o != arg0
is the same as !(o == (arg0))
.
o != arg0
is the same as !(o == (arg0))
.
the object to compare against this object for dis-equality.
false
if the receiver object is equivalent to the argument; true
otherwise.
o == arg0
is the same as if (o eq null) arg0 eq null else o.equals(arg0)
.
o == arg0
is the same as if (o eq null) arg0 eq null else o.equals(arg0)
.
the object to compare against this object for equality.
true
if the receiver object is equivalent to the argument; false
otherwise.
o == arg0
is the same as o.equals(arg0)
.
o == arg0
is the same as o.equals(arg0)
.
the object to compare against this object for equality.
true
if the receiver object is equivalent to the argument; false
otherwise.
Append the given messages starting with the given offset.
Append the given messages starting with the given offset. Add an entry to the index if needed.
It is assumed this method is being called from within a lock.
The first offset in the message set.
The messages to append.
This method is used to cast the receiver object to be of type T0
.
This method is used to cast the receiver object to be of type T0
.
Note that the success of a cast at runtime is modulo Scala's erasure semantics. Therefore the expression1.asInstanceOf[String]
will throw a ClassCastException
at runtime, while the expressionList(1).asInstanceOf[List[String]]
will not. In the latter example, because the type argument is erased as
part of compilation it is not possible to check whether the contents of the list are of the requested typed.
the receiver object.
Change the suffix for the index and log file for this log segment
Change the suffix for the index and log file for this log segment
This method creates and returns a copy of the receiver object.
This method creates and returns a copy of the receiver object.
The default implementation of the clone
method is platform dependent.
a copy of the receiver object.
Close this log segment
Close this log segment
Delete this log segment from the filesystem.
Delete this log segment from the filesystem.
This method is used to test whether the argument (arg0
) is a reference to the
receiver object (this
).
This method is used to test whether the argument (arg0
) is a reference to the
receiver object (this
).
The eq
method implements an [http://en.wikipedia.org/wiki/Equivalence_relation equivalence relation] on
non-null instances of AnyRef
:
* It is reflexive: for any non-null instance x
of type AnyRef
, x.eq(x)
returns true
.
* It is symmetric: for any non-null instances x
and y
of type AnyRef
, x.eq(y)
returns true
if and
only if y.eq(x)
returns true
.
* It is transitive: for any non-null instances x
, y
, and z
of type AnyRef
if x.eq(y)
returns true
and y.eq(z)
returns true
, then x.eq(z)
returns true
.
Additionally, the eq
method has three other properties.
* It is consistent: for any non-null instances x
and y
of type AnyRef
, multiple invocations of
x.eq(y)
consistently returns true
or consistently returns false
.
* For any non-null instance x
of type AnyRef
, x.eq(null)
and null.eq(x)
returns false
.
* null.eq(null)
returns true
.
When overriding the equals
or hashCode
methods, it is important to ensure that their behavior is
consistent with reference equality. Therefore, if two objects are references to each other (o1 eq o2
), they
should be equal to each other (o1 == o2
) and they should hash to the same value (o1.hashCode == o2.hashCode
).
the object to compare against this object for reference equality.
true
if the argument is a reference to the receiver object; false
otherwise.
This method is used to compare the receiver object (this
) with the argument object (arg0
) for equivalence.
This method is used to compare the receiver object (this
) with the argument object (arg0
) for equivalence.
The default implementations of this method is an [http://en.wikipedia.org/wiki/Equivalence_relation equivalence
relation]:
* It is reflexive: for any instance x
of type Any
, x.equals(x)
should return true
.
* It is symmetric: for any instances x
and y
of type Any
, x.equals(y)
should return true
if and
only if y.equals(x)
returns true
.
* It is transitive: for any instances x
, y
, and z
of type AnyRef
if x.equals(y)
returns true
and
y.equals(z)
returns true
, then x.equals(z)
should return true
.
If you override this method, you should verify that your implementation remains an equivalence relation.
Additionally, when overriding this method it is often necessary to override hashCode
to ensure that objects
that are "equal" (o1.equals(o2)
returns true
) hash to the same
scala.Int
(o1.hashCode.equals(o2.hashCode)
).
the object to compare against this object for equality.
true
if the receiver object is equivalent to the argument; false
otherwise.
This method is called by the garbage collector on the receiver object when garbage collection determines that there are no more references to the object.
This method is called by the garbage collector on the receiver object when garbage collection determines that there are no more references to the object.
The details of when and if the finalize
method are invoked, as well as the interaction between finalize
and non-local returns and exceptions, are all platform dependent.
Flush this log segment to disk
Flush this log segment to disk
Returns a representation that corresponds to the dynamic class of the receiver object.
Returns a representation that corresponds to the dynamic class of the receiver object.
The nature of the representation is platform dependent.
a representation that corresponds to the dynamic class of the receiver object.
Returns a hash code value for the object.
Returns a hash code value for the object.
The default hashing algorithm is platform dependent.
Note that it is allowed for two objects to have identical hash codes (o1.hashCode.equals(o2.hashCode)
) yet
not be equal (o1.equals(o2)
returns false
). A degenerate implementation could always return 0
.
However, it is required that if two objects are equal (o1.equals(o2)
returns true
) that they have
identical hash codes (o1.hashCode.equals(o2.hashCode)
). Therefore, when overriding this method, be sure
to verify that the behavior is consistent with the equals
method.
the hash code value for the object.
This method is used to test whether the dynamic type of the receiver object is T0
.
This method is used to test whether the dynamic type of the receiver object is T0
.
Note that the test result of the test is modulo Scala's erasure semantics. Therefore the expression1.isInstanceOf[String]
will return false
, while the expression List(1).isInstanceOf[List[String]]
will
return true
. In the latter example, because the type argument is erased as part of compilation it is not
possible to check whether the contents of the list are of the requested typed.
true
if the receiver object is an instance of erasure of type T0
; false
otherwise.
The last modified time of this log segment as a unix time stamp
The last modified time of this log segment as a unix time stamp
Change the last modified time for this log segment
Change the last modified time for this log segment
o.ne(arg0)
is the same as !(o.eq(arg0))
.
o.ne(arg0)
is the same as !(o.eq(arg0))
.
the object to compare against this object for reference dis-equality.
false
if the argument is not a reference to the receiver object; true
otherwise.
Calculate the offset that would be used for the next message to be append to this segment.
Calculate the offset that would be used for the next message to be append to this segment. Note that this is expensive.
Wakes up a single thread that is waiting on the receiver object's monitor.
Wakes up a single thread that is waiting on the receiver object's monitor.
Wakes up all threads that are waiting on the receiver object's monitor.
Wakes up all threads that are waiting on the receiver object's monitor.
Read a message set from this segment beginning with the first offset >= startOffset.
Read a message set from this segment beginning with the first offset >= startOffset. The message set will include no more than maxSize bytes and will end before maxOffset if a maxOffset is specified.
A lower bound on the first offset to include in the message set we read
An optional maximum offset for the message set we read
The maximum number of bytes to include in the message set we read
The message set read or null if the startOffset is larger than the largest offset in this log.
Run recovery on the given segment.
Run recovery on the given segment. This will rebuild the index from the log file and lop off any invalid bytes from the end of the log and index.
A bound the memory allocation in the case of a corrupt message size--we will assume any message larger than this is corrupt.
The number of bytes truncated from the log
Returns a string representation of the object.
Returns a string representation of the object.
The default representation is platform dependent.
a string representation of the object.
Truncate off all index and log entries with offsets >= the given offset.
Truncate off all index and log entries with offsets >= the given offset. If the given offset is larger than the largest message in this segment, do nothing.
The offset to truncate to
The number of log bytes truncated
A segment of the log. Each segment has two components: a log and an index. The log is a FileMessageSet containing the actual messages. The index is an OffsetIndex that maps from logical offsets to physical file positions. Each segment has a base offset which is an offset <= the least offset of any message in this segment and > any offset in any previous segment.
A segment with a base offset of [base_offset] would be stored in two files, a [base_offset].index and a [base_offset].log file.


