From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 10 Aug 2023 20:41:45 +0000 (+0100)
Subject: JAL-629 more tests for stdout
X-Git-Tag: Release_2_11_4_0~198^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ec4fa6981b66e78bfb467ad8bf65a56eec85f6ea;p=jalview.git

JAL-629 more tests for stdout
---

diff --git a/test/jalview/bin/CommandLineOperationsNG.java b/test/jalview/bin/CommandLineOperationsNG.java
index bbd498b..ef2f78a 100644
--- a/test/jalview/bin/CommandLineOperationsNG.java
+++ b/test/jalview/bin/CommandLineOperationsNG.java
@@ -511,6 +511,10 @@ public class CommandLineOperationsNG
             workingDir + "/uniref50-output.fa", TEST_TIMEOUT },
         { "--open examples/uniref50.fa --output -",
             workingDir + "/uniref50-output.fa", TEST_TIMEOUT },
+        { "--open examples/uniref50.fa --output=[format=blc]-",
+            workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
+        { "--open examples/uniref50.fa --output - --format blc",
+            workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
         //
     };
   }
diff --git a/test/jalview/bin/uniref50-output.blc b/test/jalview/bin/uniref50-output.blc
new file mode 100644
index 0000000..3614ef8
--- /dev/null
+++ b/test/jalview/bin/uniref50-output.blc
@@ -0,0 +1,174 @@
+>FER_CAPAA/1-97 Ferredoxin
+>FER_CAPAN/1-144 Ferredoxin, chloroplast precursor
+>FER1_SOLLC/1-144 Ferredoxin-1, chloroplast precursor
+>Q93XJ9_SOLTU/1-144 Ferredoxin I precursor
+>FER1_PEA/1-149 Ferredoxin-1, chloroplast precursor
+>Q7XA98_TRIPR/1-152 Ferredoxin I
+>FER1_MESCR/1-148 Ferredoxin-1, chloroplast precursor
+>FER1_SPIOL/1-147 Ferredoxin-1, chloroplast precursor
+>FER3_RAPSA/1-96 Ferredoxin, leaf L-A
+>FER2_ARATH/1-148 Ferredoxin-2, chloroplast precursor
+>FER_BRANA/1-96 Ferredoxin
+>FER1_ARATH/1-148 Ferredoxin-1, chloroplast precursor
+>Q93Z60_ARATH/1-118 At1g10960/T19D16_12
+>FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor
+>O80429_MAIZE/1-140 Ferredoxin
+* iteration 1
+-MMMMMMM-M-MMMM
+-AAAAAAA-A-AAAA
+----TTAA-S-SSTA
+----TTTT-T-TTVT
+-------------L-
+-------------G-
+------TT-----S-
+----PPAT-----P-
+-SSSAAAT-A-AAR-
+-VIILLLM-L-LLA-
+-SSSYYSM-S-SSP-
+-AGGGGGG-S-SSA-
+-TTTTTA--A-AAF-
+-MMMAAT--I-IIFA
+-IIIVVMM-V-VVFL
+-SSSSSSA-G-SSSS
+-TTTTTTT-T-TTSM
+-SSSSSAT-S-SSSS
+-FFFFFFF-F-FFSI
+-MLLLMAV-I-LLLL
