LOGIN
Different login ID’s have different access privileges within the system. Your login will allow you to search the database for a chemical and to be able to write a risk assessment for any chemical in the inventory.
Information retrieved on any one chemical includes - location, grade, lab manager, hazardous nature and dangerous goods class.
Once logged in, the black bar at the top of the screen shows four options
- Search chemicals
- Update & Add
- Risk Assessment
- Admin
SEARCH CHEMICALS
Search for one chemical in all locations
Enter the chemical name or CAS # of the chemical and leave the location menu showing 'ALL' .
Click on a chemical name for more details on that particular chemical container. The 'back' button on your browser will take you back to the search list.
Return a list of all chemicals in a single location.
Use the drop-down list to choose a location. Enter an asterisk, * , in the chemical name box then click 'Search'. The asterisk wildcard character represents all chemicals. Don't try to search all chemicals in all locations - there are thousands of chemicals in the system!
You can perform a wildcard search by using an asterisk in place of any group of characters within the name of a chemical e.g. entering "cop*" will return all chemicals starting with "cop", entering "b*acid" will return acids starting with "b".
Click on a chemical name for more details on that particular chemical container. The ‘back’ button on your browser will take you back to the search list.
UPDATE AND ADD
Not accessible.
RISK ASSESSMENTS
If you are using a chemical that is hazardous you will need to use the risk assessment section to help you record your risk assessment details. It is a legal requirement that before you use a chemical you must:
- identify the level of risk associated with the way that particular hazardous substance is used,
- assess the risk of harm that the chemical can cause and
- control the risk of harm.
This section is designed to make it easy to record you risk assessment details.
- Open up the OCID site and go to the 'risk assessment' section
- Search for one chemical in all locations or Return a list of all chemicals in a single location
(see the Search Chemicals section above).
- Click on 'add' next to the chemical for which you wish to create a new risk assessment*.
- Fill out the risk assessment form and click the 'Add the New Risk Assessment' button at the bottom of the page to save the assessment.
- Click the 'Search Risk Assessment' button again to see the new assessment in the list.
- By clicking 'View' you can have a look at the details of any assessment. At the bottom of the page are the buttons 'Undo Changes', 'Update' and 'Delete'. These allow you to make changes to the assessment later if needed. 'Undo Changes' removes any changes to the assessment form that have not yet been saved. 'Update' saves the assessment details. 'Delete' deletes the whole assessment.
- Print the assessment to have it signed by your supervisor once all the recommended controls are in place (you may want to remove the header/footer options in 'page setup' of your browser).
- Keep the signed assessment in a folder.


| Recorded Crime Offences (Number) by Garda Station, Type of Offence and Year |
|||||||
|---|---|---|---|---|---|---|---|
| 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | ||
| Lusk, D.M.R. Northern Division | 03 ,Attempts/threats to murder, assaults, harassments and related offences | 32 | 24 | 36 | 30 | 48 | 53 |
| 06 ,Robbery, extortion and hijacking offences | 2 | 14 | 8 | 4 | 3 | 7 | |
| 07 ,Burglary and related offences | 79 | 80 | 81 | 84 | 91 | 53 | |
| 08 ,Theft and related offences | 356 | 387 | 319 | 412 | 354 | 292 | |
| See Background Notes |


Remove conditions that promote administrative corruption - Expert
by Edmund Quaynor, GNA
Koforidua, Nov. 12, GNA - A consultant on corruption has called on the government to strive to remove the conditions that encourages administrative corruption.
Ms Clara Kasser of Tee, Consult, a private consulting firm on corruption was speaking at a sensitization workshop on how to prevent and fight corruption at Koforidua.
The workshop was organized by the Private Enterprise Federation (PEF) for private enterprises in the Eastern Region and sponsored by UK Aid, the European Union and the Danish International Development Agency (DANIDA).
Ms Kesser said business men and investors would always be pushed to pay a bribe whenever there is a delay in delivering the services they required.
She explained that to stop the corruption in the public service, the target should be aimed at removing the delays in the rendering of public service.
Ms Kesser called for the production of service charters by the public service to give a clear information about the services rendered by each agency, the duration that it takes to be served, the responsibility of the customer and the cost involved.
She said the service charter need to provide a service telephone line for complains by customers who have issues with the service rendered to them and how it would be resolved.
