...
 
Commits (10)
gff2aplot (2.0-10) unstable; urgency=medium
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Secure URI in copyright format
* Fix privacy issues by providing images, js and css locally
-- Andreas Tille <tille@debian.org> Sat, 20 Oct 2018 23:57:37 +0200
gff2aplot (2.0-9) unstable; urgency=medium
* Moved packaging from SVN to Git
......
......@@ -4,10 +4,10 @@ Uploaders: Nelson A. de Oliveira <naoliv@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10)
Standards-Version: 4.1.1
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/gff2aplot.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/gff2aplot.git
Build-Depends: debhelper (>= 11~)
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/gff2aplot
Vcs-Git: https://salsa.debian.org/med-team/gff2aplot.git
Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html
Package: gff2aplot
......
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: GFF2APLOT
Upstream-Contact: Josep Francesc ABRIL FERRANDO <jabril@imim.es>
Source: http://genome.imim.es/software/gfftools/GFF2APLOT.html
......
/* GENOME BIOINFORMATICS */
/* RESEARCH LABORATORY */
/* Global Style Sheet */
/*$Id: Genome.css,v 1.28 2003/06/03 16:35:45 gmaster Exp gmaster $*/
BODY, BLOCKQUOTE, P, CENTER,
DD, DIV, FIELDSET, PRE, FORM,
FRAME, FRAMESET, IFRAME, NOFRAMES,
OBJECT, APPLET, HR,
UL, OL, MENU {
display: block }
LI, DL, DD, DT {
display: block }
H1, H2, H3, H4, H5, H6 {
display: table-cell }
HEAD { display: none }
TABLE { display: table }
TR { display: table-row }
TBODY { display: table-row-group }
COL { display: table-column }
COLGROUP { display: table-column-group }
TD, TH { display: table-cell }
IMG { display: run-in }
TT, CODE, EM {
display: inline }
BODY {
background-color: #009F9F;
color: black;
border-collapse: collapse;
/* This does not work on newer browsers like N6 */
/* position: fixed; */
top: 0px;
bottom: auto;
left: 0px;
right: 0px;
padding: 0px;
border: 0px;
line-height/* */ : 1.33em;
}
*, .default {
top: 0;
bottom: 0;
left: 0;
right: 0;
border: 0;
padding: 0;
/* spacing: 0; */
margin: 0;
text-indent: 0;
}
.hh {
line-height/* */ : 80%;
}
.hhh {
line-height/* */ : 50%;
}
P {
margin-left: 10px;
margin-right: 10px;
margin-bottom: 10px;
text-align: justify;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: normal;
font-size: 12px;
}
TEXTAREA {
font-family: "Monospaced", "Courier", sans-serif;
font-weight: normal;
font-size: 12px;
}
INPUT, SELECT {
font-family: "Arial", "Helvetica", sans-serif;
font-weight: normal;
font-size: 12px;
}
.tbl {
vertical-align: top;
font-family: "Arial", "Helvetica", sans-serif;
/* font-weight: normal; */
font-size: 12px;
}
A:link {
color: #008080;
text-decoration: none;
}
A:visited {
color: #800000;
text-decoration: none;
}
A:hover, A:active, A:focus { text-decoration: underline; }
/* :focus { outline: thin solid invert; } */
B {
font-weight: bold;
}
I {
font-style: italic;
}
EM {
font-family: "Monospaced", "Courier", sans-serif;
font-weight: normal;
font-style: italic;
font-stretch: expanded;
color: green;
}
TT, CODE {
font-family: "Monospaced", "Courier", sans-serif;
font-weight: normal;
}
TT {
color: gray;
font-stretch: expanded;
}
.K, .T {
display: run-in
}
H1, H2, .K, .T {
color: white;
}
H1, H2, .K, .T {
font-family: "Arial", "Helvetica", sans-serif;
font-weight: bold;
font-stretch: expanded;
border: none;
line-height/* */ : 100%;
}
P H1, P H2, P H3, P .K, P .T {
color: black;
}
H1, .T {
font-size: 24px;
padding: 5px;
text-indent: 0;
}
H2, .K {
border: none;
padding: 0;
text-indent: 0;
font-size: 20px;
width: auto;
}
H3 { font-size: 16px; }
H4, UL, OL {
background-color: white;
color: black;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: bold;
font-size: 12px;
line-height/* */ : 110%;
}
MENU {
background-color: white;
