Updated screenshots.

Author: kjolley

data_downloads.rst

@@ -9,11 +9,14 @@ identifier to a sequence.  It also defines scheme, e.g. MLST, profiles.
 ***************************
 Allele sequence definitions
 ***************************
-Click the 'Allele sequences' link in the 'Downloads' section.  Depending on 
-the database, you may see either a hierarchical scheme tree or a table of 
-loci. You can choose to display links either by scheme using the scheme tree, 
-as an alphabetical list or a page of all schemes, by selecting the 
-approrpiate link at the top of the page.
+Click the 'Allele sequences' link in the 'Downloads' section. 
+
+.. image:: /images/data_downloads/download_alleles.png
+
+Depending on the database, you may see either a hierarchical scheme tree or 
+a table of loci. You can choose to display links either by scheme using the 
+scheme tree, as an alphabetical list or a page of all schemes, by selecting 
+the approrpiate link at the top of the page.
 
 Scheme tree
 ===========
@@ -93,7 +96,9 @@ appropriate link on the contents page.
 
 .. image:: /images/data_downloads/profiles.png
 
-If multiple schemes are available, you will need to select the scheme in the dropdown box and click 'Download profiles'
+If there is only one scheme available, the link will directly download the 
+profiles. If multiple schemes are available, the link will take you to an 
+intermediate page from where you can select the scheme to download.
 
 .. image:: /images/data_downloads/profiles2.png
 

data_records.rst

@@ -1,7 +1,8 @@
 ############
 Data records
 ############
-Record pages for different types of data can be accessed following a query by clicking appropriate hyperlinks.
+Record pages for different types of data can be accessed following a query 
+by clicking appropriate hyperlinks.
 
 .. index::
    pair: isolate; records 
@@ -22,7 +23,9 @@ Projects
 
 .. image:: /images/data_records/isolate_record2.png
 
-This displays a list of projects that the isolate is a member of.  Only projects that have a full description will be displayed. 
+This displays a list of projects that the isolate is a member of. Only projects
+that have a full description and the 'isolate_display' flag in their settings 
+will be displayed. 
 
 Provenance metadata
 ===================
@@ -40,7 +43,8 @@ This section includes:
   * last update times
   * links to update history
 
-The update link displays page with exact times of who and when updated the record.
+The update link displays page with exact times of who and when updated the 
+record.
 
 .. image:: /images/data_records/isolate_record7.png
 
@@ -49,28 +53,39 @@ Publications
 
 .. image:: /images/data_records/isolate_record8.png
 
-This section includes full citation for papers linked to the isolate record.  Each citation has a button that will return a dataset of all isolates linked to the paper.
+This section includes full citation for papers linked to the isolate record. 
+Each citation has a button that will return a dataset of all isolates linked 
+to the paper.
 
-If there are five or more references they will be hidden by default to avoid cluttering the page too much.  Click the 'Show/hide' button to display them in this case.
+If there are five or more references they will be hidden by default to avoid 
+cluttering the page too much.  Click the 'Show/hide' button to display them 
+in this case.
 
 Sequence bin summary
 ====================
 
 .. image:: /images/data_records/isolate_record4.png
 
-This section contains basic statistics describing the sequence bin.  Clicking the 'Display' button navigates to the :ref:`sequence bin record <sequence_bin_records>`.
+This section contains basic statistics describing the sequence bin. Clicking 
+the 'Show sequence bin' button navigates to the 
+:ref:`sequence bin record <sequence_bin_records>`.
 
 Scheme and locus data
 =====================
-A hierarchical tree displays available schemes.  Click within internal nodes to expand them. 
+A hierarchical tree displays available schemes.  Click within internal nodes 
+to expand them. 
 
 .. image:: /images/data_records/isolate_record5.png
 
-Clicking any terminal node will display data available for a scheme or group of schemes.
+Clicking any terminal node will display data available for a scheme or group 
+of schemes.
 
 .. image:: /images/data_records/isolate_record6.png
 
-Click an allele number within the scheme profile, will display the appropriate :ref:`allele definition record <allele_definition_records>`.  Clicking the green 'S' link will display the appropriate :ref:`sequence tag record <sequence_tag_records>`.
+Click an allele number within the scheme profile, will display the appropriate 
+:ref:`allele definition record <allele_definition_records>`. Clicking the green
+'S' link will display the appropriate 
+:ref:`sequence tag record <sequence_tag_records>`.
 
