[med-svn] [Git][med-team/gff2aplot][master] 10 commits: debhelper 11
Andreas Tille
gitlab at salsa.debian.org
Sat Oct 20 23:05:33 BST 2018
Andreas Tille pushed to branch master at Debian Med / gff2aplot
Commits:
f524413d by Andreas Tille at 2018-10-20T09:23:26Z
debhelper 11
- - - - -
b438f5a7 by Andreas Tille at 2018-10-20T09:23:32Z
Point Vcs fields to salsa.debian.org
- - - - -
4d77943b by Andreas Tille at 2018-10-20T09:23:32Z
Standards-Version: 4.2.1
- - - - -
469d0188 by Andreas Tille at 2018-10-20T09:23:32Z
Secure URI in copyright format
- - - - -
a137fb76 by Andreas Tille at 2018-10-20T09:41:09Z
Fix privacy breach issue
- - - - -
5d83f3d0 by Andreas Tille at 2018-10-20T12:15:25Z
More privacy issues fixed
- - - - -
5da253d7 by Andreas Tille at 2018-10-20T12:16:25Z
Upload to unstable
- - - - -
9b87f09c by Andreas Tille at 2018-10-20T21:47:42Z
Further privacy braches
- - - - -
673e5e25 by Andreas Tille at 2018-10-20T21:56:47Z
DEP3
- - - - -
0dd91f60 by Andreas Tille at 2018-10-20T21:58:21Z
Upload to unstable
- - - - -
16 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- debian/examples
- + debian/imgs/Genome.css
- + debian/imgs/Genome_forms_mozilla.css
- + debian/imgs/HowTo.css
- + debian/imgs/dmd.gif
- + debian/imgs/genome.js
- + debian/imgs/get_from_web_archive
- + debian/imgs/lhr.gif
- + debian/imgs/top.gif
- + debian/patches/fis-privacy-breach.patch
- debian/patches/series
- + debian/source/include-binaries
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+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 at debian.org> Sat, 20 Oct 2018 23:57:37 +0200
+
gff2aplot (2.0-9) unstable; urgency=medium
* Moved packaging from SVN to Git
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
@@ -4,10 +4,10 @@ Uploaders: Nelson A. de Oliveira <naoliv at debian.org>,
Andreas Tille <tille at 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
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-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 at imim.es>
Source: http://genome.imim.es/software/gfftools/GFF2APLOT.html
=====================================
debian/examples
=====================================
@@ -1 +1,2 @@
examples/*
+debian/imgs
=====================================
debian/imgs/Genome.css
=====================================
@@ -0,0 +1,376 @@
+/* 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;
+
+ }
=====================================
debian/imgs/Genome_forms_mozilla.css
=====================================
@@ -0,0 +1,92 @@
+/* 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 $*/
+
+/* TEXTAREA { */
+/* display: block; */
+/* } */
+/* INPUT { */
+/* display: inline; */
+/* } */
+/* SELECT { */
+/* display: run-in; */
+/* } */
+
+HR {
+ border: 1px inset;
+ color: black;
+}
+
+LI, DL, DD, DT {
+ display: list-item;
+}
+
+P {
+ margin-left: 5px;
+ margin-right: 5px;
+ padding-left: 10px;
+}
+
+TEXTAREA {
+ cursor: text;
+}
+
+TEXTAREA, INPUT, SELECT {
+ border-width: thin;
+ border-style: solid;
+ border-color: black;
+ vertical-align: baseline;
+}
+
+/* Redefining Sections to improve their boxes */
+.section {
+ background-color: #008080;
+ color: white;
+ margin-top: 0;
+ margin-bottom: 0;
+ margin-left: 5px;
+ padding-top: 3px;
+ padding-bottom: 3px;
+ padding-left: 5px;
+}
+
+UL, OL, DL, MENU {
+ margin-left: 30px;
+}
+UL UL, OL OL, DL DL, MENU * {
+ margin-left: 35px;
+}
+UL UL UL, OL OL OL {
+ margin-left: 40px;
+}
+OL {
+ counter-reset: gencnt;
+}
+LI:before {
+ display: marker;
+ marker-offset: 1px;
+ text-align: right;
+}
+OL LI:before {
+ content: "" counter(gencnt) ".";
+ counter-increment: gencnt;
+}
+.home {
+ line-height/* */ : 150%;
+ text-align: center;
+}
+.tit {
+ line-height/* */ : 150%;
+}
+.tgen {
+ line-height/* */ : 120%;
+}
+
+P * CENTER {
+ text-align: center;
+}
=====================================
