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Upversion to 0.8.4
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- Phylogeny import NEXUS trees #59: Closing w/limited support (not BEAST
or MrBayes rate/branch annotations or TRANSLATE block, most other)
- Phylogeny stats scrollpane/jtable UI, export phylogeny stats #58:
closing.
- Test data etc should be in the right places.
- Version string -> 0.8.4 prerelease
- UI (menu+hotkey) improvements to support the above.
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lonelyjoeparker committed Jul 10, 2017
1 parent 1a3f5c3 commit 7966948
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21 changes: 21 additions & 0 deletions junit-test-inputs/quick.phy
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BOS____001 MDHAEENEILGATKRYYVERPIFSHPVLQERLHKKDKVSDSIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFFGTSRHVSIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLHESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPAFIMGARRKAMRKYAKEVGNANMANATVVK--VDAEVDGEDGTKPEEDENEIKYPP-I--VIKSTLPEELQRFMPPGDNIHTIILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTRNRFFENPALLELLFHSIHDAVLGSQAREALAEQEGSAVPP-
CANIS__002 MDHAEENEILTASQRYYVERPIFSHPVLQERLHKKDKISDSIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFLGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLKESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPAVIMGARRKAMKEYAKEVGNANVANATVVK--VDAEVDGEDATKPEQEDDEVKYPP-I--VIKSTFPEELQRFMPPGDTIHTVILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTQNRFFENPALKELLFHSIHDAVLGSQLREALAEQEASALPP-
DASYPUS003 MDHAEENEILAATQKYYVERPIFSHPVL-ERLHRR-HVSD-IGDKLKRAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFFGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLKESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXVKEIPGIKIFQINAPIYYANSDLYSNALKRK-------------------------------------TDGEVDGEDNTKPEEDDDEVKYPP-V--VTKSTFPEELQRFMPPGDNVHTVILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTRNRFFENPALLELLFHSIHDAVLGSQVRETLAEQEASGLPPQ
EQUUS__004 MDHAEENEILAATQRYSVDRPIFSHPVLQERLHKKDKVPDSIGDKLKQAFICTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTRVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFLGTSRHISIGPFAVISLMIGAVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLQESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGQLPDTDVYIDIDAFEEVKEIPGIKIFQINAPIYYANSDLYSSALKRKTGVNPAHIMGARRKAMRKYAKEVGNANMANATVVK--VDAAVDGEDGTKPEEEEDEIKFPP-V--VTKSTFPEELQRFMPPGDNIHTIILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTQNRFFENPALKKLLFHSIHDAVLGSQVREALAEQEASAPPP-
ERINACE005 ---------------------------------------------------CTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFFGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLKESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-PSYKVLGQLPETDVYIDTDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKXXXXXXXXXXXXXXXXXXXXXX-GNANMANATVVKVVIDAEVDGEDGTKPEEEENEVKYPP-I--VIKNTFPEEIQRFMPPGDNIHTVILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTRNRFFENPALLELLFHSIHDAVLGSQLREALAEQ-ASAPPPQ
FELIS__006 MDHAEENEILAASQRYYVERPIFSHLVLQERLHKKDKISDSIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFFGTSRHVSIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLQESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPALIMGARRKAMKKYAKEVGNANMANATAVK--VDAEVDGEDATKPEEEDDEVKYPP-I--VIKSTFPEEMQRFMPPGDNIHTIILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTQNRFFENPALKELLFYSIHDAVLGSQLREALAEQEATAAPP-
HOMO___007 MDHAEENEILAATQRYYVERPIFSHPVLQERLHTKDKVPDSIADKLKQAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPIFGLYSSFYPVIMYCFLGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLKESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGKLPETDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPAVIMGARRKAMRKYAKEVGNANMANATVVK--ADAEVDGEDATKPEEEDGEVKYPP-I--VIKSTFPEEMQRFMPPGDNVHTVILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTRNRFFENPALWELLFHSIHDAVLGSQLREALAEQEASAPPS-
LOXODON008 MDHAEENEILVATQKYCVERPIFSHPVLQERLHKKDKISDSIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFATLAAVPPVFGLYSSFYPVIMYCFFGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTELCLRALTRMSN-NAMTDLRVSVQGLFLDITSSV-HVLQSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLKDSYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLAIKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGM-MQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPALIMSVRRKAMRKYAKEVGNANMANATVVK--VGAEVDGEDGTKPEEENNEMKYPP-I--VIKSTFPEELQRFMPPGDNVHTVILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLSRNRFFENPALKDLLFHSIHDAVLGSQAREALAEQEASALPPQ
MEGADER009 MDHAEETEILAATQKYYVERPIFSHSVLQERLHKKDKISDSIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYNFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFFGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFSLHESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILMVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALMTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGVKIFQINAPIYYANSDLYSSALKRKTGVNPTLIMGARRKAMKKYAKEVGNANMVNATVVK--ADAEVDGGDGTKPEEEDDEIKFPP-I--VTKSTFPEELQRFMPPGDNIHTVILDFTQVNFIDSVGVKTLSGIVKEYGDVGIYVYLAGCSPQVVNDLTQNQFFENPALLELLFHSIHDAVLGSQVREALAEQEALAPPP-
MONODEL010 MDHTQENEILIATQTYCVERPIYSYPALHGKLHKKDKVSDPIGDKIKRALSCTPKKIRNIIYMFLPICKWLPAYKPREYVFGDFVSGISTGVLHLPQGLAFAMLAAVPPVFGLYSSFYPVILYCFFGTSRHVSIGPFAVISLMIGGVAVRLVPDDMYVGGGGANSTNGTEERDAMRVKVAMSVTLLSGIIQFCLGVLRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRHSGPFSVVYSTLAVIANVKKLNICSLVVGLMCFALLLGGKEFNERFKNKLPAPIPLEIVAVIIGTGISAGFNLEESYKVDVVGSLPLGLLAPATPDSSLFHLVYVDAIAIAIVGFSVTISMAKIFAVKHGYQVDGNQELIALGICNSIGSLFQTFSISCSLSRSLVQESTGGNTQLAGCLASLLILLVILAIGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALMTVIYRTQSPTYTVLGQLPNTDVYIDIDAYEEVKEHAGIKIFQINAPIYYANSDLYNNALRRKTGVNPALIMAARRKALKKHAKELGTQGKPKSSVVK--VDAETGGEEEAKQEEQNEENAKPMTIDSLVQKTFPAELERFLPPGPNVHTMILDFSQVNFIDSVGVKTVSGILKEYGDVGIYVYLAACSAQVVNDLTRNRFFENPCVKELLFHSIHDAVLGAKVREALAQQEALAPPP-