She said the service charter need to be published and be reviewed periodically to always meet the requirements of the time.
Ms Kesser suggested that public agencies should be made to retain part of the amount realized from their service charges so that they would not need any financial support from the customers before serving them.
Earlier in a welcome address, Nana Osei Bonsu, the Chief Executive Officer of PEF explained that the workshop was to share experiences of the participants on administrative corruption.
He said the exercise was to enable PEF to gather the necessary data to engage policy makers to help remove conditions that promote administrative corruption to help reduce the frustrations that investors face when they need some service from the public sector.
GNA


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class java.lang.
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class net.nutch.ipc.
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class net.nutch.searcher.
DistributedSearch.Client
(implements net.nutch.searcher.
HitContent
, net.nutch.searcher.
HitDetailer
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class net.nutch.searcher.
DistributedSearch
class net.nutch.searcher.
DistributedSearch.Param
(implements net.nutch.io.
Writable
)
class net.nutch.searcher.
DistributedSearch.Result
(implements net.nutch.io.
Writable
)
class net.nutch.searcher.
FetchedSegments
(implements net.nutch.searcher.
HitContent
, net.nutch.searcher.
HitSummarizer
)
class net.nutch.searcher.
FieldQueryFilter
(implements net.nutch.searcher.
QueryFilter
)
class net.nutch.searcher.
Hit
(implements java.lang.
Comparable
, net.nutch.io.
Writable
)
class net.nutch.searcher.
HitDetails
(implements net.nutch.io.
Writable
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class net.nutch.searcher.
Hits
(implements net.nutch.io.
Writable
)
class net.nutch.searcher.
IndexSearcher
(implements net.nutch.searcher.
HitDetailer
, net.nutch.searcher.
Searcher
)
class net.nutch.searcher.
NutchBean
(implements net.nutch.searcher.
HitContent
, net.nutch.searcher.
HitDetailer
, net.nutch.searcher.
HitSummarizer
, net.nutch.searcher.
Searcher
)
class net.nutch.searcher.
Query
(implements java.lang.
Cloneable
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Writable
)
class net.nutch.searcher.
Query.Clause
(implements java.lang.
Cloneable
)
class net.nutch.searcher.
Query.Phrase
class net.nutch.searcher.
Query.Term
class net.nutch.searcher.
QueryFilters
class net.nutch.searcher.
RawFieldQueryFilter
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QueryFilter
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class net.nutch.ipc.
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class net.nutch.searcher.
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class net.nutch.searcher.
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Summary
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class java.lang.
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class java.lang.
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class net.nutch.searcher.
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interface net.nutch.searcher.
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interface net.nutch.searcher.
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interface net.nutch.searcher.
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Copyright © 2005 The Nutch Organization.


Hi there! Welcome to dStock Watch.
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Introduction
This introduction is based on this article, (c) James Simpson.
The nested set model is a particular technique for representing nested sets (also known as trees or hierarchies) in
relational databases. The term was apparently introduced by Joe Celko; others describe the same technique without naming
it or using different terms. (Source: Wikipedia)
A typical example of a tree structure is an organigram of an organisation. We'll be using this to explain how nested sets work.
The above diagram is indicating that each node is aware of all its descendants, and vice versa. For example, we can see easily
enough from the diagram that Ben and Angela are "children" of Bill. We can also see that Tim and James are "children" of Ben.
This ultimately gives us a link between each member of the hierarchy.
For us to represent this we need to store two more values per node, that define the relationship between the nodes of the
tree structure. These are shown on the diagram in blue and red. We call these Left (red values)
and Right (blue values) pointers.
These values are stored on the table, this is all we need to fully represent a nested sets hierarchy.
Those who are into Mathematics know that you can use a different diagram to represent tree structures:
Although this might look confusing at first, and certainly more difficult to read, it is immediately clear why this is called
nested sets, and why this way of storing hierarchical data in a flat table is efficient: you can directly see the relation
between parent and children (all children are contained within their parent), and every node is aware of its parent, and all
its descendants. Using this representation you can clearly see that all pointers line up beautifully. This will come in very
handy when we need to access the tree.
Storing multiple tree structures in a single table
You can store multiple tree structures into a single database table. To make this possible, you can add a tree-id
column to the table. The tree-id identifies the tree the node belongs to.
