commit
4767bb4686
6 changed files with 765 additions and 0 deletions
-
2.gitignore
-
675LICENSE.md
-
21specification.md
-
1src/.gitignore
-
2src/Makefile
-
64src/testing.def.R
@ -0,0 +1,2 @@ |
|||
.DS_Store |
|||
/data |
@ -0,0 +1,675 @@ |
|||
### GNU GENERAL PUBLIC LICENSE |
|||
|
|||
Version 3, 29 June 2007 |
|||
|
|||
Copyright (C) 2007 Free Software Foundation, Inc. |
|||
<https://fsf.org/> |
|||
|
|||
Everyone is permitted to copy and distribute verbatim copies of this |
|||
license document, but changing it is not allowed. |
|||
|
|||
### Preamble |
|||
|
|||
The GNU General Public License is a free, copyleft license for |
|||
software and other kinds of works. |
|||
|
|||
The licenses for most software and other practical works are designed |
|||
to take away your freedom to share and change the works. By contrast, |
|||
the GNU General Public License is intended to guarantee your freedom |
|||
to share and change all versions of a program--to make sure it remains |
|||
free software for all its users. We, the Free Software Foundation, use |
|||
the GNU General Public License for most of our software; it applies |
|||
also to any other work released this way by its authors. You can apply |
|||
it to your programs, too. |
|||
|
|||
When we speak of free software, we are referring to freedom, not |
|||
price. Our General Public Licenses are designed to make sure that you |
|||
have the freedom to distribute copies of free software (and charge for |
|||
them if you wish), that you receive source code or can get it if you |
|||
want it, that you can change the software or use pieces of it in new |
|||
free programs, and that you know you can do these things. |
|||
|
|||
To protect your rights, we need to prevent others from denying you |
|||
these rights or asking you to surrender the rights. Therefore, you |
|||
have certain responsibilities if you distribute copies of the |
|||
software, or if you modify it: responsibilities to respect the freedom |
|||
of others. |
|||
|
|||
For example, if you distribute copies of such a program, whether |
|||
gratis or for a fee, you must pass on to the recipients the same |
|||
freedoms that you received. You must make sure that they, too, receive |
|||
or can get the source code. And you must show them these terms so they |
|||
know their rights. |
|||
|
|||
Developers that use the GNU GPL protect your rights with two steps: |
|||
(1) assert copyright on the software, and (2) offer you this License |
|||
giving you legal permission to copy, distribute and/or modify it. |
|||
|
|||
For the developers' and authors' protection, the GPL clearly explains |
|||
that there is no warranty for this free software. For both users' and |
|||
authors' sake, the GPL requires that modified versions be marked as |
|||
changed, so that their problems will not be attributed erroneously to |
|||
authors of previous versions. |
|||
|
|||
Some devices are designed to deny users access to install or run |
|||
modified versions of the software inside them, although the |
|||
manufacturer can do so. This is fundamentally incompatible with the |
|||
aim of protecting users' freedom to change the software. The |
|||
systematic pattern of such abuse occurs in the area of products for |
|||
individuals to use, which is precisely where it is most unacceptable. |
|||
Therefore, we have designed this version of the GPL to prohibit the |
|||
practice for those products. If such problems arise substantially in |
|||
other domains, we stand ready to extend this provision to those |
|||
domains in future versions of the GPL, as needed to protect the |
|||
freedom of users. |
|||
|
|||
Finally, every program is threatened constantly by software patents. |
|||
States should not allow patents to restrict development and use of |
|||
software on general-purpose computers, but in those that do, we wish |
|||
to avoid the special danger that patents applied to a free program |
|||
could make it effectively proprietary. To prevent this, the GPL |
|||
assures that patents cannot be used to render the program non-free. |
|||
|
|||
The precise terms and conditions for copying, distribution and |
|||
modification follow. |
|||
|
|||
### TERMS AND CONDITIONS |
|||
|
|||
#### 0. Definitions. |
|||
|
|||
"This License" refers to version 3 of the GNU General Public License. |
|||
|
|||
"Copyright" also means copyright-like laws that apply to other kinds |
|||
of works, such as semiconductor masks. |
|||
|
|||
"The Program" refers to any copyrightable work licensed under this |
|||
License. Each licensee is addressed as "you". "Licensees" and |
|||
"recipients" may be individuals or organizations. |
|||
|
|||
To "modify" a work means to copy from or adapt all or part of the work |
|||
in a fashion requiring copyright permission, other than the making of |
|||
an exact copy. The resulting work is called a "modified version" of |
|||
the earlier work or a work "based on" the earlier work. |
|||
|
|||
A "covered work" means either the unmodified Program or a work based |
|||
on the Program. |
|||
|
|||
To "propagate" a work means to do anything with it that, without |
|||
permission, would make you directly or secondarily liable for |
|||
