genevalidator 1.6.2 → 1.6.3

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data/README.md

@@ -1,63 +1,113 @@
-# GeneValidator - Identify problems with predicted genes 
+# GeneValidator - Identify problems with predicted genes
 [![Build Status](https://travis-ci.org/wurmlab/genevalidator.svg?branch=master)](https://travis-ci.org/wurmlab/genevalidator)
 [![Gem Version](https://badge.fury.io/rb/genevalidator.svg)](http://badge.fury.io/rb/genevalidator)
 [![Dependency Status](https://gemnasium.com/wurmlab/GeneValidator.svg)](https://gemnasium.com/wurmlab/GeneValidator)
 [![Scrutinizer Code Quality](https://scrutinizer-ci.com/g/wurmlab/GeneValidator/badges/quality-score.png?b=master)](https://scrutinizer-ci.com/g/wurmlab/GeneValidator/?branch=master)
 [![Test Coverage](https://codeclimate.com/github/wurmlab/GeneValidator/badges/coverage.svg)](https://codeclimate.com/github/wurmlab/GeneValidator)
 
+
+
+
 ## Introduction
-The goal of GeneValidator is to identify problems with gene predictions and provide useful information based on the similarities to genes in public databases. The results produced will make provide evidence on how sequencing curation may be done and will be useful in improving or trying out new approaches for gene prediction tools. The main target of this tool are biologists who wish to validate the data produced in their labs.
+GeneValidator helps in identifing problems with gene predictions and provide useful information extracted from analysing orthologs in BLAST databases. The results produced can be used by biocurators and researchers who need accurate gene predictions.
+
+If you would like to use GeneValidator on a few sequences, see our online [GeneValidator Web App](http://genevalidator.sbcs.qmul.ac.uk) - [http://genevalidator.sbcs.qmul.ac.uk](http://genevalidator.sbcs.qmul.ac.uk).
+
 
 If you use GeneValidator in your work, please cite us as follows:
+> "Dragan M<sup>&Dagger;</sup>, Moghul MI<sup>&Dagger;</sup>, Priyam A, Bustos C & Wurm Y (<em>in prep.</em>) GeneValidator: identify problematic gene predictions"
 
-"Dragan M, Moghul MI, Priyam A & Wurm Y (<em>in prep.</em>) GeneValidator: identify problematic gene predictions"
 
 
-#### Related projects 
-[GeneValidatorApp](https://github.com/wurmlab/GeneValidatorApp) - A Web App wrapper for GeneValidator.<br>
-[GeneValidatorApp-API](https://github.com/wurmlab/GeneValidatorApp-API) - An easy to use API for GeneValidatorApp to allow you to use GeneValidator within your web applications.
 
 
-### Validations
-Currently, it is possible to run the following validations with GeneValidator
 
-* Length validation by clusterization (a graph is dynamically produced)
-* Length validation by ranking
-* Check gene merge (a graph is dynamically produced)
-* Check duplications
-* Reading frame validation (for nucleotides)
-* Main ORF validation (for nucleotides) (a graph is dynamically produced)
-* Validation based on multiple alignment (a graph is dynamically produced)
+## Validations
+GeneValidator runs the following validation on all input sequences:
+
+- **Length:** GeneValidator compares the length of the query sequence to the lengths of the most significant BLAST hits using hierarchical clustering and a rank test. This can suggest that the query is too short or too long. Graphs are dynamically produced for this validation.
+- **Coverage:** GeneValidator determines whether hit regions match the query sequence more than once using a Wilcoxon test. Significance suggests that the query includes duplicated regions (e.g., resulting from merging of tandem gene duplication).
+- **Conserved Regions:** GeneValidator performs multiple alignment of the ten most significant BLAST hits, derive a Position Specific Scoring Matrix Profile, and align this profile to the query. Results of this identify potentially missing or extra regions. Graphs are dynamically produced for this validation.
+- **Different genes:** We expect the query sequence to encode a single protein-coding gene. GeneValidator first determines whether the BLAST HSPs map to multiple regions of the query by testing for deviation from unimodality of HSP start and stop coordinates. If this is the case, GeneValidator performs a linear regression between HSP start and stop coordinates (each datapoint is weighted proportionally to the significance of the corresponding HSP). We empirically determined that regression slopes of 0.4 to 1.2 indicate that the query prediction combines two different genes. Graphs are dynamically produced for this validation.
+
+GeneValidator also runs a further two validation on cDNA sequences:
+
+- **Ab initio Open Reading Frame (ORF):** Presence of more than one major ORF occurs in the presence of a frameshift, retained intron, or merged genes.
+- **Similarity-based ORFs:** We expect all BLAST hits to align within a single ORF. This test is more sensitive than the previous when a query has many BLAST hits.
 
-It is also possible to add your own custom validations to GeneValidator. 
+Each analysis of each query returns a binary result (good vs. potential problem) according to p-value or an empirically determined cutoff. The results for each query are combined into an overall quality score from 0 to 100. Each analysis of each query returns a binary result (good vs. potential problem) according to p-value or an empirically determined cutoff. The results for each query are combined into an overall quality score from 0 to 100.
 
-## Installation Requirements
+
+
+
+
+## Installation
+### Installation Requirements
 * Ruby (>= 2.0.0)
-* NCBI BLAST+ (>= 2.2.30+)
+* NCBI BLAST+ (>= 2.2.30+) (download [here](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)).
 * MAFFT installation (download [here](http://mafft.cbrc.jp/alignment/software/)).
-* Mozilla FireFox - In order to dynamically produce graphs for some of the validation, GeneValidator relies on dependency called 'd3'. Unfortunately, at this moment of time, d3 only works in Firefox (download [here](https://www.mozilla.org/en-GB/firefox/new/)).
+* A web browser - [Mozilla FireFox](https://www.mozilla.org/en-GB/firefox/new/) & Safari are recommended. At the moment, it is not possible to use Chrome to view the results locally (as chrome does not allow ajax to local files). To avoid this, simply use a different browser (like Firefox or Safari) or start a local server in the results folder.
 
 Please see [here](https://gist.github.com/IsmailM/b783e8a06565197084e6) for more help with installing the prerequisites.
-  
-## Installation
-1) Type the following command in the terminal
+
+### Installation
+Simply run the following command in the terminal.
 
 ```bash
-$ gem install genevalidator
+gem install genevalidator
 ```
 
+If that doesn't work, try `sudo gem install genevalidator` instead.
 
-## Usage 
-1) After installing, GeneValidator can be run by typing the following command in the terminal:
+##### Running From Source (Not Recommended)
+It is also possible to run from source. However, this is not recommended.
+
+```bash
+# Clone the repository.
+git clone https://github.com/wurmlab/genevalidator.git
 
+# Move into GeneValidator source directory.
+cd GeneValidator
+
+# Install bundler
+gem install bundler
+
+# Use bundler to install dependencies
+bundle install
+
+# Optional: run tests, build documentation and build the gem from source
+bundle exec rake
+
+# Run GeneValidator.
+bundle exec genevalidator -h
+# note that `bundle exec` executes GeneValidator in the context of the bundle
+
+# Alternativaly, install GeneValidator as a gem
+bundle exec rake install
+genevalidator -h
+```
+
+
+
+
+
+
+## Usage
+Verify GeneValidator installed by running the following command in the terminal:
+
+```
+genevalidator
+```
+
+You should see the following output.
 
 ```bash
 USAGE:
-    $ genevalidator [OPTIONS] Input_File
-    
+    genevalidator [OPTIONS] Input_File
+
 ARGUMENTS:
     Input_File: Path to the input fasta file containing the predicted sequences.
-    
+
 OPTIONAL ARGUMENTS
     -v, --validations <String>       The Validations to be applied.
                                      Validation Options Available (separated by coma):
@@ -71,12 +121,12 @@ OPTIONAL ARGUMENTS
                                        align = Validating based on multiple alignment
     -d, --db [BLAST_DATABASE]        Path to the BLAST database
                                      GeneValidator also supports remote databases:
-                                     e.g.   $ genevalidator -d "swissprot -remote" Input_File
+                                     e.g.   genevalidator -d "swissprot -remote" Input_File
     -e, --extract_raw_seqs           Produces a fasta file of the raw sequences of all BLAST hits in the
                                      supplied BLAST output file. This fasta file can then be provided to
                                      GeneValidator with the "-r", "--raw_sequences" argument
-    -j, --json_file [JSON_FILE]      Generate GV results from a json file (or a subset of a json file)
-                                     produced from GeneValidator
+    -j, --json_file [JSON_FILE]      Generate HTML report from a JSON file (or a subset of a JSON file)
+                                     produced by GeneValidator
     -x [BLAST_XML_FILE],             Provide GeneValidator with a pre-computed BLAST XML output
         --blast_xml_file             file (BLAST -outfmt option 5).
     -t [BLAST_TABULAR_FILE],         Provide GeneValidator with a pre-computed BLAST tabular output
@@ -85,62 +135,92 @@ OPTIONAL ARGUMENTS
         --blast_tabular_options      See BLAST+ manual pages for more details
     -n, --num_threads num_of_threads Specify the number of processor threads to use when running
                                      BLAST and Mafft within GeneValidator.
-    -f, --fast                       Run BLAST on all sequences together (rather than separately)
-                                     to speed up the analysis.
-                                     However, this means that there will be a longer wait before the
-                                     results can be viewed (as GeneValidator will need to run BLAST
-                                     on all sequences before producing any results).
-                                     The speed difference will be more apparent on larger input files
     -r, --raw_sequences [raw_seq]    Supply a fasta file of the raw sequences of all BLAST hits present
                                      in the supplied BLAST XML or BLAST tabular file.
-    -m, --mafft_bin [MAFFT_PATH]     Path to MAFFT bin folder (is added to $PATH variable)
-    -b, --blast_bin [BLAST_PATH]     Path to BLAST+ bin folder (is added to $PATH variable)
+    -b, --binaries [binaries]        Path to BLAST and MAFFT bin folders (is added to $PATH variable)
+                                     To be provided as follows:
+                                     e.g.   genevalidator -b /blast/bin/path/ -b /mafft/bin/path/
         --version                    The version of GeneValidator that you are running.
     -h, --help                       Show this screen.
 ```
 
