Update user manual (#160)

BioJulia · Jun 20, 2021 · 87f806c · 87f806c
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![Latest Release](https://img.shields.io/github/release/BioJulia/BioSequences.jl.svg)](https:/BioJulia/BioSequences.jl/releases/latest)
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https:/BioJulia/BioSequences.jl/blob/master/LICENSE)
 [![Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/BioSequences.jl/stable)
-[![Pkg Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+[![Pkg Status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Chat](https://img.shields.io/gitter/room/BioJulia/BioSequences.svg)](https://gitter.im/BioJulia/BioSequences.jl)
 
 

diff --git a/docs/make.jl b/docs/make.jl
@@ -14,7 +14,8 @@ makedocs(
  "Pattern matching and searching" => "sequence_search.md",
  "Iteration" => "iteration.md",
  "Counting" => "counting.md",
- "I/O" => "io.md"
+ "I/O" => "io.md",
+ "Interfaces" => "interfaces.md"
  ],
  authors = "Ben J. Ward, D.C.Jones, Kenta Sato, The BioJulia Organisation and other contributors."
 )

diff --git a/docs/src/construction.md b/docs/src/construction.md
@@ -67,33 +67,12 @@ julia> LongSequence{DNAAlphabet{2}}([DNA_T, DNA_T, DNA_A, DNA_G, DNA_C])
 5nt DNA Sequence:
 TTAGC
 
-julia> DNAMer{5}([DNA_T, DNA_T, DNA_A, DNA_G, DNA_C])
-DNA 5-mer:
-TTAGC
-
-julia> RNAMer{5}([RNA_U, RNA_U, RNA_A, RNA_G, RNA_C])
-RNA 5-mer:
-UUAGC
-
-julia> # Works, but is not type-stable
-
-julia> DNAMer([DNA_T, DNA_T, DNA_A, DNA_G, DNA_C])
-DNA 5-mer:
-TTAGC
-
-julia> RNAMer([RNA_U, RNA_U, RNA_A, RNA_G, RNA_C])
-RNA 5-mer:
-UUAGC
 ```
 
 ### Constructing sequences from other sequences
 
 You can create sequences, by concatenating other sequences together:
 ```jldoctest
-julia> LongDNASeq(LongDNASeq("ACGT"), LongDNASeq("NNNN"), LongDNASeq("TGCA"))
-12nt DNA Sequence:
-ACGTNNNNTGCA
-
 julia> LongDNASeq("ACGT") * LongDNASeq("TGCA")
 8nt DNA Sequence:
 ACGTTGCA
@@ -108,24 +87,6 @@ TATATATATATATATATATA
 
 ```
 
-You can also construct long sequences from kmer sequences, and vice versa:
-
-```jldoctest
-julia> m = DNAMer{5}([DNA_T, DNA_T, DNA_A, DNA_G, DNA_C])
-DNA 5-mer:
-TTAGC
-
-julia> LongSequence(m)
-5nt DNA Sequence:
-TTAGC
-
-julia> # round trip from mer to long sequence back to mer.
-
-julia> DNAMer(LongSequence(m))
-DNA 5-mer:
-TTAGC
-```
-
 Sequence views (`LongSubSeq`s) are special, in that they do not own their own data,
 and must be constructed from a `LongSequence` or another `LongSubSeq`:
 
@@ -150,10 +111,7 @@ true
 
 ## Conversion of sequence types
 
-Sometimes you can convert between sequence types without construction / having
-to copy data. for example, despite being separate types, `LongDNASeq` and
-`LongRNASeq` can freely be converted between efficiently, without copying the
-underlying data:
+You can convert between sequence types.
 ```jldoctest
 julia> dna = dna"TTANGTAGACCG"
 12nt DNA Sequence:
@@ -163,9 +121,6 @@ julia> rna = convert(LongRNASeq, dna)
 12nt RNA Sequence:
 UUANGUAGACCG
 
-julia> dna.data === rna.data # underlying data are same
-true
-
 ```
 
 Sequences can be converted explicitly and implicitly, into arrays and strings:
@@ -181,7 +136,7 @@ julia> dnastr = convert(String, dna)
 julia> # Implicit conversion to string - putting dna sequence in String vector 
 
 julia> arr = String[dna]
-1-element Array{String,1}:
+1-element Vector{String}:
  "TTANGTAGACCG"
  
 ```

diff --git a/docs/src/dev_docs/bitindex.md b/docs/src/dev_docs/bitindex.md
diff --git a/docs/src/dev_docs/sequences/biosequence.md b/docs/src/dev_docs/sequences/biosequence.md
diff --git a/docs/src/dev_docs/symbols.md b/docs/src/dev_docs/symbols.md
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -3,7 +3,7 @@
 [![Latest Release](https://img.shields.io/github/release/BioJulia/BioSequences.jl.svg)](https:/BioJulia/BioSequences.jl/releases/latest)
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https:/BioJulia/BioSequences.jl/blob/master/LICENSE)
 [![Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/BioSequences.jl/stable)
-[![Pkg Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+[![Pkg Status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Chat](https://img.shields.io/gitter/room/BioJulia/BioSequences.svg)](https://gitter.im/BioJulia/BioSequences.jl)