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SparkyJr.
Menu
{{ports[port].short || "Serial Ports"}}
{{port.short}}
{{baudrate || "Baudrate"}}
{{baudrate}}
connect
exit
Select Pattern
Select Color
set {{address}} {{long}}
Set
Let's get you connected
1
Plug in your SparkyJr.
(Serial Device)
2
Select a Serial Port
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Select a Baudrate
(factory install is 115200)


--- title: Direct Evidence Of Role Of Sleep In Memory Formation Is Uncovered layout: post ---
A Rutgers University, Newark and Collége de France, Paris research team has pinpointed for the first time the mechanism that takes place during sleep that causes learning and memory formation to occur.


I really enjoyed reading Jesse Storimer’s recent post, 4 Months of ebook Sales, about the sales of his book “Working with Unix Processes”. His feelings echo my own regarding my book, “Build Awesome Command-Line Applications in Ruby”:
I’m ecstatic with the results so far, but I have no idea how they compare.
Our books complement each other quite well, and came out around the same time. He wrote his largely on his own, going the self-publishing route, while I wrote mine with the Pragmatic Programmers. I thought I’d write a similar piece from my experience going the “traditional” route.
Beginning
I wrote an initial draft of “Build Awesome Command-Line Applications in Ruby” over November 2010, as part of PragProWriMo. I wrote almost every day, and had about 170 pages of Markdown written at the end. I hadn’t thought too far ahead, but in January of 2011, I decided to submit it to the Prags and see if they were interested.
To my surprise and excitement they decided to go forward with it! I had no idea what to expect, but figured that since I had a good 75% of a “real” book done, it shouldn’t be too much more work for me to finish up the first draft and clean it up. Boy was I wrong.
I spent the next 11 months on the book, reaching “done” by February of this year. That may seem like a long time (it certainly did to me). The reason it took “so long” was entirely due to working with a publisher and editor, but I don’t mean that as a negative. It actually needed to take that long, and the book I shipped was markedly better than anything I would’ve done on my own.
Developing
The Prags don’t just take your manuscript, spell-check it and ship it. They assign a development editor to each book. I had no idea what this was; I thought editors fixed spelling and grammar mistakes. Instead, John Osborn, my editor, provided deep and insightful feedback on every aspect of the book. Did the sections flow together? Are the titles consistent? Did the examples make sense? Of course, I had created plenty of passive voice, subject/verb disagreement and other “advanced grammar mishaps” to keep John quite busy.
Identifying these issues in your own work is hard. It’s also just not possible to get real, usable feedback on your work. Friends and colleagues just won’t give you the brutal, honest feedback you sometimes need. It had been a long time since I’ve been given this sort of feedback, and it hurt a bit (at first) to read comments like these:
- “The overall premise of the book is not immediately clear.”
- “The audience level remains unclear.”
- “After a while…it just gets wearing. Why should I bother to read yet one more example when I know that I’ll be told this was the wrong way to do it?”
These came after John and I had spent a lot of time working my initial manuscript into something publishable, and had gotten a lot of positive feedback from the tech reviewers. Based on the publisher feedback, we were looking at an almost total rewrite, and I wasn’t too happy about it. But, I really believed in the book and wasn’t about to quit now, so I trusted the publishers. Recognizing their experience, I treated this as a learning opportunity. So we persevered.
Persevering
Three chapters later, it was so clear to me that I had been wrong that I couldn’t believe I had felt otherwise. And, I never would’ve gotten there without such honest feedback and a literal team of professionals1 working to make my book as good as it could be. In the end, the book bears little resemblance to what I had produced during PragProWriMo, and, while I probably could’ve gotten that into a “sellable” shape, it would not have been nearly as good.
 Was it worth it? Absolutely. But, how has it been selling?
On the one hand, I’m not sure. I don’t know how many copies of my book will “pay for” the development costs, or how many will make the publishers “happy” with the result (I’ve put off asking in case the answer is “way more than you’ve sold”). I do know that I’ve sold more than I thought I would, and although I’d love to sell more, I’m really happy with how it’s done.
Performing
As of this post, I’ve sold around 3,000 copies from the Pragmatic Programmers online store2. I don’t yet know how many I’ve sold from other channels such as Amazon or Barnes & Noble – hopefully a lot – but sales from the Prags’ store alone feels like more than I was expecting.
Of course, I don’t make as much per book as Jesse does3; that team I mentioned doesn’t come free. But, being featured on the Pragmatic Programmers’ website is unbeatable promotion. This certainly drove a lot of sales. It’s my hope that sales are higher than they would’ve been had the Prags published a version of the book I had originally written, but there’s no way to know for sure.
Now, I don’t mean to imply Jesse’s book is poorly written; it’s not at all. Would it be better if it were edited professionally? I suppose that depends on what you mean? Would it be better written? Certainly; most writing improves with editing and revising. Would it have sold more? Would it have sold enough to cover the costs and time of editing? Again, there’s no way to know.
So where does this leave us? I know that working with John and the Prags has made me a better writer, but would I be confident enough to “go it alone”? Given my lack of notability, I feel I benefit greatly from having my work published and distributed by the Prags. Further, knowing my writing style and abilities as I do, my work will be much higher quality with a team of professionals in my corner.
That being said, I’d still love to try self-publishing at some point, but I’d really love to read a book by Jesse developed with the Pragmatic Programmers.
- In addition to John, Dave, and Andy, the Prags employ copy editors, sysadmins, indexers, and probably many others that I don’t even know about that turn my XML and code into a beautiful book to read on paper as well as every reading device there is. ↩
- The breakdown is about 10% paper/90% electronic, which seems about right. ↩
- It’s worth pointing out that the Prag’s contract is very generous compared to most other publishers. ↩