A tree-id may either be an integer or a string, and it can be auto-generated for you when you create a new tree, in case integers
are used. Integers also make it easier to use the tree-id as a foreign key in a one-to-many relation, and their index lookup
in the database is faster. It's strongly suggested you don't use a string value as a tree-id.
Table structure
You can add as many columns to the table as you want, but to be able to work, the Nestedset Model requires certain
columns to be present:
- Left node pointer, default column name is 'left_id'
- Right node pointer, default column name is 'right_id'
- Tree id, a required column only if the table contains multiple trees (no default)
The actual names of the columns used for these functions can be configured in the model. Altough not strictly needed,
several methods require a "title" or "name" field. The name of this column can be configured in the model as well.
If you use a method that requires it to be present, but you haven't defined it, an exception will be thrown.
This is a minumal stucture for a nested sets table:
CREATE TABLE `tree` (
`id` int(11) unsigned NOT NULL AUTO_INCREMENT,
`left_id` int(11) unsigned NOT NULL,
`right_id` int(11) unsigned NOT NULL,
`tree_id` int(11) unsigned NOT NULL,
`name` varchar(50),
PRIMARY KEY (`id`),
KEY `left_id` (`left_id`), // optional, might speed up certain lookups
KEY `right_id` (`right_id`), // optional, might speed up certain lookups
)
Configuration
The Nestedset Model adds an additional property, $_tree, to the model, with which you can configure the model:
- left_field defines the name of the table column that is used to store the tree's left pointer. The column name defaults to "left_id".
- right_field defines the name of the table column that is used to store the tree's right pointer. The column name defaults to "right_id".
- tree_field defines the name of the table column that is used to store the tree's id, a value that uniquely identifies a tree in case you
want to store multiple trees in a single table. If you use a numeric value as tree-id, the model can automatically assign it when you
create new tree root nodes. If it is not numeric, you have to supply the value before you call save(). There is no default value.
- title_field defines the name of the table column that is used to store the tree node's title or name. It is optional, the
Model works well without it, but it is required for some of the models methods. Where applicable this is mentioned in the documentation
of the method. There is no default value.
The next section show you what a basic Nestedset model looks like, and how you configure it.
Defining the model
Using the nested sets model is as easy as extending \Orm\Model_Nestedset instead of \Orm\Model.
This marks your model as being a nested sets model, adds a lot of methods to manipulate trees and nodes, and changes
the default behaviour of the delete() and save() methods to make sure the tree stays consistent.
<?php
class Model_Tree extends \Orm\Model_Nestedset
{
/**
* @var string name of the table to be used by this model
*/
protected static $_table_name = 'tree';
/**
* @var array array of object properties
*/
protected static $_properties = array(
'id',
'left_id',
'right_id',
'tree_id',
'name',
);
/**
* @var array array with the tree configuration
*/
protected static $_tree = array(
'left_field' => 'left_id', // name of the tree node left index field
'right_field' => 'right_id', // name of the tree node right index field
'tree_field' => 'tree_id', // name of the tree node tree index field
'title_field' => 'name', // name of the tree node title field
);
}
?>
As you can see, a pretty standard ORM model configuration. The only additional class property is $_tree, which defines
the tree configuration. The model is then set up like a normal ORM model, including any relations
or other properties that you wish to use.
Using the model
Based on the example in the introduction and the model defined above, let's start by creating this tree.
<?php
// Bill, our MD, is the root of the tree
$bill = Model_Tree::forge(array('name' => 'Bill'));
// if you save a new node, it will automatically become a tree root node
$bill->save();
// give our MD some subordinates
$angela = Model_Tree::forge(array('name' => 'Angela'));
$ben = Model_Tree::forge(array('name' => 'Ben'));
// they are children of Bill in the tree
$angela->child($bill)->save();
$ben->child($bill)->save();
// add the rest of Customer service
$henry = Model_Tree::forge(array('name' => 'Henry'));
$henry->child($angela)->save();
$nicola = Model_Tree::forge(array('name' => 'Nicola'));
$nicola->child($angela)->save();
// and the development team
$kerry = Model_Tree::forge(array('name' => 'Kerry'));
$kerry->child($ben)->save();
// a sibling of Kerry is a child of Ben too...
