ if (torange.size() % 2 == 1)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Couldn't parse the protein alignment range correctly");
+ }
+ // finally, build the map
+ int[] frommap = new int[fromrange.size()], tomap = new int[torange
+ .size()];
+ int p = 0;
+ for (Integer ip : fromrange)
+ {
+ frommap[p++] = ip.intValue();
+ }
+ p = 0;
+ for (Integer ip : torange)
+ {
+ tomap[p++] = ip.intValue();
+ }
+
+ return new MapList(frommap, tomap, 3, 1);
+ }
+
+ private List<SequenceI> findNames(AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching,
+ List<String> list)
+ {
+ List<SequenceI> found = new ArrayList<SequenceI>();
+ for (String seqId : list)
+ {
+ SequenceI seq = findName(align, seqId, relaxedIdMatching, newseqs);
+ if (seq != null)
+ {
+ found.add(seq);
+ }
+ }
+ return found;
+ }
+
private AlignmentI lastmatchedAl = null;
private SequenceIdMatcher matcher = null;
}
private SequenceI findName(AlignmentI align, String seqId,
- boolean relaxedIdMatching)
+ boolean relaxedIdMatching, List<SequenceI> newseqs)
{
SequenceI match = null;
if (relaxedIdMatching)
{
matcher = new SequenceIdMatcher(
(lastmatchedAl = align).getSequencesArray());
+ if (newseqs != null)
+ {
+ matcher.addAll(newseqs);
+ }
}
match = matcher.findIdMatch(seqId);
}
else
{
match = align.findName(seqId, true);
+ if (match == null && newseqs != null)
+ {
+ for (SequenceI m : newseqs)
+ {
+ if (seqId.equals(m.getName()))
+ {
+ return m;
+ }
+ }
+ }
+
+ }
+ if (match==null && newseqs!=null)
+ {
+ match = new SequenceDummy(seqId);
+ if (relaxedIdMatching)
+ {
+ matcher.addAll(Arrays.asList(new SequenceI[]
+ { match }));
+ }
+ // add dummy sequence to the newseqs list
+ newseqs.add(match);
}
return match;
}
-
public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
{
if (sf.getDescription() == null)
final String errorMessage = "Couldn't load file " + title + "\n"
+ error;
- if (raiseGUI)
+ // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
+ // bits ?
+ if (raiseGUI && Desktop.desktop != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
*/
package jalview.io;
+import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.util.MessageManager;
import java.io.BufferedReader;
public File inFile = null;
+ /**
+ * a viewport associated with the current file operation. May be null. May
+ * move to different object.
+ */
private AlignViewportI viewport;
- public int index = 1; // sequence counter for FileParse object created from
+ /**
+ * specific settings for exporting data from the current context
+ */
+ private AlignExportSettingI exportSettings;
- // same data source
+ /**
+ * sequence counter for FileParse object created from same data source
+ */
+ public int index = 1;
+ /**
+ * separator for extracting specific 'frame' of a datasource for formats that
+ * support multiple records (e.g. BLC, Stockholm, etc)
+ */
protected char suffixSeparator = '#';
/**
throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
}
+ /**
+ *
+ * @return true if this FileParse is configured for Export only
+ */
+ public boolean isExporting()
+ {
+ return !error && dataIn == null;
+ }
+
+ /**
+ *
+ * @return true if the data source is valid
+ */
public boolean isValid()
{
return !error;
{
this.viewport = viewport;
}
+
+ /**
+ * @return the currently configured exportSettings for writing data.
+ */
+ public AlignExportSettingI getExportSettings()
+ {
+ return exportSettings;
+ }
+
+ /**
+ * Set configuration for export of data.
+ *
+ * @param exportSettings
+ * the exportSettings to set
+ */
+ public void setExportSettings(AlignExportSettingI exportSettings)
+ {
+ this.exportSettings = exportSettings;
+ }
+
+ /**
+ * method overridden by complex file exporter/importers which support
+ * exporting visualisation and layout settings for a view
+ *
+ * @param avpanel
+ */
+ public void configureForView(AlignmentViewPanel avpanel)
+ {
+ if (avpanel!=null) {
+ setViewport(avpanel.getAlignViewport());
+ }
+ // could also set export/import settings
+ }
}
*/
package jalview.io;
-import jalview.api.AlignViewportI;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
/**
* Additional formatting methods used by the application in a number of places.