| sample_frac.sf |
Tidyverse methods for sf objects (remove .sf suffix!) |
| sample_n.sf |
Tidyverse methods for sf objects (remove .sf suffix!) |
| select.sf |
Tidyverse methods for sf objects (remove .sf suffix!) |
| semi_join.sf |
Tidyverse methods for sf objects (remove .sf suffix!) |
| separate.sf |
Tidyverse methods for sf objects (remove .sf suffix!) |
| separate_rows.sf |
Tidyverse methods for sf objects (remove .sf suffix!) |
| sf |
Create sf object |
| sf-defunct |
Deprecated functions in 'sf' |
| sf.colors |
plot sf object |
| sfc |
Create simple feature geometry list column |
| sf_extSoftVersion |
Provide the external dependencies versions of the libraries linked to sf |
| sf_project |
directly transform a set of coordinates |
| sf_proj_info |
Transform or convert coordinates of simple feature |
| sgbp |
Methods for dealing with sparse geometry binary predicate lists |
| slice.sf |
Tidyverse methods for sf objects (remove .sf suffix!) |
| spread.sf |
Tidyverse methods for sf objects (remove .sf suffix!) |
| st |
Create simple feature from a numeric vector, matrix or list |
| stars |
functions only exported to be used internally by stars |
| st_agr |
get or set relation_to_geometry attribute of an 'sf' object |
| st_agr<- |
get or set relation_to_geometry attribute of an 'sf' object |
| st_area |
Compute geometric measurements |
| st_as_binary |
Convert sfc object to an WKB object |
| st_as_binary.sfc |
Convert sfc object to an WKB object |
| st_as_binary.sfg |
Convert sfc object to an WKB object |
| st_as_grob |
Convert sf* object to a grob |
| st_as_sf |
Convert foreign object to an sf object |
| st_as_sf.data.frame |
Convert foreign object to an sf object |
| st_as_sf.lpp |
Convert foreign object to an sf object |
| st_as_sf.map |
Convert foreign object to an sf object |
| st_as_sf.ppp |
Convert foreign object to an sf object |
| st_as_sf.psp |
Convert foreign object to an sf object |
| st_as_sf.sf |
Convert foreign object to an sf object |
| st_as_sf.sfc |
Convert foreign object to an sf object |
| st_as_sf.Spatial |
Convert foreign object to an sf object |
| st_as_sfc |
Convert foreign geometry object to an sfc object |
| st_as_sfc.bbox |
Convert foreign geometry object to an sfc object |
| st_as_sfc.blob |
Convert foreign geometry object to an sfc object |
| st_as_sfc.character |
Convert foreign geometry object to an sfc object |
| st_as_sfc.factor |
Convert foreign geometry object to an sfc object |
| st_as_sfc.list |
Convert foreign geometry object to an sfc object |
| st_as_sfc.map |
Convert foreign geometry object to an sfc object |
| st_as_sfc.pq_geometry |
Convert foreign geometry object to an sfc object |
| st_as_sfc.raw |
Convert foreign geometry object to an sfc object |
| st_as_sfc.SpatialLines |
Convert foreign geometry object to an sfc object |
| st_as_sfc.SpatialMultiPoints |
Convert foreign geometry object to an sfc object |
| st_as_sfc.SpatialPixels |
Convert foreign geometry object to an sfc object |
| st_as_sfc.SpatialPoints |
Convert foreign geometry object to an sfc object |
| st_as_sfc.SpatialPolygons |
Convert foreign geometry object to an sfc object |
| st_as_sfc.WKB |
Convert foreign geometry object to an sfc object |
| st_as_text |
Return Well-known Text representation of simple feature geometry or coordinate reference system |
| st_as_text.crs |
Return Well-known Text representation of simple feature geometry or coordinate reference system |
| st_as_text.sfc |
Return Well-known Text representation of simple feature geometry or coordinate reference system |
| st_as_text.sfg |
Return Well-known Text representation of simple feature geometry or coordinate reference system |
| st_axis_order |
Retrieve coordinate reference system from object |
| st_bbox |
Return bounding of a simple feature or simple feature set |
| st_bbox.CIRCULARSTRING |
Return bounding of a simple feature or simple feature set |
| st_bbox.COMPOUNDCURVE |
Return bounding of a simple feature or simple feature set |
| st_bbox.CURVEPOLYGON |
Return bounding of a simple feature or simple feature set |
| st_bbox.Extent |
Return bounding of a simple feature or simple feature set |
| st_bbox.GEOMETRYCOLLECTION |
Return bounding of a simple feature or simple feature set |
| st_bbox.LINESTRING |
Return bounding of a simple feature or simple feature set |
| st_bbox.MULTICURVE |
Return bounding of a simple feature or simple feature set |
| st_bbox.MULTILINESTRING |
Return bounding of a simple feature or simple feature set |
| st_bbox.MULTIPOINT |
Return bounding of a simple feature or simple feature set |
| st_bbox.MULTIPOLYGON |
Return bounding of a simple feature or simple feature set |
| st_bbox.MULTISURFACE |
Return bounding of a simple feature or simple feature set |
| st_bbox.numeric |
Return bounding of a simple feature or simple feature set |
| st_bbox.POINT |
Return bounding of a simple feature or simple feature set |
| st_bbox.POLYGON |
Return bounding of a simple feature or simple feature set |
| st_bbox.POLYHEDRALSURFACE |
Return bounding of a simple feature or simple feature set |
| st_bbox.Raster |
Return bounding of a simple feature or simple feature set |
| st_bbox.sf |
Return bounding of a simple feature or simple feature set |
| st_bbox.sfc |
Return bounding of a simple feature or simple feature set |
| st_bbox.Spatial |
Return bounding of a simple feature or simple feature set |
| st_bbox.TIN |
Return bounding of a simple feature or simple feature set |
| st_bbox.TRIANGLE |
Return bounding of a simple feature or simple feature set |
| st_bind_cols |
Bind rows (features) of sf objects |
| st_boundary |
Geometric unary operations on simple feature geometry sets |
| st_buffer |
Geometric unary operations on simple feature geometry sets |
| st_cast |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.CIRCULARSTRING |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.COMPOUNDCURVE |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.CURVE |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.GEOMETRYCOLLECTION |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.LINESTRING |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.MULTICURVE |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.MULTILINESTRING |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.MULTIPOINT |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.MULTIPOLYGON |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.MULTISURFACE |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.POINT |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.POLYGON |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.sf |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.sfc |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast.sfc_CIRCULARSTRING |
Cast geometry to another type: either simplify, or cast explicitly |
| st_cast_sfc_default |
Coerce geometry to MULTI* geometry |
| st_centroid |
Geometric unary operations on simple feature geometry sets |
| st_collection_extract |
Given an object with geometries of type 'GEOMETRY' or 'GEOMETRYCOLLECTION', return an object consisting only of elements of the specified type. |
| st_collection_extract.sf |
Given an object with geometries of type 'GEOMETRY' or 'GEOMETRYCOLLECTION', return an object consisting only of elements of the specified type. |
| st_collection_extract.sfc |
Given an object with geometries of type 'GEOMETRY' or 'GEOMETRYCOLLECTION', return an object consisting only of elements of the specified type. |
| st_collection_extract.sfg |
Given an object with geometries of type 'GEOMETRY' or 'GEOMETRYCOLLECTION', return an object consisting only of elements of the specified type. |
| st_combine |
Combine or union feature geometries |
| st_contains |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_contains_properly |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_convex_hull |
Geometric unary operations on simple feature geometry sets |
| st_coordinates |
retrieve coordinates in matrix form |
| st_covered_by |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_covers |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_crop |
crop an sf object to a specific rectangle |
| st_crop.sf |
crop an sf object to a specific rectangle |
| st_crop.sfc |
crop an sf object to a specific rectangle |
| st_crosses |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_crs |
Retrieve coordinate reference system from object |
| st_crs.bbox |
Retrieve coordinate reference system from object |
| st_crs.character |
Retrieve coordinate reference system from object |
| st_crs.CRS |
Retrieve coordinate reference system from object |
| st_crs.crs |
Retrieve coordinate reference system from object |
| st_crs.numeric |
Retrieve coordinate reference system from object |
| st_crs.sf |
Retrieve coordinate reference system from object |
| st_crs.sfc |
Retrieve coordinate reference system from object |
| st_crs<- |
Retrieve coordinate reference system from object |
| st_crs<-.sf |
Retrieve coordinate reference system from object |
| st_crs<-.sfc |
Retrieve coordinate reference system from object |
| st_difference |
Geometric operations on pairs of simple feature geometry sets |
| st_difference.sfc |
Geometric operations on pairs of simple feature geometry sets |
| st_dimension |
Dimension, simplicity, validity or is_empty queries on simple feature geometries |
| st_disjoint |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_distance |
Compute geometric measurements |
| st_drivers |
Get GDAL drivers |
| st_drop_geometry |
Get, set, or replace geometry from an sf object |
| st_equals |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_equals_exact |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_filter |
spatial join, spatial filter |
| st_filter.sf |
spatial join, spatial filter |
| st_geometry |
Get, set, or replace geometry from an sf object |
| st_geometry.sf |
Get, set, or replace geometry from an sf object |
| st_geometry.sfc |
Get, set, or replace geometry from an sf object |
| st_geometry.sfg |
Get, set, or replace geometry from an sf object |
| st_geometry<- |
Get, set, or replace geometry from an sf object |
| st_geometrycollection |
Create simple feature from a numeric vector, matrix or list |
| st_geometry_type |
Return geometry type of an object |
| st_graticule |
Compute graticules and their parameters |
| st_interpolate_aw |
Areal-weighted interpolation of polygon data |
| st_intersection |
Geometric operations on pairs of simple feature geometry sets |
| st_intersection.sf |
Geometric operations on pairs of simple feature geometry sets |
| st_intersection.sfc |
Geometric operations on pairs of simple feature geometry sets |
| st_intersects |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_is |
test equality between the geometry type and a class or set of classes |
| st_is_empty |
Dimension, simplicity, validity or is_empty queries on simple feature geometries |
| st_is_longlat |
Assert whether simple feature coordinates are longlat degrees |
| st_is_simple |
Dimension, simplicity, validity or is_empty queries on simple feature geometries |
| st_is_valid |
Dimension, simplicity, validity or is_empty queries on simple feature geometries |
| st_is_within_distance |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_jitter |
jitter geometries |
| st_join |
spatial join, spatial filter |
| st_join.sf |
spatial join, spatial filter |
| st_layers |
List layers in a datasource |
| st_length |
Compute geometric measurements |
| st_linestring |
Create simple feature from a numeric vector, matrix or list |
| st_line_merge |
Geometric unary operations on simple feature geometry sets |
| st_line_sample |
Sample points on a linear geometry |
| st_make_grid |
Create a regular tesselation over the bounding box of an sf or sfc object |
| st_make_valid |
Make an invalid geometry valid |
| st_multilinestring |
Create simple feature from a numeric vector, matrix or list |
| st_multipoint |
Create simple feature from a numeric vector, matrix or list |
| st_multipolygon |
Create simple feature from a numeric vector, matrix or list |
| st_m_range |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.CIRCULARSTRING |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.COMPOUNDCURVE |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.CURVEPOLYGON |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.GEOMETRYCOLLECTION |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.LINESTRING |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.MULTICURVE |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.MULTILINESTRING |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.MULTIPOINT |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.MULTIPOLYGON |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.MULTISURFACE |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.numeric |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.POINT |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.POLYGON |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.POLYHEDRALSURFACE |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.sf |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.sfc |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.TIN |
Return 'm' range of a simple feature or simple feature set |
| st_m_range.TRIANGLE |
Return 'm' range of a simple feature or simple feature set |
| st_nearest_feature |
get index of nearest feature |
| st_nearest_points |
get nearest points between pairs of geometries |
| st_nearest_points.sf |
get nearest points between pairs of geometries |
| st_nearest_points.sfc |
get nearest points between pairs of geometries |
| st_nearest_points.sfg |
get nearest points between pairs of geometries |
| st_node |
Geometric unary operations on simple feature geometry sets |
| st_normalize |
Normalize simple features |
| st_overlaps |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_point |
Create simple feature from a numeric vector, matrix or list |
| st_point_on_surface |
Geometric unary operations on simple feature geometry sets |
| st_polygon |
Create simple feature from a numeric vector, matrix or list |
| st_polygonize |
Geometric unary operations on simple feature geometry sets |
| st_precision |
Get precision |
| st_precision<- |
Get precision |
| st_read |
Read simple features or layers from file or database |
| st_read.character |
Read simple features or layers from file or database |
| st_read.DBIObject |
Read simple features or layers from file or database |
| st_read_db |
Deprecated functions in 'sf' |
| st_read_db, |
Deprecated functions in 'sf' |
| st_relate |
Compute DE9-IM relation between pairs of geometries, or match it to a given pattern |
| st_reverse |
Geometric unary operations on simple feature geometry sets |
| st_sample |
sample points on or in (sets of) spatial features |
| st_sample.sf |
sample points on or in (sets of) spatial features |
| st_sample.sfc |
sample points on or in (sets of) spatial features |
| st_sample.sfg |
sample points on or in (sets of) spatial features |
| st_segmentize |
Geometric unary operations on simple feature geometry sets |
| st_set_agr |
get or set relation_to_geometry attribute of an 'sf' object |
| st_set_crs |
Retrieve coordinate reference system from object |
| st_set_geometry |
Get, set, or replace geometry from an sf object |
| st_set_precision |
Get precision |
| st_sf |
Create sf object |
| st_sfc |
Create simple feature geometry list column |
| st_shift_longitude |
Shift or re-center geographical coordinates for a Pacific view |
| st_shift_longitude.sf |
Shift or re-center geographical coordinates for a Pacific view |
| st_shift_longitude.sfc |
Shift or re-center geographical coordinates for a Pacific view |
| st_simplify |
Geometric unary operations on simple feature geometry sets |
| st_snap |
Geometric operations on pairs of simple feature geometry sets |
| st_sym_difference |
Geometric operations on pairs of simple feature geometry sets |
| st_touches |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_transform |
Transform or convert coordinates of simple feature |
| st_transform.sf |
Transform or convert coordinates of simple feature |
| st_transform.sfc |
Transform or convert coordinates of simple feature |
| st_transform.sfg |
Transform or convert coordinates of simple feature |
| st_triangulate |
Geometric unary operations on simple feature geometry sets |
| st_union |
Combine or union feature geometries |
| st_viewport |
Create viewport from sf, sfc or sfg object |
| st_voronoi |
Geometric unary operations on simple feature geometry sets |
| st_within |
Geometric binary predicates on pairs of simple feature geometry sets |
| st_wrap_dateline |
Transform or convert coordinates of simple feature |
| st_wrap_dateline.sf |
Transform or convert coordinates of simple feature |
| st_wrap_dateline.sfc |
Transform or convert coordinates of simple feature |
| st_wrap_dateline.sfg |
Transform or convert coordinates of simple feature |
| st_write |
Write simple features object to file or database |
| st_write.data.frame |
Write simple features object to file or database |
| st_write.sf |
Write simple features object to file or database |
| st_write.sfc |
Write simple features object to file or database |
| st_write_db |
Deprecated functions in 'sf' |
| st_zm |
Drop or add Z and/or M dimensions from feature geometries |
| st_z_range |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.CIRCULARSTRING |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.COMPOUNDCURVE |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.CURVEPOLYGON |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.GEOMETRYCOLLECTION |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.LINESTRING |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.MULTICURVE |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.MULTILINESTRING |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.MULTIPOINT |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.MULTIPOLYGON |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.MULTISURFACE |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.numeric |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.POINT |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.POLYGON |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.POLYHEDRALSURFACE |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.sf |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.sfc |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.TIN |
Return 'z' range of a simple feature or simple feature set |
| st_z_range.TRIANGLE |
Return 'z' range of a simple feature or simple feature set |
| summarise |
Tidyverse methods for sf objects (remove .sf suffix!) |
| summarise.sf |
Tidyverse methods for sf objects (remove .sf suffix!) |
| summary.sfc |
Summarize simple feature column |


