bioroebe 0.12.24 → 0.13.31

data/doc/README.gen

@@ -10,239 +10,193 @@ DEFAULT_HEADER
 <img src="https://i.imgur.com/AfduheY.png" style="margin: 4px; margin-left: 12px;"/>
 
 The **<span style="color: darkblue">above pictures</span>**,
-more or less, represent DNA - in particular a **dsDNA helix**
-(a **double-stranded DNA helix**).
+more or less, represent DNA or, more generally, information in biological
+systems. In particular the very left picture used to represented a
+<b>dsDNA helix</b> (a **double-stranded DNA helix**), but it no longer
+really like a dsDNA helix, due to my failed attempts at 'improving' it over
+the years. One day I should really should re-do that image ...
 
-The very left picture no longer looks like a dsDNA helix, though, due to
-my attempts to 'improve' it over the years and failing hard at that.
-I really should re-do that image one day.
-
-The other two images are more recent. For instance, the second picture (the one
+The other images are more recent. For instance, the second picture (the one
 that is almost in the middle) shows a schematic for a dsDNA helix. Of course
-DNA does not look like this at all whatsoever (hydrogen bonds can not possibly
-ever look as depicted like that, aside from the spacing being incorrect), but
-it is a pretty picture nonetheless - so let's go with pretty for the fancy
-visual show effects! \o/
+DNA does not look like this at all whatsoever - hydrogen bonds can not possibly
+ever look as depicted like that, aside from the spacing being incorrect 
+anyway - but it is a pretty picture nonetheless, so let's go with pretty,
+for the fancy visual show effects! \o/
 
 Minor nitpick: keep in mind that DNA in regular cells is right-handed, so if
 you see a DNA double helix displayed that is going in the left direction then
-this is technically incorrect. So the image on the very right hand side is
-showing two dsDNA where one is evidently "incorrect" - but we could reason
-about it still being correct if we assume that one of the two dsDNA molecules
-shown is a synthetic one for a mirror cell, similar to racemases and epimers
-in chemistry.
+this is <b>technically incorrect</b>. So the image on the very right hand side
+is showing two dsDNA where one is evidently "<b>incorrect</b>", since it is
+a mirror image - but we could reason about it still being correct <b>if</b> we
+were to assume that one of the two dsDNA molecules shown is a synthetic one
+for a mirror cell, similar to how racemases and epimers (in chemistry) may
+be defined.
 
 The last image, that is the fourth image from left, shows a dsDNA helix. It
 is a bit better than the other pictures because it is **somewhat** more
 accurate. The distance between the two helices is <b>2nm</b>, so this
 picture kind of shows this somewhat more accurate. The distance between
 two adjacent nucleotide pairs is <b>3.4 nm</b> - so that kind of fits
-for the fourth image; not quite perfect, but somewhat close to that.
+the distance shown in the fourth image; not quite perfect, but somewhat
+close to that.
 
 ## About the BioRoebe project: History and Goals
 
 The **BioRoebe project** was initially created in the year **2007** - 
-or at the least close to 2007, give or take, under **another name**.
+or at the least close towards that year, give or take, under <b>another
+name</b>.
 
 I was using the project for quite some time for my own, personal
 use cases in regards to **bioinformatics** and **molecular biology**;
-just a small hobby project, for very small, minor tasks. In many
-ways the project is still **just a hobby project** really - it's
-not a professional suite of software, and won't be for the
-foreseeable time either due to time constraints alone.
+just a small hobby project, for very small, minor tasks.
+
+In many ways the project is still **just a hobby project** really -
+it's not a professional suite of software, and won't be for the
+foreseeable time either, due to time constraints alone.
 
-In **early 2013**, the project was finally published on
+In **early 2013**, the project was finally <b>published</b> on
 **rubygems.org**, which has been its new home ever since - 
 and probably will remain its home, for a very long time to come.
-It is hard to predict the future accurately, though.
-
-Nonetheless, since as of **2013** the project has grown considerably
-in size. That makes describing the project a bit difficult, too, since
-the **use cases** for the project have increased, changed and been adapted
-over the years. There is not merely 'one' use case only - the **bioroebe**
-gem is **a toolset project**. Different people make use of different
-tools. Even programming languages may vary - while most of the
-bioroebe project is written in ruby, there are some (smaller)
-parts written in Java as well and I do not rule out using Python or
-other programming languages to do specific tasks either. Some parts
-of the bioroebe project are more widely (and often) used; other parts
-refer to **niche use cases** and thus are less frequently used.
+It is hard to predict the future accurately, though. Perhaps I
+may use the project for additional professional work in the future -
+I don't know yet.
+
+Nonetheless, since as of the year **2013**, the project has grown
+considerably in size. That makes describing the project a bit difficult,
+too, since the **use cases** for the project have increased, changed
+and been adapted over the years. More code, and more use cases, 
+begetting more (and better) documentation. That makes sense, right?
+
+So there is not merely 'one' use case only for this project - the
+**bioroebe** gem is ultimately <b>a toolset project</b>. Different
+people make use of different tools. Even programming languages may
+vary when it comes to this project - while most of the bioroebe project is
+written in <b>ruby</b>, there are some (smaller) parts written in Java as
+well and I do not rule out using Python or other programming languages to
+do specific tasks either in the long run, including C++, C or any other
+programming language. Some parts of the bioroebe project are more widely
+(and often) used; other parts refer to **niche use cases** and thus
+are less frequently used.
 
 Despite the plethora of options supported by this project, the
 **BioRoebe project** has several very important
 <span style="color: darkblue; font-weight: bold">goals</span>
-that are still **valid as of today** and stand out compared to
-other goals of lesser importance.
+that are still **valid as of today** and <b>stand out compared to
+other goals of lesser importance</b>.
 