$james = Model_Tree::forge(array('name' => 'James'));
$james->sibling($kerry)->save();
// assign the teams benjamin to Kerry
$tim = Model_Tree::forge(array('name' => 'Tim'));
$tim->child($kerry)->save();
?>
As you can see, creating a tree and adding tree nodes is pretty straitforward. One of the main differences between the
Nestedset model and other ORM models, it that is has methods that operate on other model objects. You don't just query
the model, or save an object, you do it in relation to another object in the tree. That doesn't mean you can't use the
traditional methods, Model::find() and Model::query() still work like for any other ORM model.
Let's move on to describing the methods that are available for getting information out of our tree and manupulating the
tree structure.
Behavioral changes
In addition to the primary key, which is read-only in every ORM model object once set, a Nestedset model doesn't allow
you to make changes to the left- and right pointers of the node, and to the tree-id if defined. Attempting to do so, either
via assigment, using a call to set() or by using unset(), will result in a InvalidArgumentException.
save($cascade = null, $use_transaction = false)
The save method works exactly the same as the regular model's implementation.
However, when you use this method on new tree node objects, additional functionality is added to make sure the tree structure
stays consistent. When you call it on an object and you have used one of the collection methods documented below, the
new object is inserted in the tree relative to the object passed to the collection method.
If you haven't used a collection method, save will assume you want to insert a new root node. If the model is
a multi-tree model, it will create a new root with the next available tree-id (if the id is numeric. If not, assign a new
tree-id to the node object yourself).
If a root node can not be created because one already exists, an OutOfBoundsException will be thrown. If
the tree-id is not numeric, and you haven't supplied one manually, the result is unpredicable!
delete($cascade = null, $use_transaction = false)
The delete method works exactly the same as the regular model's implementation.
If the node you delete is not a leaf node (i.e. is has children), all descendants of the node will move one level up in the
tree, they will become descendants of the nodes parent. If you want to delete an entire (subsection of the) tree, use the
delete_tree() method instead.
You can not use the delete() method on a root node if the root node has more then one child node.
Doing so would create an inconsistent tree, as you can't have multiple nodes at the highest level. Trying do to so
will throw a DomainException!
Collection methods
Collection methods are methods that allow you to perform an operation, either a get() or a save(),
on a part of a nestedset tree. Some methods are available for both, some are only relevant for one. For clarity, they are documented
seperately. Using a collection method on an operation that doesn't support it will cause an OutOfBoundsException to
be thrown.
Collection methods for getting nodes
Like with standard ORM models, you can use the get() method to return an array of objects, and the
get_one() method to return a single object. If a collection method is supposed to return a single result,
like for example root(), get() will return an array with that single object. If
a collection method returns multiple objects, like for example children(), get_one()
will return the first object from the result set. It is undetermined which one that will be.
get() and get_one() return null if no result was found.
root()
The root method allows you to get the root of the tree of the object you call this method on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the root of the tree $henry belongs to
$root = $henry->root()->get_one();
// echos 'true'
echo $root == $bill ? 'true' : 'false';
// get the root of a specific tree
$root = Model_Tree::forge()->set_tree_id($mytreeid)->root()->get_one();
|
roots()
The roots method allows you to get all the root nodes. If the model is not a multi-tree model,
only the one root node is returned.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get all roots in the tree
$roots = $henry->roots()->get();
// echos 'true' (there's only one root in the tree)
echo reset($roots) == $bill ? 'true' : 'false';
// get alls root without having an existing object
$roots = Model_Tree::forge()->roots()->get();
|
parent()
The parent method allows you to get the parent node of the object you call this method on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the parent of $nicola
$parent = $nicola->parent()->get_one();
// echos 'true'
echo $parent == $angela ? 'true' : 'false';
// returns null, it won't work without a node tree context
$parent = Model_Tree::forge()->parent()->get_one();
|
children()
The children method allows you to get all child nodes of the object you call this method on.
Note that this returns only children, no grandchildren. If you are interested in the entire sub-tree, use
the descendants method instead.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the children of $angela
$children = $angela->children()->get();
// echos 'true'
echo $children == array($henry->id => $henry, $nicola->id => $nicola) ? 'true' : 'false';
// returns null, it won't work without a current node context
$parent = Model_Tree::forge()->children()->get();
|
ancestors()
The ancestors method allows you to get all ancestor nodes of the object you call this method on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the ancestors of $henry
$ancestors = $henry->children()->get();
// echos 'true'
echo $ancestors == array($bill->id => $bill, $angela->id => $angela) ? 'true' : 'false';
// returns null, it won't work without a current node context
$parent = Model_Tree::forge()->ancestors()->get();
|
Ancestors are returned in order of their position in the tree, with the root node first.
descendants()
The descendants method allows you to get all descendant nodes of the object you call this method on.