#include <stdio.h>
int main()
{
/* Traditional Hello World program */
printf("Hello World");
return 0;
}
Computer executes simple instructions sequentially. Consider the assembly below:
MOV r0, #1 /* save 1 in register 0 */
MOV r1, #1 /* save 1 in register 1 */
ADD r0, r0, r1 /* add r0 and r1 and save it in r0 */
This is hardware dependent, and verbose for some more complex programs.
Comments are texts that are intended for human read only, and will be ignored by the compiler.
Single line comments starts with //
and continue to the end of the line.
/*
and ends with */
. Note that it is not required to be multi-line.// a comment using the entire line
printf("foo"); // a comment using only the end of a line
/* comment spanning
multiple lines */
printf(/*a comment in the middle of a line*/ "bar");
Data in programs have types, such as integer, floating point (represented using scientific notation), string (text) etc, with the following usages:
Memory layout. Data are stored in memory as bits and bytes, which on their own has no meaning. Type defines the interpretation of the memory.
For example 1000 0000
can represent 128 for integer, but it can also represent -128 for another type of integer (int8_t
).
Checking. Different types may be incompatible from each other, or the conversion may cause loss of information that requires programmer's attention.
Compiler performs type checking to make sure that the programmer uses the right type on the right place. For example, not putting a text into a math function.
Note: The memory layout for the same type in different architecture may be different. Search memory alignment and endianness for more details.
int8_t
is -128 to 127, when you add 1 to 127, it would overflow to -128. (assuming two's complement is used)int
long
short
, and unsigned
for unsigned integers. However, the standard only specified the minimum size of the integers, the actual size is implementation dependent. For fixed size integers which are mainly used in embedded development, use stdint.h
.float
for single-precision, double
for double-precision and long double
for even higher precision.char
.bool
.Integers and floating point numbers support basic arithmetic operations, including +
(addition), -
(subtraction), *
(multiplication), /
(division), %
(mod).
Integers and numbers support comparison which would return boolean, including ==
(equal), >
(larger than), <
(smaller than), >=
(larger than or equal to), <=
(larger than or equal to), !=
(not equal).
Integers also support bitwise operations, including &
(bitwise and), |
(bitwise or), ~
(bitwise not), ^
(bitwise xor), <<
(left shift), >>
(right shift).
Booleans support logical operations, including &&
(logical and), ||
(logical or), !
(logical not). Logical and and logical or would have a short-circuiting behavior, as the second operand (the right one) will not be evaluated if the result can be deduced from the first operand, thus may reduce processing time if used wisely.
Operators have different precedence, parenthesis (()
) can be used to change the precedence like in ordinary arithmetic.
5 * (1 + 1)
Inputs to the program are called parameters, and evaluated value of the function is called the return value. Format of function call is <name>(<param1>, <param2>, ...)
:
sin(1)
printf("1 + 1 = %d", 1 + 1)
exit()
Functions that can be defined entirely by its input and output mapping are called pure functions. Effects of the function apart from returning the return value are called side effects
. For example, printf
is not a pure function, and its side effect is printing to stdout of the terminal. Note that side effects may be desired feature of a function.
Expression would evaluate to a single value.
Statements are similar to instructions, are executed sequentially, together with expressions are building blocks of complicated programs.
Expressions become statements by appending a semicolon (;
) after them:
1 + 1;
sin(PI/4);
2 + 2 >= 4;
Statements can be combined into a compound statement (also called blocks) using a pair of braces ({}
):
{
1 + 1;
sin(PI/4);
2 + 2 >= 4;
}
Computer programs store data in variables.
Declaration of variable: angle brackets denote terms that should be replaced, square brackets denote optional component, note that this is not the complete format)
<type> <name> [= <value>];
Examples:
int a; // declare an integer called a with random value (not initialized)
bool b = true; // declare a boolean called b assigned with value true
Variables have scope, global (the entire program) if not declared inside any function, or local to the block of code it is in. Variable names should be unique within its scope, and only the code within the scope of the variable have access to the variable.
int globalVariableA; // global
void someFunction() {
int localVariable; // local to the function
{
int localVariable2; // local to this block only
}
// has no access to localVariable2 and knows nothing about it
}
Variables can be modified by assigning it with another value:
int a = 0; // originally a is 0
a = 5; // it is 5 now
but cannot do so if declared as constant:
const int a = 0;
a = 5; // this would not compile as it is not allowed
Variables not initialized should not be read, as the value is undefined (it can be anything).
int a;
printf("%d", a); // does not make sense, it can be anything
Variables declared in a block would shadow the variable outside with the same name.
int a = 0;
{
int a;
a = 5; // you are changing the variable a inside this block,
// instead of the one outside
printf("%d\n", a); // 5
}
printf("%d\n", a); // 0
Compound assignment operators: a += b
means a = a + b
. Similar operators: +=
, -=
, *=
, /=
, %=
, &=
, |=
, ^=
, <<=
, >>=
.
Increment and decrement: a++
evaluates to a
, and then add 1 to a
. ++a
add 1 to a
, and then evaluate to a
. The same goes to decrement --
operator.
int a = 0;
printf("%d\n", a++); // 0, a = 1 now
printf("%d\n", ++a); // 2, a = 2 now
We may want to execute statements conditionally, i.e. do something only when certain condition is met. We would use if
block to do so.
if (<condition boolean>)
<statement>
else if (<condition boolean>)
<statement>
...
else
<statement>
if (1 + 1 > 2)
printf("1 + 1 > 2");
else if (1 + 1 == 2)
printf("1 + 1 = 2");
else
printf("1 + 1 < 2");
Condition operator is an operator that would evaluate to 2 different values depending on the condition. <condition> ? <value when true> : <value when false>
.
(1 + 1 == 2)? 1 : 0 // 1
(1 + 1 > 2)? 1 : 0 // 0
Programs may do repetitive task via loops, which repeat certain statements.
while loop: check the condition, execute statement and repeat if condition is true.
while (<condition>)
<statement>
do-while loop: execute statement, check the condition and repeat if true.
do
<statement>
while (<condition>);
for-loop: syntactic sugar for while loop.
for (<initial>; <condition>; <action>)
<statement>
Run the initial statement once, check condition, run statement, action and repeat if condition is true. Example:
for (int i = 0; i < 10; i++)
printf("%d\n", i);
Function is a set of statements together to perform a task, may take parameters (input data, same as variables), and may evaluate to a value (called return value). For example, sin
function takes a double, computes the sine value and returns a double.
Function Declaration: tells the compiler the name, parameters and the return type of a function.
<type> <name>(<type> <parameter name>, ...);
double sin(double rad);
Function Definition: defines how the function run, basically the declaration with the function body. (statements to be run, with a return statement to return the evaluated value)
<type> <name>(<type> <parameter name>, ...)
{
<statements>
return <value>;
}
Functions can have no return value, the type of this kind of functions are void
.
void printSine(double rad)
{
printf("%lf", sin(rad));
}
Return statements would stop the execution of the function, yielding the control back to the caller.
int foo()
{
if (true)
return 1; // the function basically terminates here
printf("foobar"); // this will never be run (dead code)
}
Void functions can use return statement to yield the control back to the caller also.
void bar()
{
if (true)
return; // the function basically terminates here
printf("foobar"); // this will never be run
}
Different types have different representation in memory, so we may need to convert data to do operations between 2 data of different type.
1 + 1.0 // int + double, int will be converted into double
Type conversion take place during assignment to different variable of different type, or when operation involves two data of different types. Type with smaller range will be converted to the type with larger range. For example integers will be converted to float, but float will not be converted to integers normally.
When we want to force type conversion, we would use type casting. For example, converting from float to integer which may cause loss of information.
int a = (int)1.234;
Operators would return the same type as the operands. For example, integer division would give integer. So we may cast integer to float explicitly to get a float result:
double a = 1 / 2; // 0
double b = (double)1 / 2; // 0.5


The Internet
The Internet is a vast network that connects computers all over the world. Through the Internet, people can share information and communicate from anywhere with an Internet connection.
|
Browser Wars
The browser wars originally referred to a period of intense competition between Netscape and Microsoft over which web browser would come to dominate the market. Microsoft’s Internet Explorer (IE) ...
|
Dotcom Bubble
The dotcom bubble is a stock market bubble that was caused by speculation in dotcom or internet-based businesses from 1995 to 2000. The companies were largely those with a “.com” domain on their internet address.
|
TCP/IP
(Transmition Control Protocol/Internet Protocol)CP/IP is also used as a communications protocol in a private computer network.t also manages how a message is assembled into smaller packets before they are then transmitted over the internet.
|
WWW
Stands for "World Wide Web." It is important to know that this is not a synonym for the Internet. The World Wide Web, or just "the Web," as ordinary people call it, is a subset of the Internet. The Web consists of pages that can be accessed using a Web browser. |
IP Address
An IP address is a unique address that identifies a device on the internet or a local network. IP stands for "Internet Protocol," which is the set of rules governing the format of data sent via the internet or local network. |


Initializing...
| SOC: | |
| Device MAC: | |
| Wi-Fi Mode: | |
| Your IP: | |
| FlashMode: | |
| Configured Boot Partition: | |
| Actual Boot Partition: | |
| Idle Partition: | |
| Idle Partition Content: | |
| Bootloader: |
You'll need a firmware backup to restore this device's factory firmware after converting with esp2ino. It's often difficult to get firmware for IoT devices and, due to copyright concerns, third parties (like esp2ino) are reluctant to host these files for you.
⚠ esp2ino does not currently support restoring from backups! It may one day. You should keep this backup just in case.