-The **primary purpose** for this project - that is the **main use
-case**, if but one has to be named - is to be able to quickly help
-in regards to **bioinformatics-related tasks**, and associated
+The <b>primary purpose</b> of this project - that is the <b>main use
+case</b>, if but one has to be named - is <b>to be able to quickly help
+in regards to bioinformatics-related tasks</b>, and associated
 <b>wet-lab</b>-related use cases from within molecular biology.
 
 For example, the project should allow its users to run it on
-a **local computer**, on a **remote computer**, be used on
+a <b>local computer</b>, on a **remote computer**, be used on
 the commandline, via **different GUIs** or via the **www**
-or on a smartphone/mobile device in the long run.
+or on a smartphone/mobile device in the long run. Flexible use
+cases all the way down the rabbit hole.
 
-**There should be no limitation in where and how the project should
-or could be run**, including the possibility to run it on as many
+<b>There should be no limitation in where and how the project should
+or could be run</b>, including the possibility to run it on as many
 different operating systems as possible (at the least if ruby is
 available on that operating system; or possibly Java as an
-additional option one day). This is why the project has to 
-try to **stay as flexible as possible** - we must support
-different operating systems, with all their quirks and
-unique oddities, if this is doable.
+additional option one day, including jruby-SWING bindings). This
+is why the project has to try to **stay as flexible as possible** -
+we <b>must</b> support different operating systems, with all their
+quirks and unique oddities, if this is doable.
 
 Note that this goal also applies to **programming languages**,
-as pointed out already. While the primary focus for the **bioroebe**
+as pointed out above. While the primary focus for the **bioroebe**
 project is (and will remain) on ruby, I specifically **do not** exclude
 the possibility that languages such as Java, C/C++ or even Python may
 be included and used in this project. In fact: since as of **2021**,
 Java-specific parts will be extended in the bioroebe project as well.
+
 In the long run I would like to support both ruby and Java from the
-get go. The primary question that is relevant here in regards
-to different programming languages is that of <b>use case</b>;
+get go, on an equal level. The primary question that is relevant here in
+regards to different programming languages is that of <b>use case</b>;
 <b>usability</b> and <b>usefulness</b>, and then <b>maintainability
-of the code base</b> as well, as a secondary consideration.
+of the code base</b> as well, as a secondary consideration. Documentation
+is also equally important, so I will try to improve the documentation
+systematically - both from a user's point of view, but also from
+the point of view of other developers who may try to make use of
+this project.
 
 The bioroebe project additionally has to **solve real problems**,
 in particular from a molecular biology point of view. Most
 bioinformatics-related toolkits were written by experts in the 
 field who tend to have a strong background in **mathematics** and
 **informatics**. While that is a perfectly fine background to have,
-and most definitely an **asset**, I simply came from the "<i>other</i>"
-side - molecular biology and molecular genetics. This makes for
-a difference in thinking too, because I tend to be closer towards
-the side of, say, synthetic biology, than on the side of 
+and most definitely an **asset**, I myself came from the "<i>other</i>"
+side of the medal - molecular biology and molecular genetics. This makes
+for a difference in thinking too, because I tend to be closer towards
+the side of, say, <b>synthetic biology</b>, than on the side of 
 (bio)mathematics or statistics, due to my own interests in the
-way how I think or approach a given problem set. It's different
-to a primary in-silico driven approach. Nonetheless, the **bioroebe
-project** attempts to remain as flexible as possible, including 
-exploring other ways in how a given problem set can be solved.
-
-When the bioroebe project was initially created, I wanted it to be
-**more natural** to people who may not necessarily excel at designing
-(or even understanding) algorithms. Not that algorithms should
-be neglected, mind you, for efficiency reasons alone; but the
-primary view for the whole BioRoebe suite of programs will be
-to focus on "real" biology first and foremost, not just
-<i>in-silico</i> dry runs or simulations, per se. Although most
-of the fields of bioinformatics is dominated by mathematicians and
-computer scientists, I know that there are plenty of people who
-come from a simpler **molecular biology**-specific background. So the
-project tries to cater primarily to the latter group, without trying
-to exclude anyone else. This also includes the focus on
-**documentation** - while the documentation is far from perfect,
-I try to polish it every now and then. The aim here is to make
-the documentation useful for "Average Joe" - the common user,
-at the least from a wet-lab focus on molecular biology.
+way how I think or approach a given problem set. I find life fascinating,
+more so than computer systems - thus, biological information is
+more appealing to me than computer-stored information.
+
+It is most definitely a different view to primarily in-silico driven
+approaches. Nonetheless, the **bioroebe project** attempts to remain
+as flexible as possible, including exploring other ways in how a
+given problem set can be solved.
+
+When the bioroebe project was initially created, many years ago, I wanted it
+to be <b>more natural</b> to people who may not necessarily excel at designing
+(or even understanding) algorithms. Not that algorithms should be neglected,
+mind you, for <b>efficiency reasons</b> alone; but the primary view for the
+whole BioRoebe suite of programs will be to focus on "real" biology first
+and foremost, not just <i>in-silico</i> dry runs or simulations, per se.
+
+Although most of the fields of bioinformatics is dominated by mathematicians
+and computer scientists, I know that there are plenty of people who come from
+a simpler **molecular biology**-specific background. So the project tries to
+cater primarily to the latter group, without trying to exclude anyone else.
+This also includes the focus on **documentation** - while the documentation
+right now is far from perfect, I try to polish it every now and then. The 
+main aim here is to make the documentation useful for "Average Joe" - the
+common user, at the least from a wet-lab focus on molecular biology.
 