-Please type `genevalidator -h` into your terminal to see this information in your terminal. 
+
+
+
 
 ## Example Usage Scenarios
 
-##### Local Database, with custom number of threads (in this case 8)
+#### Simplest Usage (using NCBI remote BLAST servers)
+This runs BLAST on NCBI remote Swiss-Prot BLAST database. As such this is suitable for analyses on less than 10 sequences.
 
 ```bash
-$ genevalidator -d 'Path-to-local-BLAST-db' -n 8 Input_FASTA_File
+genevalidator INPUT_FASTA_FILE
 ```
-##### Local Database, with the fast mode, with custom number of threads (in this case 8)
-Internally, GV will run BLAST on all input sequences before analysing any sequences (instead of running BLAST on each sequence and then analysing the sequence).
+
+#### Using a local BLAST database.
+GeneValidator would run BLAST on each query against the provided BLAST database and then run the validation analyses.
 
 ```bash
-$ genevalidator -d 'Path-to-local-BLAST-db' -n 8 -f Input_FASTA_File
+genevalidator -d DATABASE_PATH -n NUM_THREADS INPUT_FASTA_FILE
 ```
 
-##### Local Database, with pre-computed BLAST XML file, with custom number of threads (in this case 8)
+#### Running BLAST separately
+At times, it may be more suitable to run the resource-heavy BLAST separately and then pass the BLAST output file to GeneValidator. This may be the case if one is analysing a large number of input sequence and would like to run the time- and resource-consuming BLAST process on a faster machine (i.e a cluster).
 
-```bash
-$  blast(p/x) -db SwissProt -out Path-to-XML-file -num_threads 8 -outfmt 5 -query Input_FASTA_File
-$  genevalidator -d 'local-or-remote-BLAST-db' -n 8 -x 'Path-to-XML-file' Input_FASTA_File
+GeneValidator supports the XML and tabular BLAST output formats.
+
+```
+# Run BLAST (XML output)
+blast(p/x) -db DATABASE_PATH -num_threads NUM_THREADS -outfmt 5 -out BLAST_XML_FILE -query INPUT_FASTA_FILE
+
+# Optional: Generate a fasta file for the BLAST hits.
+# Note: this works best if you use the same database used to create the BLAST OUTPUT file.
+genevalidator -d DATABASE_PATH -e -x BLAST_XML_FILE
+
+# Run GeneValidator
+## If you ran the previous command (i.e. if you produced fasta file for the BLAST hits)
+genevalidator -n NUM_THREADS -x BLAST_XML_FILE -r RAW_SEQUENCES_FILE INPUT_FASTA_FILE
+
+## If you did not run the previous command (this will run the previous command for you)
+genevalidator -d DATABASE_PATH -n NUM_THREADS -x BLAST_XML_FILE INPUT_FASTA_FILE
 ```
 
-##### Local Database, with pre-computed BLAST XML file, with custom number of threads (in this case 8)
+This is the same, but using the BLAST tabular output.
 
 ```bash
-$ blast(p/x) -db SwissProt -out Path-to-tabular-file -num_threads 8 -outfmt "7 qseqid sseqid sacc slen qstart qend sstart send length qframe pident nident evalue qseq sseq" -query Input_FASTA_File
-$ genevalidator -d 'local-or-remote-BLAST-db' -n 8 -t 'Path-to-tabular-file' -o 'qseqid sseqid sacc slen qstart qend sstart send length qframe pident evalue' Input_FASTA_File 
+# Run BLAST (tabular output)
+blast(p/x) -db DATABASE_PATH -num_threads NUM_THREADS -outfmt '7 qseqid sseqid sacc slen qstart qend sstart send length qframe pident nident evalue qseq sseq' -out BLAST_TAB_FILE -query INPUT_FASTA_FILE
+
+# Optional: Generate a fasta file for the BLAST hits.
+# Note: this works best if you use the same database used to create the BLAST OUTPUT file.
+genevalidator -d DATABASE_PATH -e -t BLAST_TAB_FILE -o 'qseqid sseqid sacc slen qstart qend sstart send length qframe pident nident evalue qseq sseq'
+
+# Run GeneValidator
+## If you ran the previous command (i.e. if you produced fasta file for the BLAST hits)
+genevalidator -n NUM_THREADS -t BLAST_TAB_FILE -o 'qseqid sseqid sacc slen qstart qend sstart send length qframe pident nident evalue qseq sseq' -r RAW_SEQUENCES_FILE INPUT_FASTA_FILE
+
+## If you did generate the BLAST hits fasta file (this will run the previous command for you)
+genevalidator -d DATABASE_PATH -n NUM_THREADS -t BLAST_TAB_FILE -o 'qseqid sseqid sacc slen qstart qend sstart send length qframe pident nident evalue qseq sseq' INPUT_FASTA_FILE
+
 ```
 
 
+
+
 ## Output
 The output produced by GeneValidator is presented in three manners.
 
-#### HTML Output 
-Firstly, the output is produced as a colourful, HTML file. This file is titled 'results.html' (found in the 'html' folder) and can be opened in a web browser (please use Mozilla Firefox). This file contains all the results in an easy-to-view manner with graphical visualisations. See exemplar html output [here](http://wurmlab.github.io/tools/genevalidator/exemplar_data/protein_input/) (protein input data) and [here](http://wurmlab.github.io/tools/genevalidator/exemplar_data/genetic_input/) (DNA input data).
+#### HTML Output
+Firstly, the output is produced as a colourful, HTML file. This file is titled 'results.html' (found in the 'html' folder) and can be opened in a web browser (please use a supported browser - See [Installation Requirements](#installation-requirements)). This file contains all the results in an easy-to-view manner with graphical visualisations. See exemplar HTML output [here](http://wurmlab.github.io/tools/genevalidator/exemplar_data/protein_input/) (protein input data) and [here](http://wurmlab.github.io/tools/genevalidator/exemplar_data/genetic_input/) (DNA input data).
 
 #### JSON Output
 The output is also produced in JSON. GeneValidator is able to re-generate results for any JSON files (or derived JSON files) with that were previously generated by the program. This means that you are able to use the JSON file in your own analysis pipelines and then use GeneValidator to produce the HTML output for the analysed JSON file.
 
 #### Terminal Output
-Lastly, a summary of the results is also outputted in the terminal to provide quick feedback on the results.
+Lastly, a tabular summary of the results is also outputted in the terminal to provide quick feedback on the results. The terminal output can be piped to tools like `awk` and `sed` or redirected to a file for further processing.
+
+
+
 
 
 ## Analysing the JSON output
@@ -154,38 +234,29 @@ After installing node:
 $ npm install -g json
 ```
 
-### Filtering the results 
-
-- Extract sequences that have an overall score of 100
+### Filtering the results
 
 ```bash
-$ json -f INPUT_JSON_FILE -c 'this.overall_score == 100' > OUTPUT_JSON_FILE
-```
 
-- Extract sequences that have an overall score of over 70
+# Extract sequences that have an overall score of 100
+$ json -f INPUT_JSON_FILE -c 'this.overall_score == 100' > OUTPUT_JSON_FILE
 
-```bash
+# Extract sequences that have an overall score of over 70
 $ json -f INPUT_JSON_FILE -c 'this.overall_score > 70' > OUTPUT_JSON_FILE
-```
-
-- Extract sequences that have more than 50 hits
 
-```bash
+# Extract sequences that have more than 50 hits
 $ json -f INPUT_JSON_FILE -c 'this.no_hits > 50' > OUTPUT_JSON_FILE
-```
 
-- Sort the JSON based on the overall score (ascending - 0 to 100)
-
-```bash
+# Sort the JSON based on the overall score (ascending - 0 to 100)
 $ json -f INPUT_JSON_FILE -A -e 'this.sort(function(a,b) {return (a.overall_score > b.overall_score) ? 1 : ((b.overall_score > a.overall_score) ? -1 : 0);} );' > OUTPUT_JSON_FILE
-```
 
-- Sort the JSON based on the overall score (decending - 100 to 0)
-
-```bash
+# Sort the JSON based on the overall score (decending - 100 to 0)
 json -f INPUT_JSON_FILE -A -e 'this.sort(function(a,b) {return (a.overall_score < b.overall_score) ? 1 : ((b.overall_score < a.overall_score) ? -1 : 0);} );' > OUTPUT_JSON_FILE
 ```
 
-## Other Resources
 
-* [Full Documentation](http://wurmlab.github.io/tools/genevalidator/documentation/v1/)
+
+
+## Related projects
+[GeneValidatorApp](https://github.com/wurmlab/GeneValidatorApp) - A Web App wrapper for GeneValidator.<br>
+[GeneValidatorApp-API](https://github.com/wurmlab/GeneValidatorApp-API) - An easy to use API for GeneValidatorApp to allow you to use GeneValidator within your web applications.

