Refresh images on data export pages to reflect new icons.

data_downloads.rst

@@ -1,24 +1,32 @@
 ####################
 Definition downloads
 ####################
-The sequence definition database defines alleles, i.e. links an allele identifier to a sequence.  It also defines scheme, e.g. MLST, profiles.
+The sequence definition database defines alleles, i.e. links an allele 
+identifier to a sequence.  It also defines scheme, e.g. MLST, profiles.
 
 .. _download_alleles:
 
 ***************************
 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.  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
 ===========
 .. image:: /images/data_downloads/alleles.png
 
-You can drill down through the tree by clicking branch nodes.  Clicking the labels of internal nodes will display tables of all schemes belonging to that scheme group.  Clicking the labels of terminal nodes will display that single scheme table.
+You can drill down through the tree by clicking branch nodes.  Clicking the 
+labels of internal nodes will display tables of all schemes belonging to that 
+scheme group.  Clicking the labels of terminal nodes will display that single 
+scheme table.
 
 .. image:: /images/data_downloads/alleles2.png
 
-Click the green download link for the required locus
+Click the download link for the required locus
 
 .. image:: /images/data_downloads/alleles3.png
 
@@ -54,11 +62,13 @@ Alleles will be downloaded in FASTA format, e.g. ::
 
 Alphabetical list
 =================
-Loci can be displayed in an alphabetical list.  Loci will be grouped in to tables by initial letter.  If common names are set for loci, they will be listed by both primary and common names.
+Loci can be displayed in an alphabetical list.  Loci will be grouped in to 
+tables by initial letter.  If common names are set for loci, they will be 
+listed by both primary and common names.
 
 .. image:: /images/data_downloads/alleles4.png
 
-Click the green download links for the required locus.
+Click the download links for the required locus.
 
 All loci by scheme
 ==================
@@ -70,14 +80,16 @@ Click the green download links for the required locus.
 
 Download locus table
 ====================
-The locus table can be downloaded in tab-delimited text or Excel formats by clicking the links following table display.
+The locus table can be downloaded in tab-delimited text or Excel formats by 
+clicking the links following table display.
 
 .. image:: /images/data_downloads/alleles6.png
 
 **************************
 Scheme profile definitions
 **************************
-Scheme profiles, e.g. those for MLST, can be downloaded by clicking the appropriate link on the contents page.
+Scheme profiles, e.g. those for MLST, can be downloaded by clicking the 
+appropriate link on the contents page.
 
 .. image:: /images/data_downloads/profiles.png
 

data_export.rst

@@ -5,11 +5,15 @@ Data export plugins
 *********************
 Isolate record export
 *********************
-You can export the entire isolate recordset by clicking the 'Export dataset' link in the Export section of the main contents page.
+You can export the entire isolate recordset by clicking the 'Export dataset' 
+link in the Export section of the main contents page.
 
 .. image:: /images/data_export/isolate_export.png
 
-Alternatively, you can export the recordsets of isolates returned from a database query by clicking the ‘Dataset’ button in the Export list at the bottom of the results table. Please note that the list of functions here may vary depending on the setup of the database.
+Alternatively, you can export the recordsets of isolates returned from a 
+database query by clicking the ‘Dataset’ button in the Export list at the 
+bottom of the results table. Please note that the list of functions here may 
+vary depending on the setup of the database.
 
 .. image:: /images/data_export/isolate_export2.png
 
@@ -30,19 +34,28 @@ Advanced options
 
 The options fieldset has the following options.
 
-* Include locus common names - any common name for the locus is displayed in parentheses following the primary name.
-* Export allele numbers - the allele designation is included for any locus included.
-* Use one row per field - this is an alternative output format where instead of each locus and field having a separate column, each field is export on a separate row.
-* Include isolate field in row - the name of the isolate is included as a separate column when exporting in 'one row per field' fomrmat.
-* Export full allele designation record - export sender, curator and datestamp information as separate rows when exporting allele designation data.
+* Include locus common names - any common name for the locus is displayed in 
+  parentheses following the primary name.
+* Export allele numbers - the allele designation is included for any locus 
+  included.
+* Use one row per field - this is an alternative output format where instead 
+  of each locus and field having a separate column, each field is export on a 
+  separate row.
+* Include isolate field in row - the name of the isolate is included as a 
+  separate column when exporting in 'one row per field' fomrmat.
+* Export full allele designation record - export sender, curator and datestamp 
+  information as separate rows when exporting allele designation data.
 