*/
public class FormatAdapter extends AppletFormatAdapter
{
- public FormatAdapter(AlignViewportI viewport)
+ public FormatAdapter(AlignmentViewPanel viewpanel)
{
- super(viewport);
+ super(viewpanel);
init();
}
init();
}
+ public FormatAdapter(AlignmentPanel alignPanel,
+ AlignExportSettingI settings)
+ {
+ super(alignPanel, settings);
+ }
+
private void init()
{
if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
return this.formatSequences(format, alignment, suffix);
}
- public Alignment readFile(String inFile, String type, String format)
+ public AlignmentI readFile(String inFile, String type, String format)
throws java.io.IOException
{
- Alignment al = super.readFile(inFile, type, format);
+ AlignmentI al = super.readFile(inFile, type, format);
return al;
}
public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
- Alignment al = (Alignment) super.readFromFile(source, format);
+ AlignmentI al = super.readFromFile(source, format);
return al;
}
}
/**
- * Create a flat file representation of a given view or selected region of a view
+ * Create a flat file representation of a given view or selected region of a
+ * view
+ *
* @param format
- * @param av
+ * @param ap
+ * alignment panel originating the view
* @return String containing flat file
*/
- public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+ public String formatSequences(String format, AlignmentViewPanel ap,
+ boolean selectedOnly)
{
- return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+ return formatSequences(format, getCacheSuffixDefault(format), ap,
+ selectedOnly);
}
--- /dev/null
+package jalview.io;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.List;
+
+/**
+ * A GFF3 File parsing wrapper for the tangled mess that is FeaturesFile.
+ *
+ * This class implements the methods relied on by FileLoader/FormatAdapter in
+ * order to allow them to load alignments directly from GFF2 and GFF3 files that
+ * contain sequence data and alignment information.
+ *
+ * Major issues:
+ *
+ * 1. GFF3 files commonly include mappings between DNA, RNA and Protein - so
+ * this class needs a dataset AlignmentI context to create alignment codon
+ * mappings.
+ *
+ * 2. A single GFF3 file can generate many distinct alignments. Support will be
+ * needed to allow several AlignmentI instances to be generated from a single
+ * file.
+ *
+ *
+ * @author jprocter
+ *
+ */
+public class Gff3File extends FeaturesFile
+{
+
+ /**
+ *
+ */
+ public Gff3File()
+ {
+ super();
+ }
+
+ /**
+ * @param source
+ * @throws IOException
+ */
+ public Gff3File(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public Gff3File(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * @param parseImmediately
+ * @param source
+ * @throws IOException
+ */
+ public Gff3File(boolean parseImmediately, FileParse source)
+ throws IOException
+ {
+ super(parseImmediately, source);
+ }
+
+ /**
+ * @param parseImmediately
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public Gff3File(boolean parseImmediately, String inFile, String type)
+ throws IOException
+ {
+ super(parseImmediately, inFile, type);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.FeaturesFile#print()
+ */
+ @Override
+ public String print()
+ {
+ // TODO GFF3 writer with sensible defaults for writing alignment data
+
+ // return super.printGFFFormat(seqs, visible);
+ return ("Not yet implemented.");
+ }
+
+ AlignmentI dataset;
+
+ List<AlignmentI> alignments;
+ @Override
+ public void parse()
+ {
+ AlignViewportI av = getViewport();
+ if (av != null)
+ {
+ if (av.getAlignment() != null)
+ {
+ dataset = av.getAlignment().getDataset();
+ }
+ if (dataset == null)
+ {
+ // working in the applet context ?
+ dataset = av.getAlignment();
+ }
+ }
+ else
+ {
+ dataset = new Alignment(new SequenceI[]
+ {});
+ }
+
+ boolean parseResult = parse(dataset, null, null, false, true);
+ if (!parseResult)
+ {
+ // pass error up somehow
+ }
+ if (av != null)
+ {
+ // update viewport with the dataset data ?