data/Rakefile

@@ -9,7 +9,7 @@ task install: [:build] do
 end
 
 desc 'Runs tests, generates documentation, builds gem (default)'
-task :build => [:test, :doc] do
+task build: [:test, :doc] do
   sh 'gem build genevalidator.gemspec'
 end
 

data/aux/files/css/genevalidator.compiled.min.css

@@ -0,0 +1,16 @@
+/*Bootstrap*/
+/*!
+ * Bootstrap v3.1.1 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
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+// TableSorter
+/*!
+* TableSorter 2.17.7 min - Client-side table sorting with ease!
+* Copyright (c) 2007 Christian Bach
+*/
+!function(h){h.extend({tablesorter:new function(){function d(){var a=arguments[0],b=1<arguments.length?Array.prototype.slice.call(arguments):a;if("undefined"!==typeof console&&"undefined"!==typeof console.log)console[/error/i.test(a)?"error":/warn/i.test(a)?"warn":"log"](b);else alert(b)}function q(a,b){d(a+" ("+((new Date).getTime()-b.getTime())+"ms)")}function n(a){for(var b in a)return!1;return!0}function r(a,b,c){if(!b)return"";var g,e=a.config,l=e.textExtraction||"",d="",d="basic"===l?h(b).attr(e.textAttribute)|| b.textContent||b.innerText||h(b).text()||"":"function"===typeof l?l(b,a,c):"function"===typeof(g=f.getColumnData(a,l,c))?g(b,a,c):b.textContent||b.innerText||h(b).text()||"";return h.trim(d)}function v(a){var b,c,g=a.config,e=g.$tbodies=g.$table.children("tbody:not(."+g.cssInfoBlock+")"),l,x,k,h,m,B,u,s,t,n=0,v="",w=e.length;if(0===w)return g.debug?d("Warning: *Empty table!* Not building a parser cache"):"";g.debug&&(t=new Date,d("Detecting parsers for each column"));b=[];for(c=[];n<w;){l=e[n].rows; if(l[n])for(x=g.columns,k=0;k<x;k++){h=g.$headers.filter('[data-column="'+k+'"]:last');m=f.getColumnData(a,g.headers,k);s=f.getParserById(f.getData(h,m,"extractor"));u=f.getParserById(f.getData(h,m,"sorter"));B="false"===f.getData(h,m,"parser");g.empties[k]=f.getData(h,m,"empty")||g.emptyTo||(g.emptyToBottom?"bottom":"top");g.strings[k]=f.getData(h,m,"string")||g.stringTo||"max";B&&(u=f.getParserById("no-parser"));s||(s=!1);if(!u)a:{h=a;m=l;B=-1;u=k;for(var A=void 0,K=f.parsers.length,H=!1,z="",A= !0;""===z&&A;)B++,m[B]?(H=m[B].cells[u],z=r(h,H,u),h.config.debug&&d("Checking if value was empty on row "+B+", column: "+u+': "'+z+'"')):A=!1;for(;0<=--K;)if((A=f.parsers[K])&&"text"!==A.id&&A.is&&A.is(z,h,H)){u=A;break a}u=f.getParserById("text")}g.debug&&(v+="column:"+k+"; extractor:"+s.id+"; parser:"+u.id+"; string:"+g.strings[k]+"; empty: "+g.empties[k]+"\n");c[k]=u;b[k]=s}n+=c.length?w:1}g.debug&&(d(v?v:"No parsers detected"),q("Completed detecting parsers",t));g.parsers=c;g.extractors=b}function w(a){var b, c,g,e,l,x,k,p,m,n,u,s=a.config,t=s.$table.children("tbody"),v=s.extractors,w=s.parsers;s.cache={};s.totalRows=0;if(!w)return s.debug?d("Warning: *Empty table!* Not building a cache"):"";s.debug&&(p=new Date);s.showProcessing&&f.isProcessing(a,!0);for(l=0;l<t.length;l++)if(u=[],b=s.cache[l]={normalized:[]},!t.eq(l).hasClass(s.cssInfoBlock)){m=t[l]&&t[l].rows.length||0;for(g=0;g<m;++g)if(n={child:[]},x=h(t[l].rows[g]),k=[],x.hasClass(s.cssChildRow)&&0!==g)c=b.normalized.length-1,b.normalized[c][s.columns].$row= b.normalized[c][s.columns].$row.add(x),x.prev().hasClass(s.cssChildRow)||x.prev().addClass(f.css.cssHasChild),n.child[c]=h.trim(x[0].textContent||x[0].innerText||x.text()||"");else{n.$row=x;n.order=g;for(e=0;e<s.columns;++e)"undefined"===typeof w[e]?s.debug&&d("No parser found for cell:",x[0].cells[e],"does it have a header?"):(c=r(a,x[0].cells[e],e),c="undefined"===typeof v[e].id?c:v[e].format(c,a,x[0].cells[e],e),c="no-parser"===w[e].id?"":w[e].format(c,a,x[0].cells[e],e),k.push(s.ignoreCase&&"string"=== typeof c?c.toLowerCase():c),"numeric"===(w[e].type||"").toLowerCase()&&(u[e]=Math.max(Math.abs(c)||0,u[e]||0)));k[s.columns]=n;b.normalized.push(k)}b.colMax=u;s.totalRows+=b.normalized.length}s.showProcessing&&f.isProcessing(a);s.debug&&q("Building cache for "+m+" rows",p)}function z(a,b){var c=a.config,g=c.widgetOptions,e=a.tBodies,l=[],d=c.cache,k,p,m,r,u,s;if(n(d))return c.appender?c.appender(a,l):a.isUpdating?c.$table.trigger("updateComplete",a):"";c.debug&&(s=new Date);for(u=0;u<e.length;u++)if(k= h(e[u]),k.length&&!k.hasClass(c.cssInfoBlock)){m=f.processTbody(a,k,!0);k=d[u].normalized;p=k.length;for(r=0;r<p;r++)l.push(k[r][c.columns].$row),c.appender&&(!c.pager||c.pager.removeRows&&g.pager_removeRows||c.pager.ajax)||m.append(k[r][c.columns].$row);f.processTbody(a,m,!1)}c.appender&&c.appender(a,l);c.debug&&q("Rebuilt table",s);b||c.appender||f.applyWidget(a);a.isUpdating&&c.$table.trigger("updateComplete",a)}function D(a){return/^d/i.test(a)||1===a}function E(a){var b,c,g,e,l,x,k,p=a.config; p.headerList=[];p.headerContent=[];p.debug&&(k=new Date);p.columns=f.computeColumnIndex(p.$table.children("thead, tfoot").children("tr"));e=p.cssIcon?'<i class="'+(p.cssIcon===f.css.icon?f.css.icon:p.cssIcon+" "+f.css.icon)+'"></i>':"";p.$headers=h(a).find(p.selectorHeaders).each(function(k){c=h(this);b=f.getColumnData(a,p.headers,k,!0);p.headerContent[k]=h(this).html();l=p.headerTemplate.replace(/\{content\}/g,h(this).html()).replace(/\{icon\}/g,e);p.onRenderTemplate&&(g=p.onRenderTemplate.apply(c, [k,l]))&&"string"===typeof g&&(l=g);h(this).html('<div class="'+f.css.headerIn+'">'+l+"</div>");p.onRenderHeader&&p.onRenderHeader.apply(c,[k]);this.column=parseInt(h(this).attr("data-column"),10);this.order=D(f.getData(c,b,"sortInitialOrder")||p.sortInitialOrder)?[1,0,2]:[0,1,2];this.count=-1;this.lockedOrder=!1;x=f.getData(c,b,"lockedOrder")||!1;"undefined"!==typeof x&&!1!==x&&(this.order=this.lockedOrder=D(x)?[1,1,1]:[0,0,0]);c.addClass(f.css.header+" "+p.cssHeader);p.headerList[k]=this;c.parent().addClass(f.css.headerRow+ " "+p.cssHeaderRow).attr("role","row");p.tabIndex&&c.attr("tabindex",0)}).attr({scope:"col",role:"columnheader"});C(a);p.debug&&(q("Built headers:",k),d(p.$headers))}function F(a,b,c){var g=a.config;g.$table.find(g.selectorRemove).remove();v(a);w(a);I(g.$table,b,c)}function C(a){var b,c,g,e=a.config;e.$headers.each(function(l,d){c=h(d);g=f.getColumnData(a,e.headers,l,!0);b="false"===f.getData(d,g,"sorter")||"false"===f.getData(d,g,"parser");d.sortDisabled=b;c[b?"addClass":"removeClass"]("sorter-false").attr("aria-disabled", ""+b);a.id&&(b?c.removeAttr("aria-controls"):c.attr("aria-controls",a.id))})}function G(a){var b,c,g=a.config,e=g.sortList,l=e.length,d=f.css.sortNone+" "+g.cssNone,k=[f.css.sortAsc+" "+g.cssAsc,f.css.sortDesc+" "+g.cssDesc],p=["ascending","descending"],m=h(a).find("tfoot tr").children().add(g.$extraHeaders).removeClass(k.join(" "));g.$headers.removeClass(k.join(" ")).addClass(d).attr("aria-sort","none");for(b=0;b<l;b++)if(2!==e[b][1]&&(a=g.$headers.not(".sorter-false").filter('[data-column="'+e[b][0]+ 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n.getMinutes()}),Bc.minutes=Bc.minute.range,Bc.minutes.utc=Bc.minute.utc.range,Bc.hour=Ci(function(n){var t=n.getTimezoneOffset()/60;return new $c(36e5*(Math.floor(n/36e5-t)+t))},function(n,t){n.setTime(n.getTime()+36e5*Math.floor(t))},function(n){return n.getHours()}),Bc.hours=Bc.hour.range,Bc.hours.utc=Bc.hour.utc.range,Bc.month=Ci(function(n){return n=Bc.day(n),n.setDate(1),n},function(n,t){n.setMonth(n.getMonth()+t)},function(n){return n.getMonth()}),Bc.months=Bc.month.range,Bc.months.utc=Bc.month.utc.range;var Ml=[1e3,5e3,15e3,3e4,6e4,3e5,9e5,18e5,36e5,108e5,216e5,432e5,864e5,1728e5,6048e5,2592e6,7776e6,31536e6],xl=[[Bc.second,1],[Bc.second,5],[Bc.second,15],[Bc.second,30],[Bc.minute,1],[Bc.minute,5],[Bc.minute,15],[Bc.minute,30],[Bc.hour,1],[Bc.hour,3],[Bc.hour,6],[Bc.hour,12],[Bc.day,1],[Bc.day,2],[Bc.week,1],[Bc.month,1],[Bc.month,3],[Bc.year,1]],bl=[[ji("%Y"),Vt],[ji("%B"),function(n){return n.getMonth()}],[ji("%b %d"),function(n){return 1!=n.getDate()}],[ji("%a %d"),function(n){return n.getDay()&&1!=n.getDate()}],[ji("%I %p"),function(n){return n.getHours()}],[ji("%I:%M"),function(n){return n.getMinutes()}],[ji(":%S"),function(n){return n.getSeconds()}],[ji(".%L"),function(n){return n.getMilliseconds()}]],_l=ho(bl);xl.year=Bc.year,Bc.scale=function(){return so(vo.scale.linear(),xl,_l)};var wl={range:function(n,t,e){return vo.range(+n,+t,e).map(fo)}},Sl=xl.map(function(n){return[n[0].utc,n[1]]}),El=[[co("%Y"),Vt],[co("%B"),function(n){return n.getUTCMonth()}],[co("%b %d"),function(n){return 1!=n.getUTCDate()}],[co("%a %d"),function(n){return n.getUTCDay()&&1!=n.getUTCDate()}],[co("%I %p"),function(n){return n.getUTCHours()}],[co("%I:%M"),function(n){return n.getUTCMinutes()}],[co(":%S"),function(n){return n.getUTCSeconds()}],[co(".%L"),function(n){return n.getUTCMilliseconds()}]],kl=ho(El);return Sl.year=Bc.year.utc,Bc.scale.utc=function(){return so(vo.scale.linear(),Sl,kl)},vo.text=dt(function(n){return n.responseText}),vo.json=function(n,t){return vt(n,"application/json",go,t)},vo.html=function(n,t){return vt(n,"text/html",po,t)},vo.xml=dt(function(n){return n.responseXML}),vo}();