MUS____011 MDHAEENEIPAETQRYYVERPIFSHPVLQERLHVKDKVTESIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFFGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLHESYSVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGICNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSSALKRKTGVNPALIMGARRKAMRKYAKEVGNANVANATVVK--VDAEVDGENATKPEEEDDEVKFPP-I--VIKTTFPEELQRFLPQGENVHTVILDFTQVNFVDSVGVKTLAGIVKEYGDVGIYVYLAGCSPQVVNDLTRNNFFENPALKELLFHSIHDAVLGSQVREAMAEQEATASLP-
MYOTIS_012 MDHAEETEILAAAQKYYVDRPIFSHLALQEILHTKDKIPDSIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFFGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLAGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFSLHESYNVDVVGSLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLGNKHGYQVDGNQELIALGLCNSIGSLFQTFAISCSLSRSLVQEGTGGKTQLAGCLASLMILMVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALMTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSSALKRKTGVNPAFIMGARRKAMKKYAKEVGNANLANATIIK--ADGEVDGEDATKTEEEDDEIKFPP-V--VIKTTIPEELQRFMPPGDNVHTVILDFTQVNFIDSVGVKTLSGIVKEYGDVGIYVYLAGCSAQVVNDLTSNFFFENPALKELLFHSIHDAVLGSQLREALAEQEALTPPP-
OCHOTON013 MDHAEEQAPLAAPERYRVERPIFSHPVLQERLHTKDKVADSIGDKLKQAFTFTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQ-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-PFAVISLMIGGVAVRLVPDDIVIPGGVNSTNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNIKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKMPAPIPLEFFAVVMGTGISAGFNLKESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAVVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFADLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGQLPETDVYIDIDAFEEIKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVDPAVIMGARRKAMRKYAKEVGNVNMASAIMVKPAQDAEVDGESA-KPEDDDGEVKFPP-I--VVRGAFPEELQRFMPPREHIHTIILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVTDLTQNRFFENPALKELLFYSIHDAVLSSQVREALAAQEALAAPPQ
ORYCTOL014 MDHAEENGALAAAQRYCVERPIFSHPVLQERLHKKDKVADSIGDKLKQASTYTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFLGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNIKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLKESYSVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFADLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPAVIMGARRKAMRKYAKEVGNANIANATVAK--VDAEVDGENTPKPEEEEEEVKYPP-I--VVRSTFPEELQRFMPPGDGVHTIILDFTQVNFIDSVGVKTVAGIVKEYGDVGIYVYLAGCSAQVVNDLTRNRFFENPALKELLFYSIHDAVLGSQVREAMAEQEALAAPA-
PAN____015 MDHAEENEILAATQRYYVERPIFSHPVLQERLHTKDKVPDSIADKLKQAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPIFGLYSSFYPVIMYCFLGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLKESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLEQLPETDVYIDIDAYEEGKKIPGIKIFQINAPIYYANSDLYSNALKRKTGMNPAVIMGARRKAMRKYAKEVG-INMANATVVKATQDAEVDGEDATKPEEEDGEVKYPP-I--VIKSTFPEEMQRFMPPGDNVHTVILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTRNRFFENPALWELLFHSIHDAVLGSQLREALAEQEASAPPS-
PTEROPU016 MDHAEENEILAATQRYYVERPIFSHPVLQERLHKKDKIPDSIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVFMYCFFGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLHESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILMVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALMTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPALIMGARRKAMRKYAKEVGNANMANAAVVK--ADAEVDGEDGTKPEEE-DEVKYPP-I--VIKNTFPEELQRFMPPGDNIHTVILDFTQVNFIDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTQNQFFENPALRELLFHSIHDAVLGSHVREALAEQEASAPAT-
RHINOLO017 MDHAEETEILAATERYYVERPIFSHLVLQERLHKKDKISDSIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYNFKEYVLGDLVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFFGTSRHISIGPFAVISLMIGGVAVRLVPDDIAVPGGVNATNGTEF-RDALRVKVAMSVTLLAGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFGLHESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSTGSLFQTFAISCSLSRSLVQEGIGGKTQLAGCLASLMILMVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELVIWLSTFVSSLFLGLDYGLITAVIIALMTVIYRTQSPTYTVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPSFILGARRKAMKKYAKEGGNINIANATDVK--ADAEVDAEDGTKPEEEEDEVKYPP-V--VIKSTFPEELQRFMPPLENVHTIILDFTQVNFIDSVGVKTLQGIVKEYGDVGIYVYLAGCSAQVVSDLTRNRFFENPALLDLLFHSIHDAVLGSLVREALEEKEAAAATP-
SOREX__018 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------VVMGTGISAGFNLKESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALLTVIYRTQSPSYKVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPALIMGARRKAMKKYAKEVGNENIANATVVKVV-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX---IVKEYGDVGIYVYLAGCSAQVVNDLTRNRFFENPAMLELLFHSIHDAVLGSLVREALAEQETSAPAPQ
TURSIOP019 MDHVEETEILAATQRYYVERPIFSHPVLQERLHKKDKISESIGDKLKQAFTCTPKKIRNIIYMFLPITKWLPAYRFKEYVLGDIVSGISTGVLQLPQGLAFAMLAAVPPVFGLYSSFYPVIMYCFFGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNSTEA-RDALRVKVAMSVTLLTGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFSLHESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGNQELIALGLCNSTGSLFQTFAISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQAVLSAIVIVNLKGMFMQFSDLPFFWRTSKIELTIWLTTFVSSLFLGLDYGLITAVIIALMTVIYRTQSPSYIVLGQLPDTDVYIDIDAYEEVKEVPGIKIFQINAPIYYANSDLYSSALKRKTGVNPAFILGARRKAMKKYAKEVGNANMANATVVK--VDAEVDAEDGTKPEEEEDEIKYPP-I--VTKSTLPEELQRFMPPGDNVHTIILDFTQVNFMDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVSDLTQNQFFENPALLDLLFHSIHDAVLGSQVREALAEQEATAAPP-
VICUGNA020 ---------------------------------------------------CTPKKIRNIIYMFLPITKWLPAYKFKEYVLGDLVSGISTGVLQLPQ-XXXXXXXXXXXXXXXXXXXQKESMYCFLGTSRHISIGPFAVISLMIGGVAVRLVPDDIVIPGGVNATNGTEA-RDALRVKVAMSVTLLSGIIQFCLGVCRFGFVAIYLTEPLVRGFTTAAAVHVFTSMLKYLFGVKTKRYSGIFSVVYSTVAVLQNVKNLNVCSLGVGLMVFGLLLGGKEFNERFKEKLPAPIPLEFFAVVMGTGISAGFNLKESYNVDVVGTLPLGLLPPANPDTSLFHLVYVDAIAIAIVGFSVTISMAKTLANKHGYQVDGN-ELIALGLCNSIGSLFQTFSISCSLSRSLVQEGTGGKTQLAGCLASLMILLVILATGFLFESLPQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXVKEIPGIKIFQINAPIYYANSDLYSNALKRKTGVNPAFIMGARRKAMKKYAKEVGNANMANATVIK-VTDAEVDGTDGTKPEEEEDEIKYPP-V--VIKNTFPEELQRFMPPGDNVHTIILDFTQVNFIDSVGVKTVAGIVKEYGDVGIYVYLAGCSAQVVNDLSRNRFFENPALLELLFHSIHDAVLGSQVREALAEQEALAAPPP
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ public class CONTEXTVersion extends Version {
/**
* Version string: assumed to be in format x.x.x
*/
private static final String VERSION = "0.8.3";
private static final String VERSION = "0.8.4";

