bioroebe 0.12.24 → 0.13.31

data/doc/blosum/blosum.md

@@ -0,0 +1,4 @@
+This file describes the references towards BLOSUM.
+
+There are different BLOSUM matrices out there and they can be found 
+in either blosum/ or the yaml/ subdirectory of the bioroebe project.

data/doc/compatibility/BIO_PHP.md

@@ -17,21 +17,23 @@ First, some more relevant links:
 
 Status of the rewrites:
 
-  Restriction digest of DNA                       |                           | http://www.biophp.org/minitools/restriction_digest/demo.php
-  Find Palindromic Sequences                      | [IMPLEMENTED FULLY]
-  Protein to DNA                                  | [IMPLEMENTED FULLY]
-  Sequence manipulation and data                  | [not implemented yet]
-  Melting Temperature (Tm) Calculator             | [not implemented yet]
-  PCR Amplification                               | [will not be implemented] | http://www.biophp.org/minitools/pcr_amplification/
-  Microsatellite Repeats Finder                   | [not implemented yet]
-  Alignment of DNA/Protein sequences              | http://www.biophp.org/functions/alignment_of_dna/
-  DNA to protein                                  | [not implemented yet]
-  Microarray analysis: adaptive quantification    | [not implemented yet]
-  Protein sequence information                    | [not implemented yet]
-  Reduced alphabets for proteins                  | [not implemented yet]
-  Chaos Game Representation                       | [not implemented yet]
-  GC-, AT-, KETO- and oligo-skews generator       | [not implemented yet]
-  Oligonucleotide Frequency                       | [not implemented yet]
-  Oligonucleotides for distance among sequences   | [not implemented yet]
-  Random DNA                                      | http://www.biophp.org/functions/random_dna/
-  Useful formulas                                 |
+  Name                                            |        Status              | Remote URL
+--------------------------------------------------|----------------------------|---------------------------------------
+  Restriction digest of DNA                       |                            | http://www.biophp.org/minitools/restriction_digest/demo.php
+  Find Palindromic Sequences                      |  [IMPLEMENTED FULLY]       |
+  Protein to DNA                                  |  [IMPLEMENTED FULLY]
+  Sequence manipulation and data                  |  [not implemented yet]
+  Melting Temperature (Tm) Calculator             |  [not implemented yet]
+  PCR Amplification                               |  [will not be implemented] | http://www.biophp.org/minitools/pcr_amplification/
+  Microsatellite Repeats Finder                   |  [not implemented yet]
+  Alignment of DNA/Protein sequences              |                            | http://www.biophp.org/functions/alignment_of_dna/
+  DNA to protein                                  |  [not implemented yet]
+  Microarray analysis: adaptive quantification    |  [not implemented yet]
+  Protein sequence information                    |  [not implemented yet]
+  Reduced alphabets for proteins                  |  [not implemented yet]
+  Chaos Game Representation                       |  [not implemented yet]
+  GC-, AT-, KETO- and oligo-skews generator       |  [not implemented yet]
+  Oligonucleotide Frequency                       |  [not implemented yet]
+  Oligonucleotides for distance among sequences   |  [not implemented yet]
+  Random DNA                                      |                            | http://www.biophp.org/functions/random_dna/
+  Useful formulas                                 |                            |

data/doc/compatibility/README.md

@@ -1,3 +1,2 @@
-This directory may contain documentation in regards to other
-software suites - in particular bio-php and the Emboss software
-suite.
+This directory may contain documentation in regards to other software
+suites - in particular bio-php and the Emboss software suite.

data/doc/compatibility/emboss.md

@@ -6,10 +6,12 @@ either via some webinterface or as its own standalone file.
 