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From:Jackson Karl To:Geaccone Tracy Sent:2017-01-11T04:37:57.0000000Z Subject:FW: 2002 Budget Timeline
Hi
Are we okay with the time line? John B. thinks that we are, but I wanted to confirm with you.
Karl
----- Forwarded by Karl Jackson/Houston/Eott on 08/27/01 03:08 PM -----
Rod Hayslett/ENRON@enronXgate 08/23/01 06:21 AM To: Tracy Geaccone/ENRON@enronXgate cc: Karl Jackson/Houston/Eott@Eott Subject: FW: 2002 Budget Timeline
We may have a problem here. Tracy, make sure Karl is aware of the change in the schedule here.
Please see the attached file for the timeline for the 2002 budget process. We have asked Barney Brasher to handle further distribution of the timeline to appropriate persons at ETS. Thanks
Karl Jackson
713-993-5402
***********
EDRM Enron Email Data Set has been produced in EML, PST and NSF format by ZL Technologies, Inc. This Data Set is licensed under a Creative Commons Attribution 3.0 United States License <http://creativecommons.org/licenses/by/3.0/us/> . To provide attribution, please cite to "ZL Technologies, Inc. (http://www.zlti.com)."
***********
California


Start wizard
Wizard in a modal
This is the first step
Path 1
Path 2
This is the path 1
This is the path 2
This is the last step


Savegame Editor for The legend of Zelda: BOTW
by
Marc Robledo
See on GitHub
Donate
|
Add item
|
Close file
Save changes
Stats
Rupees
Mons
Gerudo relic remaining uses
Goron relic remaining uses
Rito relic remaining uses
Motorcycle
Playtime
Max. hearts
1
2 hearts
3 hearts
4 hearts
5 hearts
6 hearts
7 hearts
8 hearts
9 hearts
10 hearts
11 hearts
12 hearts
13 hearts
14 hearts
15 hearts
16 hearts
17 hearts
18 hearts
19 hearts
20 hearts
21 hearts
22 hearts
23 hearts
24 hearts
25 hearts
26 hearts
27 hearts
28 hearts
29 hearts
30 hearts
Max. stamina
1 wheel
1 wheel+1/5
1 wheel+2/5
1 wheel+3/5
1 wheel+4/5
2 wheels
2 wheels+1/5
2 wheels+2/5
2 wheels+3/5
2 wheels+4/5
3 wheels
Coordinates
Current Link coordinates (XYZ)
Map
Weapons
Bows
Shields
Clothes
Materials
Food
Other
Horses
Edit horse 0
Edit horse 1
Edit horse 2
Edit horse 3
Edit horse 4
Edit untamed horse
Current horse coordinates (XYZ)
Completionism
Korok seeds
Get all
Add pins to Map
Defeated Hinox
Defeat all
Add pins to Map
Defeated Talus
Defeat all
Add pins to Map
Defeated Molduga
Defeat all
Add pins to Map
Hyrule Compendium
Set to stock
Visited locations
Visit all
Add pins to Map
Map Pins
Clear
Name
Saddles
Reins
Type
Change horse


You likely landed on this page because you're watching the dev keynote at World of Watson. This is far from prime production, so excuse the mess. Feel free to share feedback with me or just chat on Twitter @stefania_kaz
You likely landed on this page because you're watching the dev keynote at World of Watson. This is far from prime production, so excuse the mess. Feel free to share feedback with me or just chat on Twitter @stefania_kaz


A Little Girl Turns Into an Angry Kaiju in the Adorable First Trailer for Dino Girl Gauko
by James WhitbrookMove over, Retsuko – Netflix has another anime star in town with a bit of an anger problem. But Naoko doesn’t turn to heavy metal to channel her feelings. She turns to something else, rather literally!
Gizmodo's got an exclusive look at the first trailer for Dino Girl Gauko, a brand new short-form anime from Hitoshi Mogi. Set in a Japan filled with weird and wonderful monsters living alongside humans, Dino Girl Gauko follows tween poetry lover Naoko Watanabi. But Naoko has a bit of a secret – when she gets angry, she turns into a fire-breathing dinosaur!
It’s all very cute, but like Aggretsuko before it, there’s a relatablity to Naoko’s struggles with her emotions even as her transformative outbursts come across as funny. She might not have the stresses of office life like Retusko to contend with at her young age, but Naoko still has frustrations that are all too familiar to us all.
Well, except for the part where we don’t turn into dinos. Dino Girl Gauko’s 20-episode debut season – with each episode running roughly seven minutes – lands on Netflix November 22.
Image: Netflix


Australia
The Most Iconic Places to Visit Down Under
Created by Elyse Waterman
List of Unique Places to See
- Bondi Beach
A popular beach and the name of the surrounding suburb in Sydney, New South Wales, Australia. It is located 4 miles east of the Sydney central business district in the Eastern suburbs. Bondi, North Bondi, and Bondi Junction are neighboring suburbs. Bondi Beach is one of the most visited tourist sites in Australia, and it is worth the hype. This iconic stretch of fine sand and curling waves is one of the world’s most famous beach destinations. - Bondi Beach Icebergs
Located at the southern end of Bondi Beach, Bondi Icebergs Club is an international landmark, and no trip to Sydney is completely without a visit to our pool and clubhouse. Bondi Icebergs has been the home of winter swimming since 1929. The famous pool is open to visitors all year round. Located above the pool is a fully licensed clubhouse. It is open to both members and guests, and all visitors are welcome to enjoy sweeping views over the pool and Bondi beach as they drink or dine on the sunny balcony. - Great Ocean Road
See the towering 12 Apostles, get up close to native wildlife, and take in iconic surf breaks, pristine rainforest and misty waterfalls along the spectacular Great Ocean Road. Get outdoors on bushwalking, surfing and mountain biking expeditions or take the cultural route through galleries, museums and heritage attractions. Feast on spectacular views and local produce along the way. - Nimbin
Nimbin is a village in the Northern Rivers area of the Australian state of New South Wales. Nimbin is notable for the prominence of its environmental initiatives such as permaculture, sustainability, and self-sufficiency, as well as the cannabis counterculture. Writer Austin Pick described his initial impressions of the village this way: "It is as if a smoky avenue of Amsterdam has been placed in the middle of the mountains behind frontier-style building facades. ... Nimbin is a strange place indeed." - Combi Cafe
This hipster cafe is the epitome of chill, Australian vibes. Offering a wide variety of selections, from their famous array of raw organic superfood smoothies to their handmade crunchy granola - you’re bound to find something you love at this intimate little cafe.


Use ETCD as a Filesystem With ETCD-FS!
Gilt Principal Systems Engineer Jonathan Leibiusky is a fan of ETCD: CoreOS’s extremely powerful, highly-available key value store for shared configuration and service discovery, inspired by Apache ZooKeeper* and written in Go. Jon thought it would be great if ETCD could also be used as a filesystem. Companies that have already deployed apps that read a configuration file from a local filesystem might want to load these config files to something like ETCD and ensure a consistent view across a cluster of nodes. Given that the Filesystem API is super-stable, widely known and supported, and simple, using ETCD in this manner would make a lot of sense.
With this in mind, Jon has created ETCD-FS, which allows you to mount ETCD as a FUSE filesystem. In other words, every existing application can basically start using ETCD as regular files and directories without lots of effort. Implemented in Go, ETCD-FS uses Han-Wen Nienhuys’s go-fuse module and CoreOS’s go-etcd module and works like this:
- Every file maps to a key in ETCD
- Every directory maps to a directory in ETCD
- The content of every file maps to the value of the key in ETCD
How to Install ETCD-FS:
Clone the project and build it:
make build
This generates an executable file etcdfs
. You can mount ETCD as a filesystem by running etcdfs MOUNT_PATH ETCD_ENDPOINT
. For example:
./etcds /tmp/foobar http://localhost:4001
Then you can access /tmp/foobar
and use etcd as a filesystem.
To unmount it:
fusermount -u /tmp/foobar
What ETCD-FS Supports:
Basic filesystem operations, such as:
- Reading/Writing files
- Creating/Deleting files
- Creating/Deleting directories
What’s Next for ETCD-FS
Jon would like to enable users to mount a filesystem to a specific ETCD node (not necessarily or always the root). Less than a week old, ETCD-FS is a work in progress–but Jon creates quickly, so expect this project to become more and more exciting in short order!
* ETCD differs from ZooKeeper in that it’s based on the Raft Consensus Algorithm; ZooKeeper has its own consensus algorithm, called Zab.)