 So, <b>how</b> can the BioRoebe project be helpful to its users?
 
 The **BioRoebe** project can be used to solve (some) problems
 related to **biology**, **molecular biology**, **genetics**
-and, last but not least, **bioinformatics**.
+and, last but not least, **bioinformatics**, perhaps even
+<b>synthetic biology</b>.
 
 For example, say that you quickly wish to **reverse-translate a
-sequence of amino acids**, and select all possible codons,
-or <b>the most likely codon candidate</b>; or just random codon
-candidates, and display that result on the commandline or via
-a www interface.
+sequence of amino acids**, and select all possible codons from
+that sequence, or <b>the most likely codon candidate(s)</b>; or
+just random codon candidates, and display that result on the
+commandline or via a www interface.
 
-This is easily possible through **BioRoebe**. How fancy and
-useful! \o/
+This is easily possible through **BioRoebe**. <b>How fancy and
+useful!</b> \o/
 
 For instance, when I do this on the commandline via bash and
-KDE konsole:
+KDE konsole, invoking the aliased binary called
+<b>revseq</b>, for <b>reverse sequence</b>:
 
-    revseq AAT # Alanine-Alanine-Threonine
+    revseq AAT # Alanine-Alanine-Threonine, so three amino acids
 
-Then it will show the following DNA sequence:
+Then on the commandline the following result will be shown,
+representing a <b>DNA sequence</b>:
 
     GCCGCCACC # These are 9 nucleotides, corresponding to the three amino acids.
 
-(This will only work if your alias of revseq points
-to the correct bin/ entry. In my case I have 
-aliased **revseq** onto **bin/deduce_most_likely_aminoacid_sequence**.
-Of course you can use any other alias, or just flat out call
-**bin/deduce_most_likely_aminoacid_sequence** directly.)
-
-## Requiring BioRoebe and starting the bioshell interface
-
-In order to require **BioRoebe**, do use a line in ruby code such
-as the following one:
-
-    require 'bioroebe'
-
-To **automatically** include the **main namespace** upon require-time,
-the following line of code can be used:
-
-    require 'bioroebe/autoinclude'
-
-Note that this will include into the Object namespace, so if you want
-to have more control over the include-action, you need to first require
-the bioroebe project, and then include it onto the target namespace
-that you wish to use specifically, such as a subclass or another 
-module. If you do not need to autoinclude then I recommend to
-simply use the first variant how to require the bioroebe gem - that
-should suffice. The reason why the file called **autoinclude.rb**
-exists is mostly due to laziness, so we can type less. We can omit
-<b>include Bioroebe</b> after all.
-
-The **BioRoebe** project comes with a file called **bin/bioshell**,
-which allows you to start this project from a typical shell, such
-as **bash**, by issuing this command on the command prompt:
-
-    bioshell
-
-You can also load up the project and run it from within a .rb file
-or during an **IRB session**, by doing the following:
-
-    require 'bioroebe'
-
-    Bioroebe::BioShell[]
-
-Or alternatively, which may be more convenient to type:
-
-    require 'bioroebe'
-
-    Bioroebe.start_shell # No need to use the [], unlike the example shown above
-
-## Usage of the BioRoebe project
-
-Not all subcomponents within the **BioRoebe** project have received
-equal attention and thus, the **quality** of these subcomponents may
-often differ, to word this nicely.
-
-Patches and contributions to extend functionality, improve the
-documentation, fix existing bugs or improve the usability and
-general quality of the project, are welcome. Take note that I
-in general tend to add **new** entries at the bottom of this file
-here (README.gen or README.md, respectively); use the navigation
-menu on the **top right** of this page to quickly jump to these
-entries. Sometimes headers change a bit, but by and large content
-is rarely removed; so if you ever found something in the past,
-you should be able to find it again in the future - except for
-when APIs are removed. These may be omitted in the documentation.
-That's quite rare, though.
-
-I will move entries that have received updates with more recent
-releases to the ~bottom of this very page here - that way it should
-be a bit easier to keep up to date with what has changed within
-this project. It is admittedly becoming a fairly large project,
-which is why I try to keep things somewhat organized.
-
-In the long run I will also, most likely, publish the documentation
-in a "booklet" format such as https://yaml.readthedocs.io/en/latest/.
-That way one may be more easily able to read individual
-subchapters.
+(This will only work if your alias of <b>revseq</b> points
+to the correct bin/ entry as well; I keep the rcfiles gem for
+that, which includes all the aliases I use. In my case I have 
+aliased **revseq** onto **bin/deduce_most_likely_aminoacid_sequence**
+actually, as can be seen in the rcfiles gem. Of course you can use
+any other alias, or just flat out call **bin/deduce_most_likely_aminoacid_sequence**
+directly. I just like to be succinct and to-the-point whenever 
+possible, so the revseq alias suits the way how my brain works.)
 
 ## Differences and Compatibility towards BioRuby
 
-This subsection will explain some of the philosophical - and, more
-importantly, **practical** - differences between **BioRoebe** and
-**BioRuby**, as both projects have somewhat similar, hence **shared
-goals**.
+This subsection will explain some of the philosophical - and, more importantly,
+**practical** - differences between **BioRoebe** and **BioRuby**, as both projects
+have somewhat similar, hence <b>shared goals</b>.
 
 One philosophical difference, for example, is that BioRoebe is less
 focused on bioinformatics as such, and more focused on **molecular
@@ -340,6 +294,106 @@ instead, they can do so, too - see the <b>API</b> for codon tables
 lateron. Simply define your own constants and pass them to the
 appropriate methods.
 