+ }
+ else
+ {
+ setSeqs(dataset.getSequencesArray());
+ }
+
+ }
+
+ @Override
+ public void addProperties(AlignmentI al)
+ {
+ super.addProperties(al);
+ if (dataset.getCodonFrames() != null)
+ {
+ AlignmentI ds = (al.getDataset() == null) ? al : al.getDataset();
+ for (AlignedCodonFrame codons : dataset.getCodonFrames())
+ {
+ ds.addCodonFrame(codons);
+ }
+ }
+ }
+}
package jalview.io;
import java.io.IOException;
+import java.io.StringReader;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
{
try
{
- StringBuilder htmlData = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null)
- {
- htmlData.append(currentLine);
+ Element content = null;
+ Document doc = null;
+ try {
+ StringBuilder htmlData = new StringBuilder();
+ String currentLine;
+ while ((currentLine = nextLine()) != null)
+ {
+ htmlData.append(currentLine);
+ }
+
+ doc = Jsoup.parse(htmlData.toString());
+ } catch (OutOfMemoryError oom) {
+ errormessage = "Not enough memory to process HTML document";
+ throw new IOException(errormessage);
}
-
- Document doc = Jsoup.parse(htmlData.toString());
- Element content = doc.getElementById("seqData");
- String alignmentJsonString = content.val();
-
- JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
+ content = doc.getElementById("seqData");
+
+ JSONFile jsonFile = new JSONFile().parse(new StringReader(content.val()));
this.seqs = jsonFile.getSeqs();
this.seqGroups = jsonFile.getSeqGroups();
this.annotations = jsonFile.getAnnotations();
this.columnSelection = jsonFile.getColumnSelection();
} catch (Exception e)
{
- e.printStackTrace();
+ errormessage = "Failed to extract data from HTML document.";
+ throw new IOException("Unexpected exception whilst extracting JSon from HTML.",e);
}
}
package jalview.io;
+import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
-import jalview.gui.AnnotationPanel;
-import jalview.gui.FeatureRenderer;
import jalview.gui.HTMLOptions;
import jalview.math.AlignmentDimension;
import jalview.util.MessageManager;
FeatureRenderer fr;
AlignmentPanel ap;
- AnnotationPanel annotationPanel;
public HtmlSvgOutput(File file, AlignmentPanel ap)
{
-
- this.av = ap.av;
- this.ap = ap;
- av.setFeatureRenderer(new FeatureRenderer(ap));
- this.annotationPanel = ap.getAnnotationPanel();
+ this.av = ap.av;
+ this.ap = ap;
+ fr = ap.cloneFeatureRenderer();
generateHtmlSvgOutput(file);
}
String titleSvgData = g1.getSVGDocument();
String alignSvgData = g2.getSVGDocument();
- String jsonData = JSONFile.getJSONData(av);
+ String jsonData = JSONFile.getJSONData(ap);
String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
out.write(htmlData.getBytes());
*/
public class IdentifyFile
{
+ public static final String GFF3File = "GFF v2 or v3";
+
/**
* Identify a datasource's file content.
*
}
data = data.toUpperCase();
- if ((data.indexOf("# STOCKHOLM") > -1))
+ if (data.startsWith("##GFF-VERSION"))
+ {
+ reply = GFF3File;
+ break;
+ }
+ if (data.indexOf("# STOCKHOLM") > -1)
{
reply = "STH";
break;
package jalview.io;
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-
-import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureRenderer;
import jalview.api.FeaturesDisplayedI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import java.awt.Color;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+
public class JSONFile extends AlignFile implements ComplexAlignFile
{
private ColourSchemeI colourScheme;
private FeatureRenderer fr;
- private JSONExportSettings jsonExportSettings;
-
private List<int[]> hiddenColumns;
private ColumnSelection columnSelection;
@Override
public void parse() throws IOException
{
- StringBuilder jsonStringBuilder = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null)
- {
- jsonStringBuilder.append(currentLine);
- }
- parse(jsonStringBuilder.toString());
+ parse(getReader());
}
-
@Override
public String print()
{
String jsonOutput = null;
try
{
- if (getJsonExportSettings() == null)