infringement under applicable copyright law, except executing it on a |
|||
computer or modifying a private copy. Propagation includes copying, |
|||
distribution (with or without modification), making available to the |
|||
public, and in some countries other activities as well. |
|||
|
|||
To "convey" a work means any kind of propagation that enables other |
|||
parties to make or receive copies. Mere interaction with a user |
|||
through a computer network, with no transfer of a copy, is not |
|||
conveying. |
|||
|
|||
An interactive user interface displays "Appropriate Legal Notices" to |
|||
the extent that it includes a convenient and prominently visible |
|||
feature that (1) displays an appropriate copyright notice, and (2) |
|||
tells the user that there is no warranty for the work (except to the |
|||
extent that warranties are provided), that licensees may convey the |
|||
work under this License, and how to view a copy of this License. If |
|||
the interface presents a list of user commands or options, such as a |
|||
menu, a prominent item in the list meets this criterion. |
|||
|
|||
#### 1. Source Code. |
|||
|
|||
The "source code" for a work means the preferred form of the work for |
|||
making modifications to it. "Object code" means any non-source form of |
|||
a work. |
|||
|
|||
A "Standard Interface" means an interface that either is an official |
|||
standard defined by a recognized standards body, or, in the case of |
|||
interfaces specified for a particular programming language, one that |
|||
is widely used among developers working in that language. |
|||
|
|||
The "System Libraries" of an executable work include anything, other |
|||
than the work as a whole, that (a) is included in the normal form of |
|||
packaging a Major Component, but which is not part of that Major |
|||
Component, and (b) serves only to enable use of the work with that |
|||
Major Component, or to implement a Standard Interface for which an |
|||
implementation is available to the public in source code form. A |
|||
"Major Component", in this context, means a major essential component |
|||
(kernel, window system, and so on) of the specific operating system |
|||
(if any) on which the executable work runs, or a compiler used to |
|||
produce the work, or an object code interpreter used to run it. |
|||
|
|||
The "Corresponding Source" for a work in object code form means all |
|||
the source code needed to generate, install, and (for an executable |
|||
work) run the object code and to modify the work, including scripts to |
|||
control those activities. However, it does not include the work's |
|||
System Libraries, or general-purpose tools or generally available free |
|||
programs which are used unmodified in performing those activities but |
|||
which are not part of the work. For example, Corresponding Source |
|||
includes interface definition files associated with source files for |
|||
the work, and the source code for shared libraries and dynamically |
|||
linked subprograms that the work is specifically designed to require, |
|||
such as by intimate data communication or control flow between those |
|||
subprograms and other parts of the work. |
|||
|
|||
The Corresponding Source need not include anything that users can |
|||
regenerate automatically from other parts of the Corresponding Source. |
|||
|
|||
The Corresponding Source for a work in source code form is that same |
|||
work. |
|||
|
|||
#### 2. Basic Permissions. |
|||
|
|||
All rights granted under this License are granted for the term of |
|||
copyright on the Program, and are irrevocable provided the stated |
|||
conditions are met. This License explicitly affirms your unlimited |
|||
permission to run the unmodified Program. The output from running a |
|||
covered work is covered by this License only if the output, given its |
|||
content, constitutes a covered work. This License acknowledges your |
|||
rights of fair use or other equivalent, as provided by copyright law. |
|||
|
|||
You may make, run and propagate covered works that you do not convey, |
|||
without conditions so long as your license otherwise remains in force. |
|||
You may convey covered works to others for the sole purpose of having |
|||
them make modifications exclusively for you, or provide you with |
|||
facilities for running those works, provided that you comply with the |
|||
terms of this License in conveying all material for which you do not |
|||
control copyright. Those thus making or running the covered works for |
|||
you must do so exclusively on your behalf, under your direction and |
|||
control, on terms that prohibit them from making any copies of your |
|||
copyrighted material outside their relationship with you. |
|||
|
|||
Conveying under any other circumstances is permitted solely under the |
|||
conditions stated below. Sublicensing is not allowed; section 10 makes |
|||
it unnecessary. |
|||
|
|||
#### 3. Protecting Users' Legal Rights From Anti-Circumvention Law. |
|||
|
|||
No covered work shall be deemed part of an effective technological |
|||
measure under any applicable law fulfilling obligations under article |
|||
11 of the WIPO copyright treaty adopted on 20 December 1996, or |
|||