This allows you to fetch an entire sub-tree.The result will NOT include the start node itself.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the descendants of $ben
$descendants = $ben->descendants()->get();
// echos 'true'
echo $descendants == array($kerry->id => $kerry, $tim->id => $tim, $james->id => $james) ? 'true' : 'false';
// returns null, it won't work without a current node context
$parent = Model_Tree::forge()->descendants()->get();
|
Descendants are returned in order of their position in the tree.
leaf_descendants()
The leaf_descendants method allows you to get leaf descendant nodes of the object you call this method on.
Unlike the descendants method, this method only returns nodes that do not have
children (the leafs of the tree).
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the leaf descendants of $ben
$descendants = $ben->leaf_descendants()->get();
// echos 'true'. Note that $kerry is not returned now, as that has a child object
echo $descendants == array($tim->id => $tim, $james->id => $james) ? 'true' : 'false';
// returns null, it won't work without a current node context
$parent = Model_Tree::forge()->leaf_descendants()->get();
|
Leaf descendants are returned in order of their position in the tree.
siblings()
The siblings method allows you to get all sibling nodes of the object you call this method on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the siblings of $kerry
$siblings = $kerry->siblings()->get();
// echos 'true'
echo $siblings == array($kerry->id => $kerry, $james->id => $james) ? 'true' : 'false';
// returns null, it won't work without a current node context
$parent = Model_Tree::forge()->siblings()->get();
|
Siblings are returned in order of their position in the tree. Note that the result set will include the current node!
child()
The child method is an alias for the last_child method.
first_child()
The first_child method allows you to get the first child node of the object you call this method on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the first child of $bill
$child = $bill->first_child()->get_one();
// echos 'true'
echo $child == $angela ? 'true' : 'false';
// returns null, it won't work without a current node context
$parent = Model_Tree::forge()->first_child()->get_one();
|
last_child()
The last_child method allows you to get the last child node of the object you call this method on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the last child of $bill
$child = $bill->last_child()->get_one();
// echos 'true'
echo $child == $ben ? 'true' : 'false';
// returns null, it won't work without a current node context
$parent = Model_Tree::forge()->last_child()->get_one();
|
sibling()
The sibling method is an alias for the next_sibling method.
previous_sibling()
The previous_sibling method allows you to get the previous_sibling node of the object you call this method on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the previous sibling of $nicola
$sibling = $nicola->previous_silbing()->get_one();
// echos 'true'
echo $sibling == $henry ? 'true' : 'false';
// returns null, it won't work without a current node context
$parent = Model_Tree::forge()->previous_sibling()->get_one();
// will return null too, $henry has no previous sibling
$sibling = $henry->previous_silbing()->get_one();
|
next_sibling()
The next_sibling method allows you to get the next sibling node of the object you call this method on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the next sibling of $henry
$sibling = $henry->next_silbing()->get_one();
// echos 'true'
echo $sibling == $nicola ? 'true' : 'false';
// returns null, it won't work without a current node context
$parent = Model_Tree::forge()->previous_sibling()->get_one();
// will return null too, $nicola has no previous sibling
$sibling = $nicola->next_silbing()->get_one();
|
path($addroot = true)
The path method returns the path to the current node as a string, using the column identified
by the "title_field" in the models tree configuration.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $addpath |
true |
If false, the root node will be excluded from the result. |
|
| Returns |
Model_Nestedset, for chaining. |
| Throws |
OutOfBoundsException, if the model doesn't define a "title_field" column. |
| Example |
// get the path to Tim, returns "Bill/Ben/Kerry/Tim"
$path = $tim->path()->get();
// get the path to Nicola, returns "Bill/Angela/Nicola"
$path = $nicola->path()->get();
// get the path to Kerry, and exclude the boss. returns "Ben/Kerry"
$path = $kerry->path(false)->get();
|
Collection methods for saving nodes
Like with a standard ORM model, save() will either insert the object as a new record in the table,
or it updates an existing record in case the object was retrieved from the database.
