diff --git a/js/dotplot.js b/js/dotplot.js
index 7654019..59fb8ce 100755
--- a/js/dotplot.js
+++ b/js/dotplot.js
@@ -24,20 +24,6 @@ init_pars( {
'breakid': '',
'strict': 10
});
-const goc = {
- left: 80,
- right: 40,
- width: 200,
- "top": 20,
- bottom: 40,
- height: 200
-};
-const dot_margin = {
- "top": 30,
- right: 60,
- bottom: goc.top + goc.bottom,
- left: goc.left + goc.right
-};
var margin = {};
var scales = {};
@@ -99,6 +85,20 @@ function draw_plot() {
if (win_height == 0) {
win_height = Math.floor( $( window ).height() * height_percent );
}
+ const goc = {
+ left: 80,
+ right: 40,
+ width: Math.min(win_width * 0.2, 200),
+ "top": 20,
+ bottom: 40,
+ height: Math.min(win_height * 0.2, 200)
+ };
+ const dot_margin = {
+ "top": 30,
+ right: 60,
+ bottom: goc.top + goc.bottom,
+ left: goc.left + goc.right
+ };
var offset = $("#canvas").offset();
var stats = {
@@ -487,9 +487,8 @@ function draw_plot() {
if (get_par( 'show_goc' ) == false) {
gocx_container.style({ "display": "none" });
gocy_container.style({ "display": "none" });
- }
-
- // FIlter data
+ } else {
+ // Filter data
const goc1 = data.gocs[get_par("sp1")].filter(function(d) { return d.pos >= get_par( 'start1' ) && d.pos <= get_par( 'end1' ) });
const goc2 = data.gocs[get_par("sp2")].filter(function(d) { return d.pos >= get_par( 'start2' ) && d.pos <= get_par( 'end2' ) });
@@ -517,68 +516,70 @@ function draw_plot() {
.attr("stroke-width", "2")
.attr("fill", "none");
- // Add GOC X axes
- const gocx_axes = gocx_container.append("g")
- .attr( "name", "gocx_axes" )
- .attr( "class", "svg_axes" )
-
- const gocx_xAxis = d3.svg.axis().scale( scales.x ).orient( "bottom" );
- gocx_axes.append("g")
- .attr("transform", "translate(" + 0 + "," + goc.height + ")")
- .attr("class", "x axis")
- .call(gocx_xAxis);
-
- const gocx_yAxis = d3.svg.axis().scale( gocx_scale ).orient( "left" );
- gocx_axes.append("g")
- .attr("class", "y axis")
- .call(gocx_yAxis);
- const gocx_yAxis_right = d3.svg.axis().scale( gocx_scale ).orient( "right" );
- gocx_axes.append("g")
- .attr("transform", "translate(" + (win_width - margin.left - margin.right) + "," + 0 + ")")
- .attr("class", "y axis")
- .call(gocx_yAxis_right);
-
- // Add GOC Y axes
- const gocy_axes = gocy_container.append("g")
- .attr( "name", "gocy_axes" )
- .attr( "class", "svg_axes" )
-
- const gocy_yAxis = d3.svg.axis().scale( scales.y ).orient( "left" );
- gocy_axes.append("g")
- .attr("class", "y axis")
- .call(gocy_yAxis);
-
- const gocy_xAxis = d3.svg.axis().scale( gocy_scale ).orient( "bottom" );
- gocy_axes.append("g")
- .attr("transform", "translate(" + 0 + "," + (win_height - margin.top - margin.bottom) + ")")
- .attr("class", "y axis")
- .call(gocy_xAxis);
-
- const gocy_xAxis_top = d3.svg.axis().scale( gocy_scale ).orient( "top" );
- gocy_axes.append("g")
- .attr("class", "y axis")
- .call(gocy_xAxis_top);
-
-// #### EDIT IN PROGRESS
- // Add GOC labels
- var texts = svg.append("g");
-
- texts.append("text")
- .attr("class", "y_goc label")
- .attr("text-anchor", "middle")
- .attr("x", 180)
- .attr("y", 485)
- .text( "GOC" );
- texts.append("text")
- .attr("class", "x_goc label")
- .attr("text-anchor", "middle")
- .attr("y", margin.left - 40)
- .attr("x", -567)
- .attr("transform", "rotate(-90)")
- .text( "GOC" );
-// #####
+ // Add GOC X axes
+ const gocx_axes = gocx_container.append("g")
+ .attr( "name", "gocx_axes" )
+ .attr( "class", "svg_axes" )
+
+ const gocx_xAxis = d3.svg.axis().scale( scales.x ).orient( "bottom" );
+ gocx_axes.append("g")
+ .attr("transform", "translate(" + 0 + "," + goc.height + ")")
+ .attr("class", "x axis")
+ .call(gocx_xAxis);
+