color: black;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: normal;
font-size: 12px;
line-height/* */ : 110%;
list-style: outside;
list-style-type: circle;
}
UL {
list-style: outside;
list-style-type: disc;
}
OL {
list-style: outside;
list-style-type: decimal;
}
UL, OL, DL, MENU {
margin-left: 5px;
margin-right: 10px;
}
UL UL, OL OL, MENU * {
margin-left: 10px;
margin-right: 10px;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: normal;
font-size: 12px;
}
UL UL UL, OL OL OL {
margin-left: 15px;
margin-right: 10px;
}
LI {
background-color: white;
color: black;
}
.lst {
font-weight: normal;
}
IMG.pnt {
padding-left: 5px;
padding-right: 0px;
}
IMG.mid {
padding-left: 5px;
}
.ppath {
color: white;
background-color: red;
font-family: "Arial", "Helvetica", sans-serif;
font-size: 12px;
font-weight: bold;
}
.path {
border: 1px solid #005050;
color: white;
background-color: red;
font-family: "Arial", "Helvetica", sans-serif;
font-size: 12px;
font-weight: bold;
line-height/* */ : 110%;
}
.path :link, .path :visited {
color: white;
text-decoration: none;
}
.path :visited {
font-weight: bold;
}
.userspace {
background-color: white;
color: black;
font-family: "Arial", "Helvetica", sans-serif;
font-size: 12px;
text-align: justify;
vertical-align: top;
}
.section {
background-color: #008080;
color: white;
margin-top: 0;
margin-bottom: 0;
margin-left: 5px;
padding-top: 0;
padding-bottom: 0;
}
#traila {
text-align: center;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: bold;
font-size: 15px;
text-align: left;
}
#trailb {
text-align: center;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: bold;
font-size: 12px;
color: white;
line-height/* */ : 85%;
}
#trailc {
text-align: center;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: bold;
font-size: 15px;
text-align: right;
}
.trailer {
padding: 2px;
}
.names {
font-family: "Arial", "Helvetica", sans-serif;
font-size: 12px;
color: black;
}
.links {
vertical-align: top;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: bold;
font-size: 12px;
line-height/* */ : 95%;
border: none;
padding: 0px;
}
.links :link, #traila :link, #trailc :link,
.links :visited, #traila :visited, #trailc :visited {
color: #005050;
}
.links :hover, .links :active, .links :focus,
.path :hover, .path :active, .path :focus {
text-decoration: underline;
}
.menu {
text-align: left;
vertical-align: top;
}
.title {
text-align: center;
vertical-align: middle;
}
.index {
color: white;
line-height/* */ : 100%;
text-align: center;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: bold;
font-size: 12px;
border: none;
padding: 0px;
}
.mvleft {
position: relative;
left: -15px;
}
.home {
line-height/* */ : 80%;
color: white;
font-family: "Arial", "Helvetica", sans-serif;
font-size: 22px;
font-weight: bold;
font-stretch: expanded;
text-align: center;
border: none;
}
.tit, .tgen {
color: white;
font-family: "Arial", "Helvetica", sans-serif;
font-weight: bold;
font-stretch: expanded;
border: none;
}
.tit {
font-size: 20px;
line-height/* */ : 120%;
}
.tgen {
font-size: 25px;
line-height/* */ : 100%;
}
.alt {
display: none;
}
.float-right {/* paragraph element float */
float: right;
width: 30em;
padding: 0.3em 0.3em 0.3em 0.3em;
border: 2px dotted #800000;
}
/* GENOME BIOINFORMATICS */
/* RESEARCH LABORATORY */
/* Forms "Special" Style Sheet */
/* (to apply to mozilla engine */
/* based browsers ---N6, M6, */
/* O5, ...--- and IE>5 ) */
/*$Id: Genome_forms_mozilla.css,v 1.9 2003/06/03 16:35:51 gmaster Exp $*/
/* TEXTAREA { */
/* display: block; */
/* } */
/* INPUT { */
/* display: inline; */
/* } */
/* SELECT { */
/* display: run-in; */
/* } */
HR {
border: 1px inset;
color: black;
}
LI, DL, DD, DT {
display: list-item;
}
P {
margin-left: 5px;
margin-right: 5px;
padding-left: 10px;
}
TEXTAREA {
cursor: text;
}