However, unlike a standard ORM model in a nestedset tree is is very relevant where exactly in the tree an object
is saved. If you don't specify a collection method before save, saving an existing object will just do that, identical to
normal ORM model behaviour. If you did specify a collection method, the object will be relocated in the tree when you save.
If your saving a new object, not specifing a collection method will create a new root node. If you did specify one, it will
determine where in the tree the new node will be inserted.
child($to = null)
The child method is an alias for the last_child method.
first_child($to = null)
The first_child method tells the model you want to save the object you call this method on
as the first child of the (primary key of the) node object passed.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $to |
null |
The node object or the primary key of the node which has to become the parent of the object on which this method is called. |
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// give bill a new subordinate, before Angela in the tree
$john = Model_Tree::forge(array('name' => 'John'))->first_child($bill)->save();
// promote Kerry to a subordinate of Bill
$kerry->first_child($bill)->save();
|
last_child($to = null)
The last_child method tells the model you want to save the object you call this method on
as the last child of the (primary key of the) node object passed.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $to |
null |
The node object or the primary key of the node which has to become the parent of the object on which this method is called. |
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// give bill a new subordinate, after Ben in the tree
$john = Model_Tree::forge(array('name' => 'John'))->last_child($bill)->save();
// promote Kerry to a subordinate of Bill
$kerry->last_child($bill)->save();
|
From a hierarchy perspective, first_child and last_child do the same. Only the
exact position in the tree, the relation to its siblings after the insert or relocation of the node, is different.
sibling($to = null)
The sibling method is an alias for the next_sibling method.
previous_sibling($to = null)
The previous_sibling method tells the model you want to save the object you call this method on
as the previous sibling of the (primary key of the) node object passed (just before the passed object, on the same level in the tree).
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $to |
null |
The node object or the primary key of the node which has to become the next sibling of the object on which this method is called. |
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// give bill a new subordinate, before Angela in the tree
$john = Model_Tree::forge(array('name' => 'John'))->previous_sibling($angela)->save();
// demote James to be a subordinate of Ben, besides Tim
$james->previous_sibling($tim)->save();
|
next_sibling($to = null)
The next_sibling method tells the model you want to save the object you call this method on
as the next sibling of the (primary key of the) node object passed (just after the passed object, on the same level in the tree).
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $to |
null |
The node object or the primary key of the node which has to become the previous sibling of the object on which this method is called. |
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// give bill a new subordinate, after Angela in the tree
$john = Model_Tree::forge(array('name' => 'John'))->next_sibling($angela)->save();
// demote James to be a subordinate of Ben, besides Tim
$james->next_sibling($tim)->save();
|
Test methods
Test methods are used to query a particular state of the object with regards to their position in the tree.
is_root()
The is_root method tells you if the object you're calling it on is a root node or not.
| Static |
No |
| Parameters |
None.
|
| Returns |
Bool, true if the object is a root node, false if not |
| Example |
// is Bill a root node? echo's 'true'
echo $bill->is_root() ? 'true' : 'false';
// is Tim a root node? echo's 'false'
echo $tim->is_root() ? 'true' : 'false';
|
is_leaf()
The is_leaf method tells you if the object you're calling it on is a leaf, i.e. that is doesn't have child nodes.
| Static |
No |
| Parameters |
None.
|
| Returns |
Bool, true if the object is a leaf node, false if not |
| Example |
// is Tim a leaf node? echo's 'true'
echo $tim->is_leaf() ? 'true' : 'false';
// is Angela a leaf node? echo's 'false'
echo $angela->is_leaf() ? 'true' : 'false';
|
is_child()
The is_child method tells you if the object you're calling it on is a child node, i.e. that is has
a parent node. This is the reverse of is_root(), as all non-root nodes have a parent.
| Static |
No |
| Parameters |
None.