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Beans Injection
Spring Framework: Dependencies
Let’s revist the concept of dependency injection and explore a few approaches with Spring.
Accessing Beans with Dependency Injection
Once your Beans are registered with the ApplicationContext you need a way to retrieve them and this is done through Dependency Injection. Spring provides several ways to accomplish this but we tend to use one of these techniques: constructor, property, or directly from the ApplicationContext.
Important: Dependency Injection is completely Spring managed, that is you get Beans from other Beans. The whole concept is that you retrieve a Bean from the Spring ApplicationContext and it’s the containers job to construct and wire the dependencies into your Bean before giving it back to you. If you’re creating a component via the new operator then it is “unmanaged” and Spring is unaware of it so any Spring constructs defined in your class will not work at all.
1. Injection via Constructor
The best way to wire you dependencies together are by defining them in your constructor. The reason this is favored is because it’s very obvious what your dependencies are. Additionally it makes it easy to Unit Test your code because you have the ability to inject Mocks into the constructor.
Read: stackoverflow.com: Explain why constructor inject is better than other options
@Service
class UserService { /* some code */ }
/**
* Spring will create a UserController Bean for you and all the dependencies
* needed as well (i.e., userService)
*/
@RestController
class UserController(
/**
* Spring will automatically detect that a reference to another Bean
* called userService is required and inject it here for you.
*/
var userService: UserService
){
@RequestMapping("/user/{id}")
fun findUserById(@RequestParam id: Long) = userService.findById(id) // now you can use it in your class
}
Now to test the UserController you could easily Mock out the UserService.
import org.junit.Before
import org.junit.Test
import org.junit.runner.RunWith
import org.mockito.Mockito
import org.springframework.boot.test.context.SpringBootTest
import org.springframework.test.context.junit4.SpringRunner
@RunWith(SpringRunner::class)
@SpringBootTest
class UserControllerTest{
lateinit var userController
lateinit var userService
@Before fun setup() {
// easily inject a fake mock of the UserService
userService = Mockito.mock(UserService::class.java)
userController = UserController(userService)
}
@Test
fun `easy test because of constructor injection`(){
Mockito.`when`(userService.findById(Mockito.any(Long::class.java)))
.thenReturn(User(1, "Fake User"))
// continue with test
var fakeUser: User = userController.findUserById(1);
}
}
2. Injection via Property with @Autowired
The favored alternative to constructor injection is property level injection. This approach illustrates a lot more of the Spring magic because it’s using reflection to discover properties of your class that need to be provided by Spring. Surprising to many people it can even inject private properties into your class.
This approach is very convenient in our class but things change dramatically when you want to test it.
Read: vojtechruzicka.com: Dangers of Field Injection
@Service
class UserService { /* some code */ }
/*
* Spring will create a UserController Bean for you and all the dependencies
* needed as well (i.e., userService)
*/
@RestController
class UserController{
/*
* Spring will use reflection to detect that this property is a reference to
* another Bean called userService and inject it here for you directly after
* the UserController is initialized by Spring.
*/
@Autowired
lateinit var userService: UserService
@RequestMapping("/user/{id}")
fun findUserById(@RequestParam id: Long) = userService.findById(id) // now you can use it in your class
}
lateinit is a Kotlin construct and is confusing for those new using the language with Spring. This is required because Kotlin is very strict with null safety checking. There is a short period of time where the userService property will actually be null, refer back to the Spring Bean Lifecycle section to learn more. Spring will first create your Object and then use reflection immediately after to inject these properties, lateinit essentially tells Kotin to ignore the null safety checks for this reference.
Testing code written this way is much harder because you really don’t have a good clean way to override the value with a Mock. There are two general approaches to this - define another bean as the @Primary and override it in the ApplicationContext, or using Mockito and the @InjectMocks annotation.
Mocking @Autowired Properties with @Primary
The @Primary annotation allows you to define multiple beans of the same and give Spring a hint at deciding which one to choice by default if no @Qualifier is used.
This allows you to shadow a Bean in your application with a Mock. In order to do this you need to define a test configuration and load up another Bean of the exact same type and name.
/**
* Since we're declaring a new Configuration file just for testing we have to make
* the Spring test loader aware of it by refering to it in this annotation. Notice
* that you have also include your main class because once your declare the classes
* attribute it overides the location of all configuration files!
*/
@SpringBootTest(classes = [DemoApplication::class, MyTest.TestConfig::class])
@RunWith(SpringRunner::class)
class MyTest{
/**
* This is now needed to define another Bean of the same type and mark it
* as @Primary which essentially shadows the original one.
*/
class TestConfig {
@Bean
@Primary
fun userService() = Mockito.mock(UserService::class.java)
}
/**
* Now we have to rely on Spring to provide us references to test so we
* inject them here. This is a big step away from "unit" testing.
*/
@Autowired lateinit var userService: UserService
@Autowired lateinit var userController: UserController
@Test
fun `test with mock primary bean`(){
Mockito.`when`(userService.findById(Mockito.any(Long::class.java)))
.thenReturn(User(1, "Fake User"))
// continue with test
var fakeUser: User = userController.findUserById(1);
}
}
Mocking @Autowired Properties with Mockito @InjectMocks
Mockito can eliminate that nasty bit of TestConfig code using @Mock and @InjectMocks. The concept is same as with @Primary but instead of letting Spring inject the Beans into your test class you let Mockito do it.
- @Mock - Is just like Mockito.mock(..) but registers the Mock to be used with @InjectMocks
- @InjectMocks - Is just like @Autowired but Mockito will swap out any beans with their matching Mocks declared by @Mock
Although powerful this approach can be a little dangerous.
Read: baeldung.com: Getting Started with Mockito @Mock, @Spy, @Captor and @InjectMocks Read: stackoverflow.com: @Mock and @InjectMocks Read: tedvinke.wordpress.com: Why You Should Not Use InjectMocks Annotation to Autowire Fields
@RunWith(SpringRunner::class)
@SpringBootTest
class MyTest{
@Mock
lateinit var userService: UserService
@InjectMocks
lateinit var userController: UserController
@Test
fun `test`(){
Mockito.`when`(userService.findById(Mockito.any(Long::class.java)))
.thenReturn(User(1, "Fake User"))
// continue with test
var fakeUser: User = userController.findUserById(1);
}
}
3. Injection via ApplicationContext
This approach is typically used when you are dynamically interacting with Beans during runtime, in other words you’re unsure of which Bean you need so you need to look it up. For example if you’re processing requests and need a corresponding transformer for different types of requests you wouldn’t want to inject a reference to every type of transformer.
Let’s define a few types of tranformers:
interface BrowserTransformer{
fun transform(inbound: String): String
}
@Component class ChromeTransformer : BrowserTransformer {
override fun transform(inbound: String): String = "Chrome:".plus(inbound)
}
@Component class FirefoxTransformer : BrowserTransformer{
override fun transform(inbound: String): String = "Firefox:".plus(inbound)
}
@Component class IETransformer : BrowserTransformer{
override fun transform(inbound: String): String = "IE:".plus(inbound)
}
Now you can retrieve them directly through the ApplicationContext:
@SpringBootApplication
class DemoApplication(var appContext: AbstractApplicationContext) : ApplicationRunner{
override fun run(args: ApplicationArguments?) {
var xform = appContext.getBean("firefoxTransformer", BrowserTransformer::class.java)
println(xform.transform("Hello"))
}
}
@RestController
class EchoController(var appContext: AbstractApplicationContext) {
@RequestMapping("/echo")
fun echo(str: String){
var userAgent = getUserAgent()
// this will get the corresponding bean based on its name
var xform = appContext.getBean("${userAgent}Transformer", BrowserTransformer::class.java)
return xform.transform(str)
}
fun getUserAgent(): String {
// assume this code will return the String: "IE", "firefox", or "chrome"
}
}
Testing code written this way can only be done by shadowing the original bean with @Primary in a TestConfig.
4. Injection via ObjectFactory
Spring provides a class called ObjectFactory that can be used to dispense beans, this is perfect @scope(“prototype”) beans where you want a new instance each time. You simply inject a generic typed reference of ObjectFactory.
import org.springframework.beans.factory.ObjectFactory
/**
* Bean to represent a single XLS row, we want a new instance for each row.
*/
@Component
@Scope("prototype")
class XLSRow { /*code*/ }
/**
* Bean to iterate through each XLS row and process it.
*/
@Component
class XLSProcessor(
var xlsRowFactory : ObjectFactory<XLSRow>
) {
fun processXls(xlsFile: XLSFile){
for(Row r : xlsFile.getRows()){
// spring will dispense a new bean each time this is called.
var xlsrow = xlsRowFactory.getObject()
}
}
}
Read: stackoverflow.com: How to Produce prototype objects
Exercises
Try out this exercise to get a feel for the Application Context and declaring Beans.


Nick Vandenberge
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Programming Languages:
- [Advanced] Python, C, C++
- [Intermediate] Java
Tech Domains:
- [Intermediate] BackendWeb, DevOps, ML/DL
Libraries & Frameworks:
- [Advanced] Sanic, Flask, Django, Clang(LLVM)
- [Intermediate] scikit-learn, TF, Caffe
About Server, DB & Envs:
- [Advanced] AWS, Docker, Linux, DynamoDB
- [Intermediate] PostgreSQL, MySQL
IDEs & VCS, Dev Tools:
- [Advanced] Pycharm, Vim
- [Intermediate] Github, Jupyter
Development Methodologies:
- [Intermediate] Agile with TDD


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KNP rejoices after good rainfall
Heavy rains in the Kruger National Park have brought solace to animals dying from the severe drought that plagued the park for the past few months.
by Landé WillemseTourists posted numerous photos of the rainfall on social media.
ALSO READ: Drought in KNP devastating for animals
According to myweather.com the long range weather outlook for Kruger National Park is as follows: (this includes a 14 day forecast summary)
Taking a look at Kruger National Park over the coming two weeks and the average daytime maximum temperature will be around 33°C, with a high for the two weeks of 39°C expected on the afternoon of Friday 29th.
The mean minimum temperature will be 23°C, dipping to its lowest on the morning of Tuesday 26th at 19°C. The next 14 days will have some days seeing a little precipitation and some days with rain.
The indicators are that Thursday 21st will have the most precipitation with an accumulation of around 9.0mm. On the whole winds are likely to be light.