TEXTAREA, INPUT, SELECT {
border-width: thin;
border-style: solid;
border-color: black;
vertical-align: baseline;
}
/* Redefining Sections to improve their boxes */
.section {
background-color: #008080;
color: white;
margin-top: 0;
margin-bottom: 0;
margin-left: 5px;
padding-top: 3px;
padding-bottom: 3px;
padding-left: 5px;
}
UL, OL, DL, MENU {
margin-left: 30px;
}
UL UL, OL OL, DL DL, MENU * {
margin-left: 35px;
}
UL UL UL, OL OL OL {
margin-left: 40px;
}
OL {
counter-reset: gencnt;
}
LI:before {
display: marker;
marker-offset: 1px;
text-align: right;
}
OL LI:before {
content: "" counter(gencnt) ".";
counter-increment: gencnt;
}
.home {
line-height/* */ : 150%;
text-align: center;
}
.tit {
line-height/* */ : 150%;
}
.tgen {
line-height/* */ : 120%;
}
P * CENTER {
text-align: center;
}
/* GENOME INFORMATICS */
/* RESEARCH LABORATORY */
/* GFFTOOLS HowTo Style Sheet */
/*$Id: HowTo.css,v 1.2 2003/05/30 17:50:58 gmaster Exp $*/
H3 {
display: block;
line-height: 75%;
padding-bottom: 0px;
border-bottom: 0px;
margin-bottom: 0px;
margin-top: 8px;
}
.home {
line-height: 80%;
color: white;
font-family: "Arial", "Helvetica", sans-serif;
font-size: 18px;
font-weight: bold;
font-stretch: expanded;
text-align: center;
border: none;
}
.ytbl, .rtbl {
vertical-align: top;
font-family: "Arial", "Helvetica", sans-serif;
font-size: 12px;
}
.ytbl {
background: #FAFAD2; /* light yellow */
}
.rtbl {
background: #FFCCAA; /* light red */
}
.codebg {
display: table-cell;
background: #DDFFDD;
}
.codefg {
font-family: "Monospaced", "Courier", sans-serif;
font-weight: normal;
font-size: 12px;
color: #000000;
}
/*
FILE ARCHIVED ON 18:54:24 Apr 04, 2005 AND RETRIEVED FROM THE
INTERNET ARCHIVE ON 09:49:07 Oct 20, 2018.
JAVASCRIPT APPENDED BY WAYBACK MACHINE, COPYRIGHT INTERNET ARCHIVE.
ALL OTHER CONTENT MAY ALSO BE PROTECTED BY COPYRIGHT (17 U.S.C.
SECTION 108(a)(3)).
*/
/*
playback timings (ms):
LoadShardBlock: 197.985 (3)
esindex: 0.009
captures_list: 216.277
CDXLines.iter: 12.375 (3)
PetaboxLoader3.datanode: 191.824 (4)
exclusion.robots: 0.193
exclusion.robots.policy: 0.18
RedisCDXSource: 2.583
PetaboxLoader3.resolve: 79.838 (2)
load_resource: 101.02
*/
\ No newline at end of file
//
// Genome.js
//
// $Id: Genome.js,v 1.5 2003/06/03 16:37:01 gmaster Exp $
//
// ### JavaScript Error Checking ###
onerror = myOnError;
msgArray = new Array();
urlArray = new Array();
lnoArray = new Array();
function myOnError(msg, url, lno) {
msgArray[msgArray.length] = msg;
urlArray[urlArray.length] = url;
lnoArray[lnoArray.length] = lno;
return true;
}
function displayErrors() {
if (msgArray.length == 0) {
// document.write('<tr><td class="path">This page is being displayed on <B>' + navName + '</B> ' + brNum + ' [NS4==' + NS4 + '] </td></tr>');
return true;
}
for (var i=0; i < msgArray.length; i++) {
document.writeln('<tr><td class="path"><TABLE width=400 border=1 cellpadding=1 cellspacing=0>');
document.writeln('<TR><TH class="path" width=50 align=right>Error in file:&nbsp;&nbsp;</TH><TD class="path"> ' + urlArray[i] + '</TD></TR>');
document.writeln('<TR><TH class="path" width=50 align=right>Line number:&nbsp;&nbsp;</TH><TD class="path"> ' + lnoArray[i] + '</TD></TR>');
document.writeln('<TR><TH class="path" width=50 align=right>Message:&nbsp;&nbsp;</TH><TD class="path"> ' + msgArray[i] + '</TD></TR>');
document.writeln('</TABLE><BR></td></tr>');
}
return true;
}
function reportErrors() {
if (msgArray.length == 0) {
// document.write('<tr><td class="path">This page is being displayed on <B>' + navName + '</B> ' + brNum + ' [NS4==' + NS4 + '] </td></tr>');
return true;
}
for (var i=0; i < msgArray.length; i++) {
document.writeln('<table class="trailer" border=0 cellpadding=0 cellspacing=0 width="100%">');
document.writeln('<tr><td class="path">');
