update docs

.readthedocs.yaml

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+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/soure/conf.py

docs/requirements.txt

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+Sphinx==8.0.2
+sphinx-rtd-theme==2.0.0

docs/source/index.rst

@@ -18,4 +18,6 @@ documentation for details.
    install
    window
    usage
+   others
+   output
 

docs/source/others.rst

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+Other Features
+==============
+
+Mapping Analysis
+----------------
+
+The mapping analysis will locate the found repeats into gene features (CDS, UTR, intron, exon). Before mapping, you should import gtf or gff annotation files.
+
+Go to **Toolbar**, and then click |locate| to perform mapping analysis. After mapping, the repeats mapped in gene exon (pink), intron (green), CDS (purple), 3'UTR (blue), 5'UTR (yellow) will be marked as different colors in table.
+
+	.. figure:: _static/annotcolor.png
+
+Design Primer
+-------------
+
+Krait2 use `primer3 <https://primer3.org/>`_ to design primers. Before primer design, you can set corresponding parameters for primer3. The meaning of primer3 tags can be found in `primer3 manual <https://primer3.org/manual.html>`_.
+
+	.. figure:: _static/primersetting.png
+		:width: 500
+		:align: center
+
+First, you should select some repeats in table, and then click |primer| to design primers. If primer designed successfully, the primers will be displayed in Primer result table.
+
+	.. figure:: _static/primerresults.png
+		:align: center
+
+The description of each column in primer result table:
+
+.. list-table:: 
+	:header-rows: 1
+	:align: center
+
+	* - Column
+	  - Description
+	* - ID
+	  - unique identifier generated by Krait
+	* - locus
+	  - repeat identifier which is composed of repeat type, input file id and repeat id
+	* - entry
+	  - primer entry id, each locus may has multiple designed primers
+	* - product size
+	  - product size
+	* - strand
+	  - forward or reverse
+	* - Tm
+	  - melting temperatures for forward and reverse primers
+	* - GC content
+	  - GC content for forward and reverse primers
+	* - 3' End stability
+	  - 3' end stability for forward and reverse primers
+	* - primer sequences
+	  - primer sequences for forward and reverse primers
+
+Click the row in primer table, you can view the primer sequence location in input sequence file. The sequences enclosed by the dotted boxes are the positions of the primers.
+
+	.. figure:: _static/primerseq.png
+		:align: center
+
+
+Perform Statistics
+------------------
+
+After searching repeat, you can click |statistics| to perform statistics analysis.
+
+Motif Standardization
+^^^^^^^^^^^^^^^^^^^^^
+
+**Level 0**
+
+no standardization will be performed
+
+**Level 1**
+
+Similar motifs. For example, CA can be viewed as AC. ATGcan represent TGA and GAT
+
+**Level 2**
+
+Reverse complementary motifs, including Level 1. For example, CAT is a reverse complementary motif of ATG. ATG can represent TGA, 
+GAT, CAT, ATC and TCA
+
+**Level 3**
+
+Complementary motifs, including Level 1 and Level 2. For example, TAC is a complementary motif of ATG. ATG can represent TGA,GAT, 
+CAT, ATC, TCA, TAC, ACT and CTA
+
+**Level 4**
+
+Reverse motifs, including Level 1, Level 2 and Level 3. For example, GTA is a reverse motif of ATG. ATG can represent TGA,GAT, CAT, 
+ATC, TCA, TAC, ACT, CTA, GTA, TAG and AGT
+
+
+
+Filter Tables
+-------------
+
+The repeats in current table can be filtered by setting different conditions according to each column. Go to **Toolbar** and click |filter| to open filter dialog.
+
+	.. figure:: _static/filterdialog.png
+		:width: 500
+		:align: center
+
+Click |plus| to add filter condition, click |minus| to remove current filter condition, click |clear| to clear all filter conditions, after setting filters, you can click |update| update table to do filter and update the rows in current table.
+
+
+.. |locate| image:: _static/locating.svg
+	:width: 20
+.. |primer| image:: _static/primer.svg
+	:width: 20
+.. |statistics| image:: _static/statistics.svg
+	:width: 20
+.. |filter| image:: _static/filter.svg
+	:width: 20
+.. |plus| image:: _static/plus.svg
+	:width: 20
+.. |minus| image:: _static/minus.svg
+	:width: 20
+.. |clear| image:: _static/clear.svg
+	:width: 20
+.. |update| image:: _static/update.svg
+	:width: 20

docs/source/output.rst

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+Export Results
+==============
+
+Export Result Tables
+--------------------
+
+Krait2 supports exporting results to csv or tsv formatted file.
+
+Go to **File** menu, click **Export selected rows...** to export selected rows in current table into a file.
+
+Go to **File** menu, click **Export current table...** to export all rows in current table into a file.
+
+Go to **File** menu, click **Export all tables...** to open exporting dialog. You can export all tables for current input file or for all input files. You can also select csv or tsv as output format.
+
+	.. figure:: _static/exportdialog.png
+		:width: 400
+		:align: center
+
+
+Export Statistics Report
+------------------------
+
+Krait2 allows users to export html formatted statistical report file.
+
+Go to **File** menu, click **Export statistics report...** to export html file. 

docs/source/usage.rst

@@ -207,6 +207,7 @@ The description of each column in GTRs table:
 	* - motif
 	  - repeat unit of GTR
 
+
 .. |ssr| image:: _static/ssr.svg
 	:width: 20
 .. |cssr| image:: _static/cssr.svg