 Overview:
 
+  name                 | Status                                                       | remote URL
+-------------------------------------------------------------------------------------------------
   aligncopy            |
   aligncopypair        |
   biosed               |
-  cgplot               | https://www.bioinformatics.nl/cgi-bin/emboss/cpgplot
+  cgplot               |                                                              | https://www.bioinformatics.nl/cgi-bin/emboss/cpgplot
   codcopy              |
   cutseq               | [90% IMPLEMENTED; missing output format possibilities]
   degapseq             |
@@ -17,8 +19,8 @@ Overview:
   entret               |
   extractalig          |
   extractfeat          |
-  extractseq           |
-  featcopy             |
+  extractseq           | implemented via Bioroebe.extractseq                          | https://www.bioinformatics.nl/cgi-bin/emboss/extractseq
+  featcopy             | 
   featmerge            |
   featreport           |
   feattext             |

data/doc/{extensive_usage_example.md → extensive_usage_example/extensive_usage_example.md}

@@ -1,7 +1,9 @@
 This file here attempts to note down what should be possible and doable 
-within the Bioroebe main sequence class.
+within the Bioroebe main sequence class. The reader of this file is
+assumed to be new, as far as the bioroebe gem is concerned.
 
-It is closely modelled towards this file here from the bioruby project:
+The .md file here is also closely modelled towards the following file,
+from the bioruby project:
 
     https://raw.githubusercontent.com/bioruby/bioruby/master/doc/Tutorial.rd
 

data/doc/{instructions_for_the_taxonomy_subproject.md → instructions_for_the_taxonomy_subproject/instructions_for_the_taxonomy_subproject.md}

@@ -11,7 +11,7 @@ the following URL:
 
 === INSTALLATION
 
-The taxonomy-related code is distributed with the bioroebe project,
+The taxonomy-related code is distributed within the bioroebe project,
 so if you install the latter then you will also have the Taxonomy
 submodule available.
 
@@ -20,20 +20,22 @@ The archetypical way to install bioroebe is through this way:
     gem install bioroebe
 
 Sometimes you may not have server-wide access or it may be unwanted
-to install it globally.
+to install the bioroebe-gem globally.
 
-In this case, you can install bioroebe into the home directory by
+In this case, you can install bioroebe into the home directory, by
 using the --user-install comandline switch.
 
-Example:
+Example for this:
 
     gem install --user-install bioroebe
 
-If you have a local .gem then you can also install this, e. g.
-via:
+If you have a local .gem then you can also install this, e. g. via:
 
     gem install --user-install ./*.gem
 
+In other words, to refer to the current working directory via
+the leading ./ part.
+
 The Taxonomy module itself can be used primarily for the following
 three main tasks:
 
@@ -45,7 +47,7 @@ three main tasks:
 
     ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
 
-  This URL is assigned to the constant called REMOTE_URL, in 
+  This URL is assigned to the constant called REMOTE_URL, in
   the file constants/constants.rb of the Taxonomy module.
 
   You can obtain the file path of this file inside the interactive
@@ -69,12 +71,13 @@ three main tasks:
   from localome/ as well.
 
   This is the dataset that derives from local datasets.
-  The directory that will fetch this dataset is derived from 
+
+  The directory that will fetch this dataset is derived from
   incoming/.
 
 (3)
 
-- Query data from the dataset interactively, via the file 
+- Query data from the dataset interactively, via the file
   interactive.rb, but also from the commandline directly.
 
   Note Bene: all commands that work from the file interactive.rb
@@ -92,14 +95,14 @@ Without further ado, let's start:
     'update ncbi' as instruction to use should suffice:
 
       update ncbi
-      update_ncbi # <-- This works as well, if you dislike the ' ' 
+      update_ncbi # <-- This works as well, if you dislike the ' '
 
     This instruction will attempt to download the Taxonomy database,
     extract the archive, generate the necessary .sql files and
     then connect to postgresql, so that it can then add this
     information into the postgresql database.
 
-    For this to work, a connection to the database should be 
+    For this to work, a connection to the database should be
     established prior to running this command.
 
     Note that the login information is stored in the file
@@ -127,10 +130,10 @@ Without further ado, let's start:
     see the constant DOWNLOAD_DIR. Simply set it to another directory
     if you wish to change the download location.
 
-    Also note that generating the .sql files and populating the 
+    Also note that generating the .sql files and populating the
     postgresql table from that information, may take about an
     hour. This could possibly be optimized by using COPY rather
-    than INSERT INTO statements, but it seemed better to not 
+    than INSERT INTO statements, but it seemed better to not
     spend too much time into researching how to optimize and
     instead see that more features are made possible in general.
 
@@ -142,7 +145,7 @@ Without further ado, let's start:
     This requires a working postgresql database at present as well.
 
