diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..cdacafa --- /dev/null +++ b/.gitignore @@ -0,0 +1,11 @@ +public/user_data/* +!public/user_data/.htaccess +public/user_uploads/* +!public/user_uploads/.htaccess + + +*.delta +!public/sample.delta +python_env +reproducibility + diff --git a/.htaccess b/.htaccess new file mode 100644 index 0000000..a8c4ceb --- /dev/null +++ b/.htaccess @@ -0,0 +1,8 @@ +RewriteEngine On +RewriteBase /assemblytics/ + +RewriteCond %{THE_REQUEST} /public/([^\s?]*) [NC] +RewriteRule ^ %1 [L,NE,R=302] + +RewriteRule ^((?!public/).*)$ public/$1 [L,NC] + diff --git a/Assemblytics_variant_charts.R b/Assemblytics_variant_charts.R deleted file mode 100755 index 4e7660f..0000000 --- a/Assemblytics_variant_charts.R +++ /dev/null @@ -1,156 +0,0 @@ -library(ggplot2) -library(plyr) - -args<-commandArgs(TRUE) -output_prefix <- args[1] -abs_min_var <- as.numeric(args[2]) -abs_max_var <- as.numeric(args[3]) - - -filename <- paste(output_prefix,".Assemblytics_structural_variants.bed",sep="") - -bed <- read.csv(filename, sep="\t", quote='', header=TRUE) - -names(bed)[1:11] <- c("chrom","start","stop","name","size","strand","type","ref.dist","query.dist","contig_position","method.found") - -# bed$type <- factor(bed$type, levels = c("Insertion","Deletion","Repeat_expansion","Repeat_contraction","Tandem_expansion","Tandem_contraction")) - -bed$type <- revalue(bed$type, c("Repeat_expansion"="Repeat expansion", "Repeat_contraction"="Repeat contraction", "Tandem_expansion"="Tandem expansion", "Tandem_contraction"="Tandem contraction")) - -types.allowed <- c("Insertion","Deletion","Repeat expansion","Repeat contraction","Tandem expansion","Tandem contraction") -bed$type <- factor(bed$type, levels = types.allowed) - -theme_set(theme_bw(base_size = 12)) - - -library(RColorBrewer) -# display.brewer.all() - -color_palette_name <- "Set1" -big_palette<-brewer.pal(9,"Set1")[c(1,2,3,4,5,7)] - -# Nature-style formatting for publication using commas (e.g.: 7,654,321) -comma_format<-function(num) { - formatC(abs(num),format="f",big.mark=",",drop0trailing = TRUE) -} - - - -############### FOR LOG PLOT ############### -alt <- bed - -alt[alt$type=="Deletion",]$size <- -1*alt[alt$type=="Deletion",]$size -alt[alt$type=="Repeat contraction",]$size <- -1*alt[alt$type=="Repeat contraction",]$size -alt[alt$type=="Tandem contraction",]$size <- -1*alt[alt$type=="Tandem contraction",]$size - -alt$Type <- "None" -if (nrow(alt[alt$type %in% c("Insertion","Deletion"),]) > 0) { - alt[alt$type %in% c("Insertion","Deletion"),]$Type <- "Indel" -} -if (nrow(alt[alt$type %in% c("Tandem expansion","Tandem contraction"),]) > 0) { - alt[alt$type %in% c("Tandem expansion","Tandem contraction"),]$Type <- "Tandem" -} -if (nrow(alt[alt$type %in% c("Repeat expansion","Repeat contraction"),]) > 0) { - alt[alt$type %in% c("Repeat expansion","Repeat contraction"),]$Type <- "Repeat" -} - -############################################# - - - -####### Run plotting with various size ranges and with either all variants or only indels ###### -var_size_cutoffs <- c(abs_min_var,10,50,500,abs_max_var) -var_size_cutoffs <- var_size_cutoffs[var_size_cutoffs>=abs_min_var & var_size_cutoffs<=abs_max_var] - -for (to_png in c(TRUE,FALSE)) { - indels_only = FALSE -# for (indels_only in c(TRUE,FALSE)) { - var_type_filename <- "all_variants" - if (indels_only) { - var_type_filename <- "indels" - } - for (i in seq(1,length(var_size_cutoffs)-1)) { - min_var <- var_size_cutoffs[i] - max_var <- var_size_cutoffs[i+1] - if (min_var < abs_max_var && max_var > abs_min_var) - { - types_to_plot = types.allowed - if (indels_only) { - types_to_plot <- c("Insertion","Deletion") - } - filtered_bed <- bed[bed$size>=min_var & - bed$size<=max_var & - bed$type %in% types_to_plot,] - filtered_bed$type <- factor(filtered_bed$type,levels=types_to_plot) - binwidth <- max_var/100 - if (binwidth < 1) { - binwidth <- 1 - } - - if (nrow(filtered_bed)>0) { - if (to_png) { - png(paste(output_prefix,".Assemblytics.size_distributions.", var_type_filename, ".", min_var, "-",max_var, ".png", sep=""),1000,1000,res=200) - } else { - pdf(paste(output_prefix,".Assemblytics.size_distributions.", var_type_filename, ".", min_var, "-",max_var, ".pdf", sep="")) - } - - print(ggplot(filtered_bed,aes(x=size, fill=type)) + - geom_histogram(binwidth=binwidth) + - scale_fill_manual(values=big_palette,drop=FALSE) + - facet_grid(type ~ .,drop=FALSE) + - labs(fill="Variant type",x="Variant size",y="Count",title=paste("Variants",comma_format(min_var),"to", comma_format(max_var),"bp")) + - scale_x_continuous(labels=comma_format,expand=c(0,0),limits=c(min_var,max_var)) + - scale_y_continuous(labels=comma_format,expand=c(0,0)) + - theme( - strip.text=element_blank(),strip.background=element_blank(), - plot.title = element_text(vjust=3), - axis.text=element_text(size=8), - panel.grid.minor = element_line(colour = NA), - panel.grid.major = element_line(colour = NA) - ) - ) - - dev.off() - } else { - print("No variants in plot:") - print(paste("min_var=",min_var)) - print(paste("max_var=",max_var)) - } - - } - - } - - - # LOG PLOT: - if (to_png) { - png(paste(output_prefix,".Assemblytics.size_distributions.", var_type_filename, ".log_all_sizes.png", sep=""),width=2000,height=1000,res=200) - } else { - pdf(paste(output_prefix,".Assemblytics.size_distributions.", var_type_filename, ".log_all_sizes.pdf", sep="")) - } - - print(ggplot(alt,aes(x=size, fill=type,y=..count..+1)) + - geom_histogram(binwidth=abs_max_var/100) + - scale_fill_manual(values=big_palette,drop=FALSE) + - facet_grid(Type ~ .,drop=FALSE) + - labs(fill="Variant type",x="Variant size",y="Log(count + 1)",title=paste("Variants",comma_format(abs_min_var),"to", comma_format(abs_max_var),"bp")) + - scale_x_continuous(labels=comma_format,expand=c(0,0),limits=c(-1*abs_max_var,abs_max_var)) + - # scale_y_continuous(labels=comma_format,expand=c(0,0)) + - scale_y_log10(labels=comma_format,expand=c(0,0)) + - annotation_logticks(sides="l") + - theme( - strip.text=element_blank(),strip.background=element_blank(), - plot.title = element_text(vjust=3), - axis.text=element_text(size=8), - panel.grid.minor = element_line(colour = NA), - panel.grid.major = element_line(colour = NA) - ) - ) - dev.off() -# } -} - -############################################################################## - - - diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..a6e8d68 --- /dev/null +++ b/LICENSE @@ -0,0 +1,22 @@ + +The MIT License (MIT) + +Copyright (c) 2016 Maria Nattestad + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md index 4b91d64..7d74e1f 100644 --- a/README.md +++ b/README.md @@ -4,19 +4,47 @@ Assemblytics is available online at http://assemblytics.com Please cite our paper in Bioinformatics: http://www.ncbi.nlm.nih.gov/pubmed/27318204 -If you prefer to run Assemblytics from the command-line this repository contains all the code, from unique anchor filtering and calling variants to creating the output plots and summary tables. +The preprint is still freely available on the BioRxiv: https://www.biorxiv.org/content/10.1101/044925v1 -The whole web application can also be downloaded and run locally, utilizing the graphical user interface and giving the added benefit of the interactive dot plot which is only available in the web version: https://github.com/marianattestad/assemblytics_web +There are three ways to use Assemblytics: +1. Use the hosted online version at http://assemblytics.com. This is the easiest option. +2. Run it from the command-line. For this you need only the contents of the `scripts/` directory. See instructions below. +3. Run the full web app from a local server. See instructions below. +Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference. -To run Assemblytics on the command-line, simply copy all the scripts in this repository into your path and make them executable (chmod +x script_name) if necessary. +## Dependencies +- R + - ggplot2 + - plyr + - RColorBrewer + - scales +- Python + - argparse + - numpy -Follow the instructions at http://assemblytics.com for how to prepare your data and get a delta file for Assemblytics. +## Command-line instructions +If you prefer to run Assemblytics from the command-line the scripts/ directory contains all the code you need, from unique anchor filtering and calling variants to creating the output plots and summary tables. -Then run as: +To run Assemblytics on the command-line, keep all the scripts together inside the `scripts/` directory, either in your PATH or anywhere else you like, and make them all executable: +``` +chmod a+x scripts/Assemblytics* ``` -Assemblytics delta_file output_prefix unique_anchor_length path_to_R_scripts +Keeping the scripts together in the same folder will allow the main `Assemblytics` script to call all the other scripts that do filtering, analysis, indexing, and plotting. + +Follow the instructions at http://assemblytics.com for how to prepare your data and get a delta file for Assemblytics. +Then run Assemblytics: + +``` +scripts/Assemblytics ``` -Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference. +## Local web app instructions +The whole web application can be downloaded and run locally, utilizing the graphical user interface and giving the added benefit of the interactive dot plot which is only available in the web version and cannot run from the CLI. + +Notes for installation: +- Use a local server like [Apache](https://www.apachefriends.org/download.html) and follow the instructions there. +- Clone this repository into a folder called `assemblytics`, to make the `.htaccess` file point the server correctly to the `public/` folder, where the index.php and other pages and web app resources are located. +- Make sure to open up permissions in user_uploads and user_data so the webserver can read and write there. +- It does not contain the examples as some of these are huge files. diff --git a/public/README.md b/public/README.md new file mode 100644 index 0000000..a2cdd11 --- /dev/null +++ b/public/README.md @@ -0,0 +1,22 @@ +# Assemblytics (full web application) + +This repo contains the full Assemblytics web application. +The web app is running on assemblytics.com, and the command-line version is available at https://github.com/marianattestad/assemblytics +This repository exists so you can install it on your own servers or locally on your computer if need be. +The code here includes the interactive dot plot (which you can't use from the command-line version). + +Dependencies: +- R + - ggplot + - plyr +- Python + - argparse + - numpy + + +Notes for installation: +- Make sure to open up permissions in user_uploads and user_data so the webserver can read and write there. +- It does not contain the examples as some of these are huge files. + + + diff --git a/public/analysis.php b/public/analysis.php new file mode 100755 index 0000000..42bae9c --- /dev/null +++ b/public/analysis.php @@ -0,0 +1,133 @@ + + + + + + + + + + + + + + + + + +
+

+
+ +
+ +
+
+ +
+
+ +
+

+ All plots are available as both .png and .pdf files through the Download button below and can be used in publications. Cite Assemblytics. +

+
+
+ + +
+
+

Assembly statistics

+

+
+
+ + +
+
+

Variant summary statistics

+

+
+
+
+
+

Variant file preview

+

+
+
+ + +
+
+

Download all data

+

Download zip file of all results + +

+
+
+
+ + + + + + + + + + + + +
+
+
+

View analysis later

+
+
+ "; + ?> +
+
+
+ + + + +
+
+

Progress

+
+
+
+ Checking progress... +
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/public/check_progress.php b/public/check_progress.php new file mode 100755 index 0000000..4179e0a --- /dev/null +++ b/public/check_progress.php @@ -0,0 +1,14 @@ + diff --git a/public/cite.php b/public/cite.php new file mode 100644 index 0000000..e9e3c69 --- /dev/null +++ b/public/cite.php @@ -0,0 +1,37 @@ + + + + + + + + +
+
+
+

How to cite Assemblytics

+
+
+

Please cite Assemblytics at Bioinformatics: + +http://www.ncbi.nlm.nih.gov/pubmed/27318204 +

+
+

The code is open-source at https://github.com/MariaNattestad/assemblytics (command-line version)

+

https://github.com/MariaNattestad/Assemblytics_web (full web application)

+
+
+
+ + + + + + + + + + diff --git a/public/contact.php b/public/contact.php new file mode 100755 index 0000000..008c54c --- /dev/null +++ b/public/contact.php @@ -0,0 +1,30 @@ + + + + + + + + +
+
+
+