|
| Returns |
Bool, true if the object is a child node, false if not |
| Example |
// is Henry a root node? echo's 'true'
echo $henry->is_child() ? 'true' : 'false';
// is Bill a root node? echo's 'false'
echo $bill->is_child() ? 'true' : 'false';
|
is_child_of(Model_Nestedset $to = null)
The is_child_of method allows you to check if the object you call this method on
is a child node (a direct descendant) of the node object passed.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $to |
null |
The node which you want to check against. |
|
| Returns |
Bool, true if the object is a child node of the node passed, false if not |
| Example |
// is Ben a child node of Bill? echo's 'true'
echo $ben->is_child_of($bill) ? 'true' : 'false';
// is James a child node of Bill? echo's 'false', as it's a grandchild
echo $james->is_child_of($bill) ? 'true' : 'false';
// is Nicola a child node of Ben? echo's 'false', different part of the tree
echo $nicola->is_child_of($ben) ? 'true' : 'false';
|
is_descendant_of(Model_Nestedset $to = null)
The is_descendant_of method allows you to check if the object you call this method on
is a descendant node of the node object passed.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $to |
null |
The node which you want to check against. |
|
| Returns |
Bool, true if the object is a descendant node of the node passed, false if not |
| Example |
// is Ben a descendant node of Bill? echo's 'true'
echo $ben->is_descendant_of($bill) ? 'true' : 'false';
// is James a descendant node of Bill? echo's 'true', as it's a grandchild
echo $james->is_descendant_of($bill) ? 'true' : 'false';
// is Nicola a descendant node of Ben? echo's 'false', different part of the tree
echo $nicola->is_descendant_of($ben) ? 'true' : 'false';
|
is_parent_of(Model_Nestedset $to = null)
The is_parent_of method allows you to check if the object you call this method on
is the parent node of the node object passed.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $to |
null |
The node which you want to check against. |
|
| Returns |
Bool, true if the object is the parent node of the node passed, false if not |
| Example |
// is Bill the parent of Ben? echo's 'true'
echo $bill->is_parent_of($ben) ? 'true' : 'false';
// is Bill the parent of James? echo's 'false', as it's a grandparent
echo $bill->is_parent_of($james) ? 'true' : 'false';
|
is_ancestor_of(Model_Nestedset $to = null)
The is_ancestor_of method allows you to check if the object you call this method on
is a ancestor of the node object passed.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $to |
null |
The node which you want to check against. |
|
| Returns |
Bool, true if the object is an ancestor of the node passed, false if not |
| Example |
// is Bill an ancestor of Ben? echo's 'true'
echo $bill->is_ancestor_of($ben) ? 'true' : 'false';
// is Bill an ancestor of James? echo's 'true', as it's a grandparent
echo $bill->is_ancestor_of($james) ? 'true' : 'false';
|
is_same_model_as(Model_Nestedset $to = null)
This method is mainly used internally to avoid operations across two different Nestedset models.
is_same_tree_as(Model_Nestedset $to = null)
This method is mainly used internally to avoid operations across two different Nestedset models.
It not only checks if both objects are instances of the same model, but also if both instances belong
to the same tree in a multi-tree model.
has_parent()
The has_parent method is an alias for the is_child method.
has_children()
The has_children method is the reverse of the is_leaf method.
If an object is not a leaf, it implies it has child nodes.
has_previous_sibling()
The has_previous_sibling method tells you if the object you're calling it on has a previous sibling.
| Static |
No |
| Parameters |
None.
|
| Returns |
Bool, true if the object has a previous sibling, false if not |
| Example |
// Does James have a previous sibling? echo's 'true'
echo $james->has_previous_sibling() ? 'true' : 'false';
// Does Tim have a previous sibling? echo's 'false'
echo $tim->has_previous_sibling() ? 'true' : 'false';
|
has_next_sibling()
The has_next_sibling method tells you if the object you're calling it on has a next sibling.
| Static |
No |
| Parameters |
None.
|
| Returns |
Bool, true if the object has a next sibling, false if not |
| Example |
// Does Henry have a next sibling? echo's 'true'
echo $henry->has_next_sibling() ? 'true' : 'false';
// Does Ben have a next sibling? echo's 'false'
echo $ben->has_next_sibling() ? 'true' : 'false';
|
Miscellaneous methods
delete_tree($cascade = null, $use_transaction = false)
The delete_tree works identical to the delete() method, which the difference that
this method DOES delete all children as well.
If you use the delete_tree() method on a root node, the entire tree will be deleted!
tree_config($name = null)
You use this method to get one or all tree configuration options of the model. It is mainly used internally
to construct queries that operate on parts of the tree, or on a specific tree in a multi-tree model.
| Static |
Yes |
| Parameters |
| Param |
Default |
Description |
| $name |
null |
The name of the configuration property to return. |
|
| Returns |
A configuration value, an array of values, or null if the requested value does not exist. |
| Example |
// get the name of the tree-id column
$tree_id = Model_Tree::tree_config('tree_id');
|
get_tree_id()
You use this method to get the tree-id in a multi-tree environment. If there is a valid node to operate on, the
tree-id of that node is returned. If not, the value set using set_tree_id() is returned.