JavaScript and Html:
The main difference between javascript and html is javascript can be used to make dynamic web pages whereas html makes static, Html is sort of like a book all of its pages stay the same where javascript would be like a movie its pages can move and change.
Control flow and loops:
When you tell a computer to loop it is basically telling it to follow a routine for example getting up in the morning, having a shower, going to school or work, coming home and having dinner, then going to bed is all a loop that you might repeat each day.
The DOM:
What your internet browser displays is a web document, it is a combination of HTML, CSS, and JavaScript working together to display the webpage. There is a hierarchical structure that your browser uses to make sense of everything going on, this structure is the Document Object Manual or the DOM for short.
The DOM is made up from more than just Html elements and these elements are called nodes, nodes can be elements, attributes, text content, comments, document-related stuff, and many other things.
The DOM is without a doubt the most important piece of functions as it provides the link between all your Html, CSS, and JavaScript files essentially making it the main building block when creating a website.
Arrays and Objects:
Arrays and objects are basically the same thing the main difference between them is that arrays keep something stored using a number and with objects you can use a word/title to store something.
Functions:
Functions are basically sub programs of a main program which can be called when needed, they are really useful when wanting to use a piece of code multiple times as it means you don't need to write it out each time, this also makes your code cleaner because there is less repetitive code.


The sarus crane (Grus antigone) is a large non-migratory crane found in parts of the Indian Subcontinent, Southeast Asia and Australia.
The tallest of the flying birds, standing at a height of up to 1.8 m (5 ft 11 in),[3] they are conspicuous and iconic[4] species of open wetlands.
The water rail (Rallus aquaticus) is a bird of the rail family which breeds in well-vegetated wetlands across Europe, Asia and North Africa. Northern and eastern populations are migratory, but this species is a permanent resident in the warmer parts of its breeding range.
The Baillon's crake (Porzana pusilla) is a very small waterbird of the family Rallidae. Their breeding habitat is sedge beds in Europe, mainly in the east, and across Asia. They used to breed in Great Britain up to the mid-19th century, but the western European population declined through drainage.
The western swamphen (Porphyrio porphyrio) is a "swamp hen" in the rail family Rallidae. From its French name talève sultane, it is also known as the sultana bird. This chicken-sized bird, with its large feet, bright plumage and red bill and frontal shield is easily recognisable in its native range.
The common moorhen (Gallinula chloropus) (also known as the swamp chicken[2]) is a bird species in the family Rallidae. It is distributed across many parts of the Old World.[3] The common moorhen lives around well-vegetated marshes, ponds, canals and other wetlands. The species is not found in the polar regions or many tropical rainforests. Elsewhere it is likely the most common rail species, except for the Eurasian coot in some regions.
The Eurasian coot (Fulica atra), also known as coot, is a member of the rail and crake bird family, the Rallidae. It is found in Europe, Asia, Australia and parts of Africa. The Australian subspecies is known as the Australian coot.


10 Vim Plugins for Writers
I still remember the first time I came in contact with Vim; it was during my very first job. It was a part-time gig in a government office. A few months in, they decided to go open-source full in. Out the window went Windows and in came Linux. At the time, I was doing PHP development, and I was sorry to have to let go of my dear Dreamweaver.
I decided that if I had to work on Linux, I would go all the way, no compromises for me. That meant getting used to working on the console and learning Vim.
When one of the resident Linux gurus walked by my seat and saw my screen, he said, “Are you using Vi? Maybe you’re not so useless after all.” (Funny story, I came across him on facebook the other day. Now that he’s bald, he doesn’t look intimidating at all).
Lately, I’ve been writing a lot. I found that armed with the right plugins, Vim is a great tool writing:
- vim-pencil: my favorite writing plugin. Vim-pencil brings a ton of nice things like navigation aids, smarter undo based on punctuation, and proper soft wrapping.
- vim-ditto: ditto highlights repeated words in a paragraph, just what I need to avoid repeating words all the time.
- vim-goyo: a Writeroom lookalike for Vim, goyo removes all distracting elements like modeline and line numbers.
- vim-colors-pencil: an elegant, low contrast colorscheme geared towards writing.
- vim-litecorrect: litecorrect automatically corrects common typing errors like “teh” instead of “the”.
- vim-lexical: combined spellchecker and thesaurus. Vim-lexical lets me navigate between spell errors with
]s
,[s
and quickly find synonyms with<leader> t
- vim-textobj-sentence: a plugin for better sentence navigation. I can move between sentences with
(
and)
, I can cut a sentence withdis
. Depends on vim-textobj-user. - vim-textobj-quote: this plugin smartly creates “quotes” so I don’t have to.
- ALE: the Asynchronous Lint Engine is a polyglot analysis tool that is not limited to code. It supports a bunch of style checkers like proselint and LanguageTool.
- vim-orgmode: I’ll admit that, before I saw the errors of my ways, I communed with the one that should not be named. During the time I used Emacs, I never fully switched away from Vim, that alone should have told me something.
For my labors, I gained something invaluable: I found Org mode. For me, Org-mode is the most intuitive and straightforward way of interacting with text. This filetype plugin only implements a subset of all its features, but even so, it’s good enough for my purposes.
While not Vim-related, I also find these tools irreplaceable in my workflow:
- pandoc: a command-line markup converter. Supports dozens of formats, including Org-mode and markdown. I usually write in Org and then export to the target type.
- TitleCase.pl: John Gruber’s title case Perl script. I haven’t found a good native Title Case plugin for Vim, so I just use a
!TitleCase.pl
filter. - grip: view local Markdown files with GitHub renderer. I use it to preview how my files will look before pushing them.
Happy writing!
Tomas


Play to Unveil our Christmas Message!
Dear Player,
Thank you for sampling our holiday seasoned card.
We hope to provide many more interesting and timely experiences for you in the future.
Happly Holidays,
Origame Studios
Build Your Own Holiday Message!!!


{% extends "_base.html" %} {% block content %} Error 404: Page not found No idea what you expected to find here, but this page doesn't exist. {% endblock content %}


Pushup! a content slider built on top of jQuery Library.
You can customize various features of Pushup slider, like stickness left/right, opacity and animation speed.
To use Pushup slider create a block element, add the necessary scripts and call the Pushup slider plugin intializer.
For detail instructions Click Here.
Left Aligned Demo Right Aligned DemoMuhammad Shahbaz Saleem
Lahore, Pakistan
http://www.egrappler.com
Muhammad Shahbaz Saleem
Lahore, Pakistan
http://www.egrappler.com


CreateWizard.
The following methods are available on the Wizard object:
unknown
Dismiss
Finish
GetButtons
GetDialog
GetLayout
Returns the control class name.
Hide the control but keep the layout space free.
Returns whether the control is currently visible to the user, ignoring overlaying controls.
Set the visibility of the control to “Show”.