- {
- jsonExportSettings = new JSONExportSettings();
- jsonExportSettings.setExportAnnotations(true);
- jsonExportSettings.setExportGroups(true);
- jsonExportSettings.setExportJalviewSettings(true);
- jsonExportSettings.setExportSequenceFeatures(true);
- }
-
AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
- if (getViewport() != null)
- {
- globalColorScheme = ColourSchemeProperty
- .getColourName(getViewport()
- .getGlobalColourScheme());
- setDisplayedFeatures(getViewport().getFeaturesDisplayed());
- showSeqFeatures = getViewport().isShowSequenceFeatures();
- fr = getViewport().getFeatureRenderer();
- }
int count = 0;
for (SequenceI seq : seqs)
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
- if (jsonExportSettings.isExportJalviewSettings())
+ jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+ jsonAlignmentPojo.getAppSettings().put("application", application);
+ jsonAlignmentPojo.getAppSettings().put("version", version);
+ jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
+ jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
+ String.valueOf(showSeqFeatures));
+
+ String[] hiddenSections = getHiddenSections();
+ if (hiddenSections != null)
{
- jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
- jsonAlignmentPojo.getAppSettings().put("application", application);
- jsonAlignmentPojo.getAppSettings().put("version", version);
- jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
- jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
- String.valueOf(showSeqFeatures));
-
- String[] hiddenSections = exportHiddenSections();
- if (hiddenSections != null && getViewport().isIncludeHiddenRegion())
+ if (hiddenSections[0] != null
+ && getExportSettings()
+ .isExportHiddenColumns())
{
- if (hiddenSections[0] != null)
- {
- jsonAlignmentPojo.getAppSettings().put("hiddenCols",
- String.valueOf(hiddenSections[0]));
- }
- if (hiddenSections[1] != null)
- {
- jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
- String.valueOf(hiddenSections[1]));
- }
+ jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+ String.valueOf(hiddenSections[0]));
+ }
+ if (hiddenSections[1] != null
+ && getExportSettings()
+ .isExportHiddenSequences())
+ {
+ jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+ String.valueOf(hiddenSections[1]));
}
}
- if (jsonExportSettings.isExportAnnotations())
+ if (getExportSettings().isExportAnnotations())
{
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
- if (jsonExportSettings.isExportSequenceFeatures())
+ if (getExportSettings().isExportFeatures())
{
jsonAlignmentPojo
.setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
}
- if (jsonExportSettings.isExportGroups() && seqGroups != null
+ if (getExportSettings().isExportGroups()
+ && seqGroups != null
&& seqGroups.size() > 0)
{
for (SequenceGroup seqGrp : seqGroups)
return jsonOutput;
}
- public String[] exportHiddenSections()
+ public String[] getHiddenSections()
{
String[] hiddenSections = new String[2];
if (getViewport() == null)
}
@SuppressWarnings("unchecked")
- public JSONFile parse(String jsonAlignmentString)
+ public JSONFile parse(Reader jsonAlignmentString)
{
try
{
this.displayedFeatures = displayedFeatures;
}
- public JSONExportSettings getJsonExportSettings()
- {
- return jsonExportSettings;
- }
-
- public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
+ @Override
+ public void configureForView(AlignmentViewPanel avpanel)
{
- this.jsonExportSettings = jsonExportSettings;
- }
-
+ super.configureForView(avpanel);
+ if (isExporting())
+ {
+ setViewport(avpanel.getAlignViewport());
+ seqGroups = avpanel.getAlignment().getGroups();
+ setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+ fr = avpanel.cloneFeatureRenderer();
- public static String getJSONData(AlignViewportI av)
- {
- JSONFile jsonFile = new JSONFile();
- jsonFile.setViewport(av);
- jsonFile.seqGroups = av.getAlignment().getGroups();
- jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
+ for (SequenceI seq : getViewport().getAlignment().getSequences())
+ {
+ seqs.add(seq);
+ }
- for (SequenceI seq : av.getAlignment().getSequences())
- {
- jsonFile.seqs.add(seq);
- }
-
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : av.getAlignment()
- .getAlignmentAnnotation())
- {
- if (annot != null && !annot.autoCalculated)
+ // Add non auto calculated annotation to AlignFile
+ for (AlignmentAnnotation annot : getViewport().getAlignment()
+ .getAlignmentAnnotation())
{
- if (annot.label.equals("PDB.CATempFactor"))
+ if (annot != null && !annot.autoCalculated)
{
- continue;
+ if (annot.label.equals("PDB.CATempFactor"))
+ {
+ continue;
+ }
+ annotations.add(annot);
}
- jsonFile.annotations.add(annot);
}
+
+ globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
+ .getGlobalColourScheme());
+ setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+ showSeqFeatures = getViewport().isShowSequenceFeatures();
}
+ }
+
+
+ public static String getJSONData(AlignmentViewPanel av)
+ {
+ JSONFile jsonFile = new JSONFile();
+ jsonFile.configureForView(av);
String jsonString = jsonFile.print();
return jsonString;
}
*/
package jalview.io;
-import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
seqs.add(sequenceElements[i]);
}
- // create an alignment based on the sequences
- Alignment a = new Alignment(sequenceElements);
- // add annotations - although comments say addAnnotations
- // is used by AppletFormatAdapter, it doesn't say other
- // classes should/can not use it
- addAnnotations(a);
-
} catch (IOException e)
{
System.err.println("Exception parsing PHYLIP file " + e);
--- /dev/null
+package jalview.jbgui;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JPanel;
+
+@SuppressWarnings("serial")
+public abstract class GAlignExportSettings extends JPanel
+{
+ protected JPanel hiddenRegionConfPanel = new JPanel();
+
+ protected JPanel complexExportPanel = new JPanel();
+
+ protected JPanel optionsPanel = new JPanel();
+
+ protected JPanel actionPanel = new JPanel();
+
+ protected BorderLayout hiddenRegionLayout = new BorderLayout();
+
+ protected BorderLayout complexExportLayout = new BorderLayout();
+
+ protected BorderLayout mainLayout = new BorderLayout();
+
+ protected JCheckBox chkAll = new JCheckBox("Check All");
+
+ protected JCheckBox chkHiddenSeqs = new JCheckBox(
+ "Export Hidden Sequences");
+
+ protected JCheckBox chkHiddenCols = new JCheckBox("Export Hidden Columns");
+
+ protected JCheckBox chkExportAnnots = new JCheckBox("Export Annotations");
+
+ protected JCheckBox chkExportFeats = new JCheckBox("Export Features");
+
+ protected JCheckBox chkExportGrps = new JCheckBox("Export Groups");
+
+ JButton btnOk = new JButton("Ok");
+
+ JButton btnCancel = new JButton("Cancel");
+
+ private boolean hasHiddenSeq, hasHiddenCols, isComplexAlignFile;
+
+ boolean isComplexFormat = false;
+
+ public GAlignExportSettings(boolean hasHiddenSeq, boolean hasHiddenCols,
+ String alignFileFormat)
+ {
+ this.hasHiddenSeq = hasHiddenSeq;
+ this.hasHiddenCols = hasHiddenCols;
+ String[] complexFormats =
+ { "JSON", "HTML" };
+
+ for (String format : complexFormats)
+ {
+ if (format.equalsIgnoreCase(alignFileFormat))
+ {
+ this.isComplexAlignFile = true;
+ break;
+ }
+ }
+
+ init();
+ }
+
+ public void init()
+ {
+ hiddenRegionConfPanel.setLayout(hiddenRegionLayout);
+ complexExportPanel.setLayout(complexExportLayout);
+ setLayout(mainLayout);
+
+ chkAll.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ checkAllAction();
+ }
+ });
+
+ btnOk.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+
+ btnCancel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+
+ hiddenRegionConfPanel.add(chkAll, BorderLayout.NORTH);
+ hiddenRegionConfPanel.add(chkHiddenSeqs, BorderLayout.CENTER);
+ hiddenRegionConfPanel.add(chkHiddenCols, BorderLayout.SOUTH);
+ chkHiddenSeqs.setEnabled(hasHiddenSeq);
