debian/changelog

+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

debian/compat

-10
+11

debian/control

@@ -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

debian/copyright

-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

debian/examples

 examples/*
+debian/imgs

debian/imgs/Genome.css

+/* 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

+/*     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

+/*      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/genome.js

+//
+// 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

debian/imgs/get_from_web_archive

+# 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/patches/fis-privacy-breach.patch

+Description: Fix privacy issues by linking to local images, js and css locally
+Author: Andreas Tille <tille@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\'Investigaci&oacute; M&egrave;dica';">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 Regulaci&oacute; Gen&ograve;mica';">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 Biom&egrave;dica';">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\'Investigaci&oacute; M&egrave;dica';">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 Regulaci&oacute; Gen&ograve;mica';">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 Biom&egrave;dica';">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

+debian/imgs/top.gif
+debian/imgs/lhr.gif
+debian/imgs/dmd.gif
+