JAL-629 Updated debian helpers for new command line

diff --git a/utils/debian/debian/jalview-mailcap b/utils/debian/debian/jalview-mailcap
index 5be7ab9..62816e5 100644 (file)
--- 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 (executable)
--- 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 "$@"