+ const gocx_yAxis = d3.svg.axis().scale( gocx_scale ).orient( "left" );
+ gocx_axes.append("g")
+ .attr("class", "y axis")
+ .call(gocx_yAxis);
+ const gocx_yAxis_right = d3.svg.axis().scale( gocx_scale ).orient( "right" );
+ gocx_axes.append("g")
+ .attr("transform", "translate(" + (win_width - margin.left - margin.right) + "," + 0 + ")")
+ .attr("class", "y axis")
+ .call(gocx_yAxis_right);
+
+ // Add GOC Y axes
+ const gocy_axes = gocy_container.append("g")
+ .attr( "name", "gocy_axes" )
+ .attr( "class", "svg_axes" )
+
+ const gocy_yAxis = d3.svg.axis().scale( scales.y ).orient( "left" );
+ gocy_axes.append("g")
+ .attr("class", "y axis")
+ .call(gocy_yAxis);
+
+ const gocy_xAxis = d3.svg.axis().scale( gocy_scale ).orient( "bottom" );
+ gocy_axes.append("g")
+ .attr("transform", "translate(" + 0 + "," + (win_height - margin.top - margin.bottom) + ")")
+ .attr("class", "y axis")
+ .call(gocy_xAxis);
+
+ const gocy_xAxis_top = d3.svg.axis().scale( gocy_scale ).orient( "top" );
+ gocy_axes.append("g")
+ .attr("class", "y axis")
+ .call(gocy_xAxis_top);
+
+ // Add GOC labels
+ var texts = goc_container.append("g");
+
+ // Horizontal GOC label
+ texts.append("text")
+ .attr("class", "y_goc label")
+ .attr("text-anchor", "middle")
+ .attr("x", (margin.left * 0.8))
+ .attr("y", win_height - margin.bottom * 0.2)
+ .text( "GOC" );
+
+ // Vertical GOC label
+ texts.append("text")
+ .attr("class", "x_goc label")
+ .attr("text-anchor", "middle")
+ .attr("y", -margin.left * 0.3)
+ .attr("x", win_height - margin.bottom * 0.8)
+ .attr("transform", "rotate(90)")
+ .text( "GOC" );
+ }
- // When the graph is drawn, prepare a file to dowload it
+ // When the graph is drawn, prepare a file to download it
update_download_link( svg_style );
update_stats( stats );
}
@@ -950,11 +951,10 @@ function show_hide_button( parname, elementid, label ) {
}
update_permalink();
- if (elementid == "goc_lines") {
- console.log("Rebuild dotplot after after toggling GOC");
- draw_plot();
- }
-
+ if (elementid == "goc_lines") {
+ console.log("Rebuild dotplot after after toggling GOC");
+ draw_plot();
+ }
});
}
diff --git a/js/index.js b/js/index.js
index 7c7b8ad..81a1694 100755
--- a/js/index.js
+++ b/js/index.js
@@ -1,3 +1,5 @@
+//import { check_data_error } from "./utils.js";
+
function print_db() {
pars = {};
pars.type = 'databases';
@@ -5,12 +7,26 @@ function print_db() {
console.log(str);
console.log(format_url(urls.get_data, pars));
$.getJSON( urls.get_data, pars, function(data) {
+ error_msg = check_data_error(data);
+ if (error_msg) {
+ $( "#databases" ).append( error_msg );
+ } else {
print_db_table(data);
+ }
}).fail(function(){
console.log("Failed databases retrieval");
});
}
+function check_data_error( data ) {
+ error_msg = ""
+ if ("outcome" in data && data["outcome"] == false) {
+ console.log("Error occurred: " + data["details"]);
+ error_msg = $("").text("An error occurred: " + data["message"] + ". Check the console for more details.");
+ }
+ return error_msg;
+}
+
function get_dbs() {
var dbs = {};
diff --git a/js/ranking.js b/js/ranking.js
index e23cecd..2875324 100755
--- a/js/ranking.js
+++ b/js/ranking.js
@@ -1,5 +1,6 @@
var cached_data = {};
var cached_data_ajax = null;
+synteruptor_version = "1.0";
init_pars( {
"sp1" : "",
@@ -42,6 +43,47 @@ function prepare_csv(data) {
$("#csv_link").trigger( "click" );
}
+// Handle antismash download link
+function to_antismash(data) {
+ tool = {
+ "name": "synteruptor",
+ "version": synteruptor_version,
+ "description": "Synteny breaks explorer",
+ };
+ records = [];
+ for (var br of data) {
+ subregions = {
+ "label": "break_" + br["breakid"],
+ "start": br["loc_start1"],