+// plot.js
+var GV;GV||(GV={}),function(){"use strict";GV.toggleAllPlots=function(t){if(window.chrome&&"file:"===window.location.protocol)$("#browseralert").modal();else{var a=$(".plot_btn");a.length>30?$("#alert").modal():($("#spinner1").modal({backdrop:"static",keyboard:"false"}),"pressed"!==t.status?(t.status="pressed",$("#show_all_plots").html("Hide All Charts"),GV.showAllPlots()):(t.status="released",$("#show_all_plots").html("Show All Charts"),GV.removeAllPlots()),$("#spinner1").modal("hide"))}},GV.showAllPlots=function(){$(".plot_btn").each(function(){"pressed"!==this.status&&GV.addData(this,"all")})},GV.removeAllPlots=function(){$(".tablesorter-childRow").each(function(){$(this).remove()}),$(".plot_btn").each(function(){this.status="released"})},GV.addData=function(t,a){if(window.chrome&&"file:"===window.location.protocol)$("#browseralert").modal();else{var e=$(t).closest("tr"),r=e.attr("data-target"),n=$("#mainrow"+r);n.length&&"pressed"!==t.status?(GV.emptyChildRow(e,r,t),GV.addDataToChildRow(e,r,a)):0===n.length?(GV.createChildRow(e,r,t),GV.addDataToChildRow(e,r,a)):n.length&&GV.removeChildRow(e,n,t),$("table").trigger("update")}},GV.toggleOverviewBtn=function(){if(window.chrome&&"file:"===window.location.protocol)$("#overview").remove();else{var t="files/json/overview.json";$.getJSON(t,function(t){var a=$("<span>"+t.less+"</span><br>"),e=$("<span>"+t.evaluation+"</span><br>");$("#overview_btn").hasClass("active")?($("#overview_text").html(e),$("#overview_btn").text("Show Less"),GV.addPlot(t.data,"overview",t.type,t.title,t.footer,t.xtitle,t.ytitle)):($("#overview").find("svg").remove(),$("#overview_text").html(a),$("#overview_btn").text("Show More"))})}},GV.createChildRow=function(t,a,e){var r='<tr class="tablesorter-childRow" id="mainrow'+a+'"><td colspan="12" id="row'+a+'"><div id="'+a+'" class="expanded-child"></div></td></tr>';t.addClass("tablesorter-hasChildRow"),t.after(r),e.status="pressed"},GV.removeChildRow=function(t,a,e){t.removeClass("tablesorter-hasChildRow"),a.remove(),e.status="released"},GV.emptyChildRow=function(t,a,e){var r="#"+a,n="#"+a+"explanation";$(r).empty(),$(n).remove(),GV.resetStatusOfOtherButtons(t),e.status="pressed"},GV.resetStatusOfOtherButtons=function(t){t.find("td").each(function(){"pressed"==this.status&&(this.status="released")}),t.find(".plot_btn").each(function(){"pressed"==this.status&&(this.status="released")})},GV.addDataToChildRow=function(t,a,e){var r=t.attr("data-jsonFile");$.getJSON(r,function(t){if("all"===e)for(var r in t.validations)void 0!==t.validations[r].graphs&&GV.generatePlotCommands(t.validations[r].graphs,a);else GV.addExplanation(a,t.validations[e]),void 0!==t.validations[e].graphs&&GV.generatePlotCommands(t.validations[e].graphs,a)})},GV.generatePlotCommands=function(t,a){for(var e=0;e<t.length;e++){var r=t[e];GV.addPlot(r.data,a,r.type,r.title,r.footer,r.xtitle,r.ytitle,r.aux1,r.aux2)}},GV.addExplanation=function(t,a){var e="#row"+t,r="<p><b>Approach:</b> "+a.approach+"</p>",n="<p><b>Explanation:</b> "+a.explanation+"</p>",o="<p><b>Conclusion:</b> "+a.conclusion+"</p>",l=$('<div id="'+t+'explanation" class="alert alert-info explanation_alert" role="alert">'+r+n+o+"</div>");$(e).prepend(l)},GV.addPlot=function(t,a,e,r,n,o,l,s,i){var c;switch(c=""===n?[]:n.split(";"),e){case"scatter":GV.plot_scatter(t,a,r,n,o,l,s,i);break;case"bars":GV.plot_bars(t,a,r,c,o,l,s);break;case"simplebars":GV.plot_simple_bars(t,a,r,c,o,l);break;case"lines":null!==i&&(i=i.split(",")),GV.plot_lines(t,a,r,c,o,l,s,i);break;case"align":null!==i&&(i=i.split(",")),GV.plot_align(t,a,r,c,o,l,s,i)}},GV.color_beautification=function(t){switch(t){case"red":return d3.rgb(189,54,47);case"blue":return d3.rgb(58,135,173);case"green":return d3.rgb(70,136,71);case"yellow":return d3.rgb(255,255,51);case"orange":return d3.rgb(248,148,6);case"violet":return d3.rgb(153,0,153);case"gray":return d3.rgb(160,160,160);default:return t}},GV.plot_bars=function(t,a,e,r,n,o,l){var s={top:70,right:50,bottom:75,left:50},i=600-s.left-s.right,c=500-s.top-s.bottom,d=d3.select("#".concat(a)).append("svg").attr("width",i+s.left+s.right).attr("height",c+s.top+s.bottom).append("g").attr("transform","translate("+s.left+","+s.top+")");d.append("text").attr("x",i/2).attr("y",-45).attr("text-anchor","middle").style("font-size","16px").text(e);var p=100,u=[].concat.apply([],t),f=d3.max(u,function(t){return t.value})+3,h=d3.scale.linear().domain([0,f+f/10]).range([c,0]),x=d3.min(u,function(t){return t.key});void 0!==l&&(x=Math.min(x,l));var g=d3.max(u,function(t){return t.key});void 0!==l&&(g=Math.max(g,l));var m=d3.scale.linear().domain([x-p,g+p]).range([13,i]),v=d3.svg.axis().scale(m).orient("bottom").ticks(8),y=d3.svg.axis().scale(h).orient("left").tickFormat(d3.format("d")).ticks(8);d.append("g").attr("class","x axis").attr("transform","translate(0,"+c+")").call(v).append("text").attr("class","label").attr("x",(i-n.length)/2-50).attr("y",35).style("text-anchor","start").text(n),d.append("g").attr("class","y axis").call(y).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(c+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o),t.map(function(t){d.selectAll(".bar").data(t).enter().append("rect").attr("x",function(t){return m(t.key)}).attr("width",6).attr("y",function(t){return h(t.value)}).attr("height",function(t){return c-h(t.value)}).attr("fill",function(t){return t.main===!0?GV.color_beautification("red"):GV.color_beautification("blue")})}),void 0!==l&&(d.append("rect").attr("x",m(l)).attr("width",4).attr("y",h(f+f/10)).style("opacity",.6).attr("height",c-h(f+f/8)).attr("fill",GV.color_beautification("black")),d.append("text").attr("transform","rotate(-90)").attr("x",-f/10-35).attr("y",m(l)-5).text("query"));for(var b=0,w=0,G=0;G<r.length;G++){var V=r[G].split(",");w=w+8*V[0].length+15}for(var k=0;k<r.length;k++){var _=r[k].split(",");d.append("rect").attr("x",(i-w)/2+b).attr("y",-30).attr("width",10).attr("height",10).style("fill",GV.color_beautification(_[1].replace(/\s+/g,""))),d.append("text").attr("x",(i-w)/2+b+15).attr("y",-20).text(_[0]),b=b+8*_[0].length+15}},GV.plot_simple_bars=function(t,a,e,r,n,o){var l={top:70,right:50,bottom:75,left:50},s=600-l.left-l.right,i=500-l.top-l.bottom,c=d3.select("#".concat(a)).append("svg").attr("width",s+l.left+l.right).attr("height",i+l.top+l.bottom).append("g").attr("transform","translate("+l.left+","+l.top+")");c.append("text").attr("x",s/2).attr("y",-45).attr("text-anchor","middle").style("font-size","16px").text(e);var d=0,p=[].concat.apply([],t),u=d3.max(p,function(t){return t.value})+3,f=d3.scale.linear().domain([0,u]).range([i,0]),h=d3.min(p,function(t){return t.key}),x=d3.max(p,function(t){return t.key}),g=d3.scale.linear().domain([h-d,x+d]).range([13,s]),m=d3.svg.axis().scale(g).orient("bottom").ticks(8),v=d3.svg.axis().scale(f).orient("left").tickFormat(d3.format("d")).ticks(8);c.append("g").attr("class","x axis").attr("transform","translate(0,"+i+")").call(m).append("text").attr("class","label").attr("x",(s-n.length)/2-50).attr("y",35).style("text-anchor","start").text(n),c.append("g").attr("class","y axis").call(v).