document.writeln('<TABLE width=400 border=1 cellpadding=1 cellspacing=0>');
document.writeln('<TR><TH class="path" width=50 align=right>Error in file:&nbsp;&nbsp;</TH><TD class="path"> ' + urlArray[i] + '</TD></TR>');
document.writeln('<TR><TH class="path" width=50 align=right>Line number:&nbsp;&nbsp;</TH><TD class="path"> ' + lnoArray[i] + '</TD></TR>');
document.writeln('<TR><TH class="path" width=50 align=right>Message:&nbsp;&nbsp;</TH><TD class="path"> ' + msgArray[i] + '</TD></TR>');
document.writeln('</TABLE></td></tr>');
document.writeln('</table>');
}
return true;
}
// This script and many more are available free online at
// The JavaScript Source!! http://javascript.internet.com
// Jeff Lance (jflance@aol.com)
//-- Begin borrowed
var navName = navigator.appName ;
var brVer = navigator.userAgent;
var brNum;
var reg = new RegExp('/');
function verNumIE() {
var brVerId = brVer.indexOf('MSIE');
brNum = brVer.substr(brVerId,8);
}
function verNumOt() {
var brVerId = brVer.search(reg);
brNum = brVer.substring(brVerId+1);
}
if (navName == 'Microsoft Internet Explorer') { verNumIE() ; }
else { verNumOt() ; }
//-- End borrowed
// ### Window Size related###
// window.location.href = 'index.html';
if (window != top) { top.location.href = location.href; }
//
var NS4 = 0;
var bVer = parseFloat(brNum);
if ((bVer < 4.1) && (navName == 'Netscape')) NS4 = 1; // 4.04
function init() {
if (NS4) { setTimeout("window.onresize = redo", 1000); }
else { window.location.reload(); }
}
function redo() {
window.location.reload();
}
// window.onload = "init();";
window.onreload = "init();";
window.onresize = "init();";
function onResize() {
window.onreload = "init();";
window.onresize = "init();";
}
// ### Misc ###
function displayURL() {
var sURL = window.location.pathname ; // unescape(window.location.pathname);
document.write('<B>http://genome.crg.es' + sURL + '</B>');
}
//
function LastUpdate() {
var theDate = "";
theDate = document.lastModified;
document.write("<B>Last Updated&nbsp;<I>"+theDate+"</I>&nbsp;&copy;&nbsp;Genome BioInformatics Research Laboratory</B>");
}
//
function LastUpdateSplit() {
var theDate = "";
theDate = document.lastModified;
document.write("<B>Last Updated&nbsp;<I>"+theDate+"</I><BR>&copy;&nbsp;Genome BioInformatics Research Laboratory</B>");
}
// Expiration date: NewIcon("MM/DD/YYYY")
function NewIcon(todate) {
NewHTML(todate,"&nbsp;<IMG SRC='https://web.archive.org/web/20091211103905/http://genome.crg.es/g_icons/new_rotating.gif' WIDTH=20 HEIGHT=10 BORDER=0 ALT='NEW'>");
}
function NewHTML(todate,toput) {
exp = new Date(todate);
cur = new Date();
if (cur.getTime() < exp.getTime()) { document.write("&nbsp;"+toput); }
else { document.write("&nbsp;"); }
}
/*
FILE ARCHIVED ON 10:39:05 Dec 11, 2009 AND RETRIEVED FROM THE
INTERNET ARCHIVE ON 09:48:18 Oct 20, 2018.
JAVASCRIPT APPENDED BY WAYBACK MACHINE, COPYRIGHT INTERNET ARCHIVE.
ALL OTHER CONTENT MAY ALSO BE PROTECTED BY COPYRIGHT (17 U.S.C.
SECTION 108(a)(3)).
*/
/*
playback timings (ms):
LoadShardBlock: 59.719 (3)
esindex: 0.007
captures_list: 77.607
CDXLines.iter: 13.422 (3)
PetaboxLoader3.datanode: 65.978 (4)
exclusion.robots: 0.154
exclusion.robots.policy: 0.142
RedisCDXSource: 1.606
PetaboxLoader3.resolve: 38.191
load_resource: 51.792
*/
\ No newline at end of file
# JS and css vanished from web
wget https://web.archive.org/web/20091211103905/http://genome.imim.es/genome.js
wget https://web.archive.org/web/20050404185424/http://genome.imim.es:80/software/gfftools/gff2aplot_docs/HowTo.css
# other files
wget http://genome.imim.es/Genome.css
wget http://genome.imim.es/Genome_forms_mozilla.css
This diff is collapsed.
......@@ -2,3 +2,4 @@
03-parseblast.diff
use-dpkg-buildflags.patch
mayhem.patch
fis-privacy-breach.patch
debian/imgs/top.gif
debian/imgs/lhr.gif
debian/imgs/dmd.gif