debian/imgs/HowTo.css
=====================================
@@ -0,0 +1,67 @@
+/* GENOME INFORMATICS */
+/* RESEARCH LABORATORY */
+/* GFFTOOLS HowTo Style Sheet */
+
+/*$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
=====================================
debian/imgs/dmd.gif
=====================================
Binary files /dev/null and b/debian/imgs/dmd.gif differ
=====================================
debian/imgs/genome.js
=====================================
@@ -0,0 +1,140 @@
+//
+// 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: </TH><TD class="path"> ' + urlArray[i] + '</TD></TR>');
+ document.writeln('<TR><TH class="path" width=50 align=right>Line number: </TH><TD class="path"> ' + lnoArray[i] + '</TD></TR>');
+ document.writeln('<TR><TH class="path" width=50 align=right>Message: </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: </TH><TD class="path"> ' + urlArray[i] + '</TD></TR>');
+ document.writeln('<TR><TH class="path" width=50 align=right>Line number: </TH><TD class="path"> ' + lnoArray[i] + '</TD></TR>');
+ document.writeln('<TR><TH class="path" width=50 align=right>Message: </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 at 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 <I>"+theDate+"</I> © Genome BioInformatics Research Laboratory</B>");
+}
+//
+function LastUpdateSplit() {
+ var theDate = "";
+ theDate = document.lastModified;
+ document.write("<B>Last Updated <I>"+theDate+"</I><BR>© Genome BioInformatics Research Laboratory</B>");
+}
+// Expiration date: NewIcon("MM/DD/YYYY")
+function NewIcon(todate) {
+ NewHTML(todate," <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(" "+toput); }
+ else { document.write(" "); }
+}
+
+/*
+ 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
=====================================
debian/imgs/get_from_web_archive
=====================================
@@ -0,0 +1,7 @@
+# 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
=====================================
debian/imgs/lhr.gif
=====================================
Binary files /dev/null and b/debian/imgs/lhr.gif differ
=====================================
debian/imgs/top.gif
=====================================
Binary files /dev/null and b/debian/imgs/top.gif differ
=====================================
debian/patches/fis-privacy-breach.patch
=====================================
@@ -0,0 +1,208 @@
+Description: Fix privacy issues by linking to local images, js and css locally
+Author: Andreas Tille <tille at debian.org>
+Last-Update Sat, 20 Oct 2018 14:15:43 +0200
+
+--- a/examples/mhcregion/index.html
++++ b/examples/mhcregion/index.html
+@@ -9,12 +9,12 @@
+ <META NAME="description" CONTENT="GFF2APLOT HOWTOs: Analyzing SIM output for a syntenic sequences pair.">
+ <TITLE>GFF2APLOT HOWTOs: SIM output for a syntenic sequences pair.</TITLE>
+ <!-- <BASE HREF="http://genome.imim.es/software/gfftools/gff2aplot_docs/mhcregion/"> -->
+-<link rel=stylesheet type="text/css" href="http://genome.imim.es/Genome.css" title="Genome">
+-<link rel=stylesheet type="text/css" href="http://genome.imim.es/software/gfftools/gff2aplot_docs/HowTo.css" title="Genome">
++<link rel=stylesheet type="text/css" href="../imgs/Genome.css" title="Genome">
++<link rel=stylesheet type="text/css" href="../imgs/HowTo.css" title="Genome">
+ <STYLE type="text/css">
+- @import url(http://genome.imim.es/Genome_forms_mozilla.css);
++ @import url(file:///usr/share/doc/gff2aplot/examples/imgs/Genome_forms_mozilla.css);
+ </STYLE>
+-<SCRIPT type="text/javascript" src="http://genome.imim.es/Genome.js"></SCRIPT>
++<SCRIPT type="text/javascript" src="../imgs/Genome.js"></SCRIPT>
+ </head>
+
+ <body onResize="init();" MARGINWIDTH="2" MARGINHEIGHT="0">
+@@ -81,39 +81,39 @@
+ <a href="http://www.imim.es/"