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(i+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o),t.map(function(t){c.selectAll(".bar").data(t).enter().append("rect").attr("x",function(t){return g(t.key)}).attr("width",6).attr("y",function(t){return f(t.value)}).attr("height",function(t){return i-f(t.value)}).attr("fill",function(t){return t.main===!0?GV.color_beautification("red"):GV.color_beautification("blue")})})},GV.plot_scatter=function(t,a,e,r,n,o,l,s){var i={top:50,right:30,bottom:75,left:50},c=500-i.left-i.right,d=500-i.top-i.bottom,p=d3.scale.linear().range([0,c]),u=d3.scale.linear().range([d,0]),f=(d3.scale.category10(),d3.svg.axis().scale(p).orient("bottom").ticks(8)),h=d3.svg.axis().scale(u).orient("left").tickFormat(d3.format("d")).ticks(8),x=d3.select("#".concat(a)).append("svg").attr("width",c+i.left+i.right).attr("height",d+i.top+i.bottom).append("g").attr("transform","translate("+i.left+","+i.top+")");x.append("text").attr("x",c/2).attr("y",-25).attr("text-anchor","middle").style("font-size","16px").text(e),x.append("text").attr("x",c/2).attr("y",d+55).attr("text-anchor","middle").style("font-size","12px").text(r);var g=d3.max(t,function(t){return t.x}),m=d3.min(t,function(t){return t.x}),v=d3.max(t,function(t){return t.y}),y=d3.min(t,function(t){return t.y});if(p.domain(d3.extent(t,function(t){return t.x})).nice(),u.domain(d3.extent(t,function(t){return t.y})).nice(),x.append("g").attr("class","x axis").attr("transform","translate(0,"+d+")").call(f).append("text").attr("class","label").attr("x",(c-n.length)/2-50).attr("y",35).style("text-anchor","start").text(n),x.append("g").attr("class","y axis").call(h).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(d+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o),x.selectAll(".dot").data(t).enter().append("circle").attr("r",2).attr("cx",function(t){return p(t.x)}).attr("cy",function(t){return u(t.y)}).style("fill",function(){return GV.color_beautification("red")}).style("opacity",.6),void 0!==s&&""!==s&&void 0!==l&&""!==l){l=parseFloat(l.replace(",","."));var b=g,w=l+s*g;w>v&&(b=(v-l)/s,w=v),y>w&&(b=(y-l)/s,w=y);var G=m,V=l+s*m;V>v&&(G=(v-l)/s,V=y),y>V&&(G=(y-l)/s,V=y),x.append("line").attr("x1",p(G)).attr("y1",u(V)).attr("x2",p(b)).attr("y2",u(w)).attr("stroke-width",2).attr("stroke","black")}},GV.plot_lines=function(t,a,e,r,n,o,l,s){var i={top:70,right:50,bottom:75,left:50},c=600-i.left-i.right,d=500-i.top-i.bottom,p=d3.scale.linear().range([0,c]),u=d3.scale.linear().range([d,0]),f=(d3.scale.category10(),"");f="Open Reading Frames in all 6 Frames"===e?d3.svg.axis().scale(p).orient("bottom").ticks(0):d3.svg.axis().scale(p).orient("bottom").ticks(5);var h=d3.svg.axis().scale(u).orient("left").ticks(5),x=d3.select("#".concat(a)).append("svg").attr("width",c+i.left+i.right).attr("height",d+i.top+i.bottom).append("g").attr("transform","translate("+i.left+","+i.top+")");x.append("text").attr("x",c/2).attr("y",-35).attr("text-anchor","middle").style("font-size","16px").text(e);var g=-1;p.domain([0,d3.max(t,function(t){return t.stop})]),u.domain(d3.extent(t,function(t){return t.y})).nice(),x.append("g").attr("class","x axis").attr("transform","translate(0,"+(d+d/l)+")").call(f).append("text").attr("class","label").attr("x",(c-n.length)/2-50).attr("y",35).style("text-anchor","start").text(n),null!==s?x.append("g").attr("class","y axis").call(h.ticks(s.length).tickFormat(function(){return g+=1,s[g]})).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(d+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o):x.append("g").attr("class","y axis").call(h).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(d+o.length)/2).attr("y",-40).style("text-anchor","start").text(o),x.selectAll(".dot").data(t).enter().append("line").attr("x1",function(t){return p(t.start)}).attr("y1",function(t){return u(t.y)}).attr("x2",function(t){return p(t.stop)}).attr("x2",function(t){return p(t.stop)}).attr("y2",function(t){return u(t.y)}).attr("stroke-width",function(t){return void 0===t.dotted?"red"==t.color?d/l/2.5:d/l:d/l/5}).style("stroke-dasharray",function(t){return void 0===t.dotted?"0, 0":"2, 6"}).attr("stroke",function(t){return GV.color_beautification(t.color)});for(var m=(x.append("g").attr("class","legend").attr("height",100).attr("width",100).attr("transform","translate(-20,50)"),40),v=0,y=0;y<r.length;y++){var b=r[y].split(",");v=v+8*b[0].length+15}for(var w=0;w<r.length;w++){var G=r[w].split(",");x.append("rect").attr("x",(c-v)/2+m).attr("y",-30).attr("width",10).attr("height",10).style("fill",GV.color_beautification(G[1].replace(/\s+/g,""))),x.append("text").attr("x",(c-v)/2+m+15).attr("y",-20).text(G[0]),m=m+8*G[0].length+15}},GV.plot_align=function(t,a,e,r,n,o,l,s){var i={top:75,right:50,bottom:75,left:150},c=600-i.left-i.right,d=300-i.top-i.bottom,p=d3.scale.linear().range([0,c]),u=d3.scale.linear().range([d,0]),f=(d3.scale.category10(),d3.svg.axis().scale(p).orient("bottom").ticks(5)),h=d3.svg.axis().scale(u).orient("left").ticks(5),x=d3.select("#".concat(a)).append("svg").style("vertical-align","top").attr("width",c+i.left+i.right).attr("height",d+i.top+i.bottom).append("g").attr("transform","translate("+i.left+","+i.top+")");x.append("text").attr("x",c/2).attr("y",-35).attr("text-anchor","middle").style("font-size","16px").text(e);var g=-1;p.domain([0,d3.max(t,function(t){return t.stop})]),u.domain(d3.extent(t,function(t){return t.y})).nice(),x.append("g").attr("class","x axis").attr("transform","translate(0,"+(d+d/l)+")").call(f).append("text").attr("class","label").attr("x",(c-n.length)/2-50).attr("y",35).style("text-anchor","start").text(n),null!==s?x.append("g").attr("class","y axis").call(h.ticks(s.length).tickFormat(function(){return g+=1,s[g]})).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(d+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o):x.append("g").attr("class","y axis").call(h).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(d+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o),x.selectAll(".dot").data(t).enter().append("line").attr("x1",function(t){return p(t.start)}).attr("y1",function(t){return u(t.y)}).attr("x2",function(t){return p(t.stop)}).attr("y2",function(t){return u(t.y)}).attr("stroke-width",function(t){return-1==t.height?d/l:d/l*t.height}).attr("stroke",function(t){return GV.color_beautification(t.color)});for(var m=0,v=0,y=0;y<r.length;y++){var b=r[y].split(",");v=v+8*b[0].length+15}for(var w=0;w<r.length;w++){var G=r[w].split(",");x.append("rect").attr("x",(c-v)/2+m).attr("y",-30).attr("width",10).attr("height",10).style("fill",GV.color_beautification(G[1].replace(/\s+/g,""))),x.append("text").attr("x",(c-v)/2+m+15).attr("y",-20).text(G[0]),m=m+8*G[0].length+15}}}();
+// Script.js
+function initTableSorter(){$.tablesorter.addParser({id:"star_scores",is:function(){return!1},format:function(t,e,r,a){var s=$(r);return 1===a?s.attr("data-score")||t:t},parsed:!1,type:"numeric"}),$("table").tablesorter({headers:{1:{sorter:"star_scores"}},sortList:[[0,0]]})}$(document).ready(function(){window.chrome&&"file:"===window.location.protocol&&($("#mainbrowseralertText").text("Some features are not supported in this browser and have been disabled."),$("#browseralert").modal()),GV.toggleOverviewBtn(),initTableSorter(),$("[data-toggle='tooltip']").tooltip()}),$(document).on("click","td, .plot_btn",function(t){if($(this).hasClass("success")||$(this).hasClass("danger")){var e=$(this).attr("title"),r=e.replace(/[ \/]/g,"");GV.addData(this,r)}else $(this).hasClass("plot_btn")&&GV.addData(this,"al