Contact information

+
+
+

Science and web application by Maria Nattestad

+

Principal investigator / The Boss: Mike Schatz

+
+

For questions, email: mnattest@cshl.edu

+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/public/css/bootstrap-theme.min.css b/public/css/bootstrap-theme.min.css new file mode 100755 index 0000000..2e97597 --- /dev/null +++ b/public/css/bootstrap-theme.min.css @@ -0,0 +1,5 @@ +/*! + * Bootstrap v3.2.0 (http://getbootstrap.com) + * Copyright 2011-2014 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + */.btn-default,.btn-primary,.btn-success,.btn-info,.btn-warning,.btn-danger{text-shadow:0 -1px 0 rgba(0,0,0,.2);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075)}.btn-default:active,.btn-primary:active,.btn-success:active,.btn-info:active,.btn-warning:active,.btn-danger:active,.btn-default.active,.btn-primary.active,.btn-success.active,.btn-info.active,.btn-warning.active,.btn-danger.active{-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,.125);box-shadow:inset 0 3px 5px 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color:black; + font-size:3.5em; +} +#header_bar>h3 { + color:black; + font-size:1.5em; +} + +/* View this analysis later url*/ +#codepanel { + word-break:break-all; +} + +#submit_button { + + /*float:right;*/ + /*margin: 20px 40px 40px 40px;*/ + margin: 2% 4% 4% 4%; + +} + +/* Dropzone text */ +.dz-message { + font-size:2em; +} + +#results { + visibility: hidden; +} + +.frame { + margin:0% 2% 2% 2%; +} +.plot_frame { + margin:2% 2% 2% 2%; +} + +/* Navigation bar */ +.navbar-default { + /*background-color: #ffffff;*/ + /*border-color: #d2d2d2;*/ +} +.navbar-default .navbar-brand { + color: #000000; +} +.navbar-default .navbar-brand:hover, .navbar-default .navbar-brand:focus { + color: #000000; +} +.navbar-default .navbar-text { + color: #000000; +} +.navbar-default .navbar-nav > li > a { + color: #000000; +} +.navbar-default .navbar-nav > li > a:hover, .navbar-default .navbar-nav > li > a:focus { + color: #000000; +} +.navbar-default .navbar-nav > .active > a, .navbar-default .navbar-nav > .active > a:hover, .navbar-default .navbar-nav > .active > a:focus { + color: #000000; + background-color: #d2d2d2; +} +.navbar-default .navbar-nav > .open > a, .navbar-default .navbar-nav > .open > a:hover, .navbar-default .navbar-nav > .open > a:focus { + color: #000000; + background-color: #d2d2d2; +} +.navbar-default .navbar-toggle { + border-color: #d2d2d2; +} +.navbar-default .navbar-toggle:hover, .navbar-default .navbar-toggle:focus { + background-color: #d2d2d2; +} +.navbar-default .navbar-toggle .icon-bar { + background-color: #000000; +} +.navbar-default .navbar-collapse, +.navbar-default .navbar-form { + border-color: #000000; +} +.navbar-default .navbar-link { + color: #000000; +} +.navbar-default .navbar-link:hover { + color: #000000; +} + +@media (max-width: 767px) { + .navbar-default .navbar-nav .open .dropdown-menu > li > a { + color: #000000; + } + .navbar-default .navbar-nav .open .dropdown-menu > li > a:hover, .navbar-default .navbar-nav .open .dropdown-menu > li > a:focus { + color: #000000; + } + .navbar-default .navbar-nav .open .dropdown-menu > .active > a, .navbar-default .navbar-nav .open .dropdown-menu > .active > a:hover, .navbar-default .navbar-nav .open .dropdown-menu > .active > a:focus { + color: #000000; + background-color: #d2d2d2; + } +} + + +.panel { + margin:2% 2% 2% 2%; + #border-color:#E8E8E8; +} +.panel > .panel-heading{ + #background-color: #E8E8E8; + #background-image:none; + #border-color:#E8E8E8; + #color:black; +} + + +a.fancybox img { + border: none; + -o-transform: scale(1,1); -ms-transform: scale(1,1); -moz-transform: scale(1,1); -webkit-transform: scale(1,1); transform: scale(1,1); -o-transition: all 0.2s ease-in-out; -ms-transition: all 0.2s ease-in-out; -moz-transition: all 0.2s ease-in-out; -webkit-transition: all 0.2s ease-in-out; transition: all 0.2s ease-in-out; +} +/*a.fancybox:hover img { + position: relative; z-index: 999; -o-transform: scale(1.03,1.03); -ms-transform: scale(1.03,1.03); -moz-transform: scale(1.03,1.03); -webkit-transform: scale(1.03,1.03); transform: scale(1.03,1.03); +}*/ + diff --git a/public/css/dropzone.css b/public/css/dropzone.css new file mode 100644 index 0000000..0494d1c --- /dev/null +++ b/public/css/dropzone.css @@ -0,0 +1,388 @@ +/* + * The MIT License + * Copyright (c) 2012 Matias Meno + */ +@-webkit-keyframes passing-through { + 0% { + opacity: 0; + -webkit-transform: translateY(40px); + -moz-transform: translateY(40px); + -ms-transform: translateY(40px); + -o-transform: translateY(40px); + transform: translateY(40px); } + 30%, 70% { + opacity: 1; + -webkit-transform: translateY(0px); + -moz-transform: translateY(0px); + -ms-transform: translateY(0px); + -o-transform: translateY(0px); + transform: translateY(0px); } + 100% { + opacity: 0; + -webkit-transform: translateY(-40px); + -moz-transform: translateY(-40px); + -ms-transform: translateY(-40px); + -o-transform: translateY(-40px); + transform: translateY(-40px); } } +@-moz-keyframes passing-through { + 0% { + opacity: 0; + -webkit-transform: translateY(40px); + -moz-transform: translateY(40px); + -ms-transform: translateY(40px); + -o-transform: translateY(40px); + transform: translateY(40px); } + 30%, 70% { + opacity: 1; + -webkit-transform: translateY(0px); + -moz-transform: translateY(0px); + -ms-transform: translateY(0px); + -o-transform: translateY(0px); + transform: translateY(0px); } + 100% { + opacity: 0; + -webkit-transform: translateY(-40px); + -moz-transform: translateY(-40px); + -ms-transform: translateY(-40px); + -o-transform: translateY(-40px); + transform: translateY(-40px); } } +@keyframes passing-through { + 0% { + opacity: 0; + -webkit-transform: translateY(40px); + -moz-transform: translateY(40px); + -ms-transform: translateY(40px); + -o-transform: translateY(40px); + transform: translateY(40px); } + 30%, 70% { + opacity: 1; + -webkit-transform: translateY(0px); + -moz-transform: translateY(0px); + -ms-transform: translateY(0px); + -o-transform: translateY(0px); + transform: translateY(0px); } + 100% { + opacity: 0; + -webkit-transform: translateY(-40px); + -moz-transform: translateY(-40px); + -ms-transform: translateY(-40px); + -o-transform: translateY(-40px); + transform: translateY(-40px); } } +@-webkit-keyframes slide-in { + 0% { + opacity: 0; + -webkit-transform: translateY(40px); + -moz-transform: translateY(40px); + -ms-transform: translateY(40px); + -o-transform: translateY(40px); + transform: translateY(40px); } + 30% { + opacity: 1; + -webkit-transform: translateY(0px); + -moz-transform: translateY(0px); + -ms-transform: translateY(0px); + -o-transform: translateY(0px); + transform: translateY(0px); } } +@-moz-keyframes slide-in { + 0% { + opacity: 0; + -webkit-transform: translateY(40px); + -moz-transform: translateY(40px); + -ms-transform: translateY(40px); + -o-transform: translateY(40px); + transform: translateY(40px); } + 30% { + opacity: 1; + -webkit-transform: translateY(0px); + -moz-transform: translateY(0px); + -ms-transform: translateY(0px); + -o-transform: translateY(0px); + transform: translateY(0px); } } +@keyframes slide-in { + 0% { + opacity: 0; + -webkit-transform: translateY(40px); + -moz-transform: translateY(40px); + -ms-transform: translateY(40px); + -o-transform: translateY(40px); + transform: translateY(40px); } + 30% { + opacity: 1; + -webkit-transform: translateY(0px); + -moz-transform: translateY(0px); + -ms-transform: translateY(0px); + -o-transform: translateY(0px); + transform: translateY(0px); } } +@-webkit-keyframes pulse { + 0% { + -webkit-transform: scale(1); + -moz-transform: scale(1); + -ms-transform: scale(1); + -o-transform: scale(1); + transform: scale(1); } + 10% { + -webkit-transform: scale(1.1); + -moz-transform: scale(1.1); + -ms-transform: scale(1.1); + -o-transform: scale(1.1); + transform: scale(1.1); } + 20% { + -webkit-transform: scale(1); + -moz-transform: scale(1); + -ms-transform: scale(1); + -o-transform: scale(1); + transform: scale(1); } } +@-moz-keyframes pulse { + 0% { + -webkit-transform: scale(1); + -moz-transform: scale(1); + -ms-transform: scale(1); + -o-transform: scale(1); + transform: scale(1); } + 10% { + -webkit-transform: scale(1.1); + -moz-transform: scale(1.1); + -ms-transform: scale(1.1); + -o-transform: scale(1.1); + transform: scale(1.1); } + 20% { + -webkit-transform: scale(1); + -moz-transform: scale(1); + -ms-transform: scale(1); + -o-transform: scale(1); + transform: scale(1); } } +@keyframes pulse { + 0% { + -webkit-transform: scale(1); + -moz-transform: scale(1); + -ms-transform: scale(1); + -o-transform: scale(1); + transform: scale(1); } + 10% { + -webkit-transform: scale(1.1); + -moz-transform: scale(1.1); + -ms-transform: scale(1.1); + -o-transform: scale(1.1); + transform: scale(1.1); } + 20% { + -webkit-transform: scale(1); + -moz-transform: scale(1); + -ms-transform: scale(1); + -o-transform: scale(1); + transform: scale(1); } } +.dropzone, .dropzone * { + box-sizing: border-box; } + +.dropzone { + min-height: 150px; + border: 2px solid rgba(0, 0, 0, 0.3); + background: white; + padding: 20px 20px; } + .dropzone.dz-clickable { + cursor: pointer; } + .dropzone.dz-clickable * { + cursor: default; } + .dropzone.dz-clickable .dz-message, .dropzone.dz-clickable .dz-message * { + cursor: pointer; } + .dropzone.dz-started .dz-message { + display: none; } + .dropzone.dz-drag-hover { + border-style: solid; } + .dropzone.dz-drag-hover .dz-message { + opacity: 0.5; } + .dropzone .dz-message { + text-align: center; + margin: 2em 0; } + .dropzone .dz-preview { + position: relative; + display: inline-block; + vertical-align: top; + margin: 16px; + min-height: 100px; } + .dropzone .dz-preview:hover { + z-index: 1000; } + .dropzone .dz-preview:hover .dz-details { + opacity: 1; } + .dropzone .dz-preview.dz-file-preview .dz-image { + border-radius: 20px; + background: #999; + background: linear-gradient(to bottom, #eee, #ddd); } + .dropzone .dz-preview.dz-file-preview .dz-details { + opacity: 1; } + .dropzone .dz-preview.dz-image-preview { + background: white; } + .dropzone .dz-preview.dz-image-preview .dz-details { + -webkit-transition: opacity 0.2s linear; + -moz-transition: opacity 0.2s linear; + -ms-transition: opacity 0.2s linear; + -o-transition: opacity 0.2s linear; + transition: opacity 0.2s linear; } + .dropzone .dz-preview .dz-remove { + font-size: 14px; + text-align: center; + display: block; + cursor: pointer; + border: none; } + .dropzone .dz-preview .dz-remove:hover { + text-decoration: underline; } + .dropzone .dz-preview:hover .dz-details { + opacity: 1; } + .dropzone .dz-preview .dz-details { + z-index: 20; + position: absolute; + top: 0; + left: 0; + opacity: 0; + font-size: 13px; + min-width: 100%; + max-width: 100%; + padding: 2em 1em; + text-align: center; + color: rgba(0, 0, 0, 0.9); + line-height: 150%; } + .dropzone .dz-preview .dz-details .dz-size { + margin-bottom: 1em; + font-size: 16px; } + .dropzone .dz-preview .dz-details .dz-filename { + white-space: nowrap; } + .dropzone .dz-preview .dz-details .dz-filename:hover span { + border: 1px solid rgba(200, 200, 200, 0.8); + background-color: rgba(255, 255, 255, 0.8); } + .dropzone .dz-preview .dz-details .dz-filename:not(:hover) { + overflow: hidden; + text-overflow: ellipsis; } + .dropzone .dz-preview .dz-details .dz-filename:not(:hover) span { + border: 1px solid transparent; } + .dropzone .dz-preview .dz-details .dz-filename span, .dropzone .dz-preview .dz-details .dz-size span { + background-color: rgba(255, 255, 255, 0.4); + padding: 0 0.4em; + border-radius: 3px; } + .dropzone .dz-preview:hover .dz-image img { + -webkit-transform: scale(1.05, 1.05); + -moz-transform: scale(1.05, 1.05); + -ms-transform: scale(1.05, 1.05); + -o-transform: scale(1.05, 1.05); + transform: scale(1.05, 1.05); + -webkit-filter: blur(8px); + filter: blur(8px); } + .dropzone .dz-preview .dz-image { + border-radius: 20px; + overflow: hidden; + width: 120px; + height: 120px; + position: relative; + display: block; + z-index: 10; } + .dropzone .dz-preview .dz-image img { + display: block; } + .dropzone .dz-preview.dz-success .dz-success-mark { + -webkit-animation: passing-through 3s cubic-bezier(0.77, 0, 0.175, 1); + -moz-animation: passing-through 3s cubic-bezier(0.77, 0, 0.175, 1); + -ms-animation: passing-through 3s cubic-bezier(0.77, 0, 0.175, 1); + -o-animation: passing-through 3s cubic-bezier(0.77, 0, 0.175, 1); + animation: passing-through 3s cubic-bezier(0.77, 0, 0.175, 1); } + .dropzone .dz-preview.dz-error .dz-error-mark { + opacity: 1; + -webkit-animation: slide-in 3s cubic-bezier(0.77, 0, 0.175, 1); + -moz-animation: slide-in 3s cubic-bezier(0.77, 0, 0.175, 1); + -ms-animation: slide-in 3s cubic-bezier(0.77, 0, 0.175, 1); + -o-animation: slide-in 3s cubic-bezier(0.77, 0, 0.175, 1); + animation: slide-in 3s cubic-bezier(0.77, 0, 0.175, 1); } + .dropzone .dz-preview .dz-success-mark, .dropzone .dz-preview 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6s ease infinite; + -o-animation: pulse 6s ease infinite; + animation: pulse 6s ease infinite; } + .dropzone .dz-preview .dz-progress { + opacity: 1; + z-index: 1000; + pointer-events: none; + position: absolute; + height: 16px; + left: 50%; + top: 50%; + margin-top: -8px; + width: 80px; + margin-left: -40px; + background: rgba(255, 255, 255, 0.9); + -webkit-transform: scale(1); + border-radius: 8px; + overflow: hidden; } + .dropzone .dz-preview .dz-progress .dz-upload { + background: #333; + background: linear-gradient(to bottom, #666, #444); + position: absolute; + top: 0; + left: 0; + bottom: 0; + width: 0; + -webkit-transition: width 300ms ease-in-out; + -moz-transition: width 300ms ease-in-out; + -ms-transition: width 300ms ease-in-out; + -o-transition: width 300ms ease-in-out; + transition: width 300ms ease-in-out; } + .dropzone .dz-preview.dz-error .dz-error-message { + display: block; } + .dropzone .dz-preview.dz-error:hover .dz-error-message { + opacity: 1; + pointer-events: auto; } + .dropzone .dz-preview .dz-error-message { + pointer-events: none; + z-index: 1000; + position: absolute; + display: block; + display: none; + opacity: 0; + -webkit-transition: opacity 0.3s ease; + -moz-transition: opacity 0.3s ease; + -ms-transition: opacity 0.3s ease; + -o-transition: opacity 0.3s ease; + transition: opacity 0.3s ease; + border-radius: 8px; + font-size: 13px; + top: 130px; + left: -10px; + width: 140px; + background: #be2626; + background: linear-gradient(to bottom, #be2626, #a92222); + padding: 0.5em 1.2em; + color: white; } + .dropzone .dz-preview .dz-error-message:after { + content: ''; + position: absolute; + top: -6px; + left: 64px; + width: 0; + height: 0; + border-left: 6px solid transparent; + border-right: 6px solid transparent; + border-bottom: 6px solid #be2626; } diff --git a/public/file_upload.php b/public/file_upload.php new file mode 100755 index 0000000..80c7177 --- /dev/null +++ b/public/file_upload.php @@ -0,0 +1,16 @@ + diff --git a/public/header.html b/public/header.html new file mode 100755 index 0000000..84fa3da --- /dev/null +++ b/public/header.html @@ -0,0 +1,136 @@ + + Assemblytics + + + + + + + Assemblytics + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/public/index.php b/public/index.php new file mode 100644 index 0000000..f9ee12c --- /dev/null +++ b/public/index.php @@ -0,0 +1,110 @@ + + + + + + + + + +
+
+
+