+ chkHiddenCols.setEnabled(hasHiddenCols);
+
+ complexExportPanel.add(chkExportAnnots, BorderLayout.NORTH);
+ complexExportPanel.add(chkExportFeats, BorderLayout.CENTER);
+ complexExportPanel.add(chkExportGrps, BorderLayout.SOUTH);
+
+ if (hasHiddenSeq || hasHiddenCols)
+ {
+ optionsPanel.add(hiddenRegionConfPanel);
+ }
+
+ if (isComplexAlignFile)
+ {
+ optionsPanel.add(complexExportPanel);
+ }
+ actionPanel.add(btnCancel);
+ actionPanel.add(btnOk);
+
+ add(optionsPanel, BorderLayout.NORTH);
+ add(actionPanel, BorderLayout.SOUTH);
+
+ }
+
+
+
+ private void checkAllAction()
+ {
+ boolean isSelected = chkAll.isSelected();
+ chkHiddenSeqs.setSelected(chkHiddenSeqs.isEnabled() && isSelected);
+ chkHiddenCols.setSelected(chkHiddenCols.isEnabled() && isSelected);
+ chkExportAnnots.setSelected(isComplexAlignFile
+ && chkExportAnnots.isEnabled() && isSelected);
+ chkExportFeats.setSelected(isComplexAlignFile
+ && chkExportFeats.isEnabled() && isSelected);
+ chkExportGrps.setSelected(isComplexAlignFile
+ && chkExportGrps.isEnabled() && isSelected);
+ }
+
+ public abstract void ok_actionPerformed(ActionEvent e);
+
+ public abstract void cancel_actionPerformed(ActionEvent e);
+}
*/
package jalview.jbgui;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.io.FormatAdapter;
import jalview.util.MessageManager;
public void run()
{
String str = textfield.getText();
- Alignment al = null;
+ AlignmentI al = null;
try
{
al = new FormatAdapter().readFile(str, "Paste", "FASTA");
*/
package jalview.viewmodel;
-import java.awt.Color;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
+import java.awt.Color;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
// hasHiddenColumns = colSel.hasHiddenColumns();
}
- protected boolean hasHiddenRows = false;
-
@Override
public boolean hasHiddenRows()
{
- return hasHiddenRows;
+ return alignment.getHiddenSequences().getSize() > 0;
}
- public void setHasHiddenRows(boolean hasHiddenRows)
- {
- this.hasHiddenRows = hasHiddenRows;
- }
protected SequenceGroup selectionGroup;
setSequenceAnnotationsVisible(seq, true);
}
- hasHiddenRows = false;
hiddenRepSequences = null;
firePropertyChange("alignment", null, alignment.getSequences());
selectionGroup.addSequence(seq, false);
setSequenceAnnotationsVisible(seq, true);
}
- // JBPNote: refactor: only update flag if we modified visiblity (used to
- // do this regardless)
- if (alignment.getHiddenSequences().getSize() < 1)
- {
- hasHiddenRows = false;
- }
firePropertyChange("alignment", null, alignment.getSequences());
sendSelection();
}
alignment.getHiddenSequences().hideSequence(seq[i]);
setSequenceAnnotationsVisible(seq[i], false);
}
- hasHiddenRows = true;
firePropertyChange("alignment", null, alignment.getSequences());
}
}
import jalview.api.FeatureSettingsModelI;
-public class FeatureSettingsModel implements FeatureSettingsModelI
+public abstract class FeatureSettingsModel implements FeatureSettingsModelI
{
}
if (af != null && af.featureSettings != null)
{
- af.featureSettings.setTableData();
+ af.featureSettings.discoverAllFeatureData();
}
if (getFeatSettings() != null)
*/
package jalview.ws.dbsources;
-import java.io.File;
-import java.io.FileReader;
-import java.io.Reader;
-import java.util.Vector;
-
-import org.exolab.castor.xml.Unmarshaller;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
+import java.io.File;
+import java.io.FileReader;
+import java.io.Reader;
+import java.util.Vector;
+
+import org.exolab.castor.xml.Unmarshaller;
+
+import com.stevesoft.pat.Regex;
+
/**
* @author JimP
*
{
queries = queries.toUpperCase().replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
- Alignment al = null;
+ AlignmentI al = null;
EBIFetchClient ebi = new EBIFetchClient();
// uniprotxml parameter required since december 2007
// uniprotkb dbname changed introduced december 2008
* @param entries
* a list of n uniprot entries to be analysed.