similar laws prohibiting or restricting circumvention of such |
|||
measures. |
|||
|
|||
When you convey a covered work, you waive any legal power to forbid |
|||
circumvention of technological measures to the extent such |
|||
circumvention is effected by exercising rights under this License with |
|||
respect to the covered work, and you disclaim any intention to limit |
|||
operation or modification of the work as a means of enforcing, against |
|||
the work's users, your or third parties' legal rights to forbid |
|||
circumvention of technological measures. |
|||
|
|||
#### 4. Conveying Verbatim Copies. |
|||
|
|||
You may convey verbatim copies of the Program's source code as you |
|||
receive it, in any medium, provided that you conspicuously and |
|||
appropriately publish on each copy an appropriate copyright notice; |
|||
keep intact all notices stating that this License and any |
|||
non-permissive terms added in accord with section 7 apply to the code; |
|||
keep intact all notices of the absence of any warranty; and give all |
|||
recipients a copy of this License along with the Program. |
|||
|
|||
You may charge any price or no price for each copy that you convey, |
|||
and you may offer support or warranty protection for a fee. |
|||
|
|||
#### 5. Conveying Modified Source Versions. |
|||
|
|||
You may convey a work based on the Program, or the modifications to |
|||
produce it from the Program, in the form of source code under the |
|||
terms of section 4, provided that you also meet all of these |
|||
conditions: |
|||
|
|||
- a) The work must carry prominent notices stating that you modified |
|||
it, and giving a relevant date. |
|||
- b) The work must carry prominent notices stating that it is |
|||
released under this License and any conditions added under |
|||
section 7. This requirement modifies the requirement in section 4 |
|||
to "keep intact all notices". |
|||
- c) You must license the entire work, as a whole, under this |
|||
License to anyone who comes into possession of a copy. This |
|||
License will therefore apply, along with any applicable section 7 |
|||
additional terms, to the whole of the work, and all its parts, |
|||
regardless of how they are packaged. This License gives no |
|||
permission to license the work in any other way, but it does not |
|||
invalidate such permission if you have separately received it. |
|||
- d) If the work has interactive user interfaces, each must display |
|||
Appropriate Legal Notices; however, if the Program has interactive |
|||
interfaces that do not display Appropriate Legal Notices, your |
|||
work need not make them do so. |
|||
|
|||
A compilation of a covered work with other separate and independent |
|||
works, which are not by their nature extensions of the covered work, |
|||
and which are not combined with it such as to form a larger program, |
|||
in or on a volume of a storage or distribution medium, is called an |
|||
"aggregate" if the compilation and its resulting copyright are not |
|||
used to limit the access or legal rights of the compilation's users |
|||
beyond what the individual works permit. Inclusion of a covered work |
|||
in an aggregate does not cause this License to apply to the other |
|||
parts of the aggregate. |
|||
|
|||
#### 6. Conveying Non-Source Forms. |
|||
|
|||
You may convey a covered work in object code form under the terms of |
|||
sections 4 and 5, provided that you also convey the machine-readable |
|||
Corresponding Source under the terms of this License, in one of these |
|||
ways: |
|||
|
|||
- a) Convey the object code in, or embodied in, a physical product |
|||
(including a physical distribution medium), accompanied by the |
|||
Corresponding Source fixed on a durable physical medium |
|||
customarily used for software interchange. |
|||
- b) Convey the object code in, or embodied in, a physical product |
|||
(including a physical distribution medium), accompanied by a |
|||
written offer, valid for at least three years and valid for as |
|||
long as you offer spare parts or customer support for that product |
|||
model, to give anyone who possesses the object code either (1) a |
|||
copy of the Corresponding Source for all the software in the |
|||
product that is covered by this License, on a durable physical |
|||
medium customarily used for software interchange, for a price no |
|||
more than your reasonable cost of physically performing this |
|||
conveying of source, or (2) access to copy the Corresponding |
|||
Source from a network server at no charge. |
|||
- c) Convey individual copies of the object code with a copy of the |
|||
written offer to provide the Corresponding Source. This |
|||
alternative is allowed only occasionally and noncommercially, and |
|||
only if you received the object code with such an offer, in accord |
|||
with subsection 6b. |
|||
- d) Convey the object code by offering access from a designated |
|||
place (gratis or for a charge), and offer equivalent access to the |
|||
Corresponding Source in the same way through the same place at no |
|||
further charge. You need not require recipients to copy the |
|||
Corresponding Source along with the object code. If the place to |
|||
copy the object code is a network server, the Corresponding Source |
