docs update

docs/saturn/tiddlers/BLAST trace sequence against SATurn database.tid

@@ -0,0 +1,31 @@
+created: 20180308154252492
+modified: 20180308155003969
+title: BLAST trace sequence against SATurn database
+type: text/vnd.tiddlywiki
+
+<table style="width:100%">
+ <thead>
+  <tr>
+   <th style="width:40%">
+    Step
+   </th>
+   <th>
+    Preview
+   </th>
+  </tr>
+ </thead>
+ <tbody>
+  <tr>
+     <td>''1. Open trace and click on BLAST''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_trace_viewer_blast_button.png]]</td>
+  </tr>
+  <tr>
+     <td>''2. Select file''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_trace_viewer_align_blast_to_trace.png]]</td>
+  </tr>
+  <tr>
+     <td>Displays sequence aligned to trace along with differences highlighted in the annotation menu tree item</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_trace_viewer_align_blast_to_trace_highlighted.png]]</td>
+  </tr>
+ </tbody>
+</table>

docs/saturn/tiddlers/Debugging standalone package.tid

@@ -0,0 +1,14 @@
+created: 20180308092659163
+modified: 20180308092954881
+title: Debugging standalone package
+type: text/vnd.tiddlywiki
+
+# Launch SATurn with the Chrome Developer Tools hook enabled
+#>$SATURN/build/Saturn_dev.bat
+# Open Chrome and navigate to the following address
+#>http://localhost:9000/
+# Click on the only link to enter developer tools
+
+# Note that to do the equivalent of a hard reset to clear the cache in the  QT window you will need to click on 
+#>Network->Disable Cache
+# Then right-click in the QT window and reload the page

docs/saturn/tiddlers/Exporting as FASTA file.tid

@@ -0,0 +1,27 @@
+created: 20180308081953933
+modified: 20180308082325305
+title: Exporting as FASTA file
+type: text/vnd.tiddlywiki
+
+<table style="width:100%">
+ <thead>
+  <tr>
+   <th style="width:40%">
+    Step
+   </th>
+   <th>
+    Preview
+   </th>
+  </tr>
+ </thead>
+ <tbody>
+  <tr>
+     <td>''1.File->Export->FASTA''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_dna_editor_export_to_fasta_file.png]]</td>
+  </tr>
+  <tr>
+     <td>''2.Enter path and name of FASTA file''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_dna_editor_export_fasta.png]]</td>
+  </tr>
+ </tbody>
+</table>

docs/saturn/tiddlers/Extracting a sequence.tid

@@ -0,0 +1,32 @@
+created: 20180308080546045
+modified: 20180308080954640
+title: Extracting a sequence
+type: text/vnd.tiddlywiki
+
+<table style="width:100%">
+ <thead>
+  <tr>
+   <th style="width:40%">
+    Step
+   </th>
+   <th>
+    Preview
+   </th>
+  </tr>
+ </thead>
+ <tbody>
+  <tr>
+     <td>''1. Select the region you wish to extract''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_dna_editor_selection.png]]</td>
+  </tr>
+ <tr>
+     <td>''2. Right-click and select New From Selected''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_dna_editor_new_from_selected_item.png]]</td>
+  </tr>
+<tr>
+     <td>Extracted DNA sequence is shown loaded as a new object</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_dna_editor_extract_selected.png]]</td>
+  </tr>
+ </tbody>
+</table>
+

docs/saturn/tiddlers/Internal_ Developer Guide.tid

@@ -1,9 +1,10 @@
 created: 20180301161035796
-modified: 20180302100603489
+modified: 20180308092652187
 title: Internal: Developer Guide
 type: text/vnd.tiddlywiki
 
 #[[Configuring development environment|Internal: Configuring development environment]]
 #[[Configuring documentation environment|Internal: Configuring documentation environment]]
 #[[Building standalone packages|Internal: Building standalone packages]]
-#[[Building QT application|Internal: Building QT application]]
+#[[Building QT application|Internal: Building QT application]]
+#[[Debugging standalone package]]

docs/saturn/tiddlers/Inverse _ Complement.tid

@@ -0,0 +1,31 @@
+created: 20180308081428947
+modified: 20180308081623841
+title: Inverse / Complement
+type: text/vnd.tiddlywiki
+
+<table style="width:100%">
+ <thead>
+  <tr>
+   <th style="width:40%">
+    Step
+   </th>
+   <th>
+    Preview
+   </th>
+  </tr>
+ </thead>
+ <tbody>
+  <tr>
+     <td>''1. Select one of the options: Inverse Complement, Complement, or Inverse''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_dna_editor_inverse_complement.png]]</td>
+  </tr>
+  <tr>
+     <td>Inverse complemented sequence</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_dna_editor_inverse_complement_performed.png]]</td>
+  </tr>
+
+ </tbody>
+</table>
+
+
+