railo-context.Component coldbox.system.Bootstrap
Copyright Since 2005 ColdBox Framework by Luis Majano and Ortus Solutions, Corp www.coldbox.org | www.luismajano.com | www.ortussolutions.com Loads the framwork into memory and provides a ColdBox application.
| Property Summary | ||||
|---|---|---|---|---|
| type | property | default | serializable | required |
any
|
appHash
|
true
|
false
|
|
any
|
COLDBOX_APP_KEY
|
true
|
false
|
|
any
|
COLDBOX_APP_MAPPING
|
true
|
false
|
|
any
|
COLDBOX_APP_ROOT_PATH
|
true
|
false
|
|
any
|
COLDBOX_CONFIG_FILE
CONSTRUCTOR ********************************************. |
true
|
false
|
|
any
|
lockTimeout
|
true
|
false
|
| Constructor Summary | |
|---|---|
|
init(string COLDBOX_CONFIG_FILE, string COLDBOX_APP_ROOT_PATH, [string COLDBOX_APP_KEY], [string COLDBOX_APP_MAPPING=''])
Constructor, called by your Application CFC. |
| Method Summary | |
|---|---|
string
|
getAppHash()
|
string
|
getCOLDBOX_APP_KEY()
|
string
|
getCOLDBOX_APP_MAPPING()
|
string
|
getCOLDBOX_APP_ROOT_PATH()
|
string
|
getCOLDBOX_CONFIG_FILE()
get: CONSTRUCTOR ********************************************. |
string
|
getLockTimeout()
|
boolean
|
isFWReinit()
Verify if a reinit is sent. |
any
|
loadColdBox()
Loads the framework into application scope and executes app start procedures. |
private any
|
locateAppKey()
Locate the application key. |
any
|
onApplicationEnd([struct appScope])
ON applicaiton end. |
boolean
|
onApplicationStart()
ON application start. |
boolean
|
onMissingTemplate(any template)
ON missing template. |
boolean
|
onRequestStart(any targetPage)
On request start. |
any
|
onSessionEnd(struct sessionScope, [struct appScope])
ON session end. |
any
|
onSessionStart()
ON session start. |
any
|
processColdBoxRequest()
Process a ColdBox Request. |
private string
|
processException(any controller, any exception)
Process an exception and returns a rendered bug report. |
private any
|
processStackTrace([any str])
Process Stack trace for errors. |
any
|
reloadChecks()
Request Reload procedures. |
private Bootstrap
|
renderDataSetup(any controller, any statusCode, any statusText, any contentType, any encoding)
Process render data setup. |
any
|
setAppHash(any appHash)
|
any
|
setCOLDBOX_APP_KEY(any COLDBOX_APP_KEY)
|
any
|
setCOLDBOX_APP_MAPPING(any COLDBOX_APP_MAPPING)
|
any
|
setCOLDBOX_APP_ROOT_PATH(any COLDBOX_APP_ROOT_PATH)
|
any
|
setCOLDBOX_CONFIG_FILE(any COLDBOX_CONFIG_FILE)
set: CONSTRUCTOR ********************************************. |
any
|
setLockTimeout(any lockTimeout)
|
| Methods inherited from class railo-context.Component |
|---|
| None |
| Constructor Detail |
|---|
Constructor, called by your Application CFC
COLDBOX_CONFIG_FILE
- The override location of the config fileCOLDBOX_APP_ROOT_PATH
- The location of the app on diskCOLDBOX_APP_KEY
- The key used in application scope for this applicationCOLDBOX_APP_MAPPING
- The application mapping override, only used for Flex/SOAP apps, this is auto-calculated| Property Detail |
|---|
required
- falseserializable
- truerequired
- falseserializable
- truerequired
- falseserializable
- truerequired
- falseserializable
- trueCONSTRUCTOR ********************************************
required
- falseserializable
- truerequired
- falseserializable
- true| Method Detail |
|---|
get: CONSTRUCTOR ********************************************
Verify if a reinit is sent
Loads the framework into application scope and executes app start procedures
Locate the application key
ON applicaiton end
appScope
ON application start
ON missing template
template
On request start
targetPage
ON session end
sessionScope
appScope
ON session start
Process a ColdBox Request
Process an exception and returns a rendered bug report
controller
- The ColdBox Controllerexception
- The ColdFusion exceptionProcess Stack trace for errors
str
Request Reload procedures
Process render data setup
controller
- The ColdBox controllerstatusCode
- The status code to sendstatusText
- The status text to sendcontentType
- The content type to sendencoding
- The content encodingappHash
COLDBOX_APP_KEY
COLDBOX_APP_MAPPING
COLDBOX_APP_ROOT_PATH
set: CONSTRUCTOR ********************************************
COLDBOX_CONFIG_FILE
lockTimeout


Contributions
Apache DistributedLog is developed by an open and friendly community. Everybody is cordially welcome to join the community and contribute to Apache DistributedLog. There are several ways to interact with the community and to contribute to DistributedLog including asking questions, filing bug reports, proposing new features, joining discussions on the mailing lists, contributing code or documentation, improving the website, or testing release candidates.
Ask questions!
The Apache DistributedLog community is eager to help and to answer your questions. We have a mailing list.
File a bug report
Please let us know if you experienced a problem with DistributedLog and file a bug report. Open DistributedLog’s JIRA and click on the blue Create button at the top. Please give detailed information about the problem you encountered and, if possible, add a description that helps to reproduce the problem. Thank you very much.
Propose an improvement or a new feature
Our community is constantly looking for feedback to improve Apache DistributedLog. If you have an idea how to improve DistributedLog or have a new feature in mind that would be beneficial for DistributedLog users, please open an issue in DistributedLog’s JIRA. The improvement or new feature should be described in appropriate detail and include the scope and its requirements if possible. Detailed information is important for a few reasons:
- It ensures your requirements are met when the improvement or feature is implemented.
- It helps to estimate the effort and to design a solution that addresses your needs.
- It allow for constructive discussions that might arise around this issue.
Detailed information is also required, if you plan to contribute the improvement or feature you proposed yourself. Please read the Contribute code guide in this case as well.
We recommend to first reach consensus with the community on whether a new feature is required and how to implement a new feature, before starting with the implementation. Some features might be out of scope of the project, and it’s best to discover this early.
Help others and join the discussions
Most communication in the Apache DistributedLog community happens on the mailing list:
- The mailing list
<EMAIL_ADDRESS>is the place where DistributedLog developers exchange ideas and discuss new features, upcoming releases, and the development process in general. If you are interested in contributing code to DistributedLog, you should join this mailing list.
You are very welcome to subscribe to mailing lists.
Test a release candidate
Apache DistributedLog is continuously improved by its active community. Every few weeks, we release a new version of Apache DistributedLog with bug fixes, improvements, and new features. The process of releasing a new version consists of the following steps:
- Building a new release candidate and starting a vote (usually for 72 hours).
- Testing the release candidate and voting (
+1
if no issues were found,-1
if the release candidate has issues). - Going back to step 1 if the release candidate had issues otherwise we publish the release.
Release testing is a big effort if done by a small group of people but can be easily scaled out to more people. The DistributedLog community encourages everybody to participate in the testing of a release candidate. By testing a release candidate, you can ensure that the next DistributedLog release is working properly for your setup and help to improve the quality of releases.
Contribute code
Apache DistributedLog is maintained, improved, and extended by code contributions of volunteers. The Apache DistributedLog community encourages anybody to contribute source code. In order to ensure a pleasant contribution experience for contributors and reviewers and to preserve the high quality of the code base, we follow a contribution process that is explained in our Contribute code guide. The guide does also include instructions to setup a development environment, our coding guidelines and code style, and explains how to submit a code contribution.
Please read the Contribute code guide before you start to work on a code contribution.
Looking for an issue to work on?
We maintain a list of all known bugs, proposed improvements and suggested features in DistributedLog’s JIRA.
Also, Project Ideas is also a good page to check out for big ideas.
Contribute documentation
[TBD]
Improve the website
[TBD]
More ways to contribute…
There are many more ways to contribute to the DistributedLog community. For example you can
- give a talk about DistributedLog and tell others how you use it.
- organize a local Meetup or user group.
- talk to people about DistributedLog.
- …