|||
may be on a different server (operated by you or a third party) |
|||
that supports equivalent copying facilities, provided you maintain |
|||
clear directions next to the object code saying where to find the |
|||
Corresponding Source. Regardless of what server hosts the |
|||
Corresponding Source, you remain obligated to ensure that it is |
|||
available for as long as needed to satisfy these requirements. |
|||
- e) Convey the object code using peer-to-peer transmission, |
|||
provided you inform other peers where the object code and |
|||
Corresponding Source of the work are being offered to the general |
|||
public at no charge under subsection 6d. |
|||
|
|||
A separable portion of the object code, whose source code is excluded |
|||
from the Corresponding Source as a System Library, need not be |
|||
included in conveying the object code work. |
|||
|
|||
A "User Product" is either (1) a "consumer product", which means any |
|||
tangible personal property which is normally used for personal, |
|||
family, or household purposes, or (2) anything designed or sold for |
|||
incorporation into a dwelling. In determining whether a product is a |
|||
consumer product, doubtful cases shall be resolved in favor of |
|||
coverage. For a particular product received by a particular user, |
|||
"normally used" refers to a typical or common use of that class of |
|||
product, regardless of the status of the particular user or of the way |
|||
in which the particular user actually uses, or expects or is expected |
|||
to use, the product. A product is a consumer product regardless of |
|||
whether the product has substantial commercial, industrial or |
|||
non-consumer uses, unless such uses represent the only significant |
|||
mode of use of the product. |
|||
|
|||
"Installation Information" for a User Product means any methods, |
|||
procedures, authorization keys, or other information required to |
|||
install and execute modified versions of a covered work in that User |
|||
Product from a modified version of its Corresponding Source. The |
|||
information must suffice to ensure that the continued functioning of |
|||
the modified object code is in no case prevented or interfered with |
|||
solely because modification has been made. |
|||
|
|||
If you convey an object code work under this section in, or with, or |
|||
specifically for use in, a User Product, and the conveying occurs as |
|||
part of a transaction in which the right of possession and use of the |
|||
User Product is transferred to the recipient in perpetuity or for a |
|||
fixed term (regardless of how the transaction is characterized), the |
|||
Corresponding Source conveyed under this section must be accompanied |
|||
by the Installation Information. But this requirement does not apply |
|||
if neither you nor any third party retains the ability to install |
|||
modified object code on the User Product (for example, the work has |
|||
been installed in ROM). |
|||
|
|||
The requirement to provide Installation Information does not include a |
|||
requirement to continue to provide support service, warranty, or |
|||
updates for a work that has been modified or installed by the |
|||
recipient, or for the User Product in which it has been modified or |
|||
installed. Access to a network may be denied when the modification |
|||
itself materially and adversely affects the operation of the network |
|||
or violates the rules and protocols for communication across the |
|||
network. |
|||
|
|||
Corresponding Source conveyed, and Installation Information provided, |
|||
in accord with this section must be in a format that is publicly |
|||
documented (and with an implementation available to the public in |
|||
source code form), and must require no special password or key for |
|||
unpacking, reading or copying. |
|||
|
|||
#### 7. Additional Terms. |
|||
|
|||
"Additional permissions" are terms that supplement the terms of this |
|||
License by making exceptions from one or more of its conditions. |
|||
Additional permissions that are applicable to the entire Program shall |
|||
be treated as though they were included in this License, to the extent |
|||
that they are valid under applicable law. If additional permissions |
|||
apply only to part of the Program, that part may be used separately |
|||
under those permissions, but the entire Program remains governed by |
|||
this License without regard to the additional permissions. |
|||
|
|||
When you convey a copy of a covered work, you may at your option |
|||
remove any additional permissions from that copy, or from any part of |
|||
it. (Additional permissions may be written to require their own |
|||
removal in certain cases when you modify the work.) You may place |
|||
additional permissions on material, added by you to a covered work, |
|||
for which you have or can give appropriate copyright permission. |
|||
|
|||
Notwithstanding any other provision of this License, for material you |
|||
add to a covered work, you may (if authorized by the copyright holders |
|||
of that material) supplement the terms of this License with terms: |
|||
|
|||
- a) Disclaiming warranty or limiting liability differently from the |