+## The rewrite in November 2023
+
+The bioroebe gem was partially rewritten in November 2023.
+
+The primary goal for this rewrite was to add a jruby-SWING
+GUI that allows the user to make use of the interactive
+bioshell from a SWING GUI. This GUI works right now, but it
+is not very pretty or elegant, as the following image shows
+(you may have to scroll down a little bit, in order to
+see it):
+
+<img src="https://i.imgur.com/bVr8eIx.png" style="margin: 1em">
+
+I also made sure that this does indeed work on Windows, which
+was the primary reason this GUI was added in the first place -
+and it does indeed work on windows. \o/
+
+In the coming months this will be improved.
+
+## Usage of the BioRoebe project
+
+Not all subcomponents within the **BioRoebe** project have received equal
+attention and thus, the **quality** of these subcomponents may often
+differ, to word this nicely. In other words: the quality of the code will
+be different, with some parts being tested more than others.
+
+Patches and contributions to extend functionality, improve the documentation,
+fix existing bugs or improve the usability and general quality of the project,
+are in general welcome. Take note that I in general tend to add **new**
+entries at the bottom of this file here (README.gen or README.md, respectively);
+use the navigation menu on the **top right** of this page to quickly jump to
+these entries.
+
+Sometimes headers change a bit, but by and large content is rarely removed; so
+if you ever found something in the past, you should be able to find it again
+in the future - except for when APIs or submodules are removed. These may
+be omitted in the documentation. That's quite rare to happen, though.
+
+I will typically move entries that have received updates with more recent
+releases to the ~bottom of this very page here - that way it should be a bit
+easier to keep up to date with what has changed within this project. It is
+admittedly becoming a fairly large project, which is why I try to keep
+things somewhat organized here.
+
+In the long run I will also, most likely, publish the documentation
+in a "booklet" format such as https://yaml.readthedocs.io/en/latest/.
+That way one may be more easily able to read individual subchapters.
+
+The rest of this document shall now attempt to explain the different
+parts of the bioroebe-gem.
+
+## Requiring the BioRoebe project and starting the bioshell interface
+
+In order to require **BioRoebe** you can use the following line of
+ruby code:
+
+    require 'bioroebe'
+
+To <b>automatically</b> include the **main namespace** upon require-time,
+the following line of code can be used:
+
+    require 'bioroebe/autoinclude'
+
+Note that this will include into the Object namespace, so if you want
+to have more control over the include-action (and avoid inclusion into
+ruby's Object namespace), you need to first require the bioroebe
+project, as shown above, and then include it onto the target namespace
+that you wish to use specifically, such as a subclass or another 
+module.
+
+If you do not need to autoinclude then I recommend to simply use the
+first variant (require 'bioroebe') how to require the bioroebe gem -
+that should suffice for most use cases. The reason why the file called
+<b>autoinclude.rb</b> exists is mostly due to my inherent laziness,
+as well as a desire to be flexible, so we can ultimately type less.
+We can omit <b>include Bioroebe</b> after all in the second case.
+
+The **BioRoebe** project comes with a file called **bin/bioshell**,
+which allows you to start this project from a typical shell, similar
+to <b>bash</b>, by issuing this command on the command prompt:
+
+    bioshell
+
+(If this does not work, make sure that bin/bioshell is in your
+$PATH; you can also extract the .gem and move bin/bioshell to
+any location you desire it to be, of course.)
+
+You can also load up the project and run it from within a .rb
+file or during an **IRB session**, by doing the following:
+
+    require 'bioroebe'
+
+    Bioroebe::BioShell[]
+
+Or alternatively, which may be more convenient to type:
+
+    require 'bioroebe'
+
+    Bioroebe.start_shell # No need to use the [] here, unlike in the example shown above
+
 ## Readline support in the BioRoebe project
 
 The **BioRoebe** project will attempt to make use of **Readline**, if
@@ -384,6 +438,61 @@ Personally I recommend that people should switch to **psych** and
 give it a try. It should work fine really. But ultimately this is
 up to them.
 
+## Colours support in the Bioroebe project
+
+<b>Colours</b> can be immensely useful, at the least to most people.
+
+The bioroebe project has to support colours. The primary file
+that bundles together most of that colours-related functionality
+can be found at:
+
+    require 'bioroebe/colours/colours.rb'
+
+This, in turn, depends on the gem called <b>colours</b>.
+
+Code exists in the bioroebe project that can be used on the
+commandline to output colours, such as the following image
+shows:
+
+<img src="https://i.imgur.com/VbfOME3.png" style="margin: 1em">
+
+If you do not want or need colours, you can disable them via
+this method call:
+
+    Bioroebe.disable_colours
+
+Conversely, to enable colours again, use:
+
+    Bioroebe.enable_colours
+
+Classes that subclass from Bioroebe::CommandlineApplication will
+have a method called <b>.use_colours?</b>, which can be used
+to query whether the class at hand makes use of colours.
+
+This functionality depends on the gem called <b>colours</b>.
+
+In the past the code allowed for konsole-colours support (KDE
+konsole) and simpler terminals without RGB colour support.
+
+When the bioroebe project was rewritten in April 2020, this was 
+changed. The project now depends on the Colours module, and it
+will try to use that project to its full possibilities, including
+KDE konsole colours (RGB colours) by default. This will also include
+so called "HTML colours", such as :slateblue or :steelblue.
+
+## class Bioroebe::DetermineMissingNucleotidesPercentage
+
+The small class Bioroebe::DetermineMissingNucleotidesPercentage can be
+used to determine missing nucleotide content, in percentage.
+
+For instance, say that you know the GC content of a given
+DNA sequence is at 48%. You want to know the GC and AT
+content of that quickly, so you invoke this class.
+
+It's output may then look like this:
+
+<img src="https://i.imgur.com/txV3ZGY.png" style="margin: 1em">
+
 ## Phred quality score
 