| > The Unit Test Framework > User's guide > Test organization > Test suite > |
If you consider test cases as leaves on the test tree, the test suite can be considered as branch and the master
test suite as a trunk. Unlike real trees though, our tree in many cases consists only of leaves attached
directly to the trunk. This is common for all test cases to reside directly in the master test suite. If you do
want to construct a hierarchical test suite structure the UTF provides both manual and automated
test suite creation and registration facilities:
如果将测试用例当作测试树的叶，那么测试套件就是树枝，主测试套件就是树干。
但是和真实的树不同，我们的树在很多情况下只包含树叶，直接连在树干上。
所有的测试用例直接属于主测试套件是很平常的。
如果你确实想要构造层次化的测试套件结构，UTF 同时提供了手动和自动创建注册测试套件的工具：
The UTF models the notion of test case container - test suite - using class boost::unit_test::test_suite. For
complete class interface reference check advanced section of this documentation. Here you should only be
interested in a single test unit registration interface:
UTF 将测试用例容器的概念建模为 - 测试套件 - 使用 boost::unit_test::test_suite 类。
完整的类接口参考请参见文档的高级部分。
这里你只需要关注单个测试单元注册接口：
void test_suite::add( test_unit* tc, counter_t expected_failures = 0, int timeout = 0 );
The first parameter is a pointer to a newly created test unit. The second optional parameter -
expected_failures - defines the number of test assertions that are expected to fail within the test unit. By
default no errors are expected.
第一个参数是指向新创建的测试单元的指针。第二个可选的参数 - expected_failures
- 定义了在测试单元中期望失败的测试断言数量。默认不期望碰到错误。
| Caution | |
|---|---|
Be careful when supplying a number of expected failures for test suites. By default the UTF calculates the
number of expected failures in test suite as the sum of appropriate values in all test units that constitute
it. And it rarely makes sense to change this.
|
The third optional parameter - timeout - defines the timeout value for the test unit. As of now the UTF
isn't able to set a timeout for the test suite execution, so this parameter makes sense only for test case
registration. By default no timeout is set. See the method
boost::execution_monitor::execute
for more details about the timeout value.
第三个可选参数 - timeout - 定义了测试单元的超时时间。
现在 UTF 还不支持设置测试套件的执行超时，所以这个参数只在注册测试用例时有意义。
默认不设置超时时间。
关于超时时间更多的细节请参见方法 boost::execution_monitor::execute
。
To register group of test units in one function call the boost::unit_test::test_suite provides another add
interface covered in the advanced section of this documentation.
要在一个函数中注册一组测试单元，调用 boosot::unit_test::test_suite 提供的另外一个添加接口，在文档高级部分有介绍。


This is what we sought to discover a couple of years back. That was when we founded DevStaff, a developer community here in Heraklion, Crete. We were just preparing for our first ever meet up and we needed to come up with some way for getting people involved in the community.
Collecting emails on a piece of paper just wasn’t good enough. Remember — this is a community for developers! Clearly, we needed some better way!
And that was when we thought of GitHub. I don’t remember if I was the one who proposed it, but, even if I was, it was certainly not my own idea. I had already heard of it on some podcast somewhere and — even though I can’t remember the rest of the podcast — the GitHub idea stuck!
What better tool than GitHub, to bring a bunch of devs closer together?
Hesitations? Yes, plenty! Not everybody knows how to use it. Not everybody would already have an account on GitHub. It would make it more awkward for non-devs to participate that way. This wasn’t what GitHub was built for.
BUT.
The arguments for it were so much more overwhelming!
- If you’re a developer in 2015 (back then) who hasn’t used Git, we should really find any excuse available to help you try.
- If we’re focusing on developers, whose job essence really is learning, we shouldn’t be afraid of asking them to learn one more new tool.
- Learning how to use GitHub, the #1 place for open source projects, would make it easier for our community to start contributing more to open source! Because, OSS FTW!
- We’re picking a tool already built for developers.
- We wanted to build an open community. Choosing a tool that has served open source software so well sounded like a natural choice.
- Instead of using GitHub to build software, we’re using it to build our community. That invites us to think about our community like software. Regardless of how well this analogy works, it’s an interesting twist, you have to admit, that we thought might even invite skeptics to give it a try.
- Come on, isn’t it cool?!? Isn’t this the reason you’re reading this article anyway? :D
Long story short, we were ready to give it a try!
But this was all back then… We’re now a couple of years down the line, so it’s time for a look back…
But before we dive in, a necessary disclaimer: the below is nothing more but a personal opinion, in no way written to represent the views of the community as a whole. Hopefully, this will also spark some discussion within the community itself. ; )
Let’s now go through the jobs we hired it to do and see how well it fit our purpose.
Job #1: Introduction to the Community
We needed some way to explain what our community is about and why people should join.
Typically, in an open source project, this is handled in a README
file and that’s what we
started using as well.
In retrospect, I feel it has served us well for people who are already familiar with GitHub and know what to expect. For everybody else, we also built a website , a Facebook page and we also leveraged the meetup.com group page.
Pros: Intuitive place to look (if you know what you’re looking for). No need to have multiple websites. Simple to maintain. Free (as in beer).
Cons: We could do with better onboarding experience and a more “attractive” look and feel, aimed at new members.
Verdict: B
Job #2: Documentation
In an open source software project, after the “Quickstart guide”, you need a reference documentation: How the thing works, what the rules are, why it’s built that way, and so on.
Much of the same holds for our community. We wanted people to know — first and foremost —
what the rules are.
Being an open community, we wanted to provide clear guidelines on
how people can contribute
(the standard CONTRIBUTING
file was a natural fit). We wanted them to know why certain
“design” decisions were made along the way — like our sponsorship policy.
Pros: Version control. Open to pull requests, in case people disagree! Living document — evolves as the community grows.
Cons: Not much comes in mind here.
Verdict: A+
Job #3: Contributions
Let’s be clear. This was the big & most important one. Giving people a way to start discussions, to actively participate in the community, to share thoughts and views and provide feedback. We knew GitHub was great for that in the virtual, online world; we didn’t know yet how well it would do for a community in the physical “real” world.
DevStaff community members can contribute by (among others):
- helping us choose upcoming meetup topics,
- helping us prepare and run successful meetups,
- helping us run the community itself.
Choosing Topics
As a generic developers community, most of our meetups have been about very different topics. We are not a focused user group, nor do we all share the same love for specific technologies / stacks, as it happens with many meetup groups in most bigger cities.
Coming from a small town (~200K population), with no active communities (to the best of my knowledge, back in 2015), our goal was to establish a broad community that would serve as the networking infrastructure for all these smaller / more focused communities to spring up.
As such, our meet ups could be about anything software-related. The specifics we left up to the community. We chose GitHub issues as a way to let people propose their own topics , so that others could upvote them. The most popular topic would get selected for the upcoming meetup.
The way we would count upvotes is by using comments with 👍
. We even built a tool that
helped us count the most popular topics, which, btw, is
open source. Later on, GitHub allowed emoji
reactions, so we adapted to that and the aforementioned tool now supports that too.
(If you’re thinking of using GitHub issues for anything similar to what we did, I’d recommend you check it out. — disclaimer: I did NOT build that, so I’m not blowing my own horn here — It just made things so much simpler for us!)
The only problem here was that not all proposed topics had available speakers; but that’s not really related to GitHub. You see, people could still propose a topic even if they couldn’t or didn’t want to present.
Yet several of these topics became very popular, leaving the org team to have to get creative about finding speakers to satisfy the need. Clearly, this was not sustainable over the long term, so we quickly iterated and redefined our criteria such that the topics “with the most votes and at least 2 speakers” could be selected for upcoming meetups.
(Again, we added relevant features to our vote counting tool.)
Preparing and Running the Meet Ups
Apart from creating a separate GitHub repo for each meetup, so that presenters could upload their presentations and some sample code, etc. GitHub wasn’t much help here.
We handled most of the preparations through direct IM chats (see below, under Communication).
Running the Community Itself
I was hoping people would use GitHub issues to also raise concerns about how the community itself is ran, so that we could openly discuss and adapt to suggestions from the community. I was expecting this would be touching things like our CoC, discussion on meetup times, places, etc.
This didn’t work as well as I was hoping…
Most feedback ended up coming in, in person, at the Org Team meetups.
Overall
Even though some things didn’t go as well as I was hoping for, looking back, I can’t help but admit that it still went much better than I would have originally guessed.
Verdict: A
Job #4: Communication
Looking back, I can see 2 main forms of communication that takes place online, within the community: announcements and p2p conversations (i.e. broadcasts and unicasts). Group discussions are more limited.
For announcements, GitHub kind of worked. Take new issues for example, or new pull requests (which we used, for example to handle announcement of new job opportunities on our job board). It all worked fine, as long as people were watching the GitHub repo.
And not everyone was. Or even knew they had to do that… : (
For p2p communication, there is a complete disconnect. GitHub just fails flat out to enable that kind of interaction. Publishing a comment with an @-mention of somebody’s name, is not exactly p2p.
(Btw, I see a huge gap here. I expect GitHub to acquire some player in this space soon (the same way GitLab acquired Mattermost). )
Verdict - C: Find some other way to enable your group’s communication.
Job #5: Shared Space
One final thing I saw our community had a need for was sharing copies of digital content. Whether that was copies of presentations, or document templates, or sample code, this all fell naturally within GitHub’s reach.
Verdict — A: No major issues here. Even though you may need to provide some help / guidance to people on how to open PRs, etc.
With that I will bring this looong reflection to an end. For now, at least… I hope you found some of this useful. : )
If (you’re still reading this and) you found any good takeaways here, please feel free to drop me a line. I’d love to hear your views, suggestions and similar experiences on running a community!


