From a20d02a5acd820192158d03c4623365018848737 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Fri, 1 Oct 2021 00:08:41 +0100 Subject: [PATCH] JAL-1260 Added .gbk to GenBank extensions. Added GenBank extensions to the installer. --- src/jalview/io/FileFormat.java | 2 +- .../file_associations_auto-Info_plist.xml | 39 ++++ .../file_associations_auto-install4j8.xml | 222 ++++++++++++++------ 3 files changed, 196 insertions(+), 67 deletions(-) diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java index 1d240b2..a743694 100644 --- a/src/jalview/io/FileFormat.java +++ b/src/jalview/io/FileFormat.java @@ -244,7 +244,7 @@ public enum FileFormat implements FileFormatI return new PhylipFile(); } }, - GenBank("GenBank Flatfile", "gb", true, false) + GenBank("GenBank Flatfile", "gb, gbk", true, false) { @Override public AlignmentFileReaderI getReader(FileParse source) diff --git a/utils/install4j/file_associations_auto-Info_plist.xml b/utils/install4j/file_associations_auto-Info_plist.xml index fac86a3..2196a6a 100644 --- a/utils/install4j/file_associations_auto-Info_plist.xml +++ b/utils/install4j/file_associations_auto-Info_plist.xml @@ -197,6 +197,25 @@ CFBundleTypeExtensions +txt + +CFBundleTypeName +ENA Flatfile File +CFBundleTypeIconFile +Jalview-File.icns +CFBundleTypeRole +Editor +CFBundleTypeMIMETypes + +application/x-embl+txt + +LSIsAppleDefaultForType + + + + +CFBundleTypeExtensions + fa fasta @@ -237,6 +256,26 @@ CFBundleTypeExtensions +gb +gbk + +CFBundleTypeName +GenBank Flatfile File +CFBundleTypeIconFile +Jalview-File.icns +CFBundleTypeRole +Editor +CFBundleTypeMIMETypes + +application/x-genbank+txt + +LSIsAppleDefaultForType + + + + +CFBundleTypeExtensions + gff2 CFBundleTypeName diff --git a/utils/install4j/file_associations_auto-install4j8.xml b/utils/install4j/file_associations_auto-install4j8.xml index b14d32a..0d80644 100644 --- a/utils/install4j/file_associations_auto-install4j8.xml +++ b/utils/install4j/file_associations_auto-install4j8.xml @@ -143,9 +143,9 @@ - + - + @@ -188,9 +188,9 @@ - + - + @@ -233,9 +233,9 @@ - + - + @@ -278,9 +278,9 @@ - + - + @@ -323,9 +323,9 @@ - + - + @@ -368,9 +368,9 @@ - + - + @@ -413,9 +413,9 @@ - + - + @@ -448,8 +448,53 @@ + + + + ENA Flatfile (.txt) + Creating file associations... + + + + + + + + + + + + + + ENA Flatfile File + txt + 737 + + + Jalview-File.icns + + + + + + + + + Jalview-File.png + + + application/x-embl+txt + + + Jalview-File.ico + + + + + + - + Fasta (.fa, .fasta) Creating file associations... @@ -458,13 +503,13 @@ - + - + - + Fasta File fa,fasta @@ -494,7 +539,7 @@ - + Jalview Features (.features, .jvfeatures) Creating file associations... @@ -503,13 +548,13 @@ - + - + - + Jalview Features File features,jvfeatures @@ -538,8 +583,53 @@ + + + + GenBank Flatfile (.gb, .gbk) + Creating file associations... + + + + + + + + + + + + + + GenBank Flatfile File + gb,gbk + 737 + + + Jalview-File.icns + + + + + + + + + Jalview-File.png + + + application/x-genbank+txt + + + Jalview-File.ico + + + + + + - + Generic Features Format v2 (.gff2) Creating file associations... @@ -548,13 +638,13 @@ - + - + - + Generic Features Format v2 File gff2 @@ -584,7 +674,7 @@ - + Generic Features Format v3 (.gff3) Creating file associations... @@ -593,13 +683,13 @@ - + - + - + Generic Features Format v3 File gff3 @@ -629,7 +719,7 @@ - + JnetFile (.concise, .jnet) Creating file associations... @@ -638,13 +728,13 @@ - + - + - + JnetFile File concise,jnet @@ -674,7 +764,7 @@ - + MSF (.msf) Creating file associations... @@ -683,13 +773,13 @@ - + - + - + MSF File msf @@ -719,7 +809,7 @@ - + PFAM (.pfam) Creating file associations... @@ -728,13 +818,13 @@ - + - + - + PFAM File pfam @@ -764,7 +854,7 @@ - + PHYLIP (.phy) Creating file associations... @@ -773,13 +863,13 @@ - + - + - + PHYLIP File phy @@ -809,7 +899,7 @@ - + PileUp (.pileup) Creating file associations... @@ -818,13 +908,13 @@ - + - + - + PileUp File pileup @@ -854,7 +944,7 @@ - + PIR (.pir) Creating file associations... @@ -863,13 +953,13 @@ - + - + - + PIR File pir @@ -899,7 +989,7 @@ - + RNAML (.rnaml) Creating file associations... @@ -908,13 +998,13 @@ - + - + - + RNAML File rnaml @@ -944,7 +1034,7 @@ - + Substitution Matrix (.mat) Creating file associations... @@ -953,13 +1043,13 @@ - + - + - + Substitution Matrix File mat @@ -989,7 +1079,7 @@ - + Stockholm (.stk, .sto) Creating file associations... @@ -998,13 +1088,13 @@ - + - + - + Stockholm File stk,sto -- 1.7.10.2