 If you need support for PHRED, you could use this method:
@@ -480,28 +589,6 @@ now and then.
   TLR3    |     double-stranded RNA (dsRNA)                                          | https://en.wikipedia.org/wiki/TLR3 
   TLR4    |     binds cell-wall components of gram-negative bacteria (via their LPS) | https://en.wikipedia.org/wiki/TLR4
 
-## Enzymes
-
-This subsection will be expanded at a later time - it will be
-about enzymes in general.
-
-For now, if you need a table, as memory, for the enzyme classes,
-here is one:
-
-| Enzyme class  (EC)  |     Name         |
-|-------------------- |------------------|
-|          1          | Oxidoreductases  |
-|          2          |  Transferases    |
-|          3          |   Hydrolases     |
-|          4          |    Lyases        |
-|          5          |   Isomerases     |
-|          6          |    Ligases       |
-|          7          |    Translocases  |
-
-See wikipedia for more information:
-
-https://en.wikipedia.org/wiki/Enzyme_Commission_number#Top_level_codes
-
 ## Using Bioroebe in a project
 
 Of considerable usefulness to the end-user may be the **BioShell**.
@@ -2451,24 +2538,6 @@ And, my favourite one:
 
 https://labcalculator.net/wiki/oligo-tm
 
-## SimpleStringComparer
-
-class **SimpleStringComparer** can be used to compare two strings visually,
-similar as to how **NCBI BLAST** compares two sequences to one another.
-
-By default the output of that class will be, in colours, on the commandline,
-but you can disable this like so:
-
-    Bioroebe::SimpleStringComparer.new(ARGV) { :disable_colours }
-
-Let's look at another example:
-
-    Bioroebe::SimpleStringComparer.new('AAAAAAAAAAAAAATTTTTTTTTTTAAAAAAAAAAAATATA|GAAAAAAAAAAAAAAAATATTTTTTTTTTTTTTTTTTTTTT')
-
-This may look like so:
-
-<img src="https://i.imgur.com/kkqkpmQ.png" style="margin-left: 2em">
-
 ## Bioroebe::SanitizeNucleotideSequence
 
 class **Bioroebe::SanitizeNucleotideSequence** can be used to **sanitize
@@ -2529,7 +2598,7 @@ class will replace the older code. But it will happen.
 If you wish to make use of this class in your own projects,
 first require it:
 
-    require 'bioroebe/nucleotides/show_nucleotide_sequence.rb'
+    require 'bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb'
 
 And then you can use it to display a nucleotide sequence, 
 such as via:
@@ -3381,7 +3450,7 @@ This would colourize Lysine. K is the one amino acid letter
 for Lysine.
 
 Next, you can test whether this works. A simply way is to
-ask for the Ubiquitin sequence. Pay attention to lysine
+ask for the Ubiquitin sequence. Pay attention to <b>lysine</b>
 at position 48.
 
 From within the bioshell, you can query for the ubiquitin
@@ -4135,7 +4204,7 @@ DNA-strand**, whereas the **palindrome** occurs on the **sister
 strand**.
 
 Bioroebe supports the simple "creation" of mirror repeats, through the
-file <b>bioroebe/utility_scripts/mirror_repeat.rb</b> and the method
+file <b>bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb</b> and the method
 there called <b>Bioroebe.mirror_repeat_of()</b>.
 
 Simply pass in the sequence that you wish to mirror, such as:
@@ -4250,50 +4319,6 @@ Why is this important to understand? Well, you may wish to design
 or check that both primers in PCR, forward and reverse, would be
 correct.
 
-## Logging and Log output
-
-The **BioRoebe project** may autogenerate some files, including
-**log files**.
-
-In order to be able to do so, the bioroebe project needs the user
-to be able to access a **base directory**, the so-called
-**working base directory**. This is where bioroebe assumes
-most working files to exist.
-
-On my linux system this used to default to the directory
-called **/Depot/Bioroebe/**. On other systems, the log directory
-may default into the **user's home directory**, via a call to 
-<b>"#{File.expand_path('~')}/"</b>. (I use this presently,
-since **2020**.)
-
-This should work on most systems, but it may not be what you
-want to have or use in your own workflow. Thus, code exists 
-that allows you to designate another log directory to use.
-
-The API for this is simply called:
-
-    Bioroebe.set_log_dir()
-
-The method can be found in
-**lib/bioroebe/toplevel_methods/log_directory.rb**. 
-
-If you want to do this from within the **bioshell** itself,
-try:
-
-    set_log_dir /tmp/test
-    setlogdir /tmp/test
-
-If you use the interactive bioroebe-shell then you can use
-**home?** to determine where the log directory is on your
-system. For example, I tend to just use **/root/Bioroebe/**
-these days, when I am the superuser.
-
-Note that you can also define the environment variable
-called **BIOROEBE_DEFAULT_LOG_DIRECTORY**. If this is
-set on startup of the bioroebe-shell, then it will
-overrule the initial :default value that is used
-otherwise.
-
 ## Working with Blosum
 
 **BLOSUM** is used to sequence-align proteins; thus, it can be
@@ -4722,6 +4747,16 @@ than by phosphatases. Thus, there is a bias in regards to the
 publications that are published. This bias is not necessarily
 "existing" on the level of the cell(s) itself.
 
