From: Jim Procter Date: Mon, 24 Oct 2016 14:46:43 +0000 (+0100) Subject: Merge branch 'develop' into releases/Release_2_10_0_Branch X-Git-Tag: Release_2_10_0b1~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c3adaf9e615ef32d1e4c7624fe07b108a1b36ad7;hp=bc059a21e8d7949157f436dc706fb8d0335b3874;p=jalview.git Merge branch 'develop' into releases/Release_2_10_0_Branch --- diff --git a/examples/exampleFile.jar b/examples/exampleFile.jar index 3231974..2f9000d 100755 Binary files a/examples/exampleFile.jar and b/examples/exampleFile.jar differ diff --git a/examples/exampleFile_2_3.jar b/examples/exampleFile_2_3.jar index adf707e..1a8bef0 100644 Binary files a/examples/exampleFile_2_3.jar and b/examples/exampleFile_2_3.jar differ diff --git a/examples/exampleFile_2_7.jar b/examples/exampleFile_2_7.jar index 0b70e66..7cd9d77 100644 Binary files a/examples/exampleFile_2_7.jar and b/examples/exampleFile_2_7.jar differ diff --git a/examples/ferredoxin.nw b/examples/ferredoxin.nw index 0b949de..89ea348 100755 --- a/examples/ferredoxin.nw +++ b/examples/ferredoxin.nw @@ -1 +1 @@ -(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868); +(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER1_ARATH:64.0,FER2_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868); diff --git a/examples/plantfdx.fa b/examples/plantfdx.fa index f314c85..80d7133 100644 --- a/examples/plantfdx.fa +++ b/examples/plantfdx.fa @@ -34,18 +34,18 @@ IETHKEEELTA- ----------------------------------------------------------ATYKVKFITPEGEQ EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT IETHREEDMV-- ->FER1_ARATH/1-148 -----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ -EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV -IETHKEEAIM-- ->FER_BRANA/1-96 -----------------------------------------------------------ATYKVKFITPEGEQ -EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT -IETHKEEELV-- >FER2_ARATH/1-148 ----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT IETHKEEDIV-- +>FER_BRANA/1-96 +----------------------------------------------------------ATYKVKFITPEGEQ +EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT +IETHKEEELV-- +>FER1_ARATH/1-148 +----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ +EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV +IETHKEEAIM-- >Q93Z60_ARATH/1-118 ----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------- diff --git a/examples/uniref50.fa b/examples/uniref50.fa index 4bdbfb4..6e6c670 100755 --- a/examples/uniref50.fa +++ b/examples/uniref50.fa @@ -34,18 +34,18 @@ TIETHKEEELTA- -----------------------------------------------------------ATYKVKFITPEGE QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV TIETHREEDMV-- ->FER1_ARATH Ferredoxin-1, chloroplast precursor -MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE -QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV -VIETHKEEAIM-- ->FER_BRANA Ferredoxin ------------------------------------------------------------ATYKVKFITPEGE -QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV -TIETHKEEELV-- >FER2_ARATH Ferredoxin-2, chloroplast precursor MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV TIETHKEEDIV-- +>FER_BRANA Ferredoxin +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV +TIETHKEEELV-- +>FER1_ARATH Ferredoxin-1, chloroplast precursor +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV +VIETHKEEAIM-- >Q93Z60_ARATH At1g10960/T19D16_12 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------------------- diff --git a/examples/uniref50_mz.fa b/examples/uniref50_mz.fa index 9974fc7..725d210 100644 --- a/examples/uniref50_mz.fa +++ b/examples/uniref50_mz.fa @@ -18,11 +18,11 @@ AAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDD AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDD >FER3_RAPSA/1-66 Ferredoxin, leaf L-A ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD ->FER1_ARATH/53-118 Ferredoxin-1, chloroplast precursor +>FER2_ARATH/53-118 Ferredoxin-1, chloroplast precursor ATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD >FER_BRANA/1-66 Ferredoxin ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDD ->FER2_ARATH/53-118 Ferredoxin-2, chloroplast precursor +>FER1_ARATH/53-118 Ferredoxin-2, chloroplast precursor ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD >Q93Z60_ARATH/53-118 At1g10960/T19D16_12 ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD diff --git a/help/html/releases.html b/help/html/releases.html index 7d34557..3fe08cb 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -63,7 +63,9 @@ General Application