Instructions

+

Upload a delta file to analyze alignments of an assembly to another assembly or a reference genome

+
    +
  1. Download and install MUMmer
    2. +
  2. Align your assembly to a reference genome using nucmer (from MUMmer package) + 

    $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT

    +

    + Consult the MUMmer manual if you encounter problems

    3. +

    +
  3. Optional: Gzip the delta file to speed up upload (usually 2-4X faster) + 

    $ gzip OUT.delta
    + Then use the OUT.delta.gz file for upload. +

    4. +
  4. Upload the .delta or delta.gz file (view example) to Assemblytics
    5. +
+

+ Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference. +

+

+ The unique sequence length required represents an anchor for determining if a sequence is unique enough to safely call variants from, which is an alternative to the mapping quality filter for read alignment. +

+
+
+
+
+
+

Run Assemblytics

+
+
+ +
+ +
+ +
+
+ +
+

+

+ Description + +
+

+

+

+ Unique sequence length required + +
+

+

+

+ Maximum variant size + +
+

+

+

+ Minimum variant size + +
+

+

+ +

+
+
+
+
+
+
+ + + + + + + + + + + diff --git a/public/input_validation.php b/public/input_validation.php new file mode 100755 index 0000000..53faa11 --- /dev/null +++ b/public/input_validation.php @@ -0,0 +1,123 @@ + + + + + + + + +
+> user_data/$code/run.log');} + // $kmer_length = $_POST["kmer_length"]; + // $read_length = $_POST["read_length"]; + + + $url="analysis.php?code=$code"; + $run_url="run_algorithm.php"; + $filename="user_uploads/$code"; + + $back_button= "
"; + //$continue_button= "
"; + + $continue_button= "
+ + + + + + +
"; + + // + + if (!file_exists ($filename)) { + echo "
No file uploaded
"; + echo "$back_button"; + exit; + } + + $consistent=true; + // $myfile = fopen($filename, "r") or die("Unable to open file!"); + // $line1 = fgets($myfile); + + $myfile = gzopen($filename, "r") or die("Unable to open file!"); + $line1 = gzgets($myfile); + + + + $line1 = trim(preg_replace( '/\s+/', ' ', $line1 )); + + $array=array_map("trim",explode(' ',$line1)); + if (count($array)==2) { + // echo "GOOD first line"; + } else { + echo "Bad first line. \n"; + $consistent=false; + } + + $line2 = fgets($myfile); + $line2 = trim(preg_replace( '/\s+/', ' ', $line2 )); + + if ($line2 == "NUCMER") { + // echo "GOOD second line"; + } else { + echo "Bad second line\n"; + $consistent=false; + } + + // fclose($myfile); + gzclose($myfile); + + if ($consistent) { + // if ($previous_bins > 500) { + echo "
Great! File was uploaded and looks like a real delta file
"; + // } else { + // echo "
File was uploaded and has acceptable dimensions: $line_counter samples by $previous_bins bins, but the analysis is unlikely to work optimally without more bins. We recommend at least 500 bins for higher accuracy.
"; + // } + + if (!file_exists("user_data/$code")) { + + } + else { + echo "
File already submitted once. Please continue.
"; + } + echo "
"; + echo "$back_button"; + echo "
"; + echo "$continue_button"; + echo "
"; + } + else { + echo "
This doesn't look like a delta file. Are you sure it is the output from nucmer? The first line should list two file names separated by a space, and the second line should be the word 'NUCMER'. The remaining lines in the file specify alignments."; + echo "
"; + echo "$back_button"; + } + + + + +?> +
+ + diff --git a/public/interactive_dotplot.php b/public/interactive_dotplot.php new file mode 100644 index 0000000..bb743d9 --- /dev/null +++ b/public/interactive_dotplot.php @@ -0,0 +1,54 @@ + + + + + + + + +

+ + + + + + + + + + + + + + diff --git a/public/js/analysis_page_script.js b/public/js/analysis_page_script.js new file mode 100755 index 0000000..4d3e36b --- /dev/null +++ b/public/js/analysis_page_script.js @@ -0,0 +1,170 @@ +var analysis_path="analysis.php?code="; + +////////////////////////////////////////////////////////////// +/////// For analysis page: +////////////////////////////////////////////////////////////// + +function showProgress() { + var run_id_code=getUrlVars()["code"]; + var prog=0; + + // Check for progress and show it to the user + jQuery.ajax({ + type:"POST", + url: "check_progress.php", + dataType: 'json', + data: {code: run_id_code}, + success: function (obj) { + prog=obj; + + last_line = prog[prog.length-1]; + nickname = prog[0].slice(0,prog[0].length-1); // this cuts off the last character, which is a carriage return we don't want to pass on to the visualizer as GET + + document.getElementById("nickname_header").innerHTML = nickname.replace(/_/g," "); + + output_array = prog.slice(1,prog.length); + output_info = "" + for (var i=0;i < output_array.length; i++) { + sub_array = output_array[i].split(","); + output_info += "

" + sub_array.slice(2,sub_array.length) + "

"; + } + + document.getElementById("plot_info").innerHTML = output_info; + + // Depending on what the last line of the progress file is, show updates to the user + if (last_line.indexOf('SUMMARY,DONE') > -1) { + // Analysis finished, show a green panel declaring success + document.getElementById("plot_info").innerHTML = "Analysis completed successfully"; + document.getElementById("progress_panel").className = "panel panel-success center"; + check_plot_exists(0,nickname); + } + else if (last_line.indexOf("FAIL") > -1) { + // Analysis failed, show a red panel with error message + document.getElementById("progress_panel").className = "panel panel-danger center"; + } + else { + // Wait half a second then check again + setTimeout(function(){showProgress();},500); + } + } + }); +} + + + +function getUrlVars() { + var vars = {}; + var parts = window.location.href.replace(/[?&]+([^=&]+)=([^&]*)/gi, function(m,key,value) { + vars[key] = value; + }); + return vars; +} + +var done_making_images = false; + +function imageresize() { + var size_fraction = 3; // number of plots to fit on the page + + var top_padding = 200; + var side_padding = 0.05; + var aspect_ratio = 1; + var height = Math.min(content_width/aspect_ratio*(1-side_padding), $( window ).height()-top_padding)/size_fraction; + + $(".fluidimage").height(height + "px"); + + // Fancybox plot zooming + // http://www.dwuser.com/education/content/click-to-zoom-for-photos-adding-lightbox-effect-to-your-images/ + var addToAll = true; + var gallery = true; + var titlePosition = 'inside'; + $(addToAll ? 'img' : 'img.fancybox').each(function(){ + var $this = $(this); + var title = $this.attr('title'); + var src = $this.attr('data-big') || $this.attr('src'); + var a = $('').attr('href', src).attr('title', title); + $this.wrap(a); + }); + if (gallery) + $('a.fancybox').attr('rel', 'fancyboxgallery'); + $('a.fancybox').fancybox({ + titlePosition: titlePosition + }); + + $.noConflict(); + +} + + +var content_width = $( window ).width(); + + + +function check_plot_exists(counter,nickname) { + document.title = "Assemblytics: " + nickname; + + var run_id_code=getUrlVars()["code"]; + var plot_url_prefix="user_data/"+run_id_code + "/" + nickname + ".Assemblytics."; + var summary_table_url="user_data/"+run_id_code + "/" + nickname + ".Assemblytics_structural_variants.summary"; + var variant_preview_url="user_data/"+run_id_code + "/" + nickname + ".variant_preview.txt"; + var assembly_stats_url="user_data/"+run_id_code + "/" + nickname + ".Assemblytics_assembly_stats.txt"; + + var zip_file_url="user_data/"+run_id_code + "/" + nickname + ".Assemblytics_results.zip"; + + + var file_to_wait_for=plot_url_prefix + "size_distributions.png"; + + if (counter>=100) { + alert("Taking too long to find "+ file_to_wait_for) + } + else { + wait_then_resize(); + + jQuery.ajax({ + type:"POST", + url: "list_plots.php", + dataType: 'json', + data: {code: run_id_code}, + error: function() { + setTimeout(function(){check_plot_exists(counter+1,nickname);},500); + }, + success: function (obj) { + var plot_filenames = obj; + // Add all the plots to the page + + for (i in plot_filenames) { + plot_filename = plot_filenames[i]; + document.getElementById("container_for_all_plots").innerHTML += '
'; + } + document.getElementById("container_for_all_plots").innerHTML += '