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There are two different ways we can set up an NB classifier. The model we introduced in the previous section is the multinomial model . It generates one term from the vocabulary in each position of the document, where we assume a generative model that will be discussed in more detail in Section 13.4 (see also page 12.1.1 ).
An alternative to the multinomial model is the multivariate Bernoulli model or Bernoulli model . It is equivalent to the binary independence model of Section 11.3 (page ), which generates an indicator for each term of the vocabulary, either indicating presence of the term in the document or indicating absence. Figure 13.3 presents training and testing algorithms for the Bernoulli model. The Bernoulli model has the same time complexity as the multinomial model.
The different generation models imply different estimation strategies and different classification rules. The Bernoulli model estimates as the fraction of documents of class that contain term (Figure 13.3 , TRAINBERNOULLINB, line 8). In contrast, the multinomial model estimates as the fraction of tokens or fraction of positions in documents of class that contain term (Equation 119). When classifying a test document, the Bernoulli model uses binary occurrence information, ignoring the number of occurrences, whereas the multinomial model keeps track of multiple occurrences. As a result, the Bernoulli model typically makes many mistakes when classifying long documents. For example, it may assign an entire book to the class China because of a single occurrence of the term China.
The models also differ in how nonoccurring terms are used in classification. They do not affect the classification decision in the multinomial model; but in the Bernoulli model the probability of nonoccurrence is factored in when computing (Figure 13.3 , APPLYBERNOULLINB, Line 7). This is because only the Bernoulli NB model models absence of terms explicitly.
Worked example. Applying the Bernoulli model to the example in Table 13.1 , we have the same estimates for the priors as before: , . The conditional probabilities are:
The denominators are and because there are three documents in and one document in and because the constant in Equation 119 is 2 - there are two cases to consider for each term, occurrence and nonoccurrence.
The scores of the test document for the two classes are


Review by Lars Lindahl
Final Destination (2000)
Grade: ***1/2 (out of four)
Starring Devon Sawa, Ali Larter, Kerr Smith, Kristen Cloke, Seann William Scott, and Tony Todd.
Directed by James Wong Written by Glen Morgan, Jeffrey Reddick, and James Wong
Even if I did not know that director and co-writers James Wong and Jeffrey Reddick of the creepy Final Destination helped create the hit television show The X-Files, I would have inevitably made a connection. The similarities are very apparent from the inexplicable phenomenon- like plot, to the mysterious characters, to the overall dark, ominous settings. It would have been perfectly fitting to see FBI Agents Mulder and Scully investigate this case, they witness stuff like this on a weekly basis (in fact Mulder and Scully would have been a much more welcome change to the bland one dimensional FBI agents seen in this movie). Another more important similarity, is that both succeed in entertaining and thrilling at the same time. This is a great accomplishment for a teen horror movie, especially when compared to some of the trash, of the same genre, released in the last couple of years (Urban Legend and I Still Know What You Did Last Summer are classic examples from the bunch).
What helps Final Destination is its unique premise. Unlike your average horror flick in which some invincible psycho with a knife chases blonde cheerleaders, the villain presented is unusual, it's the Grim Reaper. This being already has predestined when and how you will die. According to the brief history lesson given in this film, everyone was meant to die at a certain time, some people at 100, others at 17, whatever Death chooses. What is unique about Death is that it's already dead, so you can't really kill it. The only way to defeat Death is to cheat it; the question is how do you do that? This dilemma is what faces Alex and a group of teenagers. Alex has been having some dreams that the airplane which will take his class on a trip to Paris will crash, leaving no survivors.  Shortly after, the plane does indeed crash leaving some of the seven survivors confused and others feeling immortal. However, Death isn't through with them yet. It gradually kills off the seven one by one, leaving those currently still alive frantically trying to trick Death again.
The plot allows for some of the most creative, original death scenes I have seen in a while. Some scenes build up the perfect amount of tension until an elaborate climax, others are so unexpected they will leave your jaw wide open in shock. Creativity and originality are two adjectives lacking in most horror films nowadays but Final Destination is not like most horror films. Sure, it has your traditional share of jerks and outsiders (Ali Larter's character is particularly annoying), but the shocks, from the beginning to the end, are extremely entertaining. Also director Wong has the sense not to take the movie too seriously. He knows its just another entertaining guilty pleasure that won't win any Academy Awards (not even a Golden Globe). The myriad of inside jokes and gags (the characters are named after famous horror directors, one character who plays a jerk is named Carter, like X-Files creator Chris Carter, and a song by John Denver, who died in a plane crash, plays whenever Death is near) show this movie is a bunch of guys having a good time making a movie. And from this, I had a great time watching the movie.
Lars Attacks! A teenager attacks a movie every week. http://www.angelfire.com/ny3/larsattacks
© 2000 Lars Lindahl
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TIN Tools
Geo-F/X has a robust proprietary library of tools that provide the capability of building TIN (triangulated irregular networks) from files of X-Y-Z coordinates or grids. The resulting net can be analyzed or mapped using threaded contours - stroked or filled.
The library can handle mesh sizes of over one million points and is optimized for very rapid execution.
The illustration below is a very simple mesh of approximately one thousand points.