+Next, a table is shown to compare some search databases:
+
+Name            | remote URL
+----------------|------------------------------------------------------------------------|
+PubMed          | https://pubmed.­ncbi.­nlm.­nih.­gov/                                       |
+Google Scholar  | https://scholar.­google.­com/                                            |
+Web of Science  | https://clarivate.com/webofsciencegroup/solutions/web-of-science/      |
+Scopus          | https://www.­scopus.­com/                                                |
+----------------|------------------------------------------------------------------------|
+
 ## Browser setting in the configuration file
 
 The browser (for opening external websites) is defined here:
@@ -4862,7 +4897,7 @@ Let's take the phage lambda of E. coli. The **refseq entry** is at:
 
 https://www.ncbi.nlm.nih.gov/nuccore/9626243
 
-The genome is **48502 bp** long (**dsDNA**).
+The genome is <b>48502 bp</b> long (<b>dsDNA</b>).
 
 The NCBI ID is: **NC_001416.1**
 
@@ -5296,44 +5331,6 @@ Try the following instruction in order to **disable** it again:
 
     no_expand_cd_aliases
 
-## UniProt
-
-UniProt is a freely accessible database of protein sequence and
-functional information. What makes it also useful for 
-bioinformatics is that you can easily query the FASTA sequence
-of a protein.
-
-Consider the protein called **A2Z669**. The **entry** to this protein
-can be found here:
-
-https://www.uniprot.org/uniprot/A2Z669
-
-And the corresponding FASTA sequence of that protein can be
-found here, if you append **.fasta** to the URL:
-
-https://www.uniprot.org/uniprot/A2Z669.fasta
-
-If you wish to save this file, from within **Bioroebe** itself,
-then you can use the following API:
-
-    Bioroebe.fetch_data_from_uniprot()
-    Bioroebe.fetch_data_from_uniprot('A2Z669')
-
-NCBI also has entries related to UniProt.
-
-Example:
-
-https://www.ncbi.nlm.nih.gov/protein/P02768
-https://www.ncbi.nlm.nih.gov/protein/P02768.2?report=fasta
-
-This has the header **RecName: Full=Serum albumin; Flags:
-PrecursorUniProtKB/Swiss-Prot: P02768.2**.
-
-From the bioroebe-shell, you can can fetch data from
-<b>Uniprot</b>, such as by issuing:
-
-    unitprot_fetch
-
 ## AminoAcid composition
 
 A small widget exists to show the amino-acid composition.
@@ -5442,11 +5439,9 @@ A bin file exists as well:
 
     bin/genbank_to_fasta
 
-This is also handled by the more generic method 
-called **Bioroebe.parse()**, which attempts to parse
-any file that may be relevant in regards to bioinformatics
-eventually. For now (**May 2021**) only a few files are 
-supported.
+This is also handled by the more generic method called <b>Bioroebe.parse()</b>,
+which attempts to parse any file that may be relevant in regards to bioinformatics
+eventually. For now (**May 2021**) only a few files are supported.
 
 A small ruby-gtk3 widget exists for this as well:
 
@@ -6053,6 +6048,7 @@ found in **bioroebe/toplevel_methods/palindromes.rb**.
 You can also use a toplevel method for this. Example:
 
     Bioroebe.palindrome_generator 4 # => "CTAG\nGATC"
+    Bioroebe.palindrome_generator(10)
 
 In **June 2020** code was added to "display" a 2D structure
 of RNA or DNA palindromes. The code for this resides in
@@ -6460,20 +6456,6 @@ You can use it as follows:
 Several commandline scripts make use of that. I found it to be
 useful to have a short visual separator ready.
 
-## Using Bioroebe.three_delimiter()
-
-The method **Bioroebe.three_delimiter()** can be used to
-split a String into a String where every third position has
-a trailing '|' token.
-
-So for instance:
-
-    Bioroebe.three_delimiter 'ATGGGGATGTAGGTA' # => "ATG|GGG|ATG|TAG|GTA"
-
-The primary reason why that was added as a toplevel method has been
-because it may be visually simpler to identify the individual codons
-via your eyes that way.
-
 ## Generating a random DNA sequence
 
 You can "generate" a random DNA sequence from the commandline
@@ -7182,6 +7164,11 @@ It will deduce the possible codons for the aminoacid sequence
 MTTAGP, and it will display the findings in RNA - thus, all
 T are U on the display on the commandline.
 
+The commandline output of the above, captured as an image,
+will be shown next:
+
+<img src="https://i.imgur.com/EUCU3sH.png" style="margin: 1em">
+
 ## Determining the possible codons for a given aminoacid
 
 If you need to quickly determine all possible codons for a specific
@@ -8952,7 +8939,7 @@ that the base is actually correct, we can use the following formula:
 P stands for <b>Probability</b>. An example to this follows next:
 
 Say that you have a quality score of 48; then, in ruby code,
-you would get an **error probability** of:
+you would get an <b>error probability</b> of:
 
     10 ** (-48 / 10.0) # => 1.584893192461114e-05
 
@@ -9520,11 +9507,14 @@ information about <b>SUMO</b>: https://en.wikipedia.org/wiki/SUMO_protein
 
 This is just a simple table, for summary purposes.
 
-Name of the organism          | Latin name                     | Number of chromosomes
-------------------------------|--------------------------------|-----------------------
+Name of the organism          | Latin name                     | Number of chromosomes (in somatic, diploid cells)
+------------------------------|--------------------------------|---------------------------------------------------
  Zebrafish                    | Danio rerio                    |         16
+ Cabbage plants               | Brassica oleracea              |         18
  House mouse                  | Mus musculus                   |         20
+ Chimpanzees                  | Pan troglodytes                |         48
  Pigeon (the domestic pigeon) | Columba livia domestica        |         80
+ Hedgehogs                    | Erinaceidae                    |         90
 
 ## Finding the consensus sequence and constructing a frequency profile
 
@@ -9797,6 +9787,9 @@ in time.
 