'; + + document.getElementById("landing_for_summary_statistics").innerHTML=''; + document.getElementById("landing_for_variant_file_preview").innerHTML='
'; + document.getElementById("landing_for_assembly_stats").innerHTML=''; + + document.getElementById("download_zip").href = zip_file_url; + + // Show all results + document.getElementById("results").style.visibility= 'visible'; + done_making_images = true; + + } + }); + + } +} + +function wait_then_resize() { + if (done_making_images == true) { + imageresize(); + } else { + setTimeout(wait_then_resize,50); + } + +} + +$(document).ready(function() { + showProgress(); + $(window).bind("resize", function(){ //Adjusts image when browser resized + imageresize(); + }); +}); diff --git a/public/js/bootstrap.min.js b/public/js/bootstrap.min.js new file mode 100755 index 0000000..7c1561a --- /dev/null +++ b/public/js/bootstrap.min.js @@ -0,0 +1,6 @@ +/*! + * Bootstrap v3.2.0 (http://getbootstrap.com) + * Copyright 2011-2014 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + */ +if("undefined"==typeof jQuery)throw new Error("Bootstrap's JavaScript 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@@ -0,0 +1,1752 @@ + +/* + * + * More info at [www.dropzonejs.com](http://www.dropzonejs.com) + * + * Copyright (c) 2012, Matias Meno + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + * THE SOFTWARE. + * + */ + +(function() { + var Dropzone, Emitter, camelize, contentLoaded, detectVerticalSquash, drawImageIOSFix, noop, without, + __slice = [].slice, + __hasProp = {}.hasOwnProperty, + __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor(); child.__super__ = parent.prototype; return child; }; + + noop = function() {}; + + Emitter = (function() { + function Emitter() {} + + Emitter.prototype.addEventListener = Emitter.prototype.on; + + Emitter.prototype.on = function(event, fn) { + this._callbacks = this._callbacks || {}; + if (!this._callbacks[event]) { + this._callbacks[event] = []; + } + this._callbacks[event].push(fn); + return this; + }; + + Emitter.prototype.emit = function() { + var args, callback, callbacks, event, _i, _len; + event = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : []; + this._callbacks = this._callbacks || {}; + callbacks = this._callbacks[event]; + if (callbacks) { + for (_i = 0, _len = callbacks.length; _i < _len; _i++) { + callback = callbacks[_i]; + callback.apply(this, args); + } + } + return this; + }; + + Emitter.prototype.removeListener = Emitter.prototype.off; + + Emitter.prototype.removeAllListeners = Emitter.prototype.off; + + Emitter.prototype.removeEventListener = Emitter.prototype.off; + + Emitter.prototype.off = function(event, fn) { + var callback, callbacks, i, _i, _len; + if (!this._callbacks || arguments.length === 0) { + this._callbacks = {}; + return this; + } + callbacks = this._callbacks[event]; + if (!callbacks) { + return this; + } + if (arguments.length === 1) { + delete this._callbacks[event]; + return this; + } + for (i = _i = 0, _len = callbacks.length; _i < _len; i = ++_i) { + callback = callbacks[i]; + if (callback === fn) { + callbacks.splice(i, 1); + break; + } + } + return this; + }; + + return Emitter; + + })(); + + Dropzone = (function(_super) { + var extend, resolveOption; + + __extends(Dropzone, _super); + + Dropzone.prototype.Emitter = Emitter; + + + /* + This is a list of all available events you can register on a dropzone object. + + You can register an event handler like this: + + dropzone.on("dragEnter", function() { }); + */ + + Dropzone.prototype.events = ["drop", "dragstart", "dragend", "dragenter", "dragover", "dragleave", "addedfile", "addedfiles", "removedfile", "thumbnail", "error", "errormultiple", "processing", "processingmultiple", "uploadprogress", "totaluploadprogress", "sending", "sendingmultiple", "success", "successmultiple", "canceled", "canceledmultiple", "complete", "completemultiple", "reset", "maxfilesexceeded", "maxfilesreached", "queuecomplete"]; + + Dropzone.prototype.defaultOptions = { + url: null, + method: "post", + withCredentials: false, + parallelUploads: 2, + uploadMultiple: false, + maxFilesize: 256, + paramName: "file", + createImageThumbnails: true, + maxThumbnailFilesize: 10, + thumbnailWidth: 120, + thumbnailHeight: 120, + filesizeBase: 1000, + maxFiles: null, + params: {}, + clickable: true, + ignoreHiddenFiles: true, + acceptedFiles: null, + acceptedMimeTypes: null, + autoProcessQueue: true, + autoQueue: true, + addRemoveLinks: false, + previewsContainer: null, + hiddenInputContainer: "body", + capture: null, + dictDefaultMessage: "Drop delta file here to upload", + dictFallbackMessage: "Your browser does not support drag'n'drop file uploads.", + dictFallbackText: "Please use the fallback form below to upload your files like in the olden days.", + dictFileTooBig: "File is too big ({{filesize}}MiB). Max filesize: {{maxFilesize}}MiB.", + dictInvalidFileType: "You can't upload files of this type.", + dictResponseError: "Server responded with {{statusCode}} code.", + dictCancelUpload: "Cancel upload", + dictCancelUploadConfirmation: "Are you sure you want to cancel this upload?", + dictRemoveFile: "Remove file", + dictRemoveFileConfirmation: null, + dictMaxFilesExceeded: "You can not upload any more files.", + accept: function(file, done) { + return done(); + }, + init: function() { + return noop; + }, + forceFallback: false, + fallback: function() { + var child, messageElement, span, _i, _len, _ref; + this.element.className = "" + this.element.className + " dz-browser-not-supported"; + _ref = this.element.getElementsByTagName("div"); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + child = _ref[_i]; + if (/(^| )dz-message($| )/.test(child.className)) { + messageElement = child; + child.className = "dz-message"; + continue; + } + } + if (!messageElement) { + messageElement = Dropzone.createElement("
"); + this.element.appendChild(messageElement); + } + span = messageElement.getElementsByTagName("span")[0]; + if (span) { + if (span.textContent != null) { + span.textContent = this.options.dictFallbackMessage; + } else if (span.innerText != null) { + span.innerText = this.options.dictFallbackMessage; + } + } + return this.element.appendChild(this.getFallbackForm()); + }, + resize: function(file) { + var info, srcRatio, trgRatio; + info = { + srcX: 0, + srcY: 0, + srcWidth: file.width, + srcHeight: file.height + }; + srcRatio = file.width / file.height; + info.optWidth = this.options.thumbnailWidth; + info.optHeight = this.options.thumbnailHeight; + if ((info.optWidth == null) && (info.optHeight == null)) { + info.optWidth = info.srcWidth; + info.optHeight = info.srcHeight; + } else if (info.optWidth == null) { + info.optWidth = srcRatio * info.optHeight; + } else if (info.optHeight == null) { + info.optHeight = (1 / srcRatio) * info.optWidth; + } + trgRatio = info.optWidth / info.optHeight; + if (file.height < info.optHeight || file.width < info.optWidth) { + info.trgHeight = info.srcHeight; + info.trgWidth = info.srcWidth; + } else { + if (srcRatio > trgRatio) { + info.srcHeight = file.height; + info.srcWidth = info.srcHeight * trgRatio; + } else { + info.srcWidth = file.width; + info.srcHeight = info.srcWidth / trgRatio; + } + } + info.srcX = (file.width - info.srcWidth) / 2; + info.srcY = (file.height - info.srcHeight) / 2; + return info; + }, + + /* + Those functions register themselves to the events on init and handle all + the user interface specific stuff. Overwriting them won't break the upload + but can break the way it's displayed. + You can overwrite them if you don't like the default behavior. If you just + want to add an additional event handler, register it on the dropzone object + and don't overwrite those options. + */ + drop: function(e) { + return this.element.classList.remove("dz-drag-hover"); + }, + dragstart: noop, + dragend: function(e) { + return this.element.classList.remove("dz-drag-hover"); + }, + dragenter: function(e) { + return this.element.classList.add("dz-drag-hover"); + }, + dragover: function(e) { + return this.element.classList.add("dz-drag-hover"); + }, + dragleave: function(e) { + return this.element.classList.remove("dz-drag-hover"); + }, + paste: noop, + reset: function() { + return this.element.classList.remove("dz-started"); + }, + addedfile: function(file) { + var node, removeFileEvent, removeLink, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2, _results; + if (this.element === this.previewsContainer) { + this.element.classList.add("dz-started"); + } + if (this.previewsContainer) { + file.previewElement = Dropzone.createElement(this.options.previewTemplate.trim()); + file.previewTemplate = file.previewElement; + this.previewsContainer.appendChild(file.previewElement); + _ref = file.previewElement.querySelectorAll("[data-dz-name]"); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + node = _ref[_i]; + node.textContent = file.name; + } + _ref1 = file.previewElement.querySelectorAll("[data-dz-size]"); + for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) { + node = _ref1[_j]; + node.innerHTML = this.filesize(file.size); + } + if (this.options.addRemoveLinks) { + file._removeLink = Dropzone.createElement("" + this.options.dictRemoveFile + ""); + file.previewElement.appendChild(file._removeLink); + } + removeFileEvent = (function(_this) { + return function(e) { + e.preventDefault(); + e.stopPropagation(); + if (file.status === Dropzone.UPLOADING) { + return Dropzone.confirm(_this.options.dictCancelUploadConfirmation, function() { + return _this.removeFile(file); + }); + } else { + if (_this.options.dictRemoveFileConfirmation) { + return Dropzone.confirm(_this.options.dictRemoveFileConfirmation, function() { + return _this.removeFile(file); + }); + } else { + return _this.removeFile(file); + } + } + }; + })(this); + _ref2 = file.previewElement.querySelectorAll("[data-dz-remove]"); + _results = []; + for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { + removeLink = _ref2[_k]; + _results.push(removeLink.addEventListener("click", removeFileEvent)); + } + return _results; + } + }, + removedfile: function(file) { + var _ref; + if (file.previewElement) { + if ((_ref = file.previewElement) != null) { + _ref.parentNode.removeChild(file.previewElement); + } + } + return this._updateMaxFilesReachedClass(); + }, + thumbnail: function(file, dataUrl) { + var thumbnailElement, _i, _len, _ref; + if (file.previewElement) { + file.previewElement.classList.remove("dz-file-preview"); + _ref = file.previewElement.querySelectorAll("[data-dz-thumbnail]"); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + thumbnailElement = _ref[_i]; + thumbnailElement.alt = file.name; + thumbnailElement.src = dataUrl; + } + return setTimeout(((function(_this) { + return function() { + return file.previewElement.classList.add("dz-image-preview"); + }; + })(this)), 1); + } + }, + error: function(file, message) { + var node, _i, _len, _ref, _results; + if (file.previewElement) { + file.previewElement.classList.add("dz-error"); + if (typeof message !== "String" && message.error) { + message = message.error; + } + _ref = file.previewElement.querySelectorAll("[data-dz-errormessage]"); + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + node = _ref[_i]; + _results.push(node.textContent = message); + } + return _results; + } + }, + errormultiple: noop, + processing: function(file) { + if (file.previewElement) { + file.previewElement.classList.add("dz-processing"); + if (file._removeLink) { + return file._removeLink.textContent = this.options.dictCancelUpload; + } + } + }, + processingmultiple: noop, + uploadprogress: function(file, progress, bytesSent) { + var node, _i, _len, _ref, _results; + if (file.previewElement) { + _ref = file.previewElement.querySelectorAll("[data-dz-uploadprogress]"); + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + node = _ref[_i]; + if (node.nodeName === 'PROGRESS') { + _results.push(node.value = progress); + } else { + _results.push(node.style.width = "" + progress + "%"); + } + } + return _results; + } + }, + totaluploadprogress: noop, + sending: noop, + sendingmultiple: noop, + success: function(file) { + if (file.previewElement) { + return file.previewElement.classList.add("dz-success"); + } + }, + successmultiple: noop, + canceled: function(file) { + return this.emit("error", file, "Upload canceled."); + }, + canceledmultiple: noop, + complete: function(file) { + if (file._removeLink) { + file._removeLink.textContent = this.options.dictRemoveFile; + } + if (file.previewElement) { + return file.previewElement.classList.add("dz-complete"); + } + }, + completemultiple: noop, + maxfilesexceeded: noop, + maxfilesreached: noop, + queuecomplete: noop, + addedfiles: noop, + previewTemplate: "
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\n \n Error\n \n \n \n \n \n \n \n
\n
" + }; + + extend = function() { + var key, object, objects, target, val, _i, _len; + target = arguments[0], objects = 2 <= arguments.length ? __slice.call(arguments, 1) : []; + for (_i = 0, _len = objects.length; _i < _len; _i++) { + object = objects[_i]; + for (key in object) { + val = object[key]; + target[key] = val; + } + } + return target; + }; + + function Dropzone(element, options) { + var elementOptions, fallback, _ref; + this.element = element; + this.version = Dropzone.version; + this.defaultOptions.previewTemplate = this.defaultOptions.previewTemplate.replace(/\n*/g, ""); + this.clickableElements = []; + this.listeners = []; + this.files = []; + if (typeof this.element === "string") { + this.element = document.querySelector(this.element); + } + if (!(this.element && (this.element.nodeType != null))) { + throw new Error("Invalid dropzone element."); + } + if (this.element.dropzone) { + throw new Error("Dropzone already attached."); + } + Dropzone.instances.push(this); + this.element.dropzone = this; + elementOptions = (_ref = Dropzone.optionsForElement(this.element)) != null ? _ref : {}; + this.options = extend({}, this.defaultOptions, elementOptions, options != null ? options : {}); + if (this.options.forceFallback || !Dropzone.isBrowserSupported()) { + return this.options.fallback.call(this); + } + if (this.options.url == null) { + this.options.url = this.element.getAttribute("action"); + } + if (!this.options.url) { + throw new Error("No URL provided."); + } + if (this.options.acceptedFiles && this.options.acceptedMimeTypes) { + throw new Error("You can't provide both 'acceptedFiles' and 'acceptedMimeTypes'. 'acceptedMimeTypes' is deprecated."); + } + if (this.options.acceptedMimeTypes) { + this.options.acceptedFiles = this.options.acceptedMimeTypes; + delete this.options.acceptedMimeTypes; + } + this.options.method = this.options.method.toUpperCase(); + if ((fallback = this.getExistingFallback()) && fallback.parentNode) { + fallback.parentNode.removeChild(fallback); + } + if (this.options.previewsContainer !== false) { + if (this.options.previewsContainer) { + this.previewsContainer = Dropzone.getElement(this.options.previewsContainer, "previewsContainer"); + } else { + this.previewsContainer = this.element; + } + } + if (this.options.clickable) { + if (this.options.clickable === true) { + this.clickableElements = [this.element]; + } else { + this.clickableElements = Dropzone.getElements(this.options.clickable, "clickable"); + } + } + this.init(); + } + + Dropzone.prototype.getAcceptedFiles = function() { + var file, _i, _len, _ref, _results; + _ref = this.files; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + file = _ref[_i]; + if (file.accepted) { + _results.push(file); + } + } + return _results; + }; + + Dropzone.prototype.getRejectedFiles = function() { + var file, _i, _len, _ref, _results; + _ref = this.files; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + file = _ref[_i]; + if (!file.accepted) { + _results.push(file); + } + } + return _results; + }; + + Dropzone.prototype.getFilesWithStatus = function(status) { + var file, _i, _len, _ref, _results; + _ref = this.files; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + file = _ref[_i]; + if (file.status === status) { + _results.push(file); + } + } + return _results; + }; + + Dropzone.prototype.getQueuedFiles = function() { + return this.getFilesWithStatus(Dropzone.QUEUED); + }; + + Dropzone.prototype.getUploadingFiles = function() { + return this.getFilesWithStatus(Dropzone.UPLOADING); + }; + + Dropzone.prototype.getAddedFiles = function() { + return this.getFilesWithStatus(Dropzone.ADDED); + }; + + Dropzone.prototype.getActiveFiles = function() { + var file, _i, _len, _ref, _results; + _ref = this.files; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + file = _ref[_i]; + if (file.status === Dropzone.UPLOADING || file.status === Dropzone.QUEUED) { + _results.push(file); + } + } + return _results; + }; + + Dropzone.prototype.init = function() { + var eventName, noPropagation, setupHiddenFileInput, _i, _len, _ref, _ref1; + if (this.element.tagName === "form") { + this.element.setAttribute("enctype", "multipart/form-data"); + } + if (this.element.classList.contains("dropzone") && !this.element.querySelector(".dz-message")) { + this.element.appendChild(Dropzone.createElement("
" + this.options.dictDefaultMessage + "
")); + } + if (this.clickableElements.length) { + setupHiddenFileInput = (function(_this) { + return function() { + if (_this.hiddenFileInput) { + _this.hiddenFileInput.parentNode.removeChild(_this.hiddenFileInput); + } + _this.hiddenFileInput = document.createElement("input"); + _this.hiddenFileInput.setAttribute("type", "file"); + if ((_this.options.maxFiles == null) || _this.options.maxFiles > 1) { + _this.hiddenFileInput.setAttribute("multiple", "multiple"); + } + _this.hiddenFileInput.className = "dz-hidden-input"; + if (_this.options.acceptedFiles != null) { + _this.hiddenFileInput.setAttribute("accept", _this.options.acceptedFiles); + } + if (_this.options.capture != null) { + _this.hiddenFileInput.setAttribute("capture", _this.options.capture); + } + _this.hiddenFileInput.style.visibility = "hidden"; + _this.hiddenFileInput.style.position = "absolute"; + _this.hiddenFileInput.style.top = "0"; + _this.hiddenFileInput.style.left = "0"; + _this.hiddenFileInput.style.height = "0"; + _this.hiddenFileInput.style.width = "0"; + document.querySelector(_this.options.hiddenInputContainer).appendChild(_this.hiddenFileInput); + return _this.hiddenFileInput.addEventListener("change", function() { + var file, files, _i, _len; + files = _this.hiddenFileInput.files; + if (files.length) { + for (_i = 0, _len = files.length; _i < _len; _i++) { + file = files[_i]; + _this.addFile(file); + } + } + _this.emit("addedfiles", files); + return setupHiddenFileInput(); + }); + }; + })(this); + setupHiddenFileInput(); + } + this.URL = (_ref = window.URL) != null ? _ref : window.webkitURL; + _ref1 = this.events; + for (_i = 0, _len = _ref1.length; _i < _len; _i++) { + eventName = _ref1[_i]; + this.on(eventName, this.options[eventName]); + } + this.on("uploadprogress", (function(_this) { + return function() { + return _this.updateTotalUploadProgress(); + }; + })(this)); + this.on("removedfile", (function(_this) { + return function() { + return _this.updateTotalUploadProgress(); + }; + })(this)); + this.on("canceled", (function(_this) { + return function(file) { + return _this.emit("complete", file); + }; + })(this)); + this.on("complete", (function(_this) { + return function(file) { + if (_this.getAddedFiles().length === 0 && _this.getUploadingFiles().length === 0 && _this.getQueuedFiles().length === 0) { + return setTimeout((function() { + return _this.emit("queuecomplete"); + }), 0); + } + }; + })(this)); + noPropagation = function(e) { + e.stopPropagation(); + if (e.preventDefault) { + return e.preventDefault(); + } else { + return e.returnValue = false; + } + }; + this.listeners = [ + { + element: this.element, + events: { + "dragstart": (function(_this) { + return function(e) { + return _this.emit("dragstart", e); + }; + })(this), + "dragenter": (function(_this) { + return function(e) { + noPropagation(e); + return _this.emit("dragenter", e); + }; + })(this), + "dragover": (function(_this) { + return function(e) { + var efct; + try { + efct = e.dataTransfer.effectAllowed; + } catch (_error) {} + e.dataTransfer.dropEffect = 'move' === efct || 'linkMove' === efct ? 'move' : 'copy'; + noPropagation(e); + return _this.emit("dragover", e); + }; + })(this), + "dragleave": (function(_this) { + return function(e) { + return _this.emit("dragleave", e); + }; + })(this), + "drop": (function(_this) { + return function(e) { + noPropagation(e); + return _this.drop(e); + }; + })(this), + "dragend": (function(_this) { + return function(e) { + return _this.emit("dragend", e); + }; + })(this) + } + } + ]; + this.clickableElements.forEach((function(_this) { + return function(clickableElement) { + return _this.listeners.push({ + element: clickableElement, + events: { + "click": function(evt) { + if ((clickableElement !== _this.element) || (evt.target === _this.element || Dropzone.elementInside(evt.target, _this.element.querySelector(".dz-message")))) { + _this.hiddenFileInput.click(); + } + return true; + } + } + }); + }; + })(this)); + this.enable(); + return this.options.init.call(this); + }; + + Dropzone.prototype.destroy = function() { + var _ref; + this.disable(); + this.removeAllFiles(true); + if ((_ref = this.hiddenFileInput) != null ? _ref.parentNode : void 0) { + this.hiddenFileInput.parentNode.removeChild(this.hiddenFileInput); + this.hiddenFileInput = null; + } + delete this.element.dropzone; + return Dropzone.instances.splice(Dropzone.instances.indexOf(this), 1); + }; + + Dropzone.prototype.updateTotalUploadProgress = function() { + var activeFiles, file, totalBytes, totalBytesSent, totalUploadProgress, _i, _len, _ref; + totalBytesSent = 0; + totalBytes = 0; + activeFiles = this.getActiveFiles(); + if (activeFiles.length) { + _ref = this.getActiveFiles(); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + file = _ref[_i]; + totalBytesSent += file.upload.bytesSent; + totalBytes += file.upload.total; + } + totalUploadProgress = 100 * totalBytesSent / totalBytes; + } else { + totalUploadProgress = 100; + } + return this.emit("totaluploadprogress", totalUploadProgress, totalBytes, totalBytesSent); + }; + + Dropzone.prototype._getParamName = function(n) { + if (typeof this.options.paramName === "function") { + return this.options.paramName(n); + } else { + return "" + this.options.paramName + (this.options.uploadMultiple ? "[" + n + "]" : ""); + } + }; + + Dropzone.prototype.getFallbackForm = function() { + var existingFallback, fields, fieldsString, form; + if (existingFallback = this.getExistingFallback()) { + return existingFallback; + } + fieldsString = "
"; + if (this.options.dictFallbackText) { + fieldsString += "