     * Note that the above two commands can be combined by issuing
-     'update all' or 'update everything', but this will also 
+     'update all' or 'update everything', but this will also
      update (overwrite) the localome table, so 'update ncbi'
      is usually better. (If we want to build up the localome
      table anew anyway, we can safely use "update localome", which
@@ -163,7 +166,7 @@ Without further ado, let's start:
     Of course you can also use 'taxonomy' without having to use the
     interactive component, i.e. from the commandline directly.
 
-    Once inside the interactive shell, typing 'help' will give 
+    Once inside the interactive shell, typing 'help' will give
     some information about the subcommands available.
 
     Now let's look at a few specific examples:
@@ -190,7 +193,7 @@ Without further ado, let's start:
 
       update ncbi      # Update the NCBI database.
       update localomes # Update the database from localomes.
-      update lineage   # Update the lineage - this is only required after 
+      update lineage   # Update the lineage - this is only required after
                        # the NCBI database was downloaded (at the weekend).
 
       update all       # This will perform both updates, first ncbi,
@@ -244,7 +247,7 @@ Without further ado, let's start:
                                            # hominis in the names table.
       search_in_localomes Blastocystis hominis # As above, but we search
                                                # in localomes rather than
-                                               # in NCBI. "slocalomes" is a 
+                                               # in NCBI. "slocalomes" is a
                                                # shorter alias to this.
 
     To sort the localome table by modtime, we can do this:
@@ -283,7 +286,7 @@ Without further ado, let's start:
 
       nodes?
       names?
- 
+
     The above two commands will fetch 10 random entries from the
     two tables, which should aid a little bit in ensuring that the
     dataset is correct.
@@ -299,7 +302,7 @@ Without further ado, let's start:
     to find out the local path as well, we need to issue this command:
 
       eukarya path
-      prokarya path # There were no entries from prokarya at the time 
+      prokarya path # There were no entries from prokarya at the time
                     # of writing this file here though.
 
     If we wish to change the path of a localome entry, we must know
@@ -356,8 +359,8 @@ Without further ado, let's start:
 
       info foo.INFO
 
-    or by simply putting the full location of the .INFO file 
-    in the interactive shell.
+    or by simply putting the full location of the .INFO file in the
+    interactive shell.
 
     Note that the code that handles parsing of .INFO files will also
     attempt to locate a corresponding .fa entry. It will first check
@@ -365,15 +368,15 @@ Without further ado, let's start:
       /data/curated/sequences/aa/ or /data/curated/sequences/nt/
 
     To parse a fasta file, we can do this:
- 
+
       pfasta foo.fa
 
     or by simply putting the full location of the .fa file in the interactive
     shell. The argument to this should be the fasta file in question of course.
- 
+
     If you quickly wish to obtain the taxtree in a tree display-like
     fashion, try these two ways:
- 
+
       taxtree  77166
       taxtree 106583
 
@@ -407,8 +410,8 @@ Without further ado, let's start:
 
 In principle, all that can be done in the interactive shell, can also
 be done from the commandline alone. The main "binary" (it is just a
-text file of course, but resides in the bin/ subdirectory) to 
-invoke is the file 'taxonomy':
+text file of course, but resides in the bin/ subdirectory) to invoke
+is the file 'taxonomy':
 
     bin/taxonomy
     taxonomy
@@ -427,7 +430,7 @@ to the user at all:
 
 == Aliases
 
-In general, for most available actions in the main menu of the Taxonomy 
+In general, for most available actions in the main menu of the Taxonomy
 module, aliases exist. So the subsection "query", for instance, can be
 shortened to "qu". In case of ambiguity, we try to decide which component
 is more important from the point of view of the Taxonomy module, so there
@@ -463,12 +466,12 @@ to this file as well. This .gem file can be used and redistributed.
 (A .gem file is Ruby's way to distribute addons, similar to perl's
 CPAN.)
 
-Permission is explicitly granted to allow the I.M.P. team to
-modify all code parts that were produced specifically for the 
-Taxonomy module in any way they see fit - in other words, the full
-content of this .gem archive is licensed to the I.M.P, in particular
-to Alex Schleiffer. This should allow modifications to everything 
-that belongs to the Taxonomy module at any moment of time.
+Permission is explicitly granted to allow the I.M.P. team to modify all code
+parts that were produced specifically for the Taxonomy module in any way they
+see fit - in other words, the full content of this .gem archive is licensed to
+the I.M.P, in particular all members of the bioinformatics group there. This
+should allow modifications to everything that belongs to the Taxonomy module
+at any moment of time.
 