 .. index::
    pair: allele definition; records 
@@ -80,13 +95,18 @@ Click an allele number within the scheme profile, will display the appropriate :
 *************************
 Allele definition records
 *************************
-An allele definition record displays information about a defined allele in a sequence definition database.
+An allele definition record displays information about a defined allele in a 
+sequence definition database.
 
 .. image:: /images/data_records/allele_definition_record.png
 
-If the allele is a member of a scheme profile, e.g. MLST, this will be listed.  In this case, there will be a button to display all profiles of that scheme that contain the allele.
+If the allele is a member of a scheme profile, e.g. MLST, this will be listed. 
+In this case, there will be a button to display all profiles of that scheme 
+that contain the allele.
 
-Similarly, if a :ref:`client database <client_databases>` has been setup for the database and the allele has been identified in an isolate, there will be a button to display all isolates that have that allele.
+Similarly, if a :ref:`client database <client_databases>` has been setup for 
+the database and the allele has been identified in an isolate, there will be 
+a button to display all isolates that have that allele.
 
 .. index::
    pair: sequence tag; records 
@@ -99,9 +119,14 @@ Sequence tag records
 
 .. image:: /images/data_records/sequence_tag_record.png
 
-A sequence tag record displays information about the location within a contig of a region associated with a locus.  The nucleotide sequence will be displayed along with upstream and downstream flanking sequence.  The length of these flanking sequences can be modified within the :ref:`general options <general_options>`.
+A sequence tag record displays information about the location within a contig 
+of a region associated with a locus.  The nucleotide sequence will be displayed
+along with upstream and downstream flanking sequence.  The length of these 
+flanking sequences can be modified within the 
+:ref:`general options <general_options>`.
 
-If the tag is for a DNA locus and it is marked as a coding sequence, the three-frame translation will also be displayed.
+If the tag is for a DNA locus and it is marked as a coding sequence, the 
+three-frame translation will also be displayed.
 
 .. index::
    pair: profile; records 
@@ -114,9 +139,14 @@ Profile records
 
 .. image:: /images/data_records/profile_record.png
 
-A profile record displays information about a scheme, e.g. MLST, profile.  Each allele number within the profile will be hyperlinked.  Clicking these will take you to the appropriate :ref:`allele definition record <allele_definition_records>`.
+A profile record displays information about a scheme, e.g. MLST, profile. 
+Each allele number within the profile will be hyperlinked.  Clicking these 
+will take you to the appropriate 
+:ref:`allele definition record <allele_definition_records>`.
 
-If a :ref:`client database <client_databases>` has been setup for the database and an isolate has the profile, there will be a button to display all isolates that have the profile.
+If a :ref:`client database <client_databases>` has been setup for the database
+and an isolate has the profile, there will be a button to display all isolates
+that have the profile.
 
 .. index::
    pair: sequence bin; records 
@@ -129,7 +159,8 @@ Sequence bin records
 
 .. image:: /images/data_records/seqbin_record.png
 
-A sequence bin record contains information about that contigs associated with an isolate record.  This includes:
+A sequence bin record contains information about the contigs associated with
+an isolate record.  This includes:
 
 * Number of contigs
 * Total length
@@ -138,6 +169,14 @@ A sequence bin record contains information about that contigs associated with an
 * N50, N90 and N95 values
 * Size distribution charts
 
-There are also links to download the contigs in FASTA or EMBL format.
+Charts show the distribution of contig sizes and the cumulative contig length
+against contig number giving a breakdown indication of contig size.
 
-Finally there is a table that shows the loci that are tagged on each contig.  Individual contigs can also be downloaded in EMBL format.
+The record includes an embedded genome browser showing the positions of
+any loci that have been tagged.
+
+There are also links to download the contigs in FASTA, Genbank or EMBL format, 
+along with annotation in GFF3 format.
+
+Finally there is a table that shows the loci that are tagged on each contig. 
+Individual contigs can also be downloaded in EMBL or Genbank format.