|||
terms of sections 15 and 16 of this License; or |
|||
- b) Requiring preservation of specified reasonable legal notices or |
|||
author attributions in that material or in the Appropriate Legal |
|||
Notices displayed by works containing it; or |
|||
- c) Prohibiting misrepresentation of the origin of that material, |
|||
or requiring that modified versions of such material be marked in |
|||
reasonable ways as different from the original version; or |
|||
- d) Limiting the use for publicity purposes of names of licensors |
|||
or authors of the material; or |
|||
- e) Declining to grant rights under trademark law for use of some |
|||
trade names, trademarks, or service marks; or |
|||
- f) Requiring indemnification of licensors and authors of that |
|||
material by anyone who conveys the material (or modified versions |
|||
of it) with contractual assumptions of liability to the recipient, |
|||
for any liability that these contractual assumptions directly |
|||
impose on those licensors and authors. |
|||
|
|||
All other non-permissive additional terms are considered "further |
|||
restrictions" within the meaning of section 10. If the Program as you |
|||
received it, or any part of it, contains a notice stating that it is |
|||
governed by this License along with a term that is a further |
|||
restriction, you may remove that term. If a license document contains |
|||
a further restriction but permits relicensing or conveying under this |
|||
License, you may add to a covered work material governed by the terms |
|||
of that license document, provided that the further restriction does |
|||
not survive such relicensing or conveying. |
|||
|
|||
If you add terms to a covered work in accord with this section, you |
|||
must place, in the relevant source files, a statement of the |
|||
additional terms that apply to those files, or a notice indicating |
|||
where to find the applicable terms. |
|||
|
|||
Additional terms, permissive or non-permissive, may be stated in the |
|||
form of a separately written license, or stated as exceptions; the |
|||
above requirements apply either way. |
|||
|
|||
#### 8. Termination. |
|||
|
|||
You may not propagate or modify a covered work except as expressly |
|||
provided under this License. Any attempt otherwise to propagate or |
|||
modify it is void, and will automatically terminate your rights under |
|||
this License (including any patent licenses granted under the third |
|||
paragraph of section 11). |
|||
|
|||
However, if you cease all violation of this License, then your license |
|||
from a particular copyright holder is reinstated (a) provisionally, |
|||
unless and until the copyright holder explicitly and finally |
|||
terminates your license, and (b) permanently, if the copyright holder |
|||
fails to notify you of the violation by some reasonable means prior to |
|||
60 days after the cessation. |
|||
|
|||
Moreover, your license from a particular copyright holder is |
|||
reinstated permanently if the copyright holder notifies you of the |
|||
violation by some reasonable means, this is the first time you have |
|||
received notice of violation of this License (for any work) from that |
|||
copyright holder, and you cure the violation prior to 30 days after |
|||
your receipt of the notice. |
|||
|
|||
Termination of your rights under this section does not terminate the |
|||
licenses of parties who have received copies or rights from you under |
|||
this License. If your rights have been terminated and not permanently |
|||
reinstated, you do not qualify to receive new licenses for the same |
|||
material under section 10. |
|||
|
|||
#### 9. Acceptance Not Required for Having Copies. |
|||
|
|||
You are not required to accept this License in order to receive or run |
|||
a copy of the Program. Ancillary propagation of a covered work |
|||
occurring solely as a consequence of using peer-to-peer transmission |
|||
to receive a copy likewise does not require acceptance. However, |
|||
nothing other than this License grants you permission to propagate or |
|||
modify any covered work. These actions infringe copyright if you do |
|||
not accept this License. Therefore, by modifying or propagating a |
|||
covered work, you indicate your acceptance of this License to do so. |
|||
|
|||
#### 10. Automatic Licensing of Downstream Recipients. |
|||
|
|||
Each time you convey a covered work, the recipient automatically |
|||
receives a license from the original licensors, to run, modify and |
|||
propagate that work, subject to this License. You are not responsible |
|||
for enforcing compliance by third parties with this License. |
|||
|
|||
An "entity transaction" is a transaction transferring control of an |
|||
organization, or substantially all assets of one, or subdividing an |
|||
organization, or merging organizations. If propagation of a covered |
|||
work results from an entity transaction, each party to that |
|||
transaction who receives a copy of the work also receives whatever |
|||
licenses to the work the party's predecessor in interest had or could |
|||
give under the previous paragraph, plus a right to possession of the |
|||
Corresponding Source of the work from the predecessor in interest, if |
