aaa182677fc86a82dd4cd7764cdb40a1476cedae hiram Wed Mar 30 12:47:51 2022 -0700 the selection menus now look like buttons with a down arrow icon and the column headers have an info icon refs #28930 diff --git src/hg/gar/garTable.pl src/hg/gar/garTable.pl index 788c45e..e0046ac 100755 --- src/hg/gar/garTable.pl +++ src/hg/gar/garTable.pl @@ -714,65 +714,65 @@ printf "\n"; } } # if ( 1 == 0 ) # count all assemblies in all clades my $totalAssemblies = 0; foreach my $c (@clades) { $totalAssemblies += $cladeCounts{$c}; } printf "\n"; printf "
\n"; printf "
\n"; printf "
\n"; -printf " choose clades to view/hide\n"; +printf " choose clades to view/hide ▼\n"; printf "
\n"; printf "
    \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
\n"; printf "
\n"; printf "
\n"; printf "
\n"; -printf " select assembly type to display\n"; +printf " select assembly type to display ▼\n"; printf "
\n"; printf "
    \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
\n"; printf "
\n"; printf "
\n"; printf "
\n"; -printf " show/hide columns\n"; +printf " show/hide columns ▼\n"; printf "
\n"; printf "
    \n"; -printf "
    • \n"; +printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
    • \n"; printf "
\n"; printf "
\n"; @@ -806,45 +806,45 @@ printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; -printf "
view/request'view' opens the genome browser for an existing assembly, 'request' opens an assembly request form.
\n"; -printf "
common namecommon name
\n"; -printf "
scientific name (count)Links to Google image search. Count shows the number of assemblies available for this orgnism.
\n"; -printf "
NCBI AssemblyLinks to NCBI resource record.
\n"; -printf "
assembly
sizeNumber of nucleotides in the assembly.
\n"; -printf "
sequence
countThe number of sequences in this assembly.
\n"; -printf "
scaffold N50
length (L50)N50 (L50) length.
\n"; -printf "
contig N50
length (L50)N50 (L50) length.
\n"; -printf "
IUCNLinks to IUCN Red List of Threatened Species (version 2021-3) CR - Critical / EN - Endangered / VU - Vulnerable
\n", $statusColors{"CR"}, $statusColors{"EN"}, $statusColors{"VU"}; -printf "
NCBI taxIDLinks to NCBI Taxonomy database.
\n"; -printf "
assembly
dateDate submitted to NCBI Assembly database.
\n"; -printf "
BioSampleBioSample ID at NCBI.
\n"; -printf "
BioProjectBioProject ID at NCBI.
\n"; -printf "
Assembly submitterPerson or group who submitted to NCBI Assembly database.
\n"; -printf "
cladeClade of this organism.
\n"; +printf "
view/request ⓘ'view' opens the genome browser for an existing assembly, 'request' opens an assembly request form.
\n"; +printf "
English common name ⓘEnglish common name
\n"; +printf "
scientific name (count) ⓘLinks to Google image search. Count shows the number of assemblies available for this orgnism.
\n"; +printf "
NCBI Assembly ⓘLinks to NCBI resource record.
\n"; +printf "
assembly
size ⓘNumber of nucleotides in the assembly.
\n"; +printf "
sequence
count ⓘThe number of sequences in this assembly.
\n"; +printf "
scaffold N50
length (L50) ⓘN50 (L50) length.
\n"; +printf "
contig N50
length (L50) ⓘN50 (L50) length.
\n"; +printf "
IUCN ⓘLinks to IUCN Red List of Threatened Species (version 2021-3) CR - Critical / EN - Endangered / VU - Vulnerable
\n", $statusColors{"CR"}, $statusColors{"EN"}, $statusColors{"VU"}; +printf "
NCBI taxID ⓘLinks to NCBI Taxonomy database.
\n"; +printf "
assembly
date ⓘDate submitted to NCBI Assembly database.
\n"; +printf "
BioSample ⓘBioSample ID at NCBI.
\n"; +printf "
BioProject ⓘBioProject ID at NCBI.
\n"; +printf "
Assembly submitter ⓘPerson or group who submitted to NCBI Assembly database.
\n"; +printf "
clade ⓘClade of this organism.
\n"; printf "\n"; printf "\n"; my %equivalentNamesUsed; # key is NCBI sciName, value is IUCN sciName my $pageSectionCount = 0; my %checkDupAsmId; # key is asmId, value is count of times seen my %cladeSciNameCounts; # key is clade, value is number of different # scientific names my %gcfGcaCounts; # key is GCF or GCA, value is count of each my $asmCountInTable = 0; # counting the rows output my %statusCounts; # key is status: CR EN VU, value is count my $totalAssemblySize = 0; # sum of all assembly sizes