Removed docs and added it to gh-pages branch

.travis.yml

@@ -4,13 +4,13 @@ jdk:
 sudo: true
 env:
   global:
-    - BUILD_CMD='mvn -X -Dskip.tests=true validate clean install'
-    - RUN_TESTS=false
+    - BUILD_CMD='mvn -Dskip.tests=true clean package'
+    - RUN_TESTS=true
 matrix:
   include:
   - jdk: oraclejdk8
     env:
-    - RUN_TESTS=false
+    - RUN_TESTS=true
 cache:
   directories:
   - "${HOME}/dependencies"
@@ -19,7 +19,7 @@ before_install:
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"
   - "source install_dependencies.sh"
-  - mvn -X validate
+  - mvn validate
 install:
   - "$BUILD_CMD"
 script:

README.md

@@ -33,13 +33,19 @@ ACT is a free tool for displaying pairwise comparisons between two or more DNA s
 
 For further information, please see the [Artemis GitHub page](http://sanger-pathogens.github.io/Artemis/)
 
-## Installation
+## Installation and Usage
 
-For instructions on how to install Artemis, please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf).
+Please refer to the relevant documentation in the Documentation section below.
 
-## Usage
+## Building the Applications From Scratch
 
-For instructions please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf)
+If you would prefer to build the applications from scratch rather than use the pre-built releases in GitHub, then you will firstly need the source code from GitHub. This can be obtained by cloning the repository:
+
+git clone http://github.com/sanger-pathogens/Artemis.git
+
+or by downloadng the source zip file for a particular release. Apache Maven and Java 8 will need to be installed beforehand, in order to build. The applications can be built by issuing the following command in the top-level folder:
+
+mvn validate clean test package
 
 ## License
 Artemis is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/artemis/blob/master/LICENSE).
@@ -49,15 +55,13 @@ For more information on how to download Artemis, please see the [Artemis GitHub
 ## Documentation
 
 The Artemis user manual is at:
-  http://www.sanger.ac.uk/science/tools/artemis
+  http://sanger-pathogens.github.io/Artemis/Artemis/
 
 The ACT user manual is at:
-  http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
-  
-The DNA plotter user manual is at:
-  http://www.sanger.ac.uk/science/tools/dnaplotter
-  
-The BAM View user manual is at:
-  http://www.sanger.ac.uk/science/tools/bamview
- 
+  http://sanger-pathogens.github.io/Artemis/ACT/
+
+The DNA plotter documentation is at:
+  http://sanger-pathogens.github.io/Artemis/Artemis/DNAPlotter/
 
+The BAM View documentation is at:
+  http://sanger-pathogens.github.io/Artemis/Artemis/BamView/

act

@@ -138,7 +138,7 @@ then
     echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ActMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ActMain $*
 result=$?
 
 exit $result

art

@@ -144,7 +144,7 @@ then
     echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ArtemisMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ArtemisMain $*
 result=$?
 
 exit $result

bamview

@@ -82,7 +82,7 @@ then
     echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.alignment.BamView $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.alignment.BamView $*
 result=$?
 
 exit $result

dnaplotter

@@ -119,7 +119,7 @@ then
     echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
 result=$?
 
 exit $result

docs/chado/ACT.html

-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"/>
-<title>Artemis - Chado tutorial</title>
-
-</head>
-<body>
-
-<h2>Generating ACT Comparison File</h2>
-
-<p>BLAST is used to generate the ACT comparison file (for more details see the <a href="http://www.sanger.ac.uk/Software/ACT/">ACT manual</a>) one of the 
-sequences needs to be made the database sequence and indexed with formatdb: 
-</p><pre>formatdb -i NC_004314.fasta -p 'F' 
-</pre>
-<p>The other sequence is the query and you can then search for matches between these: 
-</p>
-<pre>blastall -p tblastx -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_tblastx -m 8 
-</pre><p>or 
-</p>
-<pre>blastall -p blastn -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_blastn -m 8 -e 0.1
-</pre>
-<p>Use the '-m 8' option to provide the tabular output that ACT uses.
-</p><p>An alternative to this is to use <a href="http://www.webact.org">WebACT</a> or <a href="http://www.hpa-bioinfotools.org.uk/pise/double_act.html">Double ACT</a> to generate the comparison file.
-</p>
-</body>
-</html>