- MainMenuView - Class in com.mygdx.elmaze.view.menus
-
Represents the Main Menu View
- MainMenuView(ELMaze) - Constructor for class com.mygdx.elmaze.view.menus.MainMenuView
-
Creates the Main menu
- makeButton(Texture, Texture, float, float, int, int) - Static method in class com.mygdx.elmaze.view.menus.ButtonFactory
-
Creates a Button object
- makeImage(String, float, float, int, int) - Static method in class com.mygdx.elmaze.view.menus.ImageFactory
-
Creates an Image
- makeImage(String, float, float, int) - Static method in class com.mygdx.elmaze.view.menus.ImageFactory
-
Creates an Image
- makeMenu(ELMaze, MenuView.TYPE) - Static method in class com.mygdx.elmaze.view.menus.MenuFactory
-
Creates a menu view and stores them in the menu cache for future uses
- makeView(ELMaze, EntityModel) - Static method in class com.mygdx.elmaze.view.entities.ViewFactory
-
Creates an object view and stores them in the view cache for future uses
- MenuFactory - Class in com.mygdx.elmaze.view.menus
-
Implements functions related to the creation of Menus
- MenuFactory() - Constructor for class com.mygdx.elmaze.view.menus.MenuFactory
-
- MenuView - Class in com.mygdx.elmaze.view.menus
-
Represents a menu view
- MenuView(ELMaze, MenuView.TYPE) - Constructor for class com.mygdx.elmaze.view.menus.MenuView
-
Creates the menu
- MenuView.TYPE - Enum in com.mygdx.elmaze.view.menus
-
The types of menus
- MessageToClient - Class in com.mygdx.elmaze.networking
-
Message sent from Server to a Client
- MessageToClient(MessageToClient.CONTENT) - Constructor for class com.mygdx.elmaze.networking.MessageToClient
-
- MessageToClient.CONTENT - Enum in com.mygdx.elmaze.networking
-
Content of the message
- MessageToClientTest() - Method in class com.mygdx.elmaze.test.NetworkMessageTest
-
- MessageToServer - Class in com.mygdx.elmaze.networking
-
Message sent from Client to the Server, regarding the status of the Client's accelerometer
- MessageToServer(float, float) - Constructor for class com.mygdx.elmaze.networking.MessageToServer
-
- MessageToServerTest() - Method in class com.mygdx.elmaze.test.NetworkMessageTest
-
- ModelEntitiesTest - Class in com.mygdx.elmaze.test
-
- ModelEntitiesTest() - Constructor for class com.mygdx.elmaze.test.ModelEntitiesTest
-
- MPKeyboardMenuView - Class in com.mygdx.elmaze.view.menus
-
Represents the Multiplayer Keyboard menu view
- MPKeyboardMenuView(ELMaze) - Constructor for class com.mygdx.elmaze.view.menus.MPKeyboardMenuView
-
Creates the multiplayer Keyboard menu
- MPLevel1Model - Class in com.mygdx.elmaze.model.levels
-
Represents the first multiplayer level Model
- MPLevel1Model() - Constructor for class com.mygdx.elmaze.model.levels.MPLevel1Model
-
- MPLevel2Model - Class in com.mygdx.elmaze.model.levels
-
Represents the second multiplayer level Model
- MPLevel2Model() - Constructor for class com.mygdx.elmaze.model.levels.MPLevel2Model
-
Creates the second multiplayer Level
- MPLevel3Model - Class in com.mygdx.elmaze.model.levels
-
Represents the third multiplayer level Model
- MPLevel3Model() - Constructor for class com.mygdx.elmaze.model.levels.MPLevel3Model
-
Creates the third multiplayer Level
- MPLevelOneTest() - Method in class com.mygdx.elmaze.test.LevelTest
-
- MPLevelThreeTest() - Method in class com.mygdx.elmaze.test.LevelTest
-
- MPLevelTwoTest() - Method in class com.mygdx.elmaze.test.LevelTest
-
- MPMobileMenuView - Class in com.mygdx.elmaze.view.menus
-
Represents the Multiplayer Mobile menu view
- MPMobileMenuView(ELMaze) - Constructor for class com.mygdx.elmaze.view.menus.MPMobileMenuView
-
Creates the multiplayer Mobile menu
- MultiPlayerLevel - Class in com.mygdx.elmaze.controller.levels
-
Game Multiplayer level controller
- MultiPlayerLevel(MultiPlayerLevelModel) - Constructor for class com.mygdx.elmaze.controller.levels.MultiPlayerLevel
-
- MultiPlayerLevelModel - Class in com.mygdx.elmaze.model.levels
-
Represents a Multiplayer Level Model
- MultiPlayerLevelModel() - Constructor for class com.mygdx.elmaze.model.levels.MultiPlayerLevelModel
-
Creates a multiplayer Level Model


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Trust is a business theme perfectly suited legal advisers and offices, lawyers, attorneys, counsels, advocates and other legal and law related services.
Trust is a business theme perfectly suited legal advisers and offices, lawyers, attorneys, and other legal and law related services. We have started as a sole practitioner providing services to the area community. Aiming to provide high quality legal consultancy, support and results for your legal issues. Using their expertise and experience, Trust law firm documents and builds their clients' cases to obtain the best results they could achieve. Results recommend Trust as a good law firm, a trusted partner of customers’ business and a knowledgeable adviser and consultant for your legal situation
Trust is a business theme perfectly suited legal advisers and offices, lawyers, attorneys, and other legal and law related services. We have started as a sole practitioner providing services to the area community. Aiming to provide high quality legal consultancy, support and results for your legal issues. Using their expertise and experience, Trust law firm documents and builds their clients' cases to obtain the best results they could achieve. Results recommend Trust as a good law firm, a trusted partner of customers’ business and a knowledgeable adviser and consultant for your legal situation
Trust is a business theme perfectly suited legal advisers and offices, lawyers, attorneys, and other legal and law related services. We have started as a sole practitioner providing services to the area community. Aiming to provide high quality legal consultancy, support and results for your legal issues. Using their expertise and experience, Trust law firm documents and builds their clients' cases to obtain the best results they could achieve. Results recommend Trust as a good law firm, a trusted partner of customers’ business and a knowledgeable adviser and consultant for your legal situation
Trust is a business theme perfectly suited legal advisers and offices, lawyers, attorneys, and other legal and law related services. We have started as a sole practitioner providing services to the area community. Aiming to provide high quality legal consultancy, support and results for your legal issues. Using their expertise and experience, Trust law firm documents and builds their clients' cases to obtain the best results they could achieve. Results recommend Trust as a good law firm, a trusted partner of customers’ business and a knowledgeable adviser and consultant for your legal situation
Trust is a business theme perfectly suited legal advisers and offices, lawyers, attorneys, and other legal and law related services. We have started as a sole practitioner providing services to the area community. Aiming to provide high quality legal consultancy, support and results for your legal issues. Using their expertise and experience, Trust law firm documents and builds their clients' cases to obtain the best results they could achieve. Results recommend Trust as a good law firm, a trusted partner of customers’ business and a knowledgeable adviser and consultant for your legal situation
Trust is a business theme perfectly suited legal advisers and offices, lawyers, attorneys, and other legal and law related services. We have started as a sole practitioner providing services to the area community. Aiming to provide high quality legal consultancy, support and results for your legal issues. Using their expertise and experience, Trust law firm documents and builds their clients' cases to obtain the best results they could achieve. Results recommend Trust as a good law firm, a trusted partner of customers’ business and a knowledgeable adviser and consultant for your legal situation
In Trust, we are aiming to provide high quality legal consultancy, support and results for your legal issues. Aiming to provide high quality legal consultancy, support and results for your legal issues. Using their expertise and experience, Trust law firm documents and builds their clients' cases to obtain the best results they could achieve in their particular situation.
Trust has been known for doing what he says, aiming to bring favourable results for its customers as soon as possible.
Trust is abusiness theme perfectly suited legal advisers and offices, lawyers, attorneys, counsels, advocates and other legal and law related services.Trust started as a sole practitioner providing services to the area community.
In Trust, we have got a wide range of legal services. We practice general civil law for businesses, individuals, and local governments too.is abusiness theme perfectly suited legal advisers and offices, lawyers, attorneys, counsels, advocates and other legal and law related services.
Family law consists of a body of statutes and case precedents that govern the legal responsibilities between individuals who share a domestic connection.
MoreFire accidents can result in catastrophic personal injury and devastating damage. Every year, billions of dollars in property damage occurs as a result of fire.
MoreShoplifting law deals with theft crimes that occur in retail establishments. Perpetrators are shoppers who enter the establishment with permission.
MoreThe legal restrictions placed on the use of controlled drugs are aimed at preventing drug misuse. The principal offences are contained in the Misuse of Drugs Act 1971.
MoreEach lawyer at Trust law firm focuses exclusively on civil matters, we have choosed our lawyers taking into account their experience and ability to handle all cases.
CEO & Manager
CEO & Manager
Civil Lawyer
Civil Lawyer
Business Lawyer
Business Lawyer
Criminal Defence
Criminal Defence
Results recommend Trust Law Firm as a good lawyers office, a trusted partners of his customers’ business and a honest adviser and consultant for legal situation.


Turn your home into a smart home by installing Nest products, saving you money in energy costs and increasing home security. When you add Nest products to your home, they can automatically work together or with other appliances and you can control them all from one place: the Nest app.
Google Nest
Test
Nest Thermostat
The 3rd gen Nest Learning Thermostat learns what temperature you like and builds a schedule around yours, automatically adapting as your life and seasons change. Nest shows you how much energy you use every day in Energy History and every month in your Home Report. So you can see when you use more energy and how to use less.
Save on energy bills.
Since 2011, the Nest Thermostat has saved over 4 billion kWh of energy in millions of homes worldwide. And independent studies showed that it saved people an average of 10-12% on heating bills and 15% on cooling bills. So in under two years, it can pay for itself.
Nest Cam
The Nest Cam security camera is designed to help you look after your home and family – even when you’re away. With 24/7 live streaming, advanced Night Vision, activity alerts, one app for all your Nest products, and a versatile magnetic stand, Nest Cam helps you keep an eye on what matters
Put it anywhere.
With full 1080p HD video, a 130° wide-angle view and Night Vision, Nest Cam works in any room of the house, day or night. Just plug it in and set it up from your phone.
Nest Protect
The Nest Cam security camera is designed to help you look after your home and family – even when you’re away. With 24/7 live streaming, advanced Night Vision, activity alerts, one app for all your Nest products, and a versatile magnetic stand, Nest Cam helps you keep an eye on what matters
Designed to connect
If the Nest Protect in your kitchen senses danger, every Nest Protect in your home will speak up to make sure you know where the danger is – even if Wi-Fi goes down. And once you've checked that everything's OK, you can hush them from your phone over Bluetooth LE.
Not just an alarm. A guide.
What To Do in the Nest app teaches your family how to get out of the house safely. It will also pop up on your phone if the alarm goes off. You can even enter an emergency contact so it's right there when you need it.
Know what happened.
You’re not always home when there’s an emergency. So Nest Protect remembers what happened and shows you the details in a 10-day Safety History.
It helps you every month.
Nest will email you a monthly Home Report. You’ll see a summary of anything that happened and tips to help you stay safe.