" + this.options.dictFallbackText + "

"; + } + fieldsString += "
"; + fields = Dropzone.createElement(fieldsString); + if (this.element.tagName !== "FORM") { + form = Dropzone.createElement("
"); + form.appendChild(fields); + } else { + this.element.setAttribute("enctype", "multipart/form-data"); + this.element.setAttribute("method", this.options.method); + } + return form != null ? form : fields; + }; + + Dropzone.prototype.getExistingFallback = function() { + var fallback, getFallback, tagName, _i, _len, _ref; + getFallback = function(elements) { + var el, _i, _len; + for (_i = 0, _len = elements.length; _i < _len; _i++) { + el = elements[_i]; + if (/(^| )fallback($| )/.test(el.className)) { + return el; + } + } + }; + _ref = ["div", "form"]; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + tagName = _ref[_i]; + if (fallback = getFallback(this.element.getElementsByTagName(tagName))) { + return fallback; + } + } + }; + + Dropzone.prototype.setupEventListeners = function() { + var elementListeners, event, listener, _i, _len, _ref, _results; + _ref = this.listeners; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + elementListeners = _ref[_i]; + _results.push((function() { + var _ref1, _results1; + _ref1 = elementListeners.events; + _results1 = []; + for (event in _ref1) { + listener = _ref1[event]; + _results1.push(elementListeners.element.addEventListener(event, listener, false)); + } + return _results1; + })()); + } + return _results; + }; + + Dropzone.prototype.removeEventListeners = function() { + var elementListeners, event, listener, _i, _len, _ref, _results; + _ref = this.listeners; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + elementListeners = _ref[_i]; + _results.push((function() { + var _ref1, _results1; + _ref1 = elementListeners.events; + _results1 = []; + for (event in _ref1) { + listener = _ref1[event]; + _results1.push(elementListeners.element.removeEventListener(event, listener, false)); + } + return _results1; + })()); + } + return _results; + }; + + Dropzone.prototype.disable = function() { + var file, _i, _len, _ref, _results; + this.clickableElements.forEach(function(element) { + return element.classList.remove("dz-clickable"); + }); + this.removeEventListeners(); + _ref = this.files; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + file = _ref[_i]; + _results.push(this.cancelUpload(file)); + } + return _results; + }; + + Dropzone.prototype.enable = function() { + this.clickableElements.forEach(function(element) { + return element.classList.add("dz-clickable"); + }); + return this.setupEventListeners(); + }; + + Dropzone.prototype.filesize = function(size) { + var cutoff, i, selectedSize, selectedUnit, unit, units, _i, _len; + selectedSize = 0; + selectedUnit = "b"; + if (size > 0) { + units = ['TB', 'GB', 'MB', 'KB', 'b']; + for (i = _i = 0, _len = units.length; _i < _len; i = ++_i) { + unit = units[i]; + cutoff = Math.pow(this.options.filesizeBase, 4 - i) / 10; + if (size >= cutoff) { + selectedSize = size / Math.pow(this.options.filesizeBase, 4 - i); + selectedUnit = unit; + break; + } + } + selectedSize = Math.round(10 * selectedSize) / 10; + } + return "" + selectedSize + " " + selectedUnit; + }; + + Dropzone.prototype._updateMaxFilesReachedClass = function() { + if ((this.options.maxFiles != null) && this.getAcceptedFiles().length >= this.options.maxFiles) { + if (this.getAcceptedFiles().length === this.options.maxFiles) { + this.emit('maxfilesreached', this.files); + } + return this.element.classList.add("dz-max-files-reached"); + } else { + return this.element.classList.remove("dz-max-files-reached"); + } + }; + + Dropzone.prototype.drop = function(e) { + var files, items; + if (!e.dataTransfer) { + return; + } + this.emit("drop", e); + files = e.dataTransfer.files; + this.emit("addedfiles", files); + if (files.length) { + items = e.dataTransfer.items; + if (items && items.length && (items[0].webkitGetAsEntry != null)) { + this._addFilesFromItems(items); + } else { + this.handleFiles(files); + } + } + }; + + Dropzone.prototype.paste = function(e) { + var items, _ref; + if ((e != null ? (_ref = e.clipboardData) != null ? _ref.items : void 0 : void 0) == null) { + return; + } + this.emit("paste", e); + items = e.clipboardData.items; + if (items.length) { + return this._addFilesFromItems(items); + } + }; + + Dropzone.prototype.handleFiles = function(files) { + var file, _i, _len, _results; + _results = []; + for (_i = 0, _len = files.length; _i < _len; _i++) { + file = files[_i]; + _results.push(this.addFile(file)); + } + return _results; + }; + + Dropzone.prototype._addFilesFromItems = function(items) { + var entry, item, _i, _len, _results; + _results = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + if ((item.webkitGetAsEntry != null) && (entry = item.webkitGetAsEntry())) { + if (entry.isFile) { + _results.push(this.addFile(item.getAsFile())); + } else if (entry.isDirectory) { + _results.push(this._addFilesFromDirectory(entry, entry.name)); + } else { + _results.push(void 0); + } + } else if (item.getAsFile != null) { + if ((item.kind == null) || item.kind === "file") { + _results.push(this.addFile(item.getAsFile())); + } else { + _results.push(void 0); + } + } else { + _results.push(void 0); + } + } + return _results; + }; + + Dropzone.prototype._addFilesFromDirectory = function(directory, path) { + var dirReader, entriesReader; + dirReader = directory.createReader(); + entriesReader = (function(_this) { + return function(entries) { + var entry, _i, _len; + for (_i = 0, _len = entries.length; _i < _len; _i++) { + entry = entries[_i]; + if (entry.isFile) { + entry.file(function(file) { + if (_this.options.ignoreHiddenFiles && file.name.substring(0, 1) === '.') { + return; + } + file.fullPath = "" + path + "/" + file.name; + return _this.addFile(file); + }); + } else if (entry.isDirectory) { + _this._addFilesFromDirectory(entry, "" + path + "/" + entry.name); + } + } + }; + })(this); + return dirReader.readEntries(entriesReader, function(error) { + return typeof console !== "undefined" && console !== null ? typeof console.log === "function" ? console.log(error) : void 0 : void 0; + }); + }; + + Dropzone.prototype.accept = function(file, done) { + if (file.size > this.options.maxFilesize * 1024 * 1024) { + return done(this.options.dictFileTooBig.replace("{{filesize}}", Math.round(file.size / 1024 / 10.24) / 100).replace("{{maxFilesize}}", this.options.maxFilesize)); + } else if (!Dropzone.isValidFile(file, this.options.acceptedFiles)) { + return done(this.options.dictInvalidFileType); + } else if ((this.options.maxFiles != null) && this.getAcceptedFiles().length >= this.options.maxFiles) { + done(this.options.dictMaxFilesExceeded.replace("{{maxFiles}}", this.options.maxFiles)); + return this.emit("maxfilesexceeded", file); + } else { + return this.options.accept.call(this, file, done); + } + }; + + Dropzone.prototype.addFile = function(file) { + file.upload = { + progress: 0, + total: file.size, + bytesSent: 0 + }; + this.files.push(file); + file.status = Dropzone.ADDED; + this.emit("addedfile", file); + this._enqueueThumbnail(file); + return this.accept(file, (function(_this) { + return function(error) { + if (error) { + file.accepted = false; + _this._errorProcessing([file], error); + } else { + file.accepted = true; + if (_this.options.autoQueue) { + _this.enqueueFile(file); + } + } + return _this._updateMaxFilesReachedClass(); + }; + })(this)); + }; + + Dropzone.prototype.enqueueFiles = function(files) { + var file, _i, _len; + for (_i = 0, _len = files.length; _i < _len; _i++) { + file = files[_i]; + this.enqueueFile(file); + } + return null; + }; + + Dropzone.prototype.enqueueFile = function(file) { + if (file.status === Dropzone.ADDED && file.accepted === true) { + file.status = Dropzone.QUEUED; + if (this.options.autoProcessQueue) { + return setTimeout(((function(_this) { + return function() { + return _this.processQueue(); + }; + })(this)), 0); + } + } else { + throw new Error("This file can't be queued because it has already been processed or was rejected."); + } + }; + + Dropzone.prototype._thumbnailQueue = []; + + Dropzone.prototype._processingThumbnail = false; + + Dropzone.prototype._enqueueThumbnail = function(file) { + if (this.options.createImageThumbnails && file.type.match(/image.*/) && file.size <= this.options.maxThumbnailFilesize * 1024 * 1024) { + this._thumbnailQueue.push(file); + return setTimeout(((function(_this) { + return function() { + return _this._processThumbnailQueue(); + }; + })(this)), 0); + } + }; + + Dropzone.prototype._processThumbnailQueue = function() { + if (this._processingThumbnail || this._thumbnailQueue.length === 0) { + return; + } + this._processingThumbnail = true; + return this.createThumbnail(this._thumbnailQueue.shift(), (function(_this) { + return function() { + _this._processingThumbnail = false; + return _this._processThumbnailQueue(); + }; + })(this)); + }; + + Dropzone.prototype.removeFile = function(file) { + if (file.status === Dropzone.UPLOADING) { + this.cancelUpload(file); + } + this.files = without(this.files, file); + this.emit("removedfile", file); + if (this.files.length === 0) { + return this.emit("reset"); + } + }; + + Dropzone.prototype.removeAllFiles = function(cancelIfNecessary) { + var file, _i, _len, _ref; + if (cancelIfNecessary == null) { + cancelIfNecessary = false; + } + _ref = this.files.slice(); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + file = _ref[_i]; + if (file.status !== Dropzone.UPLOADING || cancelIfNecessary) { + this.removeFile(file); + } + } + return null; + }; + + Dropzone.prototype.createThumbnail = function(file, callback) { + var fileReader; + fileReader = new FileReader; + fileReader.onload = (function(_this) { + return function() { + if (file.type === "image/svg+xml") { + _this.emit("thumbnail", file, fileReader.result); + if (callback != null) { + callback(); + } + return; + } + return _this.createThumbnailFromUrl(file, fileReader.result, callback); + }; + })(this); + return fileReader.readAsDataURL(file); + }; + + Dropzone.prototype.createThumbnailFromUrl = function(file, imageUrl, callback, crossOrigin) { + var img; + img = document.createElement("img"); + if (crossOrigin) { + img.crossOrigin = crossOrigin; + } + img.onload = (function(_this) { + return function() { + var canvas, ctx, resizeInfo, thumbnail, _ref, _ref1, _ref2, _ref3; + file.width = img.width; + file.height = img.height; + resizeInfo = _this.options.resize.call(_this, file); + if (resizeInfo.trgWidth == null) { + resizeInfo.trgWidth = resizeInfo.optWidth; + } + if (resizeInfo.trgHeight == null) { + resizeInfo.trgHeight = resizeInfo.optHeight; + } + canvas = document.createElement("canvas"); + ctx = canvas.getContext("2d"); + canvas.width = resizeInfo.trgWidth; + canvas.height = resizeInfo.trgHeight; + drawImageIOSFix(ctx, img, (_ref = resizeInfo.srcX) != null ? _ref : 0, (_ref1 = resizeInfo.srcY) != null ? _ref1 : 0, resizeInfo.srcWidth, resizeInfo.srcHeight, (_ref2 = resizeInfo.trgX) != null ? _ref2 : 0, (_ref3 = resizeInfo.trgY) != null ? _ref3 : 0, resizeInfo.trgWidth, resizeInfo.trgHeight); + thumbnail = canvas.toDataURL("image/png"); + _this.emit("thumbnail", file, thumbnail); + if (callback != null) { + return callback(); + } + }; + })(this); + if (callback != null) { + img.onerror = callback; + } + return img.src = imageUrl; + }; + + Dropzone.prototype.processQueue = function() { + var i, parallelUploads, processingLength, queuedFiles; + parallelUploads = this.options.parallelUploads; + processingLength = this.getUploadingFiles().length; + i = processingLength; + if (processingLength >= parallelUploads) { + return; + } + queuedFiles = this.getQueuedFiles(); + if (!