private static final String DATE_STRING = "2011-2017";

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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ public NewickTreeRepresentation(File inputFile, TreeSet<String> names){
}
}
}
} catch (UnsupportedTreefileTypeParseException e) {
} catch (Exception e) {
// TODO Auto-generated catch block
System.err.println("tree parsing failed.");
e.printStackTrace();
Expand Down Expand Up @@ -183,7 +183,7 @@ public NewickTreeRepresentation(File inputFile){
}
}
}
} catch (UnsupportedTreefileTypeParseException e) {
} catch (Exception e) {
// TODO Auto-generated catch block
System.err.println("tree parsing failed.");
e.printStackTrace();
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Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,6 @@ public enum PhylogenyConvergenceType {
TEST_ALTERNATIVE_PHYLOGENY,
RANDOM_CONTROL_PHYLOGENY,
RAXML_RESOLVED_PARTIALLY_CONSTRAINED_PHYLOGENY,
RAXML_FULLY_RESOLVED_UNCONSTRAINED_PHYLOGENY
RAXML_FULLY_RESOLVED_UNCONSTRAINED_PHYLOGENY,
UNDEFINED
}
Original file line number Diff line number Diff line change
Expand Up @@ -146,8 +146,8 @@ private class PhylogenomicDatasetBrowserView extends JFrame{
JProgressBar taskbar;
JFileChooser alignmentsFileChooser, alignmentsDirectoryChooser, phylogeniesFileChooser, phylogeniesDirectoryChooser;
JMenuBar menuBar;
JMenu fileMenu, helpMenu, loadAlignments, loadTrees;
JMenuItem loadAlignmentsSingle, loadAlignmentsBatch, loadTreesSingle, loadTreesBatch, close, about, showPlots; // fileMenu sub-items
JMenu fileMenu, helpMenu, loadAlignments, loadTrees, exportData;
JMenuItem loadAlignmentsSingle, loadAlignmentsBatch, loadTreesSingle, loadTreesBatch, exportAlignments, exportTrees, close, about, showPlots; // fileMenu sub-items
JMenuItem help, reportBugs, contributeCode; // helpMenu sub-items