data/aux/files/js/src/plots.js

@@ -0,0 +1,814 @@
+/*
+    GV - GeneValidator's JavaScript module
+
+    Define a global GV (acronym for GeneValidator) object containing all
+    GV associated methods:
+*/
+
+//define global GV object
+var GV;
+if (!GV) {
+    GV = {};
+}
+
+//GV module
+(function () {
+  'use strict';
+  /*global window:false, $:false, d3:false*/
+  //  SHOW ALL PLOTS button
+  GV.toggleAllPlots = function (btn) {
+    if (window.chrome && (window.location.protocol === 'file:')){
+      $('#browseralert').modal();
+    } else {
+      var plotBtns = $('.plot_btn');
+      if (plotBtns.length > 30){
+        $('#alert').modal();
+      } else {
+        $('#spinner1').modal({ backdrop: 'static', keyboard: 'false' });
+        if (btn.status !== 'pressed'){
+          btn.status = 'pressed';
+          $('#show_all_plots').html('Hide All Charts');
+          GV.showAllPlots();
+        } else {
+          btn.status = 'released';
+          $('#show_all_plots').html('Show All Charts');
+          GV.removeAllPlots();
+        }
+        $('#spinner1').modal('hide');      // remove activity spinner
+      }
+    }
+  };
+
+  //iterate over the plot_btns and add data to each childRow
+  GV.showAllPlots = function () {
+    $('.plot_btn').each (function(){
+      if (this.status !== 'pressed') {
+        GV.addData(this, 'all');
+      }
+    });
+  };
+
+  GV.removeAllPlots = function () {
+    $('.tablesorter-childRow').each (function(){
+      $(this).remove();
+    });
+    $('.plot_btn').each (function(){
+      this.status = 'released';
+    });
+  };
+
+  GV.addData = function (source, val){
+    if (window.chrome && (window.location.protocol === 'file:')){
+      $('#browseralert').modal();
+    } else {
+      var $currentRow = $(source).closest('tr'),
+          target      = $currentRow.attr("data-target"),
+          $childRow   = $('#mainrow' + target);
+
+      if ($childRow.length && source.status !== 'pressed') {
+        // if you click on another td...
+        GV.emptyChildRow($currentRow, target, source);
+        GV.addDataToChildRow($currentRow, target, val);
+      } else if ($childRow.length === 0){
+        GV.createChildRow($currentRow, target, source);
+        GV.addDataToChildRow($currentRow, target, val);
+      } else if ($childRow.length) {
+        GV.removeChildRow($currentRow, $childRow, source);
+      }
+
+      $('table').trigger('update');
+    }
+  };
+
+  GV.toggleOverviewBtn = function () {
+    if (window.chrome && (window.location.protocol === 'file:')){
+      $('#overview').remove();
+    } else {
+      var jsonFile = 'files/json/overview.json';
+      $.getJSON(jsonFile, function( json ) {
+        var overview = $('<span>' + json.less + '</span><br>');
+        var full_overview  = $('<span>' + json.evaluation + '</span><br>');
+        if ( $('#overview_btn').hasClass('active')){
+          $('#overview_text').html(full_overview);
+          $('#overview_btn').text('Show Less');
+          GV.addPlot(json.data, 'overview', json.type, json.title, json.footer, json.xtitle, json.ytitle);
+        } else {
+          $('#overview').find('svg').remove();
+          $('#overview_text').html(overview);
+          $('#overview_btn').text('Show More');
+        }
+      });
+    }
+  };
+
+  GV.createChildRow = function ($currentRow, target, source) {
+    var childRowHTML = '<tr class="tablesorter-childRow" id="mainrow' + target +
+                       '"><td colspan="12" id="row' + target + '"><div id="' +
+                       target + '" class="expanded-child"></div></td></tr>';
+    $currentRow.addClass('tablesorter-hasChildRow');
+    $currentRow.after(childRowHTML);
+    source.status = 'pressed';
+  };
+
+  GV.removeChildRow = function ($currentRow, $childRow, source) {
+    $currentRow.removeClass('tablesorter-hasChildRow');
+    $childRow.remove();
+    source.status = 'released';
+  };
+
+  GV.emptyChildRow = function ($currentRow, target, source) {
+    var targetId = '#' + target;
+    var explanationId = '#' + target + 'explanation';
+    $(targetId).empty();
+    $(explanationId).remove();
+    GV.resetStatusOfOtherButtons($currentRow);
+    source.status = 'pressed';
+  };
+
+  GV.resetStatusOfOtherButtons = function ($currentRow) {
+    $currentRow.find('td').each (function(){
+      if (this.status == 'pressed') { this.status = 'released'; }
+    });
+    $currentRow.find('.plot_btn').each (function(){
+      if (this.status == 'pressed') { this.status = 'released'; }
+    });
+  };
+
+  GV.addDataToChildRow = function ($currentRow, target, val) {
+    var file = $currentRow.attr("data-jsonFile");
+
+    $.getJSON(file, function( json ) {
+      if (val === 'all'){
+        for (var i in json.validations){
+          if (json.validations[i].graphs !== undefined) {
+            GV.generatePlotCommands(json.validations[i].graphs, target);
+          }
+        }
+      } else {
+        GV.addExplanation(target, json.validations[val]);
+        if (json.validations[val].graphs !== undefined) {
+          GV.generatePlotCommands(json.validations[val].graphs, target);
+        }
+      }
+    });
+  };
+
+  GV.generatePlotCommands = function (graphs, target)  {
+    for (var g = 0; g < graphs.length; g++) {
+      var graphData = graphs[g];
+      GV.addPlot(graphData.data, target, graphData.type, graphData.title,
+                 graphData.footer, graphData.xtitle, graphData.ytitle,
+                 graphData.aux1, graphData.aux2);
+    }
+  };
+
+  GV.addExplanation = function (target, jsonData) {
+    var row = '#row' + target;
+    var approach_html = '<p><b>Approach:</b> ' + jsonData.approach + '</p>';
+    var explanation_html = '<p><b>Explanation:</b> ' + jsonData.explanation + '</p>';
+    var conclusion_html = '<p><b>Conclusion:</b> ' + jsonData.conclusion + '</p>';
+
+    var explain = $('<div id="' + target + 'explanation" class="alert alert-info explanation_alert" role="alert">' +
+                  approach_html + explanation_html + conclusion_html + '</div>');
+    $(row).prepend(explain);
+  };
+
+
+// Functions that produce the plots in D3
+  GV.addPlot = function (jsonData, target, type, title, footer, xtitle, ytitle, aux1, aux2) {
+    var legend;
+    if (footer === '') {
+      legend = [];
+    } else {
+      legend = footer.split(';');
+    }
+
+    switch(type) {
+      case 'scatter':
+        GV.plot_scatter(jsonData, target, title, footer, xtitle, ytitle, aux1, aux2);
+        break;
+      case 'bars':
+        GV.plot_bars(jsonData, target, title, legend, xtitle, ytitle, aux1);
+        break;
+      case 'simplebars':
+        GV.plot_simple_bars(jsonData, target, title, legend, xtitle, ytitle);
+        break;
+      case 'lines':
+        if (aux2 !== null) {
+          aux2 = aux2.split(',');
+        }
+        GV.plot_lines(jsonData, target, title, legend, xtitle, ytitle, aux1, aux2);
+        break;
+      case 'align':
+        if (aux2 !== null) {
+          aux2 = aux2.split(',');
+        }
+        GV.plot_align(jsonData, target, title, legend, xtitle, ytitle, aux1, aux2);
+        break;
+      default:
+        break;
+    }
+  };
+
+  GV.color_beautification = function (color) {
+    switch(color){
+      case 'red':
+        return d3.rgb(189,54,47);
+      case 'blue':
+        return d3.rgb(58,135,173);
+      case 'green':
+        return d3.rgb(70,136,71);
+      case 'yellow':
+        return d3.rgb(255,255,51);
+      case 'orange':
+        return d3.rgb(248,148,6);
+      case 'violet':
+        return d3.rgb(153,0,153);
+      case 'gray':
+        return d3.rgb(160,160,160);
+      default:
+        return color;
+    }
+  };
+
+  // bars plot
+  GV.plot_bars = function (alldata, target, title, footer, xTitle, yTitle, bar) {
+    var margin = {top: 70, right: 50, bottom: 75, left: 50},
+      width = 600 - margin.left - margin.right,
+      height = 500 - margin.top - margin.bottom;
+
+    var svg = d3.select("#".concat(target)).append("svg")
+      .attr("width", width + margin.left + margin.right)
+      .attr("height", height + margin.top + margin.bottom)
+      .append("g")
+      .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+    svg.append("text")
+      .attr("x", (width / 2))
+      .attr("y", -45)
+      .attr("text-anchor", "middle")
+      .style("font-size", "16px")
+      .text(title);
+
+    var padding = 100;
+
+    var flattened_data = [].concat.apply([], alldata);
+    var yMax = d3.max(flattened_data, function(d) { return d.value; }) + 3;
+    var y = d3.scale.linear()
+      .domain([0, yMax + yMax/10])
+      .range([height, 0]);
+
+    var xMin = d3.min(flattened_data, function(d) { return d.key; });
+    if (bar !== undefined){
+      xMin = Math.min(xMin, bar);
+    }
+
+    var xMax = d3.max(flattened_data, function(d) { return d.key; });
+    if (bar !== undefined){
+      xMax = Math.max(xMax, bar);
+    }
+
+    var x = d3.scale.linear()
+      .domain([xMin-padding, xMax+padding])
+      .range([13, width]);
+
+    var xAxis = d3.svg.axis()