(queuedFiles.length > 0)) { + return; + } + if (this.options.uploadMultiple) { + return this.processFiles(queuedFiles.slice(0, parallelUploads - processingLength)); + } else { + while (i < parallelUploads) { + if (!queuedFiles.length) { + return; + } + this.processFile(queuedFiles.shift()); + i++; + } + } + }; + + Dropzone.prototype.processFile = function(file) { + return this.processFiles([file]); + }; + + Dropzone.prototype.processFiles = function(files) { + var file, _i, _len; + for (_i = 0, _len = files.length; _i < _len; _i++) { + file = files[_i]; + file.processing = true; + file.status = Dropzone.UPLOADING; + this.emit("processing", file); + } + if (this.options.uploadMultiple) { + this.emit("processingmultiple", files); + } + return this.uploadFiles(files); + }; + + Dropzone.prototype._getFilesWithXhr = function(xhr) { + var file, files; + return files = (function() { + var _i, _len, _ref, _results; + _ref = this.files; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + file = _ref[_i]; + if (file.xhr === xhr) { + _results.push(file); + } + } + return _results; + }).call(this); + }; + + Dropzone.prototype.cancelUpload = function(file) { + var groupedFile, groupedFiles, _i, _j, _len, _len1, _ref; + if (file.status === Dropzone.UPLOADING) { + groupedFiles = this._getFilesWithXhr(file.xhr); + for (_i = 0, _len = groupedFiles.length; _i < _len; _i++) { + groupedFile = groupedFiles[_i]; + groupedFile.status = Dropzone.CANCELED; + } + file.xhr.abort(); + for (_j = 0, _len1 = groupedFiles.length; _j < _len1; _j++) { + groupedFile = groupedFiles[_j]; + this.emit("canceled", groupedFile); + } + if (this.options.uploadMultiple) { + this.emit("canceledmultiple", groupedFiles); + } + } else if ((_ref = file.status) === Dropzone.ADDED || _ref === Dropzone.QUEUED) { + file.status = Dropzone.CANCELED; + this.emit("canceled", file); + if (this.options.uploadMultiple) { + this.emit("canceledmultiple", [file]); + } + } + if (this.options.autoProcessQueue) { + return this.processQueue(); + } + }; + + resolveOption = function() { + var args, option; + option = arguments[0], args = 2 <= arguments.length ? __slice.call(arguments, 1) : []; + if (typeof option === 'function') { + return option.apply(this, args); + } + return option; + }; + + Dropzone.prototype.uploadFile = function(file) { + return this.uploadFiles([file]); + }; + + Dropzone.prototype.uploadFiles = function(files) { + var file, formData, handleError, headerName, headerValue, headers, i, input, inputName, inputType, key, method, option, progressObj, response, updateProgress, url, value, xhr, _i, _j, _k, _l, _len, _len1, _len2, _len3, _m, _ref, _ref1, _ref2, _ref3, _ref4, _ref5; + xhr = new XMLHttpRequest(); + for (_i = 0, _len = files.length; _i < _len; _i++) { + file = files[_i]; + file.xhr = xhr; + } + method = resolveOption(this.options.method, files); + url = resolveOption(this.options.url, files); + xhr.open(method, url, true); + xhr.withCredentials = !!this.options.withCredentials; + response = null; + handleError = (function(_this) { + return function() { + var _j, _len1, _results; + _results = []; + for (_j = 0, _len1 = files.length; _j < _len1; _j++) { + file = files[_j]; + _results.push(_this._errorProcessing(files, response || _this.options.dictResponseError.replace("{{statusCode}}", xhr.status), xhr)); + } + return _results; + }; + })(this); + updateProgress = (function(_this) { + return function(e) { + var allFilesFinished, progress, _j, _k, _l, _len1, _len2, _len3, _results; + if (e != null) { + progress = 100 * e.loaded / e.total; + for (_j = 0, _len1 = files.length; _j < _len1; _j++) { + file = files[_j]; + file.upload = { + progress: progress, + total: e.total, + bytesSent: e.loaded + }; + } + } else { + allFilesFinished = true; + progress = 100; + for (_k = 0, _len2 = files.length; _k < _len2; _k++) { + file = files[_k]; + if (!(file.upload.progress === 100 && file.upload.bytesSent === file.upload.total)) { + allFilesFinished = false; + } + file.upload.progress = progress; + file.upload.bytesSent = file.upload.total; + } + if (allFilesFinished) { + return; + } + } + _results = []; + for (_l = 0, _len3 = files.length; _l < _len3; _l++) { + file = files[_l]; + _results.push(_this.emit("uploadprogress", file, progress, file.upload.bytesSent)); + } + return _results; + }; + })(this); + xhr.onload = (function(_this) { + return function(e) { + var _ref; + if (files[0].status === Dropzone.CANCELED) { + return; + } + if (xhr.readyState !== 4) { + return; + } + response = xhr.responseText; + if (xhr.getResponseHeader("content-type") && ~xhr.getResponseHeader("content-type").indexOf("application/json")) { + try { + response = JSON.parse(response); + } catch (_error) { + e = _error; + response = "Invalid JSON response from server."; + } + } + updateProgress(); + if (!((200 <= (_ref = xhr.status) && _ref < 300))) { + return handleError(); + } else { + return _this._finished(files, response, e); + } + }; + })(this); + xhr.onerror = (function(_this) { + return function() { + if (files[0].status === Dropzone.CANCELED) { + return; + } + return handleError(); + }; + })(this); + progressObj = (_ref = xhr.upload) != null ? _ref : xhr; + progressObj.onprogress = updateProgress; + headers = { + "Accept": "application/json", + "Cache-Control": "no-cache", + "X-Requested-With": "XMLHttpRequest" + }; + if (this.options.headers) { + extend(headers, this.options.headers); + } + for (headerName in headers) { + headerValue = headers[headerName]; + if (headerValue) { + xhr.setRequestHeader(headerName, headerValue); + } + } + formData = new FormData(); + if (this.options.params) { + _ref1 = this.options.params; + for (key in _ref1) { + value = _ref1[key]; + formData.append(key, value); + } + } + for (_j = 0, _len1 = files.length; _j < _len1; _j++) { + file = files[_j]; + this.emit("sending", file, xhr, formData); + } + if (this.options.uploadMultiple) { + this.emit("sendingmultiple", files, xhr, formData); + } + if (this.element.tagName === "FORM") { + _ref2 = this.element.querySelectorAll("input, textarea, select, button"); + for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { + input = _ref2[_k]; + inputName = input.getAttribute("name"); + inputType = input.getAttribute("type"); + if (input.tagName === "SELECT" && input.hasAttribute("multiple")) { + _ref3 = input.options; + for (_l = 0, _len3 = _ref3.length; _l < _len3; _l++) { + option = _ref3[_l]; + if (option.selected) { + formData.append(inputName, option.value); + } + } + } else if (!inputType || ((_ref4 = inputType.toLowerCase()) !== "checkbox" && _ref4 !== "radio") || input.checked) { + formData.append(inputName, input.value); + } + } + } + for (i = _m = 0, _ref5 = files.length - 1; 0 <= _ref5 ? _m <= _ref5 : _m >= _ref5; i = 0 <= _ref5 ? ++_m : --_m) { + formData.append(this._getParamName(i), files[i], files[i].name); + } + return this.submitRequest(xhr, formData, files); + }; + + Dropzone.prototype.submitRequest = function(xhr, formData, files) { + return xhr.send(formData); + }; + + Dropzone.prototype._finished = function(files, responseText, e) { + var file, _i, _len; + for (_i = 0, _len = files.length; _i < _len; _i++) { + file = files[_i]; + file.status = Dropzone.SUCCESS; + this.emit("success", file, responseText, e); + this.emit("complete", file); + } + if (this.options.uploadMultiple) { + this.emit("successmultiple", files, responseText, e); + this.emit("completemultiple", files); + } + if (this.options.autoProcessQueue) { + return this.processQueue(); + } + }; + + Dropzone.prototype._errorProcessing = function(files, message, xhr) { + var file, _i, _len; + for (_i = 0, _len = files.length; _i < _len; _i++) { + file = files[_i]; + file.status = Dropzone.ERROR; + this.emit("error", file, message, xhr); + this.emit("complete", file); + } + if (this.options.uploadMultiple) { + this.emit("errormultiple", files, message, xhr); + this.emit("completemultiple", files); + } + if (this.options.autoProcessQueue) { + return this.processQueue(); + } + }; + + return Dropzone; + + })(Emitter); + + Dropzone.version = "4.2.0"; + + Dropzone.options = {}; + + Dropzone.optionsForElement = function(element) { + if (element.getAttribute("id")) { + return Dropzone.options[camelize(element.getAttribute("id"))]; + } else { + return void 0; + } + }; + + Dropzone.instances = []; + + Dropzone.forElement = function(element) { + if (typeof element === "string") { + element = document.querySelector(element); + } + if ((element != null ? element.dropzone : void 0) == null) { + throw new Error("No Dropzone found for given element. This is probably because you're trying to access it before Dropzone had the time to initialize. Use the `init` option to setup any additional observers on your Dropzone."); + } + return element.dropzone; + }; + + Dropzone.autoDiscover = true; + + Dropzone.discover = function() { + var checkElements, dropzone, dropzones, _i, _len, _results; + if (document.querySelectorAll) { + dropzones = document.querySelectorAll(".dropzone"); + } else { + dropzones = []; + checkElements = function(elements) { + var el, _i, _len, _results; + _results = []; + for (_i = 0, _len = elements.length; _i < _len; _i++) { + el = elements[_i]; + if (/(^| )dropzone($| )/.test(el.className)) { + _results.push(dropzones.push(el)); + } else { + _results.push(void 0); + } + } + return _results; + }; + checkElements(document.getElementsByTagName("div")); + checkElements(document.getElementsByTagName("form")); + } + _results = []; + for (_i = 0, _len = dropzones.length; _i < _len; _i++) { + dropzone = dropzones[_i]; + if (Dropzone.optionsForElement(dropzone) !== false) { + _results.push(new Dropzone(dropzone)); + } else { + _results.push(void 0); + } + } + return _results; + }; + + Dropzone.blacklistedBrowsers = [/opera.*Macintosh.*version\/12/i]; + + Dropzone.isBrowserSupported = function() { + var capableBrowser, regex, _i, _len, _ref; + capableBrowser = true; + if (window.File && window.FileReader && window.FileList && window.Blob && window.FormData && document.querySelector) { + if (!("classList" in document.createElement("a"))) { + capableBrowser = false; + } else { + _ref = Dropzone.blacklistedBrowsers; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + regex = _ref[_i]; + if (regex.test(navigator.userAgent)) { + capableBrowser = false; + continue; + } + } + } + } else { + capableBrowser = false; + } + return capableBrowser; + }; + + without = function(list, rejectedItem) { + var item, _i, _len, _results; + _results = []; + for (_i = 0, _len = list.length; _i < _len; _i++) { + item = list[_i]; + if (item !== rejectedItem) { + _results.push(item); + } + } + return _results; + }; + + camelize = function(str) { + return str.replace(/[\-_](\w)/g, function(match) { + return match.charAt(1).toUpperCase(); + }); + }; + + Dropzone.createElement = function(string) { + var div; + div = document.createElement("div"); + div.innerHTML = string; + return div.childNodes[0]; + }; + + Dropzone.elementInside = function(element, container) { + if (element === container) { + return true; + } + while (element = element.parentNode) { + if (element === container) { + return true; + } + } + return false; + }; + + Dropzone.getElement = function(el, name) { + var element; + if (typeof el === "string") { + element = document.querySelector(el); + } else if (el.nodeType != null) { + element = el; + } + if (element == null) { + throw new Error("Invalid `" + name + "` option provided. Please provide a CSS selector or a plain HTML element."); + } + return element; + }; + + Dropzone.getElements = function(els, name) { + var e, el, elements, _i, _j, _len, _len1, _ref; + if (els instanceof Array) { + elements = []; + try { + for (_i = 0, _len = els.length; _i < _len; _i++) { + el = els[_i]; + elements.push(this.getElement(el, name)); + } + } catch (_error) { + e = _error; + elements = null; + } + } else if (typeof els === "string") { + elements = []; + _ref = document.querySelectorAll(els); + for (_j = 0, _len1 = _ref.length; _j < _len1; _j++) { + el = _ref[_j]; + elements.push(el); + } + } else if (els.nodeType != null) { + elements = [els]; + } + if (!