*/
- public void addUniprotXrefs(Alignment al, Vector<UniprotEntry> entries)
+ public void addUniprotXrefs(AlignmentI al, Vector<UniprotEntry> entries)
{
final String dbVersion = getDbVersion();
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
{
return null;
}
- Alignment al = null;
+ AlignmentI al = null;
ColumnSelection alcsel = null;
int FirstSeq = -1; // the position of the query sequence in Alignment al
* @param al
* @param profileseq
*/
- private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+ private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
{
char gc = al.getGapCharacter();
int[] gapMap = profileseq.gapMap();
*/
package jalview.ws.seqfetcher;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
* @return null or a valid alignment
* @throws Exception
*/
- protected Alignment parseResult(String result) throws Exception
+ protected AlignmentI parseResult(String result) throws Exception
{
- Alignment sequences = null;
+ AlignmentI sequences = null;
String format = new IdentifyFile().Identify(result, "Paste");
if (FormatAdapter.isValidFormat(format))
{
*/
package jalview.analysis;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
*/
protected AlignmentI loadAlignment(final String data, String format) throws IOException
{
- Alignment a = new FormatAdapter().readFile(data,
+ AlignmentI a = new FormatAdapter().readFile(data,
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
protected AlignmentI loadAlignment(final String data, String format)
throws IOException
{
- Alignment a = new FormatAdapter().readFile(data,
+ AlignmentI a = new FormatAdapter().readFile(data,
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
--- /dev/null
+package jalview.datamodel;
+
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class SequenceDummyTest
+{
+ /**
+ * test for become method
+ */
+ @Test
+ public void testBecome()
+ {
+ SequenceI seq = new Sequence("OrigSeq", "ASEQUENCE");
+ SequenceFeature ofeat = new SequenceFeature("NewFeat", "somedesc", 3,
+ 12, 2.3f, "none");
+
+ SequenceDummy dummySeq = new SequenceDummy("OrigSeq");
+ dummySeq.addSequenceFeature(ofeat);
+ dummySeq.become(seq);
+ Assert.assertFalse("Dummy sequence did not become a full sequence",
+ dummySeq.isDummy());
+ Assert.assertTrue("Sequence was not updated from template", seq
+ .getSequenceAsString().equals(dummySeq.getSequenceAsString()));
+ boolean found = false;
+ for (SequenceFeature sf : dummySeq.getSequenceFeatures())
+ {
+ if (sf == ofeat)
+ {
+ found = true;
+ break;
+ }
+ }
+ Assert.assertTrue("Didn't retain original sequence feature", found);
+
+ // todo - should test all aspect of copy constructor
+ }
+}
--- /dev/null
+package jalview.io;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+
+import java.io.IOException;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class Gff3tests
+{
+
+ private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
+ exonerateOutput = "examples/testdata/exonerateoutput.gff",
+ simpleGff3file = "examples/testdata/simpleGff3.gff";
+
+ @Test
+ public void testExonerateImport()
+ {
+ // exonerate does not tag sequences after features, so we have a more
+ // conventional annotation import test here
+
+ FileLoader loader = new FileLoader(false);
+
+ AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
+ FormatAdapter.FILE);
+
+ Assert.assertEquals("Unexpected number of DNA protein associations", 0,
+ af.getViewport().getAlignment().getCodonFrames().size());
+
+ af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
+
+ Assert.assertNotEquals("Expected at least one DNA protein association",
+ 0, af.getViewport().getAlignment().getDataset()
+ .getCodonFrames().size());
+
+ }
+
+ @Test
+ public void simpleGff3FileIdentify()
+ {
+ Assert.assertEquals("Didn't recognise file correctly.",
+ IdentifyFile.GFF3File,
+ new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
+ }
+
+ @Test
+ public void simpleGff3FileClass() throws IOException
+ {
+ AlignmentI dataset = new Alignment(new SequenceI[]
+ {});
+ FeaturesFile ffile = new FeaturesFile(simpleGff3file,
+ FormatAdapter.FILE);
+
+ boolean parseResult = ffile.parse(dataset, null, null, false, false);
+ Assert.assertTrue("return result should be true", parseResult);
+ checkDatasetfromSimpleGff3(dataset);
+ }
+
+ @Test
+ public void simpleGff3FileLoader() throws IOException
+ {
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ simpleGff3file, FormatAdapter.FILE);
+ Assert.assertTrue(
+ "Didn't read the alignment into an alignframe from Gff3 File",
+ af != null);
+ checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
+ }
+
+ @Test
+ public void simpleGff3RelaxedIdMatching() throws IOException
+ {
+ AlignmentI dataset = new Alignment(new SequenceI[]
+ {});
+ FeaturesFile ffile = new FeaturesFile(simpleGff3file,
+ FormatAdapter.FILE);
+
+ boolean parseResult = ffile.parse(dataset, null, null, false, true);
+ Assert.assertTrue("return result (relaxedID matching) should be true",
+ parseResult);
+ checkDatasetfromSimpleGff3(dataset);