MOUSE
Section: Devices and Network Interfaces (4)Updated: xf86-input-mouse 1.7.0
Index Return to Main Contents
NAME
mouse - Xorg mouse input driverSYNOPSIS
Section N'34'InputDeviceN'34' Identifier N'34'idevnameN'34' Driver N'34'mouseN'34' Option N'34'ProtocolN'34' N'34'protonameN'34' Option N'34'DeviceN'34' N'34'devpathN'34' ... EndSection
DESCRIPTION
mouse is an Xorg input driver for mice. The driver supports most available mouse types and interfaces, though the level of support for types of mice depends on the OS.The mouse driver functions as a pointer input device. Multiple mice are supported by multiple instances of this driver.
SUPPORTED HARDWARE
- USB mouse
- USB (Universal Serial Bus) ports are present on most modern computers. Several devices can be plugged into this bus, including mice and keyboards. Support for USB mice is platform specific.
- PS/2 mouse
- The PS/2 mouse is an intelligent device and may have more than three buttons and a wheel or a roller. The PS/2 mouse is usually compatible with the original PS/2 mouse from IBM immediately after power up. The PS/2 mouse with additional features requires a specialized initialization procedure to enable these features. Without proper initialization, it behaves as though it were an ordinary two or three button mouse.
- Serial mouse
-
There have been numerous serial mouse models from a number of
manufacturers.
Despite the wide range of variations, there have been relatively
few protocols (data format) with which the serial mouse talks
to the host computer.
The modern serial mouse conforms to the PnP COM device specification so that the host computer can automatically detect the mouse and load an appropriate driver. This driver supports this specification and can detect popular PnP serial mouse models on most platforms.
- Bus mouse
- The bus mouse connects to a dedicated interface card in an expansion slot. Some older video cards, notably those from ATI, and integrated I/O cards may also have a bus mouse connector.
The interface type of the mouse can be determined by looking at the connector of the mouse. USB mice have a thin rectangular connector. PS/2 mice are equipped with a small, round DIN 6-pin connector. Serial mouse have a D-Sub female 9- or 25-pin connector. Bus mice have either a D-Sub male 9-pin connector or a round DIN 9-pin connector. Some mice come with adapters with which the connector can be converted to another. If you are to use such an adapter, remember that the connector at the very end of the mouse/adapter pair is what matters.
CONFIGURATION DETAILS
Depending on the X server version in use, input device options may be set in either a xorg.conf file, an xorg.conf.d snippet or in the configuration files read by the Hardware Abstraction Layer (HAL) daemon, hald(1).
Please refer to xorg.conf(5) for general configuration details and for options that can be used with all input drivers. This section only covers configuration details specific to this driver.
The driver can auto-detect the mouse type on some platforms. On some platforms this is limited to plug and play serial mice, and on some the auto-detection works for any mouse that the OS's kernel driver supports. On others, it is always necessary to specify the mouse protocol in the config file. The README document provided with this driver contains some detailed information about this.
The following driver Options are supported:
- Option N'34'ProtocolN'34' N'34'stringN'34'
- Specify the mouse protocol. Valid protocol types include:
- Auto, Microsoft, MouseSystems, MMSeries, Logitech, MouseMan, MMHitTab, GlidePoint, IntelliMouse, ThinkingMouse, ValuMouseScroll, AceCad, PS/2, ImPS/2, ExplorerPS/2, ThinkingMousePS/2, MouseManPlusPS/2, GlidePointPS/2, NetMousePS/2, NetScrollPS/2, BusMouse, SysMouse, WSMouse, USB, VUID, Xqueue.
- Not all protocols are supported on all platforms. The "Auto" protocol specifies that protocol auto-detection should be attempted. The default protocol setting is platform-specific.
- Option N'34'DeviceN'34' N'34'stringN'34'
- Specifies the device through which the mouse can be accessed. A common setting is "/dev/mouse", which is often a symbolic link to the real device. This option is mandatory, and there is no default setting. The server may however attempt to probe some default devices if this option is missing.
- Option N'34'ButtonsN'34' N'34'integerN'34'
- Specifies the number of mouse buttons. In cases where the number of buttons cannot be auto-detected, the default value is 3. The maximum number is 24.
- Option N'34'Emulate3ButtonsN'34' N'34'booleanN'34'
- Enable/disable the emulation of the third (middle) mouse button for mice which only have two physical buttons. The third button is emulated by pressing both buttons simultaneously. Default: on, until a press of a physical button 3 is detected.
- Option N'34'Emulate3TimeoutN'34' N'34'integerN'34'
- Sets the timeout (in milliseconds) that the driver waits before deciding if two buttons where pressed "simultaneously" when 3 button emulation is enabled. Default: 50.
- Option N'34'ChordMiddleN'34' N'34'booleanN'34'
- Enable/disable handling of mice that send left+right events when the middle button is used. Default: off.
- Option N'34'EmulateWheelN'34' N'34'booleanN'34'
- Enable/disable "wheel" emulation. Wheel emulation means emulating button press/release events when the mouse is moved while a specific real button is pressed. Wheel button events (typically buttons 4 and 5) are usually used for scrolling. Wheel emulation is useful for getting wheel-like behaviour with trackballs. It can also be useful for mice with 4 or more buttons but no wheel. See the description of the EmulateWheelButton, EmulateWheelInertia, XAxisMapping, and YAxisMapping options below. Default: off.
- Option N'34'EmulateWheelButtonN'34' N'34'integerN'34'
- Specifies which button must be held down to enable wheel emulation mode. While this button is down, X and/or Y pointer movement will generate button press/release events as specified for the XAxisMapping and YAxisMapping settings. If set to 0, no button is required and any motion of the device is converted into wheel events. Default: 4.
- Option N'34'EmulateWheelInertiaN'34' N'34'integerN'34'
- Specifies how far (in pixels) the pointer must move to generate button press/release events in wheel emulation mode. Default: 10.
- Option N'34'EmulateWheelTimeoutN'34' N'34'integerN'34'
- Specifies the time in milliseconds the EmulateWheelButton must be pressed before wheel emulation is started. If the EmulateWheelButton is released before this timeout, the original button press/release event is sent. Default: 200.
- Option N'34'XAxisMappingN'34' N'34'N1 N2N'34'
- Specifies which buttons are mapped to motion in the X direction in wheel emulation mode. Button number N1 is mapped to the negative X axis motion and button number N2 is mapped to the positive X axis motion. Default: no mapping.
- Option N'34'YAxisMappingN'34' N'34'N1 N2N'34'
- Specifies which buttons are mapped to motion in the Y direction in wheel emulation mode. Button number N1 is mapped to the negative Y axis motion and button number N2 is mapped to the positive Y axis motion. Default: no mapping.
- Option N'34'ZAxisMappingN'34' N'34'XN'34'
- Option N'34'ZAxisMappingN'34' N'34'YN'34'
- Option N'34'ZAxisMappingN'34' N'34'N1 N2N'34'
- Option N'34'ZAxisMappingN'34' N'34'N1 N2 N3 N4N'34'
- Set the mapping for the Z axis (wheel) motion to buttons or another axis (X or Y). Button number N1 is mapped to the negative Z axis motion and button number N2 is mapped to the positive Z axis motion. For mice with two wheels, four button numbers can be specified, with the negative and positive motion of the second wheel mapped respectively to buttons number N3 and N4. Note that the protocols for mice with one and two wheels can be different and the driver may not be able to autodetect it. Default: "4 5".
- Option N'34'ButtonMappingN'34' N'34'N1 N2 [...]N'34'
- Specifies how physical mouse buttons are mapped to logical buttons. Physical button 1 is mapped to logical button N1, physical button 2 to N2, and so forth. This enables the use of physical buttons that are obscured by ZAxisMapping. Default: "1 2 3 8 9 10 ...".
- Option N'34'FlipXYN'34' N'34'booleanN'34'
- Enable/disable swapping the X and Y axes. This transformation is applied after the InvX, InvY and AngleOffset transformations. Default: off.
- Option N'34'InvXN'34' N'34'booleanN'34'
- Invert the X axis. Default: off.
- Option N'34'InvYN'34' N'34'booleanN'34'
- Invert the Y axis. Default: off.
- Option N'34'AngleOffsetN'34' N'34'integerN'34'
- Specify a clockwise angular offset (in degrees) to apply to the pointer motion. This transformation is applied before the FlipXY, InvX and InvY transformations. Default: 0.
- Option N'34'SampleRateN'34' N'34'integerN'34'
- Sets the number of motion/button events the mouse sends per second. Setting this is only supported for some mice, including some Logitech mice and some PS/2 mice on some platforms. Default: whatever the mouse is already set to.
- Option N'34'ResolutionN'34' N'34'integerN'34'
- Sets the resolution of the device in counts per inch. Setting this is only supported for some mice, including some PS/2 mice on some platforms. Default: whatever the mouse is already set to.
- Option N'34'SensitivityN'34' N'34'floatN'34'
- Mouse movements are multiplied by this float before being processed. Use this mechanism to slow down high resolution mice. Because values bigger than 1.0 will result in not all pixels on the screen being accessible, you should better use mouse acceleration (see man xset) for speeding up low resolution mice. Default: 1.0
- Option N'34'DragLockButtonsN'34' N'34'L1 B2 L3 B4N'34'
- Sets N'34'drag lock buttonsN'34' that simulate holding a button down, so that low dexterity people do not have to hold a button down at the same time they move a mouse cursor. Button numbers occur in pairs, with the lock button number occurring first, followed by the button number that is the target of the lock button.
- Option N'34'DragLockButtonsN'34' N'34'M1N'34'
- Sets a N'34'master drag lock buttonN'34' that acts as a N'34'Meta KeyN'34' indicating that the next button pressed is to be N'34'drag lockedN'34'.
- Option N'34'ClearDTRN'34' N'34'booleanN'34'
- Enable/disable clearing the DTR line on the serial port used by the mouse. Some dual-protocol mice require the DTR line to be cleared to operate in the non-default protocol. This option is for serial mice only and is handled by the X server. Default: off.
- Option N'34'ClearRTSN'34' N'34'booleanN'34'
- Enable/disable clearing the RTS line on the serial port used by the mouse. Some dual-protocol mice require the RTS line to be cleared to operate in the non-default protocol. This option is for serial mice only and is handled by the X server. Default: off.
- Option N'34'BaudRateN'34' N'34'integerN'34'
- Set the baud rate to use for communicating with a serial mouse. This option should rarely be required because the default is correct for almost all situations. Valid values include: 300, 1200, 2400, 4800, 9600, 19200. Default: 1200.
There are some other options that may be used to control various parameters for serial port communication, but they are not documented here because the driver sets them correctly for each mouse protocol type.
SEE ALSO
Xorg(1), xorg.conf(5), Xserver(1), X(7), README.mouse.
Index
This document was created by man2html, using the manual pages.
Time: 05:33:53 GMT, December 24, 2015