+      .scale(x)
+      .orient("bottom")
+      .ticks(8);
+
+    var yAxis = d3.svg.axis()
+      .scale(y)
+      .orient("left")
+      .tickFormat(d3.format("d"))
+      .ticks(8);
+
+    svg.append("g")
+        .attr("class", "x axis")
+        .attr("transform", "translate(0," + height + ")")
+        .call(xAxis)
+      .append("text")
+        .attr("class", "label")
+        .attr("x", (width-xTitle.length)/2-50)
+        .attr("y", 35)
+        .style("text-anchor", "start")
+        .text(xTitle);
+
+     svg.append("g")
+         .attr("class", "y axis")
+        .call(yAxis)
+      .append("text")
+        .attr("class", "label")
+        .attr("transform", "rotate(-90)")
+        .attr("x", -(height+yTitle.length)/2-50)
+        .attr("y", -40)
+        .style("text-anchor", "start")
+        .text(yTitle);
+
+      alldata.map( function(data) {
+        svg.selectAll(".bar")
+          .data(data)
+          .enter().append("rect")
+            .attr("x", function(d) { return x(d.key); })
+            .attr("width", 6)
+            .attr("y", function(d) { return y(d.value); })
+            .attr("height", function(d) { return height - y(d.value); })
+            .attr("fill", function(d) { if (d.main === true) return GV.color_beautification("red"); return GV.color_beautification("blue");});
+      });
+
+      if (bar !== undefined){
+        svg.append("rect")
+          .attr("x", x(bar))
+          .attr("width", 4)
+          .attr("y", y(yMax + yMax/10))
+          .style("opacity",0.6)
+          .attr("height", height - y(yMax + yMax/8))
+          .attr("fill", GV.color_beautification("black"));
+
+        svg.append("text")
+          .attr("transform", "rotate(-90)")
+          .attr("x", -yMax/10 - 35)
+          .attr("y", x(bar) - 5)
+            .text("query");
+          }
+
+    var offset = 0;
+    var total_len = 0;
+    for (var i = 0; i < footer.length; i++) {
+      var array = footer[i].split(",");
+      total_len = total_len + array[0].length*8 + 15;
+    }
+
+    for (var j = 0; j < footer.length; j++) {
+
+      var footer_array = footer[j].split(",");
+      svg.append("rect")
+          .attr("x", (width-total_len)/2 + offset)
+          .attr("y", -30)
+          .attr("width", 10)
+          .attr("height", 10)
+          .style("fill", GV.color_beautification(footer_array[1].replace(/\s+/g, '')));
+
+      svg.append("text")
+          .attr("x", (width-total_len)/2 + offset + 15)
+          .attr("y", -20)
+          .text(footer_array[0]);
+      offset = offset + footer_array[0].length*8 + 15;
+    }
+  };
+
+  // bars plot
+  GV.plot_simple_bars = function (alldata, target, title, footer, xTitle, yTitle) {
+    var margin = {top: 70, right: 50, bottom: 75, left: 50},
+      width = 600 - margin.left - margin.right,
+      height = 500 - margin.top - margin.bottom;
+
+    var svg = d3.select("#".concat(target)).append("svg")
+      .attr("width", width + margin.left + margin.right)
+      .attr("height", height + margin.top + margin.bottom)
+      .append("g")
+        .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+    svg.append("text")
+      .attr("x", (width / 2))
+      .attr("y", -45)
+      .attr("text-anchor", "middle")
+      .style("font-size", "16px")
+      .text(title);
+
+    var padding = 0;
+
+    var flattened_data = [].concat.apply([], alldata);
+    var yMax = d3.max(flattened_data, function(d) { return d.value; }) + 3;
+    var y = d3.scale.linear()
+           .domain([0, yMax])
+           .range([height, 0]);
+
+    var xMin = d3.min(flattened_data, function(d) { return d.key; });
+    var xMax = d3.max(flattened_data, function(d) { return d.key; });
+
+    var x = d3.scale.linear()
+              .domain([xMin-padding, xMax+padding])
+              .range([13, width]);
+
+    var xAxis = d3.svg.axis()
+                  .scale(x)
+                  .orient("bottom")
+                  .ticks(8);
+
+    var yAxis = d3.svg.axis()
+                  .scale(y)
+                  .orient("left")
+                  .tickFormat(d3.format("d"))
+                  .ticks(8);
+
+    svg.append("g")
+         .attr("class", "x axis")
+         .attr("transform", "translate(0," + height + ")")
+         .call(xAxis)
+       .append("text")
+         .attr("class", "label")
+         .attr("x", (width-xTitle.length)/2-50)
+         .attr("y", 35)
+         .style("text-anchor", "start")
+         .text(xTitle);
+
+    svg.append("g")
+         .attr("class", "y axis")
+         .call(yAxis)
+       .append("text")
+         .attr("class", "label")
+         .attr("transform", "rotate(-90)")
+         .attr("x", -(height+yTitle.length)/2-50)
+         .attr("y", -40)
+         .style("text-anchor", "start")
+         .text(yTitle);
+
+    alldata.map( function(data) {
+      svg.selectAll(".bar")
+         .data(data)
+         .enter().append("rect")
+                 .attr("x", function(d) { return x(d.key); })
+                 .attr("width", 6)
+                 .attr("y", function(d) { return y(d.value); })
+                 .attr("height", function(d) { return height - y(d.value); })
+                 .attr("fill", function(d) { if (d.main === true) return GV.color_beautification("red"); return GV.color_beautification("blue");});
+    });
+  };
+
+
+  // scatter plot
+  // ecuation of the line: slope * x + yLine
+  GV.plot_scatter = function (data, target, title, footer, xTitle, yTitle, yLine, slope) {
+    var margin = {top: 50, right: 30, bottom: 75, left: 50},
+    width = 500 - margin.left - margin.right,
+    height = 500 - margin.top - margin.bottom;
+
+    var x = d3.scale.linear()
+              .range([0, width]);
+    var y = d3.scale.linear()
+              .range([height, 0]);
+
+    var color = d3.scale.category10();
+
+    var xAxis = d3.svg.axis()
+                  .scale(x)
+                  .orient("bottom")
+                  .ticks(8);
+    var yAxis = d3.svg.axis()
+                  .scale(y)
+                  .orient("left")
+                  .tickFormat(d3.format("d"))
+                  .ticks(8);
+
+    var svg = d3.select("#".concat(target)).append("svg")
+                  .attr("width", width + margin.left + margin.right)
+                  .attr("height", height + margin.top + margin.bottom)
+                  .append("g")
+                  .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+    svg.append("text")
+         .attr("x", (width / 2))
+         .attr("y", -25)
+         .attr("text-anchor", "middle")
+         .style("font-size", "16px")
+         .text(title);
+
+    svg.append("text")
+         .attr("x", (width / 2))
+         .attr("y", height+ 55)
+         .attr("text-anchor", "middle")
+         .style("font-size", "12px")
+         .text(footer);
+
+    var xMax = d3.max(data, function(d) { return d.x; });
+    var xMin = d3.min(data, function(d) { return d.x; });
+    var yMax = d3.max(data, function(d) { return d.y; });
+    var yMin = d3.min(data, function(d) { return d.y; });
+    x.domain(d3.extent(data, function(d) { return d.x; })).nice();
+    y.domain(d3.extent(data, function(d) { return d.y; })).nice();
+
+    svg.append("g")
+         .attr("class", "x axis")
+         .attr("transform", "translate(0," + height + ")")
+         .call(xAxis)
+       .append("text")
+         .attr("class", "label")
+         .attr("x", (width-xTitle.length)/2-50)
+         .attr("y", 35)
+         .style("text-anchor", "start")
+         .text(xTitle);
+
+    svg.append("g")
+         .attr("class", "y axis")
+         .call(yAxis)
+       .append("text")
+         .attr("class", "label")
+         .attr("transform", "rotate(-90)")
+         .attr("x", -(height+yTitle.length)/2-50)
+         .attr("y", -40)
+         .style("text-anchor", "start")
+         .text(yTitle);
+
+    svg.selectAll(".dot")
+         .data(data)
+       .enter().append("circle")
+         .attr("r", 2)
+         .attr("cx", function(d) { return x(d.x); })
+         .attr("cy", function(d) { return y(d.y); })
+         .style("fill", function() { return GV.color_beautification("red"); })
+         .style("opacity",0.6);
+
+    if ((slope !== undefined && slope !== "") && (yLine !== undefined && yLine !== "")){
+      yLine = parseFloat(yLine.replace(",", "."));
+      var xMaxValue = xMax;
+      var yMaxValue = yLine + slope * xMax;
+      if (yMaxValue > yMax){
+        xMaxValue = (yMax-yLine)/slope;
+        yMaxValue = yMax;
+      }
+
+      if (yMaxValue < yMin){
+        xMaxValue = (yMin-yLine)/slope;
+        yMaxValue = yMin;
+      }
+
+      var xMinValue = xMin;
+      var yMinValue = yLine + slope * xMin;
+      if (yMinValue > yMax){
+        xMinValue = (yMax-yLine)/slope;
+        yMinValue = yMin;
+      }
+
+      if (yMinValue < yMin){
+        xMinValue = (yMin-yLine)/slope;
+        yMinValue = yMin;
+      }
+
+      svg.append("line")
+           .attr("x1", x(xMinValue))
+           .attr("y1", y(yMinValue))
+           .attr("x2", x(xMaxValue))
+           .attr("y2", y(yMaxValue))