 The .gem file would allow installation by doing something like this:
 

data/doc/{legacy_paths.md → legacy_paths/legacy_paths.md}

@@ -1,6 +1,6 @@
-This small file here just is a reminder of the paths that were in
-use during February 2014 for the Taxonomy project when it was still
-a standalone project:
+This small file here just is a reminder of the paths that were in use 
+during February 2014 for the Taxonomy project when it was still a 
+standalone project:
 
   /biosw/debian5_x86_64/
   /biosw/debian5_x86_64/postgresql/8.4.16/bin

data/doc/statistics/statistics.md

@@ -23,19 +23,21 @@ https://bestgems.org/gems/bioroebe
   Rank: 5,811 of 163,391 as of 16.12.2020
   Rank: 6,314 of 167,416 as of 08.08.2021
   Rank: 6,651 of 169,613 as of 24.12.2021
+  Rank: 8,254 of 178,566 as of 01.11.2023
 
 -------------------------------------------------------------------------------
 
 Size of the bioroebe-gem itself (showing only a few snapshots):
 
-  0.0.79  -     July 19, 2015 (  86 KB)
-  0.0.414 -     July 17, 2016 ( 308 KB)
-  0.1.075 -  January 21, 2018 ( 413 KB)
-  0.3.0   -  January 18, 2018 ( 536 KB)
-  0.3.44  -    March 17, 2019 ( 578 KB)
-  0.3.77  -   August 17, 2019 ( 749 KB) # Includes a large .pdb file, though.
-  0.8.80  -   August 05, 2021 ( 949 KB)
-  0.9.75  - December 18, 2021 (1009 KB)
-  0.10.22 - December 24, 2021 (1.09 MB)
-  
+  0.0.79  -     July  19, 2015 (  86 KB)
+  0.0.414 -     July  17, 2016 ( 308 KB)
+  0.1.075 -  January  21, 2018 ( 413 KB)
+  0.3.0   -  January  18, 2018 ( 536 KB)
+  0.3.44  -    March  17, 2019 ( 578 KB)
+  0.3.77  -   August  17, 2019 ( 749 KB) # Includes a large .pdb file, though.
+  0.8.80  -   August  05, 2021 ( 949 KB)
+  0.9.75  - December  18, 2021 (1009 KB)
+  0.10.22 - December  24, 2021 (1.09 MB)
+  0.12.24 - September 12, 2023 (1.43 MB)
+
 -------------------------------------------------------------------------------

data/doc/todo/bioroebe_GUI_todo.md

@@ -2,7 +2,7 @@
 (1) → Improve the primer-design widget. It should be fully
       functional one day. See also this entry here:
       https://www.geneious.com/tutorials/primer-design-prime/
-      gtkprimerdesign
+      gtkprimerdesign; then jruby-swing primer widget.
 --------------------------------------------------------------------------------
 (2) → enable drag and drop support in the bioroebe gui
       The idea is that we can freely move FASTA sequences and .pdb files
@@ -18,3 +18,8 @@
       jruby rewriten.
       ^^^
 --------------------------------------------------------------------------------
+(4) → comparethesetwosequencesviablosum GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD----LHAHK GSGYLVGDSLTFVDLL--VAQHTADLLAANAALLDEFPQFKAHQ
+      ^^^ move this into jruby-gui
+      ^^^^^^^^^^^
+      ^^^^ we need a Compare-these-two-sequences-via-blosum widget.
+--------------------------------------------------------------------------------

data/doc/todo/bioroebe_java_todo.md

@@ -1,4 +1,4 @@
-/Depot/j/toaa ATGGCCGAGATTGTGCTGGAGCACGTCAACAAGAAT --frame1
+toaa ATGGCCGAGATTGTGCTGGAGCACGTCAACAAGAAT --frame1
 
 The frame-1 sequence is: (12 aminoacids)
 
@@ -18,5 +18,6 @@ The frame-3 sequence is: (11 aminoacids)
 
 
 ^^^^ add this in java AND add it to 
-     static native binary
+     static native binary. then describe this
+     too how to compile it