|||
the predecessor has it or can get it with reasonable efforts. |
|||
|
|||
You may not impose any further restrictions on the exercise of the |
|||
rights granted or affirmed under this License. For example, you may |
|||
not impose a license fee, royalty, or other charge for exercise of |
|||
rights granted under this License, and you may not initiate litigation |
|||
(including a cross-claim or counterclaim in a lawsuit) alleging that |
|||
any patent claim is infringed by making, using, selling, offering for |
|||
sale, or importing the Program or any portion of it. |
|||
|
|||
#### 11. Patents. |
|||
|
|||
A "contributor" is a copyright holder who authorizes use under this |
|||
License of the Program or a work on which the Program is based. The |
|||
work thus licensed is called the contributor's "contributor version". |
|||
|
|||
A contributor's "essential patent claims" are all patent claims owned |
|||
or controlled by the contributor, whether already acquired or |
|||
hereafter acquired, that would be infringed by some manner, permitted |
|||
by this License, of making, using, or selling its contributor version, |
|||
but do not include claims that would be infringed only as a |
|||
consequence of further modification of the contributor version. For |
|||
purposes of this definition, "control" includes the right to grant |
|||
patent sublicenses in a manner consistent with the requirements of |
|||
this License. |
|||
|
|||
Each contributor grants you a non-exclusive, worldwide, royalty-free |
|||
patent license under the contributor's essential patent claims, to |
|||
make, use, sell, offer for sale, import and otherwise run, modify and |
|||
propagate the contents of its contributor version. |
|||
|
|||
In the following three paragraphs, a "patent license" is any express |
|||
agreement or commitment, however denominated, not to enforce a patent |
|||
(such as an express permission to practice a patent or covenant not to |
|||
sue for patent infringement). To "grant" such a patent license to a |
|||
party means to make such an agreement or commitment not to enforce a |
|||
patent against the party. |
|||
|
|||
If you convey a covered work, knowingly relying on a patent license, |
|||
and the Corresponding Source of the work is not available for anyone |
|||
to copy, free of charge and under the terms of this License, through a |
|||
publicly available network server or other readily accessible means, |
|||
then you must either (1) cause the Corresponding Source to be so |
|||
available, or (2) arrange to deprive yourself of the benefit of the |
|||
patent license for this particular work, or (3) arrange, in a manner |
|||
consistent with the requirements of this License, to extend the patent |
|||
license to downstream recipients. "Knowingly relying" means you have |
|||
actual knowledge that, but for the patent license, your conveying the |
|||
covered work in a country, or your recipient's use of the covered work |
|||
in a country, would infringe one or more identifiable patents in that |
|||
country that you have reason to believe are valid. |
|||
|
|||
If, pursuant to or in connection with a single transaction or |
|||
arrangement, you convey, or propagate by procuring conveyance of, a |
|||
covered work, and grant a patent license to some of the parties |
|||
receiving the covered work authorizing them to use, propagate, modify |
|||
or convey a specific copy of the covered work, then the patent license |
|||
you grant is automatically extended to all recipients of the covered |
|||
work and works based on it. |
|||
|
|||
A patent license is "discriminatory" if it does not include within the |
|||
scope of its coverage, prohibits the exercise of, or is conditioned on |
|||
the non-exercise of one or more of the rights that are specifically |
|||
granted under this License. You may not convey a covered work if you |
|||
are a party to an arrangement with a third party that is in the |
|||
business of distributing software, under which you make payment to the |
|||
third party based on the extent of your activity of conveying the |
|||
work, and under which the third party grants, to any of the parties |
|||
who would receive the covered work from you, a discriminatory patent |
|||
license (a) in connection with copies of the covered work conveyed by |
|||
you (or copies made from those copies), or (b) primarily for and in |
|||
connection with specific products or compilations that contain the |
|||
covered work, unless you entered into that arrangement, or that patent |
|||
license was granted, prior to 28 March 2007. |
|||
|
|||
Nothing in this License shall be construed as excluding or limiting |
|||
any implied license or other defenses to infringement that may |
|||
otherwise be available to you under applicable patent law. |
|||
|
|||
#### 12. No Surrender of Others' Freedom. |
|||
|
|||
If conditions are imposed on you (whether by court order, agreement or |
|||
otherwise) that contradict the conditions of this License, they do not |
|||
excuse you from the conditions of this License. If you cannot convey a |
|||
covered work so as to satisfy simultaneously your obligations under |
|||
this License and any other pertinent obligations, then as a |