+-PPPRRPP-R-RRRR
+-RRRTRKK-R-RRA-
+-KKKQQ-P-S-QQA-
+-PPPPP-Q-P-QQP-
+-AAVMVTA-A-TTAA
+-VVVPPPP-P-PPPP
+-TTTMMPP-I-IITP
+-SSSSSMM-S-SSAP
+-LLLVVTM-L-LLVC
+------AA-R-RR-F
+-KKKTAAA-S-SS-S
+-PAATTLL-L-LLAS
+-IIITTPP-P-PPLP
+-PSSKTTS-S-FFPL
+-NNNATNN-A-AAAR
+-VVVFTVT-N-NNAL
+-GGGSKGG-T-TTKR
+-EEENARR-Q-QQVV
+-----F---------
+-----P---------
+-AAAGSAS-S-SSGA
+-LLLFGLL-L-LLIV
+-FFFLFFF-F-FFMA
+-GGGGGGG-G-GGGK
+-LLLLLLL-L-LLRP
+-KKKKKKK-K-KKSL
+-SSSTSST-S-SSAA
+-----V---------
+-AGGSSSG-G-SSSA
+----LTAS-T-TTSP
+----KKSR-A-AARM
+-NRRRRR--R-RRRR
+-GNNGG---G-GG-R
+-GGGDDGG-G-GG-Q
+-KRRLLRG-R-RRRL
+-VIIAAVR-V-VVLL
+-TTTVVTM-T-TTRR
+-CCCAAAT-A-AAAA
+-MMMMMMM-M-MMQQ
+AAAAAAAAAAAAAAA
+SSSSSTAATTTTTTT
+YYYYYYYYYYYYYYY
+KKKKKKKKKKKKKNN
+VVVVVVVVVVVVVVV
+KKKKKKTTKKKKKKK
+LLLLLLLLFFFFFLL
+IIIIVIVVIIIIIII
+TTTTTTTTTTTTTTT
+PPPPPPPPPPPPPPP
+DDEDDEETEEEEEEE
+GGGGGGGGGGGGGGG
+PPPPTPKNEEEEEEE
+IIIIQQQVQLQQQVV
+EEEEEEEEEEEEEEE
+FFFFFFLFVVVVVLL
+DDEEEDEQEEEEEQQ
+CCCCCCCCCCCCCVV
+PPPPPPPPDDDEEPP
+DDDDSDDDDDDEEDD
+DNDDDDDDDDDDDDD
+VVVVVVVVVVVVVVV
+YYYYYYYYYYYYYYY
+IIIIIIIIVVVVVII
+LLLLLLLLLLLLLLL
+DDDDDDDDDDDDDDD
+QQQQHHAAAAAAAQF
+AAAAAAAAAAAAAAA
+EEEEEEEEEEEEEEE
+EEEEEEEEEEEEEEE
+AAEEVVAEAAAAADE
+GGGGGGGGGGGGGGG
+HHHHIIIIIIILLII
+DDDDDEDDDDDDDDD
+LLLLLLLLLLLLLLL
+PPPPPPPPPPPPPPP
+YYYYYYYYYYYYYYF
+SSSSSSSSSSSSSSS
+CCCCCCCCCCCCCCC
+RRRRRRRRRRRRRRR
+AAAAAAAAAAAAAAA
+GGGGGGGGGGGGGGG
+SSSSSSSSSSSSSSS
+CCCCCCCCCCCCCCC
+SSSSSSSSSSSSSSS
+SSSSSSSSSSSSSSS
+CCCCCCCCCCCCCCC
+AAAAAAAAAAAAAAA
+GGGGGGGGGGGGGGG
+KKKKKKKKKKKKKKK
+IIVVVVVLVVVVVVV
+AATTVVTKVVVVVVV
+GGAAGNSTSSSSSSS
+GGGGGGGGGGGGGGG
+AASTENSSSSFSSSS
+VVVVVVVLVVVIIVV
+DDDDDNNNDDDDDDD
+QQQQQQQQQQQQQQQ
+TTSSSEDDSSSSSSS
+DDDDDDDDDDDDDDD
+GGGGGGGQQQEQQQQ
+NNNKSSSSSSSSSSS
+FFFFFFFFFFFFFYF
+LLLLLLLLLLLLLLL
+DDDDDDDDDDDDDDN
+DDEDDDDDDDDDDDD
+DDDDEEDDDEDE-GN
+QQQQQQQQQQQQ-QQ
+LLEEIIIIIIIM-IV
+EEAAEEKDAGAS-AA
+EEAAAGEEEEEE-DD
+GGGGGGGGGGGG-GG
+WWFFFWWWFFFY-WW
+VVVVVVVVVVVV-VV
+LLLLLLLLLLLL-LL
+TTTTTTTTTTTT-TT
+CCCCCCCCCCCC-CC
+VVVVVVVAAAAV-HA
+AAAAAAAAAAAA-AA
+YYYYYFYYYYYY-YY
+PPPPPPPPPPPP-PP
+QQKKTTTVTTTT-TT
+SSGCSSGSSSSS-SS
+DDDDDDDDDDDD-DD
+VVVVVVVVVVVV-VV
+TTTTVTTTTTTV-VV
+IIIIIIIIIIII-II
+EEEEEEEEEEEE-EE
+TTTTTTTTTTTT-TT
+HHHHHHHHHHHH-HH
+KKKKKKKKRKKK-KK
+EEEEEEEEEEEE-EE
+AAEEEEEEEEEE-ED
+EEEEDEEEDDEA-ED
+LLLLLLLLMILI-LL
+VVTTTTTTVVVM-TL
+GGAAAAAA-----G-
+-------------A-
+*