 ## GUIs of the bioroebe project - Graphical User Interface of the bioroebe project
 
+The bioroebe project comes with various GUI (Graphical User Interfaces), to
+help work with various aspects even for "average users".
+
 For example, <b>levensthein.rb</b> has code that allows you to
 start its <b>ruby-gtk GUI</b> component, via:
 
@@ -9806,7 +9799,8 @@ Or, in a more generic manner:
 
     bioroebe --levensthein-gui
 
-Here is a **screenshot** of the gtk2-class for <b>HammingDistance</b>.
+Here is a **screenshot** of the (old) ruby-gtk2-class for the
+<b>HammingDistance</b>.
 
 <img src="https://i.imgur.com/OT4dJiq.png" style="margin-left: 2em">
 
@@ -9912,7 +9906,7 @@ bindings in Bioroebe to ruby-tk bindings:
     19 | sizeseq                            | [NOT YET IMPLEMENTED]         |                           |
     20 | three_to_one                       | [NOT YET IMPLEMENTED]         |                           |
     21 | www_finder                         | [NOT YET IMPLEMENTED]         |                           |
-    22 | blosum_matrix_viewer               | [TINY BIT IMPLEMENTED; ~5%]   |                           |
+    22 | blosum_matrix_viewer               | [TINY BIT IMPLEMENTED; ~5%]   |                           | [PARTIALLY IMPLEMENTED]
     23 | random_sequence                    | [NOT YET IMPLEMENTED]         |                           |
 
 </div>
@@ -9952,6 +9946,12 @@ second one is jruby+swing:
 
 <img src="https://i.imgur.com/5IUbDSt.png" style="margin: 1em">
 
+In December 2023 I decided to replace all old GUIs via the
+universal-widget projects. This project allows us to, eventually,
+make use of different GUI toolkits, as well as the world wide
+web, for GUIs. This is ongoing - right now only one GUI has been
+ported (three_to_one.rb), but expect more changes in 2024 here.
+
 ### libUI support
 
 Presently, since as of **August 2021**, support for libUI in the bioroebe
@@ -10279,12 +10279,13 @@ For instance, the last CDS ranges from 2931 to 3917.
 class <b>Bioroebe::Compacter</b> can be used to sanitize a text file that
 is supposedly a FASTA sequence, such as for a DNA sequence.
 
-In September 2023 this class was partially rewritten - the old code
-was not flexible enough and confusing to me. I also added more
-commandline options to this class, to allow the user more fine-tuned
-control.
+In <b>September 2023</b> this class was partially rewritten - the old
+code was not flexible enough and confusing to me, which is a bad sign
+considering I wrote it in the first place. I also added more commandline
+options to this class during the rewrite, to allow the user more
+fine-tuned control over its behaviour.
 
-Why has this class been created in the first place?
+<b>Why</b> has this class been created in the first place?
 
 If you download data from the internet, that data may not be what
 you want it to be. It may contain numbers, rather than just 
@@ -10301,6 +10302,217 @@ such as the following example shows:
 