public PhylogenomicDatasetBrowserView(PhylogeniesView phy_view, AlignmentsView align_view){
Expand Down Expand Up @@ -213,6 +213,11 @@ void createMenuBar(){
loadTreesBatch = new JMenuItem("As directory of files (batch operation)");
loadTrees.add(loadTreesSingle);
loadTrees.add(loadTreesBatch);
exportData = new JMenu("Export alignment/tree statistics data...");
exportAlignments = new JMenuItem("Export alignment stats");
exportTrees = new JMenuItem("Export tree stats");
exportData.add(exportAlignments);
exportData.add(exportTrees);
close = new JMenuItem("Quit CONTEXT/Phylogenomic Dataset Browser");

// Instantiate the Help menu items
Expand All @@ -226,6 +231,7 @@ void createMenuBar(){
fileMenu.add(showPlots);
fileMenu.add(loadAlignments);
fileMenu.add(loadTrees);
fileMenu.add(exportData);
fileMenu.addSeparator();
fileMenu.add(close);

Expand Down Expand Up @@ -301,7 +307,8 @@ private class PhylogenomicDatasetBrowserController{
view.loadAlignmentsBatch.addActionListener(batchAddAlignmentsListener);
view.loadTreesSingle.addActionListener(phylogeniesController.getAddSinglePhylogenyButtonListener());
view.loadTreesBatch.addActionListener(phylogeniesController.getAddBatchPhylogenyButtonListener());

view.exportAlignments.addActionListener(alignmentsController.getExportAlignmentDataButtonListener());
view.exportTrees.addActionListener(phylogeniesController.getExportTreeDataButtonListener());

/* Add action listeners for other menu items */
view.about.addActionListener(new AboutMenuListener());
Expand All @@ -317,6 +324,8 @@ private class PhylogenomicDatasetBrowserController{
view.loadAlignmentsBatch.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_O, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()+1));
view.loadTreesSingle.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()));
view.loadTreesBatch.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()+1));
view.exportAlignments.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()));
view.exportTrees.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()+1));
view.close.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()));
view.help.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()));
}
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Original file line number Diff line number Diff line change
Expand Up @@ -167,6 +167,10 @@ public NewickTreeRepresentation getNewickTree() {
return newickTree;
}

public File getTreeFile() {
return treeFile;
}

public TreeNode getTreeNode() {
return treeNode;
}
Expand Down
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