|||
consequence you may not convey it at all. For example, if you agree to |
|||
terms that obligate you to collect a royalty for further conveying |
|||
from those to whom you convey the Program, the only way you could |
|||
satisfy both those terms and this License would be to refrain entirely |
|||
from conveying the Program. |
|||
|
|||
#### 13. Use with the GNU Affero General Public License. |
|||
|
|||
Notwithstanding any other provision of this License, you have |
|||
permission to link or combine any covered work with a work licensed |
|||
under version 3 of the GNU Affero General Public License into a single |
|||
combined work, and to convey the resulting work. The terms of this |
|||
License will continue to apply to the part which is the covered work, |
|||
but the special requirements of the GNU Affero General Public License, |
|||
section 13, concerning interaction through a network will apply to the |
|||
combination as such. |
|||
|
|||
#### 14. Revised Versions of this License. |
|||
|
|||
The Free Software Foundation may publish revised and/or new versions |
|||
of the GNU General Public License from time to time. Such new versions |
|||
will be similar in spirit to the present version, but may differ in |
|||
detail to address new problems or concerns. |
|||
|
|||
Each version is given a distinguishing version number. If the Program |
|||
specifies that a certain numbered version of the GNU General Public |
|||
License "or any later version" applies to it, you have the option of |
|||
following the terms and conditions either of that numbered version or |
|||
of any later version published by the Free Software Foundation. If the |
|||
Program does not specify a version number of the GNU General Public |
|||
License, you may choose any version ever published by the Free |
|||
Software Foundation. |
|||
|
|||
If the Program specifies that a proxy can decide which future versions |
|||
of the GNU General Public License can be used, that proxy's public |
|||
statement of acceptance of a version permanently authorizes you to |
|||
choose that version for the Program. |
|||
|
|||
Later license versions may give you additional or different |
|||
permissions. However, no additional obligations are imposed on any |
|||
author or copyright holder as a result of your choosing to follow a |
|||
later version. |
|||
|
|||
#### 15. Disclaimer of Warranty. |
|||
|
|||
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY |
|||
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT |
|||
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT |
|||
WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT |
|||
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR |
|||
A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND |
|||
PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE |
|||
DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR |
|||
CORRECTION. |
|||
|
|||
#### 16. Limitation of Liability. |
|||
|
|||
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING |
|||
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR |
|||
CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, |
|||
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES |
|||
ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT |
|||
NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR |
|||
LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM |
|||
TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER |
|||
PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. |
|||
|
|||
#### 17. Interpretation of Sections 15 and 16. |
|||
|
|||
If the disclaimer of warranty and limitation of liability provided |
|||
above cannot be given local legal effect according to their terms, |
|||
reviewing courts shall apply local law that most closely approximates |
|||
an absolute waiver of all civil liability in connection with the |
|||
Program, unless a warranty or assumption of liability accompanies a |
|||
copy of the Program in return for a fee. |
|||
|
|||
END OF TERMS AND CONDITIONS |
|||
|
|||
### How to Apply These Terms to Your New Programs |
|||
|
|||
If you develop a new program, and you want it to be of the greatest |
|||
possible use to the public, the best way to achieve this is to make it |
|||
free software which everyone can redistribute and change under these |
|||
terms. |
|||
|
|||
To do so, attach the following notices to the program. It is safest to |
|||
attach them to the start of each source file to most effectively state |
|||
the exclusion of warranty; and each file should have at least the |
|||
"copyright" line and a pointer to where the full notice is found. |
|||
|
|||
<one line to give the program's name and a brief idea of what it does.> |
|||
Copyright (C) <year> <name of author> |
|||
|
|||
This program is free software: you can redistribute it and/or modify |
|||
it under the terms of the GNU General Public License as published by |
|||
the Free Software Foundation, either version 3 of the License, or |
|||
(at your option) any later version. |
|||
|
|||
This program is distributed in the hope that it will be useful, |
|||
but WITHOUT ANY WARRANTY; without even the implied warranty of |
|||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