ANNIE HALL A film review by Ted Prigge Copyright 1997 Ted Prigge
Director: Woody Allen Writers: Woody Allen and Marshall Brickman Starring: Woody Allen, Diane Keaton, Tony Roberts, Carol Kane, Paul Simon, Shelly Duvall, Janet Margolin, Colleen Dewhurst, Christopher Walken, Marshall MacLuhan, Dick Cavet, John Glover, Jeff Goldblum, Beverly D'Angelo, Sigourney Weaver
When trying to pick the film in a director's oeuvre that should be referred to as his or her masterpiece, one should not go for the one that was the best over all, but the one that best represents them as a human being. Directors, contrary to popular opinion, are human beings and are trying to inject themselves into their art in one way or another. Whether it's Martin Scorsese telling stories of his home town in "Mean Streets" or Tony Scott telling homoerotic stories in "Top Gun" (you know it's true, that movie is so homoerotic, it's campy), the director has expressed himself with his piece of art, even if it is "Top Gun." Well, I pick "Annie Hall" as Woody Allen's masterpiece. I think it IS his best film, although that is up for argument but has nothing to do with whether it's his masterpiece. He has several masterpieces ("Manhattan," "Hannah and her Sisters," "Crimes and Misdemeanors," "Sleeper"), but none better represent Woody as a person.
One thing you must realize is Woody has been bad with relationships. He was married twice before meeting Diane (I think) and, well, you know all about he and Mia (I actually read her autobiography - interesting...). Well, Woody explains why he continues to go on with them after failing at them several times in this film. On the surface, it's a romantic comedy (and a damn good one at that). If you watch closely (not that closely, really), you see that it is Woody giving a theory he has and showing an example of it. His theory? Glad you asked: Love is annoying and pointless and everything, but we're in it 'cause we need it, 'cause we need to feel liked and to like someone else and perhaps change them a bit, infusing ourselves into their psyche, even if it is just for a bit.  Well, that's what I got from this film.
The film is also incredibly autobiographical, although Woody has reportedly denied it is (uh huh). Granted, some of the parts of the protagonist's life are very over-exaggerated, I'm sure something similar happened to him in his childhood. Woody plays Alvy Singer, a stand-up comedian and comic writer (big stretch). The film begins with a brilliant stand-up routine delivered to the camera as he stands in front of a blank wall. He tells some old vaudevillian jokes (example: "There are two women at a resort, and they're eating, and one of them says: 'The food here is really terrible.' And the other woman says, 'Yes, and in such small portions!'") He then goes on to explain how each applies to his life, giving an odd, universal twist on all of them. He explains that he's pretty tired of himself and how much he was in love with a girl named Annie Hall (Diane Keaton, of course, in her Oscar-Winning role), and how they are now broken up. He says he has been thinking about their relationship a lot and sifting it through his mind. And that's what we get for the next 90 minutes: sifting of his relationship, trying to figure out what went wrong and why he still wants to get into other relationships.
The film, done in a great non-linear form, expresses his views on love and friendship as we see Woody drifting from scene to scene in the most original ways possible. The funniest scene takes place when he first meets her and he goes to her apartment to drink and talk a bit. As they talk about her photography, sub-titles appear below them, stating what they are thinking at that exact moment (example - Alvy: "I wonder what she looks like naked," Annie: "He's too smart for me; hang in there.") It's possibly the most brilliant scene in the film. Another scene involves cartoons when they break up for the first time with Annie portrayed as the witch from "Snow White." Another brilliant scene takes place when Alvy eats at Annie's parents house and he comments on how different his Brooklyn family is to her New England family. Then the screen splits and we see half of Annie's family talking peacefully and the other half is Alvy's family, bickering about passover.
The film has no real plot or anything, but we see Alvy trying to form Annie into what he wants her to be, kind of like "Pygmalion" (only funnier). First off, she takes pictures beautifully, but he wants her to learn about "asthetics" and take classes on it. Second off, she sings in a club and has never taken a lesson. Woody urges her to continue singing and take lessons and all, but her voice is beautiful without them (interesting side-note: Diane is on the original 1969 cast album of "Hair" in a minor role). She's also a tad on the vapid side and sometimes has no idea what he's saying (much of her dialogue consists of "yeah, oh yeah?" but Diane does it so convincingly that it sounds totally realistic), so he convinces her to go to school and take some adult college courses. This backfires as she not only has a crush on one of her professors, but she becomes smarter and the two outgrow eachother, forgetting why they were attracted to eachother in the first place. This happens all the time with couples: they fall in love with eachother but are always trying to change them for the "better." This is probably the reason why so many divorces occur.
One of Woody's biggest pet peeves is California vs. New York. All his films (save a couple) take place in New York, mostly in Manhattan ("Play it Again, Sam" was actually filmed in California, but it was a different director). His best friend, Rob (the great Tony Roberts), is a TV actor who lives out there and Alvy uses him to not only be his designated best friend, but also part of the satire of California. He's always convincing him to come out, but Alvy doesn't want to change himself. He's lived in New York his whole life, in garbage. When he and Annie go out to California so he can do a TV special, Woody remarks about how bad it is, how superficial everyone is and how it's clean because "they dont' throw away they're garbage; they make it into TV shows."
By the end, Alvy and Annie are done for, but we already knew that. All he's left with is what he got from her, how she has rubbed off on him and he is a slightly different person. He carries around black soap she used for her complexion, and she takes later boyfriends to see "The Sorrow and the Pity," a 4-hour holocaust film Alvy dragged her to see numerous times. And at the end, Alvy has figured out why we put up with relationship: 'cause we need them.
"Annie Hall" is also one of his funniest films. He creates hilarious scenes involving some of his phobias and nebbishes. One scene towards the beginning has him being harrassed by scary guys in front of a theatre before a date with Annie where they ask him if he's been on the "Johnny Carson show." Another painfully funny scene (that's a good thing, believe me) involves Alvy sniffing a bit of coke and then sneezing into a pouch of it that had cost one of his friends about 5 grand. But his humor is more realistic and more poignant than his earlier comedies. While most of it is still for satire, much of it is more focused on the point he is trying to make. And the dialogue is so perfect that the film seems to shoot right back at the audience, reminding them of themselves.
The scenes are short and to the point, as not to waste time. It's like he makes his point and ends them, and then somehow tails them onto the next scene. One scene has Alvy and Annie in bed, but Annie's not in the mood so her spirit leaves her body and sits down to draw. Alvy is mad 'cause he wants all of her, but her body just turns to him and says, "You have my body." He wants all of it 'cause he says he's a comedian. She asks him if he's always been funny, and he says, "What is this, an interview? We're supposed to be making love!" And the scene goes to an interview he has to write for some sap.
The acting is terrific from a huge ensemble cast, many of who get small one or two scene parts. Christopher Walken gets to say his funniest speech other than his on in "Pulp Fiction." And Paul Simon gets the harsh task of playing a music producer. Shelly Duvall plays someone he sleeps with on the rebound (Why?!) and Carol Kane plays as if she's on ridlin (compared to her other performances) as Alvy's second wife. Tony Roberts, the underrated man of the 70s, plays his typical best friend, as usual.
But the acting goes to the two leads. Woody and Diane are a flawless comic duo, much better than Mia and Woody (chemistry, please?).  Woody is the usual Woody character, but seems more realistic this time since the film is more realistic. Diane creates her most memorable character (to date) and does the best acting of her entire career.
"Annie Hall" is one of two Woody films to be acknowledged highly by the Academy of Arts and Sciences (the other being "Hannah and her Sisters"). It won four out of the five oscars, including Best Original Screenplay for Woody and Marshall Brickman, Actress for Diane, Direction for Woody, and the Best Picture Oscar. The only one who didn't win was Woody, who lost to Richard Dreyfus for the "Goodbye Girl." As much as I LOVE Richard's performance in "Goodbye Girl," Woody should have won for the same reason John Wayne won in 1969 for "True Grit." Woody's a fantastic actor and he makes his character in this one his most likable and most realistic.
As I've already said, "Annie Hall" is Woody's masterpiece because it best expresses its creator. But also, because it best expresses us as the viewers as we sit watching it, meanwhile living a life where we have several failed romances and we just can't figure out why we keep going out to do it over again.
MY RATING (out of 5): *****
The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
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review and has no editorial control. Unless stated otherwise, the copyright
belongs to the author.
Please direct comments/criticisms of the review to relevant newsgroups.
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Related links: index of all rec.arts.movies.reviews reviews