+ "end": br["loc_end1"],
+ }
+ record = {
+ "name": br["gpart1"],
+ "subregions": subregions,
+ }
+ records.push(record);
+ }
+ json_data = {
+ "tool": tool,
+ "records": records,
+ }
+ return JSON.stringify(json_data, null, 4);
+}
+
+function update_antismash_link(data) {
+ $('#antismash_link').attr( "href", "" );
+ $('#antismash_link').attr( "download", "" );
+ json_data = to_antismash(data);
+ $('#antismash_link').attr('download', 'breaks_table_antismash.json');
+ $('#antismash_link').attr('href', 'data:application/csv;charset=utf-8,' + encodeURIComponent(json_data));
+}
+
+function prepare_antismash_link(data) {
+ update_antismash_link(data);
+ $("#antismash_link").off( "click" );
+ $("#antismash_link").trigger( "click" );
+}
+
// Links
function break_link(b) {
link_pars = {
@@ -144,7 +186,7 @@ function update_table(data) {
}
$table.append($body_tag);
$table.show();
- $table.stickyTableHeaders( {'fixedOffset': $("#entete")} );
+ $table.stickyTableHeaders();
$table.tablesorter();
$('tr').hover(function(e) {
@@ -216,6 +258,12 @@ function update_page(init_data) {
.on( "click", function() {
prepare_csv( data );
});
+ $( "#antismash_link" )
+ .attr( "href", "" )
+ .attr( "download", "" )
+ .on( "click", function() {
+ prepare_antismash_link( data );
+ });
}
}
diff --git a/lib_db.php b/lib_db.php
index f612132..c74c8fd 100755
--- a/lib_db.php
+++ b/lib_db.php
@@ -9,7 +9,7 @@
// Check variable type (convert if necessary)
function parseVal($dat) {
foreach ($dat as $key => $val) {
- if ( ctype_digit( $val ) ) {
+ if ( ctype_digit((string)$val) ) {
$dat[ $key ] = intval( $val );
} elseif (is_numeric($val)) {
$dat[ $key ] = floatval( $val );
@@ -30,8 +30,11 @@ function die_msg($message = '', $details = '') {
function get_available_dbs_list( $all = true , $authorised = array()) {
global $dbdir;
$files = scandir($dbdir);
- // remove dirs
$hfiles = array();
+ if (!$files) {
+ return $hfiles;
+ }
+ // remove dirs
for ($i = 0 ; $i < count($files); $i++) {
if ($files[$i] == '.'
or $files[$i] == '..'
@@ -461,8 +464,21 @@ function get_ranking_data($dbh) {
$limit = ' LIMIT 10000';
$condition = join(' AND ', $cond);
$order = ' ORDER BY ' . join(', ', $ord);
- $query = 'SELECT *, (real_size2 * 100.0 / (real_size1 + real_size2)) AS diff FROM breaks_ranking LEFT JOIN breaks_all ON breaks_ranking.breakid=breaks_all.breakid WHERE ' . $condition . $order . $limit;
+ $select = 'SELECT breaks_ranking.*, breaks_all.*';
+ $select .= ', (real_size2 * 100.0 / (real_size1 + real_size2)) AS diff ';
+ $select .= ', gleft1.loc_start AS loc_start1';
+ $select .= ', gright1.loc_end AS loc_end1';
+ $select .= ', gleft2.loc_start AS loc_start2';
+ $select .= ', gright2.loc_end AS loc_end2';
+ $from = 'FROM breaks_ranking ';
+ $joins = 'LEFT JOIN breaks_all ON breaks_ranking.breakid=breaks_all.breakid ';
+ $joins .= 'LEFT JOIN genes gleft1 ON (pnum_all_left1 = gleft1.pnum_all and breaks_all.sp1 = gleft1.sp) ';
+ $joins .= 'LEFT JOIN genes gright1 ON (pnum_all_right1 = gright1.pnum_all and breaks_all.sp1 = gright1.sp) ';
+ $joins .= 'LEFT JOIN genes gleft2 ON (pnum_all_left2 = gleft2.pnum_all and breaks_all.sp2 = gleft2.sp) ';
+ $joins .= 'LEFT JOIN genes gright2 ON (pnum_all_right2 = gright2.pnum_all and breaks_all.sp2 = gright2.sp) ';
+ $query = "$select $from $joins WHERE $condition $order $limit";
return get_db_data($dbh, $query, $vals);
+ return $query;
}
/************************************************************
diff --git a/ranking.php b/ranking.php
index f8399ef..61940a1 100755
--- a/ranking.php
+++ b/ranking.php
@@ -56,7 +56,8 @@
- Download Table (CSV)
+ Download Table (CSV)
+ Download antismash link (JSON)
No breaks