docs/saturn/tiddlers/Loading a trace with drag and drop.tid

@@ -0,0 +1,27 @@
+created: 20180308145121334
+modified: 20180308153719250
+title: Loading a trace with drag and drop
+type: text/vnd.tiddlywiki
+
+<table style="width:100%">
+ <thead>
+  <tr>
+   <th style="width:40%">
+    Step
+   </th>
+   <th>
+    Preview
+   </th>
+  </tr>
+ </thead>
+ <tbody>
+  <tr>
+     <td>''1. Drag and drop file onto workspace panel''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_trace_viewer_drag_and_drop.png]]</td>
+  </tr>
+  <tr>
+     <td>Displays trace</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_trace_viewer_trace.png]]</td>
+  </tr>
+ </tbody>
+</table>

docs/saturn/tiddlers/Loading traces from a zip file.tid

@@ -0,0 +1,29 @@
+created: 20180308145305538
+modified: 20180308153650107
+title: Loading traces from a zip file
+type: text/vnd.tiddlywiki
+
+<table style="width:100%">
+ <thead>
+  <tr>
+   <th style="width:40%">
+    Step
+   </th>
+   <th>
+    Preview
+   </th>
+  </tr>
+ </thead>
+ <tbody>
+  <tr>
+     <td>''1. File->Open->Open File''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_trace_viewer_drag_and_drop_zip.png]]</td>
+  </tr>
+<tr>
+     <td>Loads all files within the zip file</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_trace_viewer_zip_loaded.png]]</td>
+  </tr>
+
+
+ </tbody>
+</table>

docs/saturn/tiddlers/Opening a trace with File Explorer.tid

@@ -0,0 +1,27 @@
+created: 20180308143728066
+modified: 20180308155022347
+title: Opening a trace with File Explorer
+type: text/vnd.tiddlywiki
+
+<table style="width:100%">
+ <thead>
+  <tr>
+   <th style="width:40%">
+    Step
+   </th>
+   <th>
+    Preview
+   </th>
+  </tr>
+ </thead>
+ <tbody>
+  <tr>
+     <td>''1. File->Open->Open File''</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_sequence_editor_open_file.png]]</td>
+  </tr>
+  <tr>
+     <td>Displays Trace</td>
+     <td style="text-align:center;padding-top:4px;padding-bottom:4px;">[img[image_trace_viewer_trace.png]]</td>
+  </tr>
+ </tbody>
+</table>

docs/saturn/tiddlers/User Guide.tid

@@ -1,5 +1,5 @@
 created: 20180305103039051
-modified: 20180307154457566
+modified: 20180308153914137
 title: User Guide
 type: text/vnd.tiddlywiki
 
@@ -21,20 +21,24 @@ type: text/vnd.tiddlywiki
 ### [[Extracting translations]]
 ### [[Extracting part of a translation]]
 ### [[Viewing translation numbering]]
-## [[Viewing properties]]
+## [[Viewing DNA properties]]
 ## [[Viewing as FASTA]]
+## [[Exporting as FASTA file]]
+## [[Opening FASTA file|Loading FASTA using the File Browser]]
 ## Finding sequences
 ### [[Exact match]]
 ### [[Regular expression]]
 ### [[By numbered region]]
 ### [[By exact position]]
 ### [[By inverse complement]]
 ### [[Missmatch search]]
+## [[Extracting a sequence]]
 ## Customizing view
 ### [[Changing sequence block size]]
 ### [[Changing number of blocks per line]]
 ### [[Introducing an offset]]
 ### [[Introducing a frame offset]]
+## [[Inverse / Complement]]
 # [[Protein Sequence Editor]]
 # [[BLAST Sequence]]
 ## [[Performing a simple BLAST]]
@@ -49,6 +53,14 @@ type: text/vnd.tiddlywiki
 ## [[Deleting alignment from database]]
 ## [[Retrieving alignment from database]]
 ## [[Inverse complement an alignment]]
+# [[Sequencing Viewer]]
+## Opening traces
+### [[File Explorer|Opening a trace with File Explorer]]
+### [[Drag and drop|Loading a trace with drag and drop]]
+### [[With a zip file|Loading traces from a zip file]]
+## Aligning to trace
+### [[BLAST sequences within SATurn database|BLAST trace sequence against SATurn database]]
+### [[Drag and drop sequence to align|Drag and drop sequence to align trace against]]
 # [[Scripting]]
 ## [[Overview]]
 ## [[Retrieving entities from the SATurn database]]