From 4a2dd32daf665c30d1f96950f4cb0007a92e7577 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Fri, 19 May 2023 16:06:17 +0100 Subject: [PATCH] JAL-629 Updated debian helpers for new command line --- utils/debian/debian/jalview-mailcap | 44 +++++++++++++++++----------------- utils/debian/debian/wrappers/jalview | 9 +------ 2 files changed, 23 insertions(+), 30 deletions(-) diff --git a/utils/debian/debian/jalview-mailcap b/utils/debian/debian/jalview-mailcap index 5be7ab9..62816e5 100644 --- a/utils/debian/debian/jalview-mailcap +++ b/utils/debian/debian/jalview-mailcap @@ -1,22 +1,22 @@ -application/x-jalview+xml+zip; jalview -open '%s'; description="Jalview File"; nametemplate=%s.jvp; test=test -n "$DISPLAY"; priority=10 -chemical/x-cif; jalview -open '%s'; description="CIF File"; nametemplate=%s.cif; test=test -n "$DISPLAY"; priority=4 -chemical/x-mmcif; jalview -open '%s'; description="mmCIF File"; nametemplate=%s.mcif; test=test -n "$DISPLAY"; priority=4 -chemical/x-pdb; jalview -open '%s'; description="PDB File"; nametemplate=%s.pdb; test=test -n "$DISPLAY"; priority=4 -application/x-amsa+txt; jalview -open '%s'; description="AMSA File"; nametemplate=%s.amsa; test=test -n "$DISPLAY"; priority=9 -application/x-jalview-annotations+text; jalview -open '%s'; description="Jalview Annotations File"; nametemplate=%s.annotations; test=test -n "$DISPLAY"; priority=10 -application/x-jalview-biojson+json; jalview -open '%s'; description="BioJSON File"; nametemplate=%s.biojson; test=test -n "$DISPLAY"; priority=10 -application/x-blc+txt; jalview -open '%s'; description="BLC File"; nametemplate=%s.blc; test=test -n "$DISPLAY"; priority=9 -application/x-clustal+txt; jalview -open '%s'; description="Clustal File"; nametemplate=%s.aln; test=test -n "$DISPLAY"; priority=9 -application/x-fasta+txt; jalview -open '%s'; description="Fasta File"; nametemplate=%s.fa; test=test -n "$DISPLAY"; priority=9 -application/x-jalview-features+text; jalview -open '%s'; description="Jalview Features File"; nametemplate=%s.features; test=test -n "$DISPLAY"; priority=10 -application/x-gff2+txt; jalview -open '%s'; description="Generic Features Format v2 File"; nametemplate=%s.gff2; test=test -n "$DISPLAY"; priority=9 -application/x-gff3+txt; jalview -open '%s'; description="Generic Features Format v3 File"; nametemplate=%s.gff3; test=test -n "$DISPLAY"; priority=9 -application/x-jalview-jnet+text; jalview -open '%s'; description="JnetFile File"; nametemplate=%s.concise; test=test -n "$DISPLAY"; priority=10 -application/x-msf+txt; jalview -open '%s'; description="MSF File"; nametemplate=%s.msf; test=test -n "$DISPLAY"; priority=9 -application/x-pfam+txt; jalview -open '%s'; description="PFAM File"; nametemplate=%s.pfam; test=test -n "$DISPLAY"; priority=9 -application/x-phylip+txt; jalview -open '%s'; description="PHYLIP File"; nametemplate=%s.phy; test=test -n "$DISPLAY"; priority=9 -application/x-pileup+txt; jalview -open '%s'; description="PileUp File"; nametemplate=%s.pileup; test=test -n "$DISPLAY"; priority=9 -application/x-pir+txt; jalview -open '%s'; description="PIR File"; nametemplate=%s.pir; test=test -n "$DISPLAY"; priority=9 -application/rnaml+xml; jalview -open '%s'; description="RNAML File"; nametemplate=%s.rnaml; test=test -n "$DISPLAY"; priority=9 -application/x-jalview-scorematrix+text; jalview -open '%s'; description="Substitution Matrix File"; nametemplate=%s.mat; test=test -n "$DISPLAY"; priority=10 -application/x-stockholm+txt; jalview -open '%s'; description="Stockholm File"; nametemplate=%s.sto; test=test -n "$DISPLAY"; priority=9 +application/x-jalview+xml+zip; jalview '%s'; description="Jalview File"; nametemplate=%s.jvp; test=test -n "$DISPLAY"; priority=10 +chemical/x-cif; jalview '%s'; description="CIF File"; nametemplate=%s.cif; test=test -n "$DISPLAY"; priority=4 +chemical/x-mmcif; jalview '%s'; description="mmCIF File"; nametemplate=%s.mcif; test=test -n "$DISPLAY"; priority=4 +chemical/x-pdb; jalview '%s'; description="PDB File"; nametemplate=%s.pdb; test=test -n "$DISPLAY"; priority=4 +application/x-amsa+txt; jalview '%s'; description="AMSA File"; nametemplate=%s.amsa; test=test -n "$DISPLAY"; priority=9 +application/x-jalview-annotations+text; jalview '%s'; description="Jalview Annotations File"; nametemplate=%s.annotations; test=test -n "$DISPLAY"; priority=10 +application/x-jalview-biojson+json; jalview '%s'; description="BioJSON File"; nametemplate=%s.biojson; test=test -n "$DISPLAY"; priority=10 +application/x-blc+txt; jalview '%s'; description="BLC File"; nametemplate=%s.blc; test=test -n "$DISPLAY"; priority=9 +application/x-clustal+txt; jalview '%s'; description="Clustal File"; nametemplate=%s.aln; test=test -n "$DISPLAY"; priority=9 +application/x-fasta+txt; jalview '%s'; description="Fasta File"; nametemplate=%s.fa; test=test -n "$DISPLAY"; priority=9 +application/x-jalview-features+text; jalview '%s'; description="Jalview Features File"; nametemplate=%s.features; test=test -n "$DISPLAY"; priority=10 +application/x-gff2+txt; jalview '%s'; description="Generic Features Format v2 File"; nametemplate=%s.gff2; test=test -n "$DISPLAY"; priority=9 +application/x-gff3+txt; jalview '%s'; description="Generic Features Format v3 File"; nametemplate=%s.gff3; test=test -n "$DISPLAY"; priority=9 +application/x-jalview-jnet+text; jalview '%s'; description="JnetFile File"; nametemplate=%s.concise; test=test -n "$DISPLAY"; priority=10 +application/x-msf+txt; jalview '%s'; description="MSF File"; nametemplate=%s.msf; test=test -n "$DISPLAY"; priority=9 +application/x-pfam+txt; jalview '%s'; description="PFAM File"; nametemplate=%s.pfam; test=test -n "$DISPLAY"; priority=9 +application/x-phylip+txt; jalview '%s'; description="PHYLIP File"; nametemplate=%s.phy; test=test -n "$DISPLAY"; priority=9 +application/x-pileup+txt; jalview '%s'; description="PileUp File"; nametemplate=%s.pileup; test=test -n "$DISPLAY"; priority=9 +application/x-pir+txt; jalview '%s'; description="PIR File"; nametemplate=%s.pir; test=test -n "$DISPLAY"; priority=9 +application/rnaml+xml; jalview '%s'; description="RNAML File"; nametemplate=%s.rnaml; test=test -n "$DISPLAY"; priority=9 +application/x-jalview-scorematrix+text; jalview '%s'; description="Substitution Matrix File"; nametemplate=%s.mat; test=test -n "$DISPLAY"; priority=10 +application/x-stockholm+txt; jalview '%s'; description="Stockholm File"; nametemplate=%s.sto; test=test -n "$DISPLAY"; priority=9 diff --git a/utils/debian/debian/wrappers/jalview b/utils/debian/debian/wrappers/jalview index 4823bee..0f44579 100755 --- a/utils/debian/debian/wrappers/jalview +++ b/utils/debian/debian/wrappers/jalview @@ -7,11 +7,4 @@ if [ -n "${HOME}" -a \! -e ${HOME}/.jalview_properties ]; then /bin/cp /etc/jalview_properties ${HOME}/.jalview_properties fi -# check to see if $1 is set and is not start of other cli set args -OPEN="" -if [ -n "$ARG1" -a "$ARG1" = "${ARG1#-}" ]; then - # first argument exists and does not start with a "-" - OPEN="-open" -fi - -java -jar /usr/share/java/jalview.jar $OPEN "$@" +java -jar /usr/share/java/jalview.jar "$@" -- 1.7.10.2