 Molecular weight calculation
 ============================
-The plugin can also calculate the predicted molecular weight of the gene product of any allele designated in the dataset.
+The plugin can also calculate the predicted molecular weight of the gene 
+product of any allele designated in the dataset.
 
 .. image:: /images/data_export/isolate_export6.png
 
-Click the 'Export protein molecular weight' checkbox.  Additional columns (or rows depending on the output format) will be created to include the molecular weight data.
+Click the 'Export protein molecular weight' checkbox.  Additional columns 
+(or rows depending on the output format) will be created to include the 
+molecular weight data.
 
 ***************
 Sequence export
@@ -80,45 +93,59 @@ Sequences will be export in XMFA and FASTA file formats.
 
 Aligning sequences
 ==================
-By default, sequences will be exported unaligned - this is very quick since no processing is required.  You can choose to align the sequences by checking the 'Align sequences' checkbox.
+By default, sequences will be exported unaligned - this is very quick since no 
+processing is required.  You can choose to align the sequences by checking 
+the 'Align sequences' checkbox.
 
 .. image:: /images/data_export/sequence_export6.png
 
-You can also choose to use MUSCLE or MAFFT as the aligner.  MAFFT is the default choice and is usually much quicker than MUSCLE.  Both produce comparable results.
+You can also choose to use MUSCLE or MAFFT as the aligner.  MAFFT is the 
+default choice and is usually much quicker than MUSCLE.  Both produce 
+comparable results.
 
 *************
 Contig export
 *************
-The contig export plugin can be accessed by clicking the ‘Contigs’ link in the Export section of the contents page of isolate databases.
+The contig export plugin can be accessed by clicking the ‘Contigs’ link in the 
+Export section of the contents page of isolate databases.
 
 .. image:: /images/data_export/contig_export.png
 
-Alternatively, it can be accessed following a query by clicking the ‘Contigs’ button in the Export section at the bottom of the results table.
+Alternatively, it can be accessed following a query by clicking the ‘Contigs’ 
+button in the Export section at the bottom of the results table.
 
 .. image:: /images/data_export/contig_export2.png
 
-Select the isolates for which you wish to export contig data for. If the export function was accessed following a query, isolates returned in the query will be pre-selected.
+Select the isolates for which you wish to export contig data for. If the 
+export function was accessed following a query, isolates returned in the query 
+will be pre-selected.
 
 .. image:: /images/data_export/contig_export3.png
 
 At its simplest, press submit.
 
-A table will be produced with download links.  Clicking these will produce the contigs in FASTA format.
+A table will be produced with download links.  Clicking these will produce the 
+contigs in FASTA format.
 
 .. image:: /images/data_export/contig_export4.png
 
-You can also download all the data in a tar file by clicking the 'Batch download' link.
+You can also download all the data in a tar file by clicking the 'Batch 
+download' link.
 
 .. image:: /images/data_export/contig_export5.png
 
 Filtering by tagged status of contigs
 =====================================
-You can also export contigs based on the percentage of the sequence that has been tagged.  This is useful to find sequences to target for gene discovery.
+You can also export contigs based on the percentage of the sequence that has 
+been tagged.  This is useful to find sequences to target for gene discovery.
 
-In order to export contigs where at least half the sequence has been tagged (and also the remaining contigs in a separate file), select '50' in the dropdown box for %untagged.
+In order to export contigs where at least half the sequence has been tagged 
+(and also the remaining contigs in a separate file), select '50' in the 
+dropdown box for %untagged.
 
 .. image:: /images/data_export/contig_export6.png
 
-The resulting table has two download links for each isolate, one for contigs matching the condition, and one for contigs that don't match.
+The resulting table has two download links for each isolate, one for contigs 
+matching the condition, and one for contigs that don't match.
 
 .. image:: /images/data_export/contig_export7.png