+ onMouseover="window.status='Institut Municipal d\'Investigació Mèdica';">IMIM</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://www.upf.es/"
+ onMouseover="window.status='Universitat Pompeu Fabra';">UPF</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://www.crg.es/"
+ onMouseover="window.status='Centre de Regulació Genòmica';">CRG</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://www.imim.es/grib/eng/default.htm"
+ onMouseover="window.status='Grup de Recerca en Informtica Biomèdica';">GRIB</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <A HREF="http://genome.imim.es/index.html" onMouseover="window.status='Genome Informatics Research Laboratory HOME PAGE: You are Welcome!!!'">
+-<IMG SRC="http://genome.imim.es/g_icons/lhr.gif" ALT="HOME" HEIGHT=10 WIDTH=36 BORDER=0>
++<IMG SRC="../imgs/lhr.gif" ALT="HOME" HEIGHT=10 WIDTH=36 BORDER=0>
+ </A>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://genome.imim.es/main/software.html"
+ onMouseover="window.status='Software';">SOFTWARE</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#TOP"
+ onMouseover="window.status='This is the main page for GFF2APLOT.';">gff2aplot</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#HOWTOS"
+ onMouseover="window.status='GFF2APLOT Tutorials...';">HowTo</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://genome.imim.es/software/gfftools/gff2aplot_docs/mhcregion/index.html#TOP"
+ onMouseover="window.status='An Alignment from WU-BLAST';">SIM Data</a>
+@@ -164,7 +164,7 @@ Bitmaps for the examples were generated
+ <TD class="section" width=20% ALIGN=RIGHT>
+ <a href="index.html#TOP"
+ onMouseover="window.status='TOP of the PAGE';">
+-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
++<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+ </TD></TR>
+ </TABLE>
+ <P> <BR class="hh">
+@@ -188,7 +188,7 @@ $BIN/ali2gff -x "X87344" \
+ <TD class="section" width=20% ALIGN=RIGHT>
+ <a href="index.html#TOP"
+ onMouseover="window.status='TOP of the PAGE';">
+-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
++<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+ </TD></TR>
+ </TABLE>
+ <P> <BR class="hh">
+@@ -240,7 +240,7 @@ gff2aplot.pl
+ <TD class="section" width=20% ALIGN=RIGHT>
+ <a href="index.html#TOP"
+ onMouseover="window.status='TOP of the PAGE';">
+-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
++<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+ </TD></TR>
+ </TABLE>
+ <P> <BR class="hh">
+@@ -275,7 +275,7 @@ gff2aplot.pl
+ <TD class="section" width=20% ALIGN=RIGHT>
+ <a href="index.html#TOP"
+ onMouseover="window.status='TOP of the PAGE';">
+-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
++<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+ </TD></TR>
+ </TABLE>
+ <P> <BR class="hh">
+--- a/examples/wublast/index.html
++++ b/examples/wublast/index.html
+@@ -9,12 +9,12 @@
+ <META NAME="description" CONTENT="GFF2APLOT HOWTOs: Analizing data from WU-BLAST alignment output.">
+ <TITLE>GFF2APLOT HOWTOs: Plotting WU-BLAST Results.</TITLE>
+ <!-- <BASE HREF="http://genome.imim.es/software/gfftools/gff2aplot_docs/wublast/"> -->
+-<link rel=stylesheet type="text/css" href="http://genome.imim.es/Genome.css" title="Genome">
+-<link rel=stylesheet type="text/css" href="http://genome.imim.es/software/gfftools/gff2aplot_docs/HowTo.css" title="Genome">
++<link rel=stylesheet type="text/css" href="../imgs/Genome.css" title="Genome">
++<link rel=stylesheet type="text/css" href="../imgs/HowTo.css" title="Genome">
+ <STYLE type="text/css">
+- @import url(http://genome.imim.es/Genome_forms_mozilla.css);
++ @import url(file:///usr/share/doc/gff2aplot/examples/imgs/Genome_forms_mozilla.css);
+ </STYLE>
+-<SCRIPT type="text/javascript" src="http://genome.imim.es/Genome.js"></SCRIPT>
++<SCRIPT type="text/javascript" src="../imgs/Genome.js"></SCRIPT>
+ </head>
+