+ }
+
+ @Test
+ public void readGff3File() throws IOException
+ {
+ Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
+ Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
+ gff3reader.addProperties(dataset);
+ checkDatasetfromSimpleGff3(dataset);
+
+ }
+
+ private void checkDatasetfromSimpleGff3(AlignmentI dataset)
+ {
+ Assert.assertEquals("no sequences extracted from GFF3 file", 2,
+ dataset.getHeight());
+
+ SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
+ .findName("seq2");
+ Assert.assertNotNull(seq1);
+ Assert.assertNotNull(seq2);
+ Assert.assertFalse(
+ "Failed to replace dummy seq1 with real sequence",
+ seq1 instanceof SequenceDummy
+ && ((SequenceDummy) seq1).isDummy());
+ Assert.assertFalse(
+ "Failed to replace dummy seq2 with real sequence",
+ seq2 instanceof SequenceDummy
+ && ((SequenceDummy) seq2).isDummy());
+ String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
+ Assert.assertFalse("dummy replacement buggy for seq1",
+ placeholderseq.equals(seq1.getSequenceAsString()));
+ Assert.assertNotEquals("dummy replacement buggy for seq2",
+ placeholderseq.equals(seq2.getSequenceAsString()));
+ Assert.assertNotNull("No features added to seq1",
+ seq1.getSequenceFeatures());// != null);
+ Assert.assertEquals("Wrong number of features", 3,
+ seq1.getSequenceFeatures().length);
+ Assert.assertNull(seq2.getSequenceFeatures());
+ Assert.assertEquals("Wrong number of features", 0, seq2
+ .getSequenceFeatures() == null ? 0
+ : seq2.getSequenceFeatures().length);
+ Assert.assertTrue(
+ "Expected at least one CDNA/Protein mapping for seq1",
+ dataset.getCodonFrame(seq1) != null
+ && dataset.getCodonFrame(seq1).size() > 0);
+
+ }
+ // @Test
+ // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
+ // {
+ // fail("Not yet implemented");
+ // }
+ //
+ // @Test
+ // public final void testAlignFileBooleanStringString()
+ // {
+ // fail("Not yet implemented");
+ // }
+
+}
import static org.testng.AssertJUnit.assertNotNull;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
{
String jsonFile = "examples/example.json";
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = null;
+ AlignmentI al = null;
try
{
al = rf.readFile(jsonFile, AppletFormatAdapter.FILE,
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import java.io.IOException;
private void testDataExtraction(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
PhylipFile.FILE_DESC);
assertNotNull("Couldn't read supplied alignment data.", al);
public void testIO(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
PhylipFile.FILE_DESC);
assertNotNull("Couldn't read supplied alignment data.", al);
String outputfile = rf.formatSequences(PhylipFile.FILE_DESC, al, true);
- Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+ AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
public void testRnamlToStockholmIO()
{
StockholmFileTest.testFileIOwithFormat(new File(
- "examples/rna-alignment.xml"), "STH", -1, -1);
+ "examples/testdata/rna-alignment.xml"), "STH", -1, -1);
}
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
assertNotNull("Couldn't read supplied alignment data.", al);
System.out.println("Output file in '" + ioformat + "':\n"
+ outputfile + "\n<<EOF\n");
// test for consistency in io
- Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+ AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
AppletFormatAdapter.PASTE, ioformat);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
an_new.displayCharacter.trim())
|| !("" + an_or.secondaryStructure).trim().equals(
("" + an_new.secondaryStructure).trim())
- || (an_or.description != an_new.description && (an_or.description == null
- || an_new.description == null || !an_or.description
- .equals(an_new.description))))
+ || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
+ .trim().length() == 0)
+ || (an_new.description == null && an_or.description
+ .trim().length() == 0) || an_or.description
+ .trim().equals(an_new.description.trim()))))
{
System.err.println("Annotation Element Mismatch\nElement " + i
+ " in original: " + annot_or.annotations[i].toString()
package jalview.util;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
protected AlignmentI loadAlignment(final String data, String format)
throws IOException
{
- Alignment a = new FormatAdapter().readFile(data,
+ AlignmentI a = new FormatAdapter().readFile(data,
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-import java.io.*;
-import java.util.*;
+import java.io.DataInputStream;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
versions.put("48.0", "1.4");
versions.put("49.0", "1.5");
versions.put("50.0", "1.6");
+ versions.put("51.0", "1.7");
+ versions.put("52.0", "1.8");
+
}
String version = (String) versions.get(major + "."
+ minor);
version = (String) versions.get(major + ".0");
}
// System.err.println("Version "+version);
+ if (version == null)
+ {
+ versions.put(major + "." + minor, "Class v" + major + ".0");
+ }
return version;
}
git://source.jalview.org / jalview.git / commitdiff