Qiyun Zhu, Katharina Dittmar
Welcome! This page will guide you through the process of building an effective configuration file for HGTector. You may refer to Quick Start Guide or User Manual for further instructions.
Title of the task: Program mode:
Checklist
HGTector's minimum requirement is but Perl, a standard component of many systems. However, if you have some of the following tools and databases equipped in the system, you will have more options.
Network connection to BLAST servers and remote databases. By default, HGTector works with the NCBI server. All you need is a solid Internet connection.
BLAST server:
Align 2 sequences server:
Entrez search server:
Entrez fetch server:
Entrez search server:
Local BLAST program (NCBI BLAST+ or any alternatives that have compatible input/output) and local databases.
Executables of the BLAST program. Leave blank if they can be launched without their paths specified (the most common situation, same below).
blastp:
blastdbcmd:
Local BLAST database(s). You can either download from the NCBI FTP site, or build one for your own. Please refer to the official NCBI BLAST manual for instructions.
Local taxonomy database. Please download it from the NCBI FTP site, extract the contents to a local directory, and specify the directory below: [?]
All you need are two files: names.dmp and nodes.dmp. For example, type "/home/you/db/taxdump/" if they can be found under this directory. Tip: the taxonomy database should be equally or more up-to-date than the BLAST database(s).
R. HGTector calls R to perform some advanced statistical computing and graphics. To enable the communication between Perl and R, you also need to install Perl package Statistics::R.
R package diptest performs Hartigan's dip test to assess the significance of non-unimodality of weight distributions.
R package pastecs identifies local extrema of a kernel density function, in order to determine cutoffs.
R package rgl creates interactive 3D scatter plots to visualize your data.
Perl package Spreadsheet::WriteExcel. It allows the program to generate reports in Excel spreadsheet format.
Programs for multiple sequence alignment and phylogenetic tree reconstruction.
The following programs can be put together to establish an automated phylogenetics pipeline. You may need some of them if you want to conduct phylogenetical analyses on the results.
Check one if you have it, and type the command (path to the executable, and any additional arguments you like). Leave blank if not necessary.
ClustalW:
MAFFT:
Muscle:
Gblocks:
RAxML:
PhyML:
FastTree:
Input files
HGTector takes one or more protein sets (from one or more, complete or incomplete genomes) as input. Multiple formats are compatible:
Name the protein sets with short and clear file names. Place them under an "input" folder in the working directory.
Alternatively, you may provide HGTector with pre-computed BLAST results. See manual for details.
Step 1: Blaster
Blaster performs all-against-all BLASTP of input proteins in batch mode.
BLAST mode:
Extra step: Treer
Treer builds phylogenetic tree based on BLAST-sampled sequences, using external programs. Resulting trees will be appended to BLAST reports.
Realign sequences, using:
Trim unreliable regions from alignment, using:
Build phylogenetic tree, using: [?]
The tree will be appended to the BLAST report in NEXUS format. You can directly open the file to watch the tree using programs like FigTree.
AA substitution model: Number of bootstrap replicates:
Compute and record phylogenetic distance matrix [?]
Check it if you consider using phylogenetic distances instead of BLAST bit scores for the subsequent prediction.
Step 2: Analyzer
Analyzer performs statistical analysis and predicts HGT events.
Use the conventional best BLAST match ( ) method instead. [?]
If the best non-self match is distal, rather than close, then this gene (protein) is predicted as HGT-derived. This conventional method is sensitive to stochastic events that lead to pseudo positives and negatives. It is therefore depreciated. The program contains this option for comparison purpose only. Note: if BBH is chosen, the program will perform an extra reversal BLAST step on every HGT candidate, which takes some time.
Step 3: Summarizer
Summarizer generates reports in multiple ways to summarize the prediction results.
Ignore hypothetical proteins:
Summarize HGT events by putative donor group, on this rank: [?]
The best distal match organism of each putatively HGT-derived gene (protein) will be summarized by the designated taxonomic rank, to give an estimation of the putative ancient donor group of this HGT event. If no rank is specified (not recommended), the best match organism names will be used.
Summarize HGT events by functional annotation, as provided in this directory: [?]
You need to provide external sources of functional annotation information, for example, reports generated by Blast2GO. They should be placed in one directory, with their names identical to the input protein set names.
Summarize HGT events by gene orthology (evolutionary history of individual gene families).
Refer to an external gene orthology scheme file:
[?]
You can use external programs such as OrthoMCL and blastclust to infer a gene orthology scheme. The result can be directly read by this program. If this box is left blank, the program will try to locate the default orthology scheme file, taxonomy/orthology.db, which might be generated in a previous run. If it is absent, the program will compute one using the built-in function (see below).
Let the program infer gene orthology using its built-in function.
Rule: two genes are defined as (co-)orthologous if they:
Name orthologous groups if necessary (use the shortest name of all members).
Exclude ORFans (genes that only occur once in all genomes)
Generate report in: Plain text Web page (HTML) Excel spreadsheet
Task completed!
Please create a text file named "config.txt" in the working directory, then copy & paste the content below to that file.
Then, you can open a terminal, navigate into the program directory (where there's HGTector.pl), and execute this command:
perl HGTector.pl working_directory
And see how the program rolls!