@@include('../_include/header/head.html',{"search": "active"})
@@include('../_include/header/nav/search.html')
@@include('../_include/header/breadcrumb/breadcrumb.html',{"search": "active"})
@@include('../_include/footer/footer.html')
@@include('../_include/footer/foot.html')


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Absolve is a command line tool for processing Ig variable domain sequences and generating tabular results characterizing the domains (Frameworks, CDRs), germline origin, somatic hypermutation events.
Input:
* Fasta files of either DNA or amino acid sequence
* Fastq(.gz) files of single or paired-end reads
Performs:
* Detection of Ig-like sequences (HMM)
* FW, CDR, Kabat numbering (HMM)
* Germline Assignment and SHM (BWA or SSW aligner)
Output:
* Tab delimited files with annotations for each query
sequence
* Optional summary statistics for the whole dataset
Absolve is a command line executable written in C++ that links to included copies of:
When running jobs on a cluster, it is critical that some files and directories be available to the cluster worker jobs via network attached storage (NAS) so that resources and result files can be accessed and shared by the cluster worker jobs. NAS sensitive parameters are specified below as "NAS required". For non-distributed/local use of absolve, you can ignore the NAS requirement.
Non-distributed. A single-threaded/non-distributed invocation, typically fine for ~1000 sequences:
$ ./absolve.bash
Distributed. For running large datasets (NGS datasets with 100k or millions of reads) use the --distrib and --startseq and --nseqs for each job to process a different part of the input data. For example, an input dataset with 8,752 reads could be distributed this way:
computeNode1 $ ./absolve.bash --R1 /networkStorage/myinputfile_R1.fastq.gz --R2 /networkStorage/myinputfile_R2.fastq.gz -VH /networkStorage/humanVH.fa --outdir /networkStorage/absolve_results --distrib --startseq 1 --nseqs 3000Invoking absolve with no input will give you a usage summary, but each of the parameters are explained below in much greater detail.
Required field, NAS required.
The input file maybe be either DNA or Amino acid sequences in FASTA format with the suffix ".fa" or ".fasta" or ".fna"
The input file might also be a fastq file with suffix ".fastq" or ".fastq.gz" with either a paired end mate specified in --R2, or a single fastq file with sequential mate pairs in the file (e.g. the first two sequences in the fastq file are a paired-end read, the second two also form a paired-end read, etc).
NAS required.
This would be second input file for paired end reads. Note that this is a file in fastq format. Paired-end reads are only supported in fastq format.
If your input is in fasta format but the sequences are amino acid, you must invoke this flag for proper analysis. Absolve does autodetect sequence type. If this flag is omitted Absolve treats the sequences as DNA.
If this flag is invoked, absolve will include a variety of statistics with the results. Each statistics file is a tab-delimited, two column table with no header; these are basically key-value pairs, where the key is the variable of interest and the value is the count of how many times that key was observed. For example "statHCDR3.tsv" might look like this, where the first column is a particular HCDR and second is number of observations of that HCDR in your input sequences:
AR-MFDS
1
ARGAGDVDWYFDY 1
ARXXYN- 2
The (current) full set of statistics files are these, for most of them, the first column is the key, and the second column is the count:
The statRunStats.tsv is ALWAYS generated, even if this flag is not asserted.
This is a timing flag used for performance measurements, generally not needed by users.
NAS Required. These are the optional germline database files for germline classification of query sequences. Any combination or even none of these flags may be used depending on whether the user wants germline calls of any type. Databases are provided and described below, but they may also be any set of sequences for which BWA indices are built. For example you may have a specific set of heavy V sequences you want to classify against, you might do the following:
user1@comp
/home/user1/myVgenes $ ls
MyFavoriteHeavyV.fa
myQuerySeqs.fa
user1@comp /home/user1/myVgenes $ bwa index
./MyFavoriteHeavyV.fa
user1@comp /home/user1/myVgenes $ ./absolve.bash --R1
./myQuerySeqs.fa --VH ./MyFavoriteHeavyV.fa --outdir ./myresults
Including any of these alignment database flags will result in alignments of the query sequences being performed against these databases and the results reported in their respective columns. The fields will be empty if no flag and dbfile are provided. For example:
Which type of HMM to run. If sequences are known to be exclusively heavy or light, it is faster to specify just the "Heavy" or "Light" HMM. If the sequences are unknown, or they are ScFV, use the "ScFV" HMM option. If not specified, the default is "ScFV".
Which type of aligner to use. The default is "BWA" for DNA sequences and "SWA" for amino acid sequences.
For germline classification, one might also want a list of alternative "next best" hits. If this flag is asserted with say N=5, the top next best 5 hits will be reported as a comma separated list. For example, the VH field would have the next best 5 hits.
This flag is not generally used in NGS datasets, but often used on complex constructs, e.g. sequences that might have multiple heavy and/or light chains, in any number in any order. This flag will cause absolve to exhaustive search a single query sequence for all possible chains, and it will report one record per chain found. Note that this can result in multiple records per Accession in the result files. Roughly speaking, the algorithm is as follows:
while
(Heavy or Light domains are found){
Report it.
Mask it out of the query sequence so its not found
again.
}
When searching exhaustively for domains, the sensitivity can be adjusted with this parameter, a threshold on the HMM score. The default is 70.0, 55.0 will give partial Ig like sequences, 10 to 30 is probably the lowest useful sensitivity.
For normal, non-exhaustive searching, minimum HMM score threshold. If this is set, only sequences exceeding this threshold will be reported. If ommitted, no filtering is done. This is a log-odds score in base 2 (bits) so 0 is even odds, positive values are more likely to be real Ig Variable domain sequences and negative values are less likely. 70 is a high bar, 55.0 will give partial Ig like sequences, 10 to 30 is probably the lowest useful discriminative sensitivity, 0 and below are almost like no filtering at all.
Flag indicating if 'incomplete' sequences should be filtered out. Incomplete means more than 3 gaps in CDR1,FW2,CDR2,FW3. FW1,CDR3 and FW4 are forgiven.
Skip N-1 sequences and then begin processing, default 1
This is used by the dist.absolve.bash wrapper when distributing jobs on the cluster so that each job works on a distinct subset of the input sequences.
Process only N sequences after startseq. If omitted, the input files will be read to their end. Notice that nseqs applies to 'pairs of read' when R2 is specified, i.e. --nseqs 10 means read both R1 and R2 10 times for 10 paired-end reads.
flag indicating job is part of distributed batch. If flag set, /tmp will be used and the results will be finally spooled/appended to the --outdir folder with synchronization by file_lock. It is harmless to use this flag on non-distributed jobs, but it does add extra steps. This flag is also useful for "pooling" samples into the same result set as each run will append to, instead of overwriting the results. The stats files will also be dealt with appropriately, existing statistics are summed with each --distrib runs statistics. This flag is used behind the scenes by "dist.absolve.bash" to create worker/cluster jobs.
For NGS datasets, the result is very large. Specifying H or L with this flag will cause the results for each heavy or light "lineage" to be saved to separate tsv files. Lineage here means "Vallele-Jallele-CDR3Length", not the typical lineage concept. This is just a way to break up the data into sensible smaller sets. A result set would look something like:
IGHV2-5*04#IGHJ5*02#5.tsv
IGHV4-39*01#IGHJ5*01#6.tsv
IGHV3-33*06#*#15.tsv
etc...
NONE is the default, in which case all results are stored in a single file: --outdir/absolve.tsv
Absolve output files, either "absolve.tsv" or specific lineage files if the breakout option is used will have the following columns:
Accession-------The
accession from the input file
DNA-------------The full DNA
sequences from the input, mated paired end reads.
ORF-------------The highest scoring full open reading frame
Frame-----------Reading frame start (0, 1, 2) in DNA field for ORF
CH--------------Heavy chain constant region 1 call
CHpos-----------Position for CH
CHcigar---------Cigar for CH
VH--------------Heavy V germline call
VHpos-----------Position for VH
VHcigar---------Cigar for VH
VHshm-----------Somatic hypermutation estimate for VH
JH--------------Heavy J germline call
JHpos-----------Position for JH
JHcigar---------Cigar for JH
JHshm-----------Somatic hypermutation estimate for JH
CL--------------Light chain constant region call
CLpos-----------Position for CL
CLcigar---------Cigar for CL
VL--------------Light V germline
call
VLpos-----------Position for VL
VLcigar---------Cigar for VL
VLshm-----------Somatic hypermutation estimate for VL
JL--------------Light J germline call
JLpos-----------Position for JL
JLcigar---------Cigar for JL
JLshm-----------Somatic hypermutation estimate for JL
HAA-------------Amino acid sequence for just the heavy variable region
LAA-------------Amino acid sequence for just the light variable region
HDNA------------DNA sequence for just the heavy variable region
LDNA------------DNA sequence for just the light variable region
HFW1------------Heavy Framework1 AA seq
HCDR1-----------Heavy CDR1 AA seq
HFW2------------Heavy Framework2 AA seq
HCDR2-----------Heavy CDR2 AA seq
HFW3------------Heavy Framework3 AA seq
HCDR3-----------Heavy CDR3 AA seq
HFW4------------Heavy Framework4 AA seq
LFW1------------Light Framework1 AA seq
LCDR1-----------Light CDR1 AA seq
LFW2------------Light Framework2 AA seq
LCDR2-----------Light CDR2 AA seq
LFW3------------Light Framework3 AA seq
LCDR3-----------Light CDR3 AA seq
LFW4------------Light Framework4 AA seq
Llineage--------Light V allele + Light J allele + CDR3length. Useful
preliminary grouping for later calculation of finer lineages
Hlineage--------Light V allele + Light J allele + CDR3length. Useful
preliminary grouping for later calculation of finer lineages
Kabat-----------The Kabat numbering for the sequence.
HMMScore--------Log-odds of how Ig-like/similar to a variable domain
this sequence is.
PairStrategy----What method was used to mate the paired end reads,
either NT18 (overlap of 18 nt perfect match), HMM1 (a single amino acid
match in the same HMM state), HMM2 (two or more amino acid matches in
the same HMM state).


--- layout: archive title: Zulip Chat Archive permalink: /stream/113488-general/topic/image.20binder.20notation.html ---
Should we have binder notation for set.image?
set.image
it's not so compositional
Last updated: Apr 24 2020 at 19:02 UTC


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* Version:1.0.0.
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* Compiled Date:2017-07-20.
2017-07-20


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