     compacter SPRR4_protein.fasta --retain-newlines
 
+## Calculating the BLOSUM substitution score via class Bioroebe::CompareTheseTwoSequencesViaBlosum.new
+
+class Bioroebe::CompareTheseTwoSequencesViaBlosum.new is mostly an
+ad-hoc class; I wrote it quickly in 2023 to calculate the
+BLOSUM50 score.
+
+I then invoke it like this from the commandline:
+
+    comparethesetwosequencesviablosum GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD----LHAHK GSGYLVGDSLTFVDLL--VAQHTADLLAANAALLDEFPQFKAHQ
+
+This compares the two sequences:
+
+    GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD----LHAHK
+    GSGYLVGDSLTFVDLL--VAQHTADLLAANAALLDEFPQFKAHQ
+
+The score I obtained was 39.
+
+## Bioroebe::SimpleStringComparer
+
+class **SimpleStringComparer** (Bioroebe::SimpleStringComparer) can be
+used to compare two strings visually, similar as to how **NCBI BLAST**
+compares two sequences to one another.
+
+By default the output of that class will be, in colours, on the commandline,
+but you can disable this like so:
+
+    Bioroebe::SimpleStringComparer.new(ARGV) { :disable_colours }
+
+Let's look at another example:
+
+    Bioroebe::SimpleStringComparer.new('AAAAAAAAAAAAAATTTTTTTTTTTAAAAAAAAAAAATATA|GAAAAAAAAAAAAAAAATATTTTTTTTTTTTTTTTTTTTTT')
+
+This may look like so:
+
+<img src="https://i.imgur.com/kkqkpmQ.png" style="margin-left: 2em">
+
+Because different people may wish to use different colours,
+the class allows the user to change these colours via
+the commandline. Let's assume you did alias 
+simple_string_comparer to this class - then you can do the following:
+
+    simple_string_comparer 'AAAAAAAAAAAAAATTTTTTTTTTTAAAAAAAAAAAATATA|GAAAAAAAAAAAAAAAATATTTTTTTTTTTTTTTTTTTTTT' --colour-for-a-match=lightblue
+
+So you can modify the vertical bar and display it in a specific
+colour. See the following image how this may then look:
+
+<img src="https://i.imgur.com/ipaXUQT.png" style="margin: 1em">
+
+I may add more options here, to allow arbitrary styling, but
+I'll leave it at this for now - the future shows how useful
+this class may be.
+
+## Using Bioroebe.three_delimiter()
+
+The method <b>Bioroebe.three_delimiter()</b> can be used to
+split a String into a String where every third position has
+a trailing '|' token.
+
+So, for instance:
+
+    Bioroebe.three_delimiter 'ATGGGGATGTAGGTAAAA' # => "ATG|GGG|ATG|TAG|GTA|AAA"
+
+The primary reason why that was added as a toplevel method has been
+because it may be visually simpler to identify the individual codons
+via your eyes that way.
+
+The following image shows this output:
+
+<img src="https://i.imgur.com/aakm0Z9.png" style="margin: 1em">
+
+## Bioroebe.cat() - displaying the content of files
+
+If you need to display the content of files you can use the
+helper-method called <b>Bioroebe.cat()</b>. A /bin executable
+for this functionality exists as well, aptly
+called <b>bioroebe_cat</b>.
+
+## Bioroebe.extractseq
+
+Bioroebe.extractseq can be used to assemble a new sequence
+from an existing sequence. This functionality has been
+inspired by EMBOSS extractseq.
+
+Usage example:
+
+    Bioroebe.extractseq('AAAGGGTTT', '7-9','3-4') # => TTTAG
+
+So a new String is generated; 7-9 and 3-4 refer to the range,
+so first we take position 7, 8, and 9, then we add 3 and
+4, and finally return the new sequence.
+
+Note that one difference between EMBOSS extractseq and
+bioroebe extractseq is that no local file is generated
+in bioroebe; you may have to combine this by yourself
+if you desire this functionality.
+
+## Bioroebe.log_dir? - Logging and Log output
+
+Since as of <b>November 2023</b>, the bioroebe project uses a simplified approach
+when it comes to the log-directory. Before that there was also the
+Bioroebe.base_dir? in use, and I kept on forgetting what the difference
+was between these two - so the latter simply became an alias to 
+Bioroebe.log_dir? now.
+
+<b>Bioroebe.log_dir?</b> will determine where the directory resides into which
+you can put files and directories, and have the bioroebe-project
+recognize these files and directories too, in particular FASTA files.
+
+The **BioRoebe project** may autogenerate some files, including
+**log files**.
+
+In order to be able to do so, the bioroebe project needs the user
+to be able to access a **base directory**, the so-called
+**working base directory**. This is where bioroebe assumes
+most working files to exist.
+
+On my linux system this used to default to the directory
+called **/Depot/Bioroebe/**. On other systems, the log directory
+may default into the **user's home directory**, via a call to 
+<b>"#{File.expand_path('~')}/"</b>. (I use this presently,
+since **2020**.)
+
+This should work on most systems, but it may not be what you
+want to have or use in your own workflow. Thus, code exists 
+that allows you to designate another log directory to use.
+
+The API for this is simply called:
+
+    Bioroebe.set_log_dir()
+
+The method can be found in
+**lib/bioroebe/log_directory/log_directory.rb**. 
+
+If you want to do this from within the **bioshell** itself,
+try:
+
+    set_log_dir /tmp/test
+    setlogdir /tmp/test
+
+If you use the interactive bioroebe-shell then you can use
+**home?** to determine where the log directory is on your
+system. For example, I tend to just use **/root/Bioroebe/**
+these days, when I am the superuser.
+
+Note that you can also define the environment variable called
+<b>BIOROEBE_DEFAULT_LOG_DIRECTORY</b>. If this is set on startup
+of the bioroebe-shell, then it will overrule the initial :default
+value that is used otherwise.
+
+## Enzymes
+
+This subsection will be expanded at a later time - it will be
+about enzymes in general.
+
+For now, if you need a table, as memory, for the enzyme classes,
+here is one:
+
+| Enzyme class  (EC)  |     Name         |
+|-------------------- |------------------|
+|          1          | Oxidoreductases  |
+|          2          |  Transferases    |
+|          3          |   Hydrolases     |
+|          4          |    Lyases        |
+|          5          |   Isomerases     |
+|          6          |    Ligases       |
+|          7          |    Translocases  |
+
+See wikipedia for more information:
+
+https://en.wikipedia.org/wiki/Enzyme_Commission_number#Top_level_codes
+
+## UniProt and the data provided by UniProt
+
+UniProt is a freely accessible database of protein sequence and
+functional information. What makes it also useful for 
+bioinformatics is that you can easily query the FASTA sequence
+of a protein.
+
+Consider the protein called **A2Z669**. The **entry** to this protein
+can be found here:
+
+https://www.uniprot.org/uniprot/A2Z669
+
+And the corresponding FASTA sequence of that protein can be
+found here, if you append **.fasta** to the URL:
+
+https://www.uniprot.org/uniprot/A2Z669.fasta
+
+If you wish to save this file, from within **Bioroebe** itself,
+then you can use the following API:
+
+    Bioroebe.fetch_data_from_uniprot()
+    Bioroebe.fetch_data_from_uniprot('A2Z669')
+
+NCBI also has entries related to UniProt.
+
+Example:
+
+https://www.ncbi.nlm.nih.gov/protein/P02768
+https://www.ncbi.nlm.nih.gov/protein/P02768.2?report=fasta
+
+This has the header **RecName: Full=Serum albumin; Flags:
+PrecursorUniProtKB/Swiss-Prot: P02768.2**.
+
+From the bioroebe-shell, you can can fetch data from
+<b>Uniprot</b>, such as by issuing:
+
+    uniprot_fetch
+    uniprot # This alias works as well.
+    fetch_data_from_uniprot # As does this variant.
+
 ## Possibly useful links in regards to molecular biology and science in general
 
 On the www there are a myriad of links to various other external sites.