((elements != null) && elements.length)) { + throw new Error("Invalid `" + name + "` option provided. Please provide a CSS selector, a plain HTML element or a list of those."); + } + return elements; + }; + + Dropzone.confirm = function(question, accepted, rejected) { + if (window.confirm(question)) { + return accepted(); + } else if (rejected != null) { + return rejected(); + } + }; + + Dropzone.isValidFile = function(file, acceptedFiles) { + var baseMimeType, mimeType, validType, _i, _len; + if (!acceptedFiles) { + return true; + } + acceptedFiles = acceptedFiles.split(","); + mimeType = file.type; + baseMimeType = mimeType.replace(/\/.*$/, ""); + for (_i = 0, _len = acceptedFiles.length; _i < _len; _i++) { + validType = acceptedFiles[_i]; + validType = validType.trim(); + if (validType.charAt(0) === ".") { + if (file.name.toLowerCase().indexOf(validType.toLowerCase(), file.name.length - validType.length) !== -1) { + return true; + } + } else if (/\/\*$/.test(validType)) { + if (baseMimeType === validType.replace(/\/.*$/, "")) { + return true; + } + } else { + if (mimeType === validType) { + return true; + } + } + } + return false; + }; + + if (typeof jQuery !== "undefined" && jQuery !== null) { + jQuery.fn.dropzone = function(options) { + return this.each(function() { + return new Dropzone(this, options); + }); + }; + } + + if (typeof module !== "undefined" && module !== null) { + module.exports = Dropzone; + } else { + window.Dropzone = Dropzone; + } + + Dropzone.ADDED = "added"; + + Dropzone.QUEUED = "queued"; + + Dropzone.ACCEPTED = Dropzone.QUEUED; + + Dropzone.UPLOADING = "uploading"; + + Dropzone.PROCESSING = Dropzone.UPLOADING; + + Dropzone.CANCELED = "canceled"; + + Dropzone.ERROR = "error"; + + Dropzone.SUCCESS = "success"; + + + /* + + Bugfix for iOS 6 and 7 + Source: http://stackoverflow.com/questions/11929099/html5-canvas-drawimage-ratio-bug-ios + based on the work of https://github.com/stomita/ios-imagefile-megapixel + */ + + detectVerticalSquash = function(img) { + var alpha, canvas, ctx, data, ey, ih, iw, py, ratio, sy; + iw = img.naturalWidth; + ih = img.naturalHeight; + canvas = document.createElement("canvas"); + canvas.width = 1; + canvas.height = ih; + ctx = canvas.getContext("2d"); + ctx.drawImage(img, 0, 0); + data = ctx.getImageData(0, 0, 1, ih).data; + sy = 0; + ey = ih; + py = ih; + while (py > sy) { + alpha = data[(py - 1) * 4 + 3]; + if (alpha === 0) { + ey = py; + } else { + sy = py; + } + py = (ey + sy) >> 1; + } + ratio = py / ih; + if (ratio === 0) { + return 1; + } else { + return ratio; + } + }; + + drawImageIOSFix = function(ctx, img, sx, sy, sw, sh, dx, dy, dw, dh) { + var vertSquashRatio; + vertSquashRatio = detectVerticalSquash(img); + return ctx.drawImage(img, sx, sy, sw, sh, dx, dy, dw, dh / vertSquashRatio); + }; + + + /* + * contentloaded.js + * + * Author: Diego Perini (diego.perini at gmail.com) + * Summary: cross-browser wrapper for DOMContentLoaded + * Updated: 20101020 + * License: MIT + * Version: 1.2 + * + * URL: + * http://javascript.nwbox.com/ContentLoaded/ + * http://javascript.nwbox.com/ContentLoaded/MIT-LICENSE + */ + + contentLoaded = function(win, fn) { + var add, doc, done, init, poll, pre, rem, root, top; + done = false; + top = true; + doc = win.document; + root = doc.documentElement; + add = (doc.addEventListener ? "addEventListener" : "attachEvent"); + rem = (doc.addEventListener ? "removeEventListener" : "detachEvent"); + pre = (doc.addEventListener ? "" : "on"); + init = function(e) { + if (e.type === "readystatechange" && doc.readyState !== "complete") { + return; + } + (e.type === "load" ? win : doc)[rem](pre + e.type, init, false); + if (!done && (done = true)) { + return fn.call(win, e.type || e); + } + }; + poll = function() { + var e; + try { + root.doScroll("left"); + } catch (_error) { + e = _error; + setTimeout(poll, 50); + return; + } + return init("poll"); + }; + if (doc.readyState !== "complete") { + if (doc.createEventObject && root.doScroll) { + try { + top = !win.frameElement; + } catch (_error) {} + if (top) { + poll(); + } + } + doc[add](pre + "DOMContentLoaded", init, false); + doc[add](pre + "readystatechange", init, false); + return win[add](pre + "load", init, false); + } + }; + + Dropzone._autoDiscoverFunction = function() { + if (Dropzone.autoDiscover) { + return Dropzone.discover(); + } + }; + + contentLoaded(window, Dropzone._autoDiscoverFunction); + +}).call(this); diff --git a/public/js/front_page_script.js b/public/js/front_page_script.js new file mode 100755 index 0000000..fb71683 --- /dev/null +++ b/public/js/front_page_script.js @@ -0,0 +1,26 @@ +var analysis_path="analysis.php?code=" + + +////////////////////////////////////////////////////////////// +/////// For index page: +////////////////////////////////////////////////////////////// +function makeid() +{ + var text = ""; + var possible = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"; + + for( var i=0; i < 20; i++ ) + text += possible.charAt(Math.floor(Math.random() * possible.length)); + + return text; +} + +function showCode() { + var code = makeid(); + var url = analysis_path + code + document.getElementById("analysis_form").innerHTML = ''; + document.getElementById("myAwesomeDropzone").innerHTML = ''; +} + +window.onload = showCode(); + diff --git a/public/js/interactive_dotplot.js b/public/js/interactive_dotplot.js new file mode 100644 index 0000000..4d5a64c --- /dev/null +++ b/public/js/interactive_dotplot.js @@ -0,0 +1,811 @@ + + +function getUrlVars() { + var vars = {}; + var parts = window.location.href.replace(/[?&]+([^=&]+)=([^&]*)/gi, function(m,key,value) { + vars[key] = value; + }); + return vars; +} + +var run_id_code=getUrlVars()["code"]; + + +var directory="user_data/" + run_id_code + "/"; +var nickname=getUrlVars()["nickname"]; + +document.getElementById("nickname_header_dotplot").innerHTML = nickname.replace(/_/g," "); + +console.log(run_id_code) +console.log(nickname) + + +////////// Positions and sizes for drawing ////////// + +var w = window, + d = document, + e = d.documentElement, + g = d.getElementsByTagName('body')[0]; + +var svg_width; +var svg_height; + +var top_edge_padding; +var bottom_edge_padding; +var left_edge_padding; +var right_edge_padding; + +var dotplot_canvas_width; +var dotplot_canvas_height; + +var chrom_label_y_offset; +var contig_label_x_offset; +var min_pixels_to_draw = 1; +var max_num_alignments = 100000; + + +////////// Drawing/D3 objects ////////// +var svg = null; +var dotplot_container = null; +var dotplot_canvas = null; + +var dotplot_ref_axis; +var dotplot_query_axis; + +////////// Scales ////////// +var dotplot_ref_scale = d3.scale.linear(); +var dotplot_query_scale = d3.scale.linear(); + +////////// Behavior /////////// +var zoom = null; + +////////// reference x query selection /////////// + +var refs_selected = null; +var queries_selected = null; + + +////////// Data ////////// + +var loaded_ref_index = false; +var loaded_query_index = false; +var loaded_alignments = false; + +var ref_index = null; +var query_index = null; + +var matching_queries_by_ref = {}; +var matching_refs_by_query = {}; + +var coords_data = null; + +var ref_chrom_start_positions = {}; // ref_chrom_start_positions["chr1"] = 234793761 // absolute position on the dot plot +var query_chrom_start_positions = {}; // query_chrom_start_positions["JSAC01000015.1"] = 8237493 // absolute position on the dot plot +var ref_chrom_label_data = []; +var query_chrom_label_data = []; +var cumulative_ref_size = 0; +var cumulative_query_size = 0; + + +console.log("Starting"); +load_data(); +responsive_sizing(); + +function responsive_sizing() { + + // top_banner_height = 120; // without title + top_banner_height = 170; // with title + + + window_width = (w.innerWidth || e.clientWidth || g.clientWidth);//*0.98; + svg_width = window_width*0.7; + svg_height = (w.innerHeight || e.clientHeight || g.clientHeight) - top_banner_height; + + var right_panel_width = window_width-svg_width; + + // console.log(svg_width) + + top_edge_padding = svg_height*0.04; + bottom_edge_padding = svg_height*0.15; + left_edge_padding = svg_width*0.10; + right_edge_padding = svg_width*0.03; + + + //////// Create the SVG //////// + svg = d3.select("svg") + .attr("width", svg_width) + .attr("height", svg_height); + + d3.select("#panel") + .attr("width",right_panel_width) + .attr("height",svg_height); + + svg.append("rect") + .attr("width",svg_width) + .attr("height",svg_height) + .attr("class","background") + .style('fill',"none"); + + + dotplot_canvas_width = svg_width - left_edge_padding - right_edge_padding; + dotplot_canvas_height = svg_height - top_edge_padding - bottom_edge_padding; + + + // TEMPORARY: + // dotplot_canvas_width = dotplot_canvas_width/2; + + // Make it into a square + // dotplot_canvas_width = Math.min(dotplot_canvas_height,dotplot_canvas_width); + // dotplot_canvas_height = dotplot_canvas_width; + + + // Calculate positions/padding for labels, etc. + chrom_label_y_offset = bottom_edge_padding/10; + contig_label_x_offset = -left_edge_padding/10; +} + + +var info_stats = ""; +function load_data() { + console.log("Starting to load data from file"); + d3.select("#panel").style("visibility",'visible'); + message_to_user("Loading data"); + + d3.csv(directory + nickname + ".info.csv", function(error,info_input) { + if (error) throw error; + + for (var i = 0; i cumulative_ref_size) { + var xdom0 = dotplot_ref_scale.domain()[0] - dotplot_ref_scale.domain()[1] + cumulative_ref_size; + dotplot_ref_scale.domain([xdom0, cumulative_ref_size]); + } + if (dotplot_query_scale.domain()[0] < 0) { + dotplot_query_scale.domain([0, dotplot_query_scale.domain()[1] - dotplot_query_scale.domain()[0] + 0]); + } + if (dotplot_query_scale.domain()[1] > cumulative_query_size) { + var ydom0 = dotplot_query_scale.domain()[0] - dotplot_query_scale.domain()[1] + cumulative_query_size; + dotplot_query_scale.domain([ydom0, cumulative_query_size]); + } + redraw_on_zoom(); + dotplot_container.select("#ref_axis").call(dotplot_ref_axis); + dotplot_container.select("#query_axis").call(dotplot_query_axis); + }); + + dotplot_canvas.call(zoom); + + draw_chromosome_labels(); +} + +function redraw_on_zoom() { + draw_alignments(); + draw_chromosome_labels(); +} + + +function hover_alignment(d) { + d3.select("#hover_message").selectAll("p").remove(); + d3.select("#hover_message").append("p").text("Reference = " + d.ref + ": " + d.ref_start + " - " + d.ref_end) + d3.select("#hover_message").append("p").text("Query = " + d.query + ": " + d.query_start + " - " + d.query_end) + +} + + +function draw_alignment(updateSelection) { + updateSelection + .filter(filter_to_view) + .style("stroke-width",1) + .style("stroke", function(d) { + if (d.tag=="repetitive") { return "red"; + } else {return "black";} }) + .attr("fill","none") + .style("cursor", "crosshair") + .on("mouseover", hover_alignment) + + .each(function (d) { + var x1 = dotplot_ref_scale(d.abs_ref_start); + var x2 = dotplot_ref_scale(d.abs_ref_end); + var y1 = dotplot_query_scale(d.abs_query_start); + var y2 = dotplot_query_scale(d.abs_query_end); + var tangent = (y2-y1)/(x2-x1); + + var new_x1 = x1; + var new_y1 = y1; + + var found_solution_1 = true; + + /////////////////// point 1 /////////////////// + + if (x1 < 0 || y1 > dotplot_canvas_height || x1 > dotplot_canvas_width || y1 < 0) { + found_solution_1 = false + if (x1 < 0) { // left wall + var new_x = 0; + var new_y = y1 - x1 * tangent; + if (new_x >= 0 && new_x <= dotplot_canvas_width && new_y >= 0 && new_y <= dotplot_canvas_height) { + new_x1 = new_x; + new_y1 = new_y; + found_solution_1 = true; + } + } + if (found_solution_1 == false && y1 > dotplot_canvas_height) { // floor + var new_x = (dotplot_canvas_height-y1)/tangent + x1; + var new_y = dotplot_canvas_height; + if (new_x >= 0 && new_x <= dotplot_canvas_width && new_y >= 0 && new_y <= dotplot_canvas_height) { + new_x1 = new_x; + new_y1 = new_y; + found_solution_1 = true; + } + } + if (found_solution_1 == false && x1 > dotplot_canvas_width) { // right wall + var new_x = dotplot_canvas_width; + var new_y = y1+tangent*(dotplot_canvas_width-x1); + if (new_x >= 0 && new_x <= dotplot_canvas_width && new_y >= 0 && new_y <= dotplot_canvas_height) { + new_x1 = new_x; + new_y1 = new_y; + found_solution_1 = true; + } + } + if (found_solution_1 == false && y1 < 0) { // ceiling + var new_y = 0; + var new_x = x1 + (0-y1)/tangent; + if (new_x >= 0 && new_x <= dotplot_canvas_width && new_y >= 0 && new_y <= dotplot_canvas_height) { + new_x1 = new_x; + new_y1 = new_y; + found_solution_1 = true; + } + } + } + + /////////////////// point 2 /////////////////// + + var new_x2 = x2; + var new_y2 = y2; + var found_solution_2 = true; + if (x2 < 0 || y2 > dotplot_canvas_height || x2 > dotplot_canvas_width || y2 < 0) { + found_solution_2 = false; + if (x2 < 0) { // left wall + var new_x = 0; + var new_y = y1 - x1 * tangent; + if (new_x >= 0 && new_x <= dotplot_canvas_width && new_y >= 0 && new_y <= dotplot_canvas_height) { + new_x2 = new_x; + new_y2 = new_y; + found_solution_2 = true; + } + } + if (found_solution_2 == false && y2 > dotplot_canvas_height) { // floor + var new_x = (dotplot_canvas_height-y1)/tangent + x1; + var new_y = dotplot_canvas_height; + if (new_x >= 0 && new_x <= dotplot_canvas_width && new_y >= 0 && new_y <= dotplot_canvas_height) { + new_x2 = new_x; + new_y2 = new_y; + found_solution_2 = true; + } + } + if (found_solution_2 == false && x2 > dotplot_canvas_width) { // right wall + var new_x = dotplot_canvas_width; + var new_y = y1+tangent*(dotplot_canvas_width-x1); + if (new_x >= 0 && new_x <= dotplot_canvas_width && new_y >= 0 && new_y <= dotplot_canvas_height) { + new_x2 = new_x; + new_y2 = new_y; + found_solution_2 = true; + } + } + if (found_solution_2 == false && y2 < 0) { // ceiling + var new_y = 0; + var new_x = x1 + (0-y1)/tangent; + if (new_x >= 0 && new_x <= dotplot_canvas_width && new_y >= 0 && new_y <= dotplot_canvas_height) { + new_x2 = new_x; + new_y2 = new_y; + found_solution_2 = true; + } + } + } + + // console.log(found_solution_1 + " -- " + found_solution_2); + if (!(found_solution_1 && found_solution_2)) { + // Don't draw if it + new_x2 = new_x1; + new_y2 = new_y1; + } + + d3.select(this).attr({ + x1:new_x1, + y1:new_y1, + x2:new_x2, + y2:new_y2 + }) + }) + +} +function filter_to_view(d) { + if (refs_selected != null && refs_selected.indexOf(d.ref) == -1) { + return false; + } + if (queries_selected != null && queries_selected.indexOf(d.query) == -1) { + return false; + } + var x1 = dotplot_ref_scale(d.abs_ref_start); + var x2 = dotplot_ref_scale(d.abs_ref_end); + var y1 = dotplot_query_scale(d.abs_query_start); + var y2 = dotplot_query_scale(d.abs_query_end); + + // if (num_alignments_in_view >= max_num_alignments) { + // return false; + // } else { + if (!((x1 < 0 && x2 < 0) || (x1 > dotplot_canvas_width && x2 > dotplot_canvas_width) || (y1 < 0 && y2 < 0) || (y1 > dotplot_canvas_height && y2 > dotplot_canvas_height))) { + num_alignments_in_view += 1; + return true; + } else { + return false; + } + // } +} + +var current_draw_ID = 0; + +function draw_lines(svg, data, batchSize) { + num_alignments_in_view = 0; + var filtered_data = data.filter(filter_to_view); + var alignments = svg.selectAll('line.alignment').data(filtered_data); + current_draw_ID += 1; + var this_draw_ID = current_draw_ID; + + function drawBatch(batchNumber) { + return function() { + console.log("drawBatch"); + var startIndex = batchNumber * batchSize; + var stopIndex = Math.min(filtered_data.length, startIndex + batchSize); + var updateSelection = d3.selectAll(alignments[0].slice(startIndex, stopIndex)); + var enterSelection = d3.selectAll(alignments.enter()[0].slice(startIndex, stopIndex)); + var exitSelection = d3.selectAll(alignments.exit()[0].slice(startIndex, stopIndex)); + + enterSelection.each(function(d, i) { + var newElement = svg.append('line')[0][0]; + enterSelection[0][i] = newElement; + updateSelection[0][i] = newElement; + newElement.__data__ = this.__data__; + }).attr("class","alignment"); + + exitSelection.remove(); + + draw_alignment(updateSelection); + + + if (stopIndex >= filtered_data.length) { + message_to_user("Done"); + } else { + if (current_draw_ID == this_draw_ID) { + setTimeout(drawBatch(batchNumber + 1), 0); + } + } + }; + } + setTimeout(drawBatch(0), 0); +} + +function draw_alignments() { + + message_to_user("Drawing alignments"); + calculate_positions(); + + dotplot_canvas.selectAll("line.alignment").remove(); + var BATCH_SIZE = 1000; + draw_lines(dotplot_canvas.data([0]), coords_data, BATCH_SIZE); +} + + +function clear_chromosome_labels() { + dotplot_canvas.selectAll("line.chromosome").remove(); + dotplot_container.selectAll("text.chromosome").remove(); + dotplot_canvas.selectAll("line.contig").remove(); + dotplot_container.selectAll("text.contig").remove(); +} + +function draw_chromosome_labels() { + clear_chromosome_labels(); + + + ////////////////////////////// Reference labels ////////////////////////////// + + dotplot_canvas.selectAll("line.chromosome") + .data(ref_chrom_label_data) + .enter() + .append("line") + .filter(function(d) {return ((refs_selected == null || refs_selected.indexOf(d.chrom)!=-1) && (dotplot_ref_scale(d.pos) > 0 && dotplot_ref_scale(d.pos) < dotplot_canvas_width))}) + .attr("class","chromosome") + .style("stroke-width",1) + .style("stroke", "gray") + .attr("fill","none") + .attr("x1",function(d){ return dotplot_ref_scale(d.pos); }) + .attr("y1",0) + .attr("x2",function(d){ return dotplot_ref_scale(d.pos); }) + .attr("y2",dotplot_canvas_height); + + + dotplot_container.selectAll("text.chromosome") + .data(ref_chrom_label_data) + .enter() + .append("text") + .filter(function(d) {return ((refs_selected == null || refs_selected.indexOf(d.chrom)!=-1) && (!(dotplot_ref_scale(d.pos + d.length) < 0 || dotplot_ref_scale(d.pos) > dotplot_canvas_width)))}) + .attr("class","chromosome") + .attr("text-anchor", "end") + .attr("dominant-baseline","middle") + .attr("y",function(d) { + if (dotplot_ref_scale(d.pos) > 0 && dotplot_ref_scale(d.pos + d.length) < dotplot_canvas_width) { + return dotplot_ref_scale(d.pos+d.length/2); + } else if (dotplot_ref_scale(d.pos + d.length) < dotplot_canvas_width) { + // If end of chromosome is showing, put label at average of left wall and end of chromosome + return (dotplot_ref_scale(d.pos+d.length) + 0)/2; + } else if (dotplot_ref_scale(d.pos) > 0) { + // If start of chromosome is showing, put label at average of start and the right wall + return (dotplot_ref_scale(d.pos)+dotplot_canvas_width)/2; + } else { + return dotplot_canvas_width/2; + } + }) + .attr("x",function(d) {return -dotplot_canvas_height-chrom_label_y_offset;}) + .text(function(d) {return d.chrom; }) + .style("fill","gray") + .style("font-size",function(d) { return Math.min(dotplot_ref_scale(d.length) , ((bottom_edge_padding*0.8) / this.getComputedTextLength() * 14)) + "px"; }) + .attr("transform", "rotate(-90)") + .on("click",zoom_to_chromosome) + .on("contextmenu", function (d, i) { + d3.event.preventDefault(); + reset_selections(); + }); + + ////////////////////////////// Query labels ////////////////////////////// + + if (query_chrom_label_data.length < 200 || queries_selected != null) { + + dotplot_canvas.selectAll("line.contig") + .data(query_chrom_label_data) + .enter() + .append("line") + .filter(function(d) {return (dotplot_query_scale(d.pos) > 0 && dotplot_query_scale(d.pos) < dotplot_canvas_height)}) + .attr("class","contig") + .style("stroke-width",1) + .style("stroke", "gray") + .attr("fill","none") + .attr("x1",0) + .attr("y1",function(d){ return dotplot_query_scale(d.pos); }) + .attr("x2",dotplot_canvas_width) + .attr("y2",function(d){ return dotplot_query_scale(d.pos); }); + + dotplot_container.selectAll("text.contig") + .data(query_chrom_label_data) + .enter() + .append("text") + .filter(function(d) {return !(dotplot_query_scale(d.pos) < 0 || dotplot_query_scale(d.pos + d.length) > dotplot_canvas_height)}) + .attr("class","contig") + .attr("text-anchor", "end") + .attr("dominant-baseline","middle") + .attr("y",function(d) { + if (dotplot_query_scale(d.pos) < dotplot_canvas_height && dotplot_query_scale(d.pos + d.length) > 0) { + return dotplot_query_scale(d.pos+d.length/2); + } else if (dotplot_query_scale(d.pos + d.length) > 0) { + // If end of chromosome is showing, put label at average of floor and end of chromosome + return (dotplot_query_scale(d.pos+d.length) + dotplot_canvas_height)/2; + } else if (dotplot_query_scale(d.pos) < dotplot_canvas_height) { + // If start of chromosome is showing, put label at average of start and the ceiling + return (dotplot_query_scale(d.pos)+0)/2; + } else { + return dotplot_canvas_height/2; + } + }) + .attr("x",function(d) {return contig_label_x_offset;}) + .text(function(d) {return d.chrom; }) + .style("fill","gray") + .style("font-size",function(d) {return Math.min(dotplot_query_scale(d.pos)-dotplot_query_scale(d.pos + d.length), left_edge_padding*0.8 / this.getComputedTextLength() * 14) + "px"; }) + .on("click",zoom_to_contig) + .on("contextmenu", function (d, i) { + d3.event.preventDefault(); + reset_selections(); + }); + } +} + +function reset_selections(){ + refs_selected = null; + queries_selected = null; + clear_chromosome_labels(); + use_indices(); + draw_dotplot(); + draw_alignments(); +} + +function measure_shared_sequence_ref(query,ref) { + var shared_sequence = 0; + for (var i = 0; i < coords_data.length; i++) { + if (coords_data[i].ref == ref && coords_data[i].query == query) { + shared_sequence += Math.abs(dotplot_ref_scale(coords_data[i].abs_ref_end) - dotplot_ref_scale(coords_data[i].abs_ref_start)); + } + } + return shared_sequence; +} + +function measure_shared_sequence_query(query,ref) { + var shared_sequence = 0; + for (var i = 0; i < coords_data.length; i++) { + if (coords_data[i].ref == ref && coords_data[i].query == query) { + shared_sequence += Math.abs(dotplot_query_scale(coords_data[i].abs_query_end) - dotplot_query_scale(coords_data[i].abs_query_start)); + } + } + return shared_sequence; +} + +var min_shared_seq_in_pixels = 5; + +function zoom_to_chromosome(d) { + console.log("zoom to chromosome"); + console.log(d.chrom); + // console.log(matching_queries_by_ref[d.chrom]); + refs_selected = [d.chrom]; + var potential_queries_selected = matching_queries_by_ref[d.chrom]; + // console.log(queries_selected); + queries_selected = potential_queries_selected; + + use_indices(); + + + // Narrow down to queries with at least a small shared sequence + queries_selected = []; + for (var i = 0; i < potential_queries_selected.length; i++) { + if (measure_shared_sequence_ref(potential_queries_selected[i],d.chrom) >= min_shared_seq_in_pixels) { + queries_selected.push(potential_queries_selected[i]); + } + } + + clear_chromosome_labels(); + use_indices() + draw_dotplot(); + draw_alignments(); + + +} + +function zoom_to_contig(d) { + console.log(d.chrom); + console.log(matching_refs_by_query[d.chrom]); + queries_selected = [d.chrom]; + var potential_refs_selected = matching_refs_by_query[d.chrom]; + refs_selected = potential_refs_selected; + + use_indices(); + + console.log(potential_refs_selected); + // Narrow down to queries with at least a small shared sequence + refs_selected = []; + for (var i = 0; i < potential_refs_selected.length; i++) { + // console.log(potential_refs_selected[i]); + // console.log(measure_shared_sequence_query(d.chrom,potential_refs_selected[i])); + if (measure_shared_sequence_query(d.chrom,potential_refs_selected[i]) >= min_shared_seq_in_pixels) { + refs_selected.push(potential_refs_selected[i]); + } + } + console.log(refs_selected); + + clear_chromosome_labels(); + + use_indices(); + draw_dotplot(); + draw_alignments(); + +} + + +function message_to_user(message) { + d3.select("#user_message") + .text(message) +} + +window.onresize = resizeWindow; +function resizeWindow() +{ + clear_chromosome_labels(); + responsive_sizing(); + draw_dotplot(); + draw_alignments(); + +} diff --git a/public/js/jquery.min.js b/public/js/jquery.min.js new file mode 100644 index 0000000..ab28a24 --- /dev/null +++ b/public/js/jquery.min.js @@ -0,0 +1,4 @@ +/*! jQuery v1.11.1 | (c) 2005, 2014 jQuery Foundation, Inc. | jquery.org/license */ +!function(a,b){"object"==typeof 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