class: center, middle # Delving more deeply into UNIX ## Buffalo Chapter 3 ??? Notes for the _first_ slide! --- # Overview ##1) A Little Review ##2) Unix Exercise and Tutorials ##3) New UNIX material: * Standard Out and Standard Error * Creating and navigating through directories * Using wildcards * The Pipe and behold, `grep`! * Redirecting streams in pipes * Managing processes * Checking process exit status --- # A little review... -- * What are some ways you can make an analysis pipeline **reproducible**? -- * What are some ways you can make an analysis pipeline **robust**? -- * What are some other key lessons we discussed from Buffalo Chapter 1 or, better yet, that you learned in your own reading? -- * What are the kernel, the shell, and commands? --- # Unix Exercise and Tutorials: -- * As a reminder, in the `Week_01` folder of the GitHub repository, I have placed a UNIX exercise and instructions for how to log in and complete this on hpc-class -- * I would continue working through this this weekend, and, since Monday is Labor Day and there are no classes, type questions in Slack. -- * If you would like additional, basic tutorials on UNIX some online resources include: https://sites.google.com/site/eeob563/computer-labs/Lab-1
-- * And before going further: Any ideas how and when UNIX can be useful? --- class: center, middle # And now for something new... --- ## Standard Out and Standard Error --
-- * What is the difference between standard output and standard error? -- * Within the `Week_01` folder you have several examples files; once inside the folder try this: ``` $ cat file1 file2 file3 ``` -- * In the output, what is standard out and what is standard error? --- ## Standard Out and Standard Error -- * How can standard output and standard error be redirected? -- ``` $ cat file1 file2 file3 > data 2> error ``` -- * How can standard out be appended to an existing file? -- ``` $ cat file4 file5 >> data ``` --- ## Creating and navigating through directories: -- * Let's set up a project as in Buffalo Chapter 3: -- ``` $ mkdir zmays-snps $ cd zmays-snps $ mkdir data $ mkdir data/seqs scripts analysis ``` -- * Try this in your course folder and use the `ls` and `cd` commands to make sure you understand what is happening with the last line of code -- * From within the `seqs` folder, how might you navigate to the `zmays-snps` folder in one line of code? --- ## The `rm` command and why nerds use underscores in their folder/file names: -- * Let's create a folder in `zmays-snps` with a space in its name: `raw sequences` -- ``` mkdir raw\ sequences ``` -- * Now in `zmays-snps` let's create two more folders: ``` $ mkdir raw sequences ``` -- * Over the next few weeks we pile data into `raw` and `sequences` and then one night when we're under-caffeinated we decide to remove the `raw sequences` folder: ``` $ rm -rf raw sequences ``` -- * What just happened?
-- * How *should* we have removed the `raw sequences` folder? --- ## Using shell expansion to make your life easier: -- * Let's go ahead and delete the nice `zmays-snps` directory we've created: ``` $ rm -rf zmays-snps ``` -- * Note that this folder and *all its subdirectories* are erased...thank you `-rf` option -- * Now let's try creating the entire project directory in a single line of code: -- ``` $ mkdir -p zmays-snps/{data/seqs,scripts,analysis} ``` -- * Explain exactly what's going on here... -- * Note the use of the `-p` option for the `mkdir` command which allows for creation of intermediate directories as required -- * Let's use shell expansion to create some files in our reconstructed project directory: -- ``` $ cd zmays-snps/data $ touch seqs/zmays{A,B,C}_R{1,2}.fastq ``` --- ## Wildcards can make your life easier too! * Navigate into your `seqs` folder and use the `ls` command in combination with the `*` and `?` wildcards to match subsets of the files we just created -- * How do `*` and `?` match differently? -- * Let's create new `R1` and `R2` folders and use a wildcard range to move only the "A" and "B" files into these new folders: -- ``` $ mv zmays[AB]_R1* R1 $ mv zmays[AB]_R2* R2 ``` -- * Convince yourself only the appropriate files have been moved and then move the "C" files as well -- * Always be careful with wildcards, particularly when using the `rm` command. For example: -- How are these different? ``` $ rm -rf tmp-data/aligned-reads* $ rm -rf tmp-data/aligned-reads * ``` --- ##The Pipe -- * In this example, how are standard out and standard error streams being funneled? ``` $ cat file1 file2 | grep "AGGATA" | wc ``` -- * Why pipe rather than create intermediate files? -- * Behold the mighty `grep` command!! -- * Let's see what this command can do using an example from Buffalo Chapter 3... -- * First, we need to clone supplementary material for the book into hpc-class so `cd` to the top of your directory and type: ``` $ git clone https://github.com/vsbuffalo/bds-files ``` --- Suppose we're working with a program that throws an error telling us that our fasta input file has non-nucleotide characters. Let's use grep in a pipe to inspect our input file: ``` $ grep -v "^>" tb1.fasta | grep --color -i "[^ATGC]" ``` --- ## Controlling streams within pipes -- * Pipes can string together multiple programs and increase the efficiency of our analysis -- * However, imagine your pipe includes 20 programs and multiple errors are thrown to your display during the analysis -- * Which program had the issue printed to standard error? -- * Let's talk through an example of how to manage this: -- ``` $ program1 input.txt 2> program1.stderr | \ program2 2> program2.stderr > results.txt ``` -- * But what if we want to send our standard output and standard error to the same place? -- ``` $ program1 input.txt 2>&1 | grep "error" ``` --- ## But what if I really love intermediate files? -- * Sometimes you or your collaborator may need intermediate files in a pipeline for other analyses or for debugging -- * Can you retain the efficiency of the pipe while also creating intermediate files? -- * You betcha: -- ``` $ program1 input.txt | tee intermediate-file.txt | program2 > results.txt ``` --- ##Managing processes: sending programs to the background: -- * Often times our UNIX programs and pipelines will run for an extended amount of time -- * It is not terribly convenient to sit and stare at our terminal for weeks at a time -- * The running job also ties up our terminal if we're running it in the foreground (however, you can open up multiple tabs or terminals) -- * One solution to this is running your analysis in the background using the ampersand: -- ``` $ program1 input.txt > results.txt & ``` -- * This process will be run in the background, freeing up your terminal, and a process ID will be provided: -- ``` [1] 25744 ``` --- ##Managing processes: checking status and bringing to the foreground: -- * Say the next day we come to work and want to check quickly whether our analysis is still running: -- ``` $ jobs [1]+ Running program1 input.txt > results.txt ``` -- * And what if, now that we're back at work, we want to stare at the process while it runs all day? -- * This is where your process ID number will come in handy: -- ``` $ fg %25744 ``` -- * Now you can watch your process run to your heart's content -- * Question: *What happens when you run a program in the background and close your terminal application?* --- ##Managing processes: sending active programs to the background: -- * Say you start a program, realize it's going to take forever to run and then want to send it to the background... -- ``` $ program1 input.txt > results.txt $ # enter control-z here...NOT CONTROL-C!! [1]+ Stopped program1 input.txt > results.txt $ bg [1]+ program1 input.txt > results.txt ``` -- * To irrevocably kill a job type "control-c"; your job must be in the foreground for this to work --- ##Checking the exit status of a completed program * Say we come into work and find our program has completed with no errors printed to our display -- * To double-check that all has gone swimmingly, we can check the exit status by inspecting our shell variable: -- ``` $ grep -v "^>" tb1.fasta | grep --color -i "[^ATGC]" CCCCAAAGACGGACCAATCCAGCAGCTTCTACTGCTAYCCATGCTCCCCTCCCTTCGCCGCCGCCGACGC $ echo $? 0 ``` -- * You can utilize the exit status in your pipelines by implementing the shell operators `&&` and `||` -- * A few examples: -- ``` $ program1 input.txt > intermediate-results.txt && \ program2 intermediate-results.txt > results.txt ``` -- ``` $ program1 input.txt > intermediate-results.txt || \ echo "warning: an error occurred" ``` --- ##Exit status operators, `true` and `false` -- * There are two Unix commands that are very useful for understanding exit status, the shell variable and operators: `true` and `false` -- * `true` always sets the shell variable to 0 (success) -- * `false` always sets the shell variable to 1 (failure) -- * Try the following commands and see if what they return makes sense to you: ``` $ true && echo "first command was a success" $ true || echo "first command was not a success" $ false || echo "first command was not a success" $ false && echo "first command was a success" ``` --- ## Command substitution: -- * Sometimes rather than piping, we may actually want to nest commands within other commands -- * This process is called "command substitution" and here are a few examples... -- * `cd` into the `chapter-03-remedial-unix` folder of your Buffalo online materials and in your terminal type: ``` $ echo "There are $(grep -cv '^>' tb1.fasta) lines of sequence in my FASTA file." ``` -- * What is the result, and what's going on here? -- * Now `cd` into your `in_class` folder and try: -- ``` $ mkdir results-$(date +%F) $ ls ``` -- * You can name folders and files with today's date without even knowing what that is!


{% extends "global/Page.html" %} {% load otree static %} {% block content %}
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{% extends "maintainer/mbase.html" %} {% block title %}AMP Tech | Question Management{% endblock title %} {% block content %}


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