docs/chado/admin.shtml

-<!--#set var="banner" value="Artemis - Chado Admin/Developer Documentation"-->
-<!--#include virtual="/perl/header"-->
-
-
-<p>
-This page describes some of the development background and admin of
-using and setting up an Artemis and ACT connection with a Chado database.
-
-<ul>
-<li><a href="#DATABASEMANAGER">Opening the Database Manager</a>
-<li><a href="#OPENART">Opening the main Artemis/ACT window</a>
-<li><a href="#CONFIG">Option File Configuration</a>
-<li><a href="#GENEBUILDER">Opening the Standalone Gene Builder</a>
-</ul>
-
-
-
-<h3><a name="DATABASEMANAGER">Opening the Database Manager</a></h3>
-<p>
-The Artemis Database Manager is cached between sessions in the directory
-'.artemis/cache' in the users home directory. There is an option under the File menu
-to clear this cache.
-<p>
-To open the Artemis Database Manager panel (from which the browser is launched), 
-Artemis looks initially for the existence of the cvterm.name = 'top_level_seq' which 
-belongs to cv.name = 'genedb_misc'. If these exist it follows method A:
-
-<ol type="A">
-<li>
--call 'getTopLevelOrganisms' (in Organism.xml mapping). This relies on the the source 
-features (e.g. chromosome) having a featureprop with a type_id corresponding to 'top_level_seq'.
-<p>
-If the 'top_level_seq' is not implemented in the database it then follows method B:
-<p>
-</li>
-
-<li>
--call 'getOrganismsContainingSrcFeatures' (in Organism.xml mapping). This searches for those 
-organisms that contain sequences with residues and have a type_id that 
-corresponds to a cvterm name that matches:
-<p>
-*chromosome*, *sequence*, supercontig, ultra_scaffold, golden_path_region, or contig
-<p>
-</li>
-</ol>
-When the organisms with the source feature have been identified these are displayed. When 
-a user clicks on an organism it opens that node and finds the types (e.g. chromosome, contig) of source 
-features and the underlying features that have residues (getResidueFeatures in Feature.xml).
-<p>
-<h3><a name="OPENART">Opening the main Artemis/ACT window</a></h3>
-<p>
-The organismprop's are loaded lazily when a sequence is opened. If an organismprop 
-is of type 'translationTable' the value of the organismprop is then used as the 
-translation table when Artemis opens a sequence from that organism.
-<p>
-When a sequence is double clicked to open it in Artemis, most things for that sequence
-are read from the database. The iBatis statement calls made when reading an entry are
-summarised below.
-<p>
-<table border=1 cellspacing=1 cellpadding=2>
-<tr><td>Statement ID</td><td>SQL Mapping File</td><td>Description</td></tr>
-<tr><td>getFeature                         </td><td>(Feature.xml)</td> 
-   <td>Retrieves all the features and their featureloc's, featureprop's, feature_relationship's and primary dbxref</td></tr>
-<tr><td>getFeatureDbXRefsBySrcFeature      </td><td>(FeatureDbXRef.xml)</td>      
-    <td>Retrieves all secondary dbxref's</td></tr>
-<tr><td>getFeatureSynonymsBySrcFeature     </td><td>(FeatureSynonym.xml)</td>
-    <td>Retrieves feature synonyms</td></tr>
-<tr><td>getFeatureCvTermsBySrcFeature      </td><td>(FeatureCvTerm.xml)</td>
-    <td>Retrieves feature_cvterm's, feature_cvtermprop (evidence code, extra qualifiers, date).</td></tr>
-<tr><td>getFeatureCvTermDbXRefBySrcFeature </td><td>(FeatureCvTermDbXRef.xml)</td>
-    <td>Retrieves feature_cvterm_dbxref (WITH/FROM column).</td></tr>
-<tr><td>getFeatureCvTermPubBySrcFeature    </td><td>(FeatureCvTermPub.xml)</td>
-    <td>Retrieves feature_cvterm_pub's.</td></tr>
-</table>
-<p>
-Artemis constructs an internal GFF3 stream from these calls for the selected sequence. 
-This is then read in the same way as a GFF3 file as an Artemis DatabaseDocumentEntry
-(which extends GFFDocumentEntry) and creating GFFStreamFeatures.
-<p>
-If the lazy load option is selected from the Database Manager's File menu, then only
-getFeature is called. The resulting GFFStreamFeature object is marked as lazy loading
-and FeatureDbXRefs, FeatureSynonyms, FeatureCvTerms, FeatureCvTermDbXRefs
-and FeatureCvTermPubs are read from the database for a feature when the Gene Builder is opened.
-<p>
-The feature_relationship (from getFeature) is used to create the gene hierarchy; 'part_of'a
-and 'derives_from' relationships become Parent and Derives_from in GFF3 terms. If the 
-feature_relationship type_id does not correspond to one of these terms (derives_from, 
-part_of, proper_part_of, partof, producedby) then the object_id is recorded as a qualifer 