+           .attr("stroke-width", 2)
+           .attr("stroke", "black");
+    }
+  };
+
+  // line plot
+  // maximum 80 lines
+  GV.plot_lines = function (data, target, title, footer, xTitle, yTitle, no_lines, yValues) {
+    var margin = {top: 70, right: 50, bottom: 75, left: 50},
+    width = 600 - margin.left - margin.right,
+    height = 500 - margin.top - margin.bottom;
+
+    var x = d3.scale.linear()
+              .range([0, width]);
+    var y = d3.scale.linear()
+              .range([height, 0]);
+
+    var color = d3.scale.category10();
+    var xAxis = '';
+    if (title === 'Open Reading Frames in all 6 Frames') {
+      xAxis = d3.svg.axis()
+                    .scale(x)
+                    .orient("bottom")
+                    .ticks(0);
+    } else {
+      xAxis = d3.svg.axis()
+                    .scale(x)
+                    .orient("bottom")
+                    .ticks(5);
+    }
+
+    var yAxis = d3.svg.axis()
+                  .scale(y)
+                  .orient("left")
+                  .ticks(5);
+
+    var svg = d3.select("#".concat(target)).append("svg")
+                .attr("width", width + margin.left + margin.right)
+                .attr("height", height + margin.top + margin.bottom)
+                .append("g")
+                .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+    svg.append("text")
+         .attr("x", (width / 2))
+         .attr("y", -35)
+         .attr("text-anchor", "middle")
+         .style("font-size", "16px")
+         .text(title);
+
+    var idx = -1;
+
+    x.domain([0, d3.max(data, function(d) { return d.stop; })]);
+    y.domain(d3.extent(data, function(d) { return d.y; })).nice();
+
+    svg.append("g")
+         .attr("class", "x axis")
+         .attr("transform", "translate(0," + (height + height/no_lines) + ")")
+         .call(xAxis)
+       .append("text")
+         .attr("class", "label")
+         .attr("x", (width-xTitle.length)/2-50)
+         .attr("y", 35)
+         .style("text-anchor", "start")
+         .text(xTitle);
+
+    if (yValues !== null){
+      svg.append("g")
+           .attr("class", "y axis")
+           .call(yAxis.ticks(yValues.length)
+                      .tickFormat(function() {
+                         idx = idx + 1;
+                         return yValues[idx];
+                      }))
+         .append("text")
+           .attr("class", "label")
+           .attr("transform", "rotate(-90)")
+           .attr("x", -(height+yTitle.length)/2-50)
+           .attr("y", -40)
+           .style("text-anchor", "start")
+           .text(yTitle);
+      } else {
+        svg.append("g")
+             .attr("class", "y axis")
+             .call(yAxis)
+           .append("text")
+             .attr("class", "label")
+             .attr("transform", "rotate(-90)")
+             .attr("x", -(height+yTitle.length)/2)
+             .attr("y", -40)
+             .style("text-anchor", "start")
+             .text(yTitle);
+      }
+
+      svg.selectAll(".dot")
+         .data(data)
+      .enter().append("line")
+              .attr("x1", function(d) { return x(d.start); })
+              .attr("y1", function(d) { return y(d.y); })
+              .attr("x2", function(d) { return x(d.stop); })
+              .attr("x2", function(d) { return x(d.stop); })
+              .attr("y2", function(d) { return y(d.y); })
+              .attr("stroke-width", function(d) {
+                if (d.dotted === undefined) {
+                  if (d.color == "red" ) {
+                    return height/no_lines/2.5;
+                  } else {
+                    return height/no_lines;
+                  }
+                } else {
+                  return height/no_lines/5;
+                }
+              })
+              .style("stroke-dasharray", function(d) { if (d.dotted === undefined) return ("0, 0"); return ("2, 6");})
+              .attr("stroke", function(d) { return GV.color_beautification(d.color); });
+
+    // add legend
+    var legend = svg.append("g")
+                    .attr("class", "legend")
+                    .attr("height", 100)
+                    .attr("width", 100)
+                    .attr('transform', 'translate(-20,50)');
+
+    var offset = 40;
+    var total_len = 0;
+    for (var i = 0; i < footer.length; i++) {
+      var array = footer[i].split(",");
+      total_len = total_len + array[0].length*8 + 15;
+    }
+
+    for (var j = 0; j < footer.length; j++) {
+      var footer_array = footer[j].split(",");
+      svg.append("rect")
+           .attr("x", (width-total_len)/2 + offset)
+           .attr("y", -30)
+           .attr("width", 10)
+           .attr("height", 10)
+           .style("fill", GV.color_beautification(footer_array[1].replace(/\s+/g, '')));
+
+      svg.append("text")
+           .attr("x", (width-total_len)/2 + offset + 15)
+           .attr("y", -20)
+           .text(footer_array[0]);
+      offset = offset + footer_array[0].length*8 + 15;
+    }
+  };
+
+  // line plot
+  // maximum 80 lines
+  GV.plot_align = function (data, target, title, footer, xTitle, yTitle, no_lines, yValues) {
+    var margin = {top: 75, right: 50, bottom: 75, left: 150},
+    width = 600 - margin.left - margin.right,
+    height = 300 - margin.top - margin.bottom;
+
+    var x = d3.scale.linear()
+              .range([0, width]);
+    var y = d3.scale.linear()
+              .range([height, 0]);
+
+    var color = d3.scale.category10();
+
+    var xAxis = d3.svg.axis()
+                      .scale(x)
+                      .orient("bottom")
+                      .ticks(5);
+
+    var yAxis = d3.svg.axis()
+                      .scale(y)
+                      .orient("left")
+                      .ticks(5);
+
+    var svg = d3.select("#".concat(target)).append("svg")
+                .style("vertical-align", "top")
+                .attr("width", width + margin.left + margin.right)
+                .attr("height", height + margin.top + margin.bottom)
+                .append("g")
+                .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+    svg.append("text")
+         .attr("x", (width / 2))
+         .attr("y", -35)
+         .attr("text-anchor", "middle")
+         .style("font-size", "16px")
+         .text(title);
+
+    var idx = -1;
+
+    x.domain([0, d3.max(data, function(d) { return d.stop; })]);
+    y.domain(d3.extent(data, function(d) { return d.y; })).nice();
+
+    svg.append("g")
+         .attr("class", "x axis")
+         .attr("transform", "translate(0," + (height+height/no_lines) + ")")
+         .call(xAxis)
+       .append("text")
+         .attr("class", "label")
+         .attr("x", (width-xTitle.length)/2-50)
+         .attr("y", 35)
+         .style("text-anchor", "start")
+         .text(xTitle);
+
+    if (yValues !== null){
+      svg.append("g")
+           .attr("class", "y axis")
+           .call(yAxis.ticks(yValues.length)
+                      .tickFormat(function() {
+                        idx = idx + 1;
+                        return yValues[idx];
+                      }))
+           .append("text")
+           .attr("class", "label")
+           .attr("transform", "rotate(-90)")
+           .attr("x", -(height+yTitle.length)/2-50)
+           .attr("y", -40)
+           .style("text-anchor", "start")
+           .text(yTitle);
+    } else {
+      svg.append("g")
+           .attr("class", "y axis")
+           .call(yAxis)
+         .append("text")
+           .attr("class", "label")
+           .attr("transform", "rotate(-90)")
+           .attr("x", -(height+yTitle.length)/2-50)
+           .attr("y", -40)
+           .style("text-anchor", "start")
+           .text(yTitle);
+    }
+
+    svg.selectAll(".dot")
+       .data(data)
+       .enter().append("line")
+                 .attr("x1", function(d) { return x(d.start); })
+                 .attr("y1", function(d) { return y(d.y); })
+                 .attr("x2", function(d) { return x(d.stop); })
+                 .attr("y2", function(d) { return y(d.y); })
+                 .attr("stroke-width", function(d) { if (d.height == -1) return height/no_lines; return (height/no_lines * d.height) ; })
+                 .attr("stroke", function(d) { return GV.color_beautification(d.color); });
+
+    var offset = 0;
+    var total_len = 0;
+    for (var i = 0; i < footer.length; i++) {
+      var array = footer[i].split(",");
+      total_len = total_len + array[0].length*8 + 15;
+    }
+
+    for (var j = 0; j < footer.length; j++) {
+      var footer_array = footer[j].split(",");
+      svg.append("rect")
+           .attr("x", (width-total_len)/2 + offset)
+           .attr("y", -30)
+           .attr("width", 10)
+           .attr("height", 10)
+           .style("fill", GV.color_beautification(footer_array[1].replace(/\s+/g, '')));
+
+      svg.append("text")
+           .attr("x", (width-total_len)/2 + offset + 15)
+           .attr("y", -20)
+           .text(footer_array[0]);
+      offset = offset + footer_array[0].length*8 + 15;
+    }
+  };
+}());