+ <body onResize="init();" MARGINWIDTH="2" MARGINHEIGHT="0">
+@@ -81,39 +81,39 @@
+ <a href="http://www.imim.es/"
+ onMouseover="window.status='Institut Municipal d\'Investigació Mèdica';">IMIM</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://www.upf.es/"
+ onMouseover="window.status='Universitat Pompeu Fabra';">UPF</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://www.crg.es/"
+ onMouseover="window.status='Centre de Regulació Genòmica';">CRG</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://www.imim.es/grib/eng/default.htm"
+ onMouseover="window.status='Grup de Recerca en Informtica Biomèdica';">GRIB</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <A HREF="http://genome.imim.es/index.html" onMouseover="window.status='Genome Informatics Research Laboratory HOME PAGE: You are Welcome!!!'">
+-<IMG SRC="http://genome.imim.es/g_icons/lhr.gif" ALT="HOME" HEIGHT=10 WIDTH=36 BORDER=0>
++<IMG SRC="../imgs/lhr.gif" ALT="HOME" HEIGHT=10 WIDTH=36 BORDER=0>
+ </A>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://genome.imim.es/main/software.html"
+ onMouseover="window.status='Software';">SOFTWARE</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#TOP"
+ onMouseover="window.status='This is the main page for GFF2APLOT.';">gff2aplot</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#HOWTOS"
+ onMouseover="window.status='GFF2APLOT Tutorials...';">HowTo</a>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+-<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
++<IMG SRC="../imgs/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
+ </td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
+ <a href="http://genome.imim.es/software/gfftools/gff2aplot_docs/wublast/index.html#TOP"
+ onMouseover="window.status='An Alignment from WU-BLAST';">WU-BLAST Data</a>
+@@ -163,7 +163,7 @@ Bitmaps for the examples were generated
+ <TD class="section" width=20% ALIGN=RIGHT>
+ <a href="index.html#TOP"
+ onMouseover="window.status='TOP of the PAGE';">
+-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
++<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+ </TD></TR>
+ </TABLE>
+ <P> <BR class="hh">
+@@ -212,7 +212,7 @@ $BIN/parseblast.pl --verbose --no-frame
+ <TD class="section" width=20% ALIGN=RIGHT>
+ <a href="index.html#TOP"
+ onMouseover="window.status='TOP of the PAGE';">
+-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
++<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+ </TD></TR>
+ </TABLE>
+ <P> <BR class="hh">
+@@ -263,7 +263,7 @@ gff2aplot.pl
+ <TD class="section" width=20% ALIGN=RIGHT>
+ <a href="index.html#TOP"
+ onMouseover="window.status='TOP of the PAGE';">
+-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
++<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+ </TD></TR>
+ </TABLE>
+ <P> <BR class="hh">
+@@ -313,7 +313,7 @@ gff2aplot.pl
+ <TD class="section" width=20% ALIGN=RIGHT>
+ <a href="index.html#TOP"
+ onMouseover="window.status='TOP of the PAGE';">
+-<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
++<IMG class="pnt" SRC="../imgs/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
+ </TD></TR>
+ </TABLE>
+ <P> <BR class="hh">
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@
03-parseblast.diff
use-dpkg-buildflags.patch
mayhem.patch
+fis-privacy-breach.patch
=====================================
debian/source/include-binaries
=====================================
@@ -0,0 +1,4 @@
+debian/imgs/top.gif
+debian/imgs/lhr.gif
+debian/imgs/dmd.gif
+
View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/compare/adac41139a97edb6f5f8088df8ef92ab8f317275...0dd91f60236262da22b5927f5421e363e1ab52bc
--
View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/compare/adac41139a97edb6f5f8088df8ef92ab8f317275...0dd91f60236262da22b5927f5421e363e1ab52bc
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