-value. This is used to read orthologous_to and paralogous_to relations. The qualifier 
-values for these are lazily stored (as ClusterLazyQualifierValue.java). When Artemis 
-displays these qualifiers in the Gene Builder it then queries the database further to 
-list the related genes.
-<p>
-Other properties that have a featureloc association with a feature
-are found by calling getLazySimilarityMatches (Feature.xml). Artemis then
-constructs lazy loading qualifiers (QualifierLazyLoading.java) from this that query
-the database further only when that qualifier is needed. This is used for
-blast/fasta similarity and polypeptide_domains.
-
-<p>
-The gene hierarchy is stored internally by the ChadoCanonicalGene.java object and is based
-on the Parent/Derives_from relationships. It stores the related children of the gene.
-The spliced features (exon, pseudogenic_exon) are combined into a single Artemis 
-Feature. The joined exons become an Artemis CDS feature (GFFStreamFeature), which stores 
-the uniquenames of the original exons in the database.
-
-<p>
-<h3><a name="CONFIG">Artemis Chado Configuration</a></h3>
-
-This is an example extract from the Artemis options file for the chado related options:
-
-<p>
-<pre style="color: #0000FF;">
-#
-# CHADO DATABASE OPTIONS 
-#
-# chado gene model features default types
-chado_exon_model=CDS
-#chado_transcript=transcript
-
-# infer CDS and UTR features from gene model
-chado_infer_CDS_UTR=no
-
-# provide a list of available servers
-chado_servers = \
-  workshop localhost:10101/workshop?user \
-  GeneDB db.genedb.org:5432/snapshot?genedb_ro
-
-# define how product qualifiers are stored (as a cv or as a featureprop)
-product_cv=yes
-product_cvname = genedb_products
-# cv containing synonym names
-synonym_cvname = genedb_synonym_type
-
-# set default delete behaviour to make things obsolete, if
-# this is not provided the default is to permanently delete
-set_obsolete_on_delete=yes
-
-# list of features to record residues for in the database
-# - these are included when inserting or updating their featurelocs
-sequence_update_features = polypeptide mRNA rRNA tRNA snRNA snoRNA
-</pre>
-
-<p>
-Artemis combines the exons stored in chado and describes it as a 'CDS' 
-feature by default. The <b>chado_exon_model</b> flag in the options file 
-allows this to be changed. 
-<p>
-When a gene model is created in Artemis it creates the transcript as a 'mRNA' 
-feature by default. The <b>chado_transcript</b> flag in the options file allows this 
-to be changed.
-<p>
-For Artemis the default gene model representation is described in the <a href="overview.shtml#GENE">
-overview</a>. In this representation the UTRs are explicitly created in the database.
-However the gmod loader (gmod_bulk_load_gff3.pl) does not create the UTRs and they can 
-be inferred from the exon and protein features. If the gmod loader is used then Artemis
-can infer the CDS and UTR features by setting <b>chado_infer_CDS_UTR=yes</b> in the 
-options file. Adjusting the polypeptide boundaries in the Gene Builder will result in the generation 
-or deletion of UTRs.
-
-<p>
-A list of available databases can be configured in the options file with the <b>chado_servers</b> flag.
-For each database an alias is given followed by its location (host:port/database?user), each alias
-is displayed in a drop down menu in the login box.
-<p>
-If product qualifiers are stored as an ontology (in cvterm) then set <b>product_cv=yes</b>
-and set <b>product_cvname</b> is set to the name of the controlled vocabulary (cv) used in chado.
-<p>
-When features are deleted in Artemis the default behaviour can be set to make these
-features obsolete rather than permanently delete them from the database.
-
-<a name="GENEBUILDER"></a><h3>Opening the Standalone Gene Builder</h3>
-<p>
-The Gene Builder can be launched on its own without opening up Artemis. The following
-opens up a window which lets you type in a gene name to be opened:
-
- <pre>
- java -mx500m -Dibatis -Dchado="localhost:5432/database?" \
-      -Djdbc.drivers=org.postgresql.Driver -classpath artemis.jar \
-      uk.ac.sanger.artemis.components.genebuilder.GeneEdit
- </pre>
-
-Alternatively the gene name can be given as an argument:
- <pre>
- java -mx500m -Dibatis -Dchado="db.genedb.org:5432/snapshot?genedb_ro" \
-      -Djdbc.drivers=org.postgresql.Driver -Dshow_log -Dread_only \
-      -classpath jar_build/artemis.jar:etc 
-       uk.ac.sanger.artemis.components.genebuilder.GeneEdit PFA0010c
- </pre>
-
-