|||
GNU General Public License for more details. |
|||
|
|||
You should have received a copy of the GNU General Public License |
|||
along with this program. If not, see <https://www.gnu.org/licenses/>. |
|||
|
|||
Also add information on how to contact you by electronic and paper |
|||
mail. |
|||
|
|||
If the program does terminal interaction, make it output a short |
|||
notice like this when it starts in an interactive mode: |
|||
|
|||
<program> Copyright (C) <year> <name of author> |
|||
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. |
|||
This is free software, and you are welcome to redistribute it |
|||
under certain conditions; type `show c' for details. |
|||
|
|||
The hypothetical commands \`show w' and \`show c' should show the |
|||
appropriate parts of the General Public License. Of course, your |
|||
program's commands might be different; for a GUI interface, you would |
|||
use an "about box". |
|||
|
|||
You should also get your employer (if you work as a programmer) or |
|||
school, if any, to sign a "copyright disclaimer" for the program, if |
|||
necessary. For more information on this, and how to apply and follow |
|||
the GNU GPL, see <https://www.gnu.org/licenses/>. |
|||
|
|||
The GNU General Public License does not permit incorporating your |
|||
program into proprietary programs. If your program is a subroutine |
|||
library, you may consider it more useful to permit linking proprietary |
|||
applications with the library. If this is what you want to do, use the |
|||
GNU Lesser General Public License instead of this License. But first, |
|||
please read <https://www.gnu.org/licenses/why-not-lgpl.html>. |
@ -0,0 +1,21 @@ |
|||
# Specifications for the script |
|||
|
|||
**Use the Nontarget** |
|||
|
|||
- Clusters should have large enough number of fragments (3+ maybe) |
|||
- nontarget has a pattern match function. |
|||
- Check for chlorinated compounds (has n+2, n+4, ...) |
|||
|
|||
- GPL License (good) |
|||
- Script to get output for all of the results |
|||
|
|||
- tabbed-deliminated text file |
|||
|
|||
- Which clusters contain chlorinated compounds, how many fragments, what other |
|||
isotopes. |
|||
|
|||
## format |
|||
|
|||
- Readable by R. |
|||
- Manipulatable by Tidyverse |
|||
- Include it in script? |
@ -0,0 +1 @@ |
|||
config.R |
@ -0,0 +1,2 @@ |
|||
testing.R: |
|||
cp ./testing.def.R ./testing.R |
@ -0,0 +1,64 @@ |
|||
library("nontarget") |
|||
library("purrr") |
|||
library("enviPat") |
|||
library("stringr") |
|||
|
|||
# Configurations ############################################################# |
|||
# file : decides which file to read in data from ############################# |
|||
file <- "~/Documents/dwalker/pattern/data/data.txt" |
|||
# separator: decides separator of file ####################################### |
|||
separator <- "," |
|||
|
|||
############################################################################## |
|||
# Read in the Table ########################################################## |
|||
table <- read.table(file, header=TRUE, sep=separator) |
|||
|
|||
# Organize the tables by number ############################################## |
|||
fragments <- max(table[,"Spectra_Number"]) |
|||
|
|||
|
|||
# The algorithm below guarantees linear complexity of looking up data points.# |
|||
|
|||
# minint is the lower bound of the interval. ################################# |
|||
# maxint is the upper bound of the interval that contains the fragment. ###### |
|||
# initialized memoizes as to whether or not each fragment number exists. ##### |
|||
minint <- unlist(map(1:fragments, function(x) 0)) |
|||
maxint <- unlist(map(1:fragments, function(x) 0)) |
|||
initialized <- unlist(map(1:fragments, function(x) FALSE)) |
|||
|
|||
|
|||
# Set all of the intervals ################################################### |
|||
for (i in seq(1, nrow(table))) { |
|||
fragment <- table[i, "Spectra_Number"] |
|||
if (! initialized[fragment]) { |
|||
minint[fragment] <- i |
|||
} |
|||
maxint[fragment] <- max(maxint[fragment], i) |
|||
initialized[fragment] <- TRUE |
|||
} |
|||
|
|||
getdata <- function(fragment, key) { |
|||
if (! initialized[fragment]) { |
|||
stop(str_interp("Fragment $[d]{fragment} does not exist in the data set", |
|||
list(fragment=fragment))) |
|||
} |
|||
return(table[minint[fragment]:maxint[fragment],key]) |
|||
} |
|||
|
|||
# Add all data frames as necessary for evaluation. ############################ |
|||
getdataframe <- function (fragment) { |
|||
mz <- getdata(fragment, "mz") |
|||
time <- getdata(fragment, "time") |
|||
Intensity <- getdata(fragment, "Intensity") |
|||
return(data.frame(mz=mz, time=time, Intensity=Intensity)) |
|||
} |
|||
|
|||
# Incomplete: cannot get pattern.search function to work per cluster. ######### |
|||
# Incomplete: Get the diagnostics for a cluster and turn them into a portable# |
|||
# format. (such as through tinyverse) ######################################## |
|||
|
|||
diagnostics <- function(fragment) { |
|||
points <- getdataframe(fragment) |
|||
} |
|||
|
|||
############################################################################## |
Write
Preview
Loading…
Cancel
Save
Reference in new issue