If no tree-id has been set, an exception is thrown. This method is mainly used internally to make sure queries
run in the context of the current tree in a multi-tree environment.
| Static |
No |
| Parameters |
None.
|
| Returns |
mixed, the tree-id of the current tree, or the default tree-id set. |
| Example |
// get the tree_id (returns 1)
$current_tree = $bill->get_tree_id();
|
set_tree_id($tree = null)
You use this method to set the tree-id in a multi-tree environment. You mainly use this when you want to
run a get() or get_one() but you don't have an existing node to work on.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $tree |
null |
The tree-id of the tree to select. If no value, or null, is passed, the stored tree-id is reset. |
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// get the root of a tree without having a previous node to work with
$root = Model_Tree::forge()->set_tree_id($mytreeid)->get_one();
|
build_query()
The build_query method returns an ORM query object, like Model_Nestedset::query()
but with an added where clause in case of a multi-tree model, to make sure the query runs in the context of the
current tree. It requires a tree-id to be available, so if you call this on a new object, use set_tree_id to make
sure a valid id is defined.
| Static |
No |
| Parameters |
None.
|
| Returns |
an ORM Query object. |
| Example |
// get all nodes in the current tree with an enabled status set
$enabled = Model_Tree::forge()
->set_tree_id($mytreeid)
->build_query()
->where('enabled', '=', 1)
->get();
// using an existing object, this will use the tree-id of the $bill object
$enabled = $bill
->build_query()
->where('enabled', '=', 1)
->get();
|
get_query()
The get_query method returns an ORM query object, but unlike build_query()
this method requires a collection methods to be used. It allows you to use the standard Model methods to
constuct a first selection of nodes, and use the returned Query object to fine-tune the query.
| Static |
No |
| Parameters |
None.
|
| Returns |
an ORM Query object. |
| Example |
// get all child nodes of Bill with an enabled status set
$enabled = $bill
->children()
->get_query()
->where('enabled', '=', 1)
->get();
|
count_children()
The count_children method returns the number of children (direct descendants) of the object you're calling it on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Integer |
| Example |
// Get the number of Bill's children, echo's 2
echo $bill->count_children();
// Get the number of Kerry's children, echo's 1
echo $kerry->count_children();
// Get the number of Tim's children, echo's 0
echo $tim->count_children();
// echo's 0 too, a new object can't have children
echo Model_Tree::forge()->count_children();
|
count_descendants()
The count_descendants method returns the number of descendants of the object you're calling it on.
| Static |
No |
| Parameters |
None.
|
| Returns |
Integer |
| Example |
// Get the number of Bill's descendants, echo's 7
echo $bill->count_descendants();
// Get the number of Ben's children, echo's 3
echo $ben->count_descendants();
// echo's 0, a new object can't have descendants
echo Model_Tree::forge()->count_descendants();
|
depth()
The depth method returns the depth or level the current node is in the tree, where
the level of the root node is 0.
| Static |
No |
| Parameters |
None.
|
| Returns |
Mixed, integer or false if the current object is not valid |
| Example |
// Get the level of Bill in the organisation
echo $bill->depth(); // echo's 0, he's top dog!
// Get the level of Angela in the organisation
echo $angela->depth(); // echo's 1, as she's an N+1
// Get the level of Tim in the organisation
echo $tim->depth(); // echo's 3, as low as you can go...
// returns false, you can't get the depth of a new node
$result = Model_Tree::forge()->depth();
|
dump_tree($as_object = false, $children = 'children', $path = 'path', $pathuri = null)
The dump_tree method returns the entire tree, using the current object as root node
into a multi-dimensional array.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $as_object |
false |
If true, it will return a hierarchical tree of objects instead of a multi-dimensional array. |
| $children |
'children' |
data for child nodes will be added to a property or array key with this name. |
| $path |
'path' |
a property by this name is created and will contain the path to the node, starting at the root.
This requires the 'title_field' to be configured!
|
| $pathuri |
null |
This argument requires an existing table column as input. If defined, it will create a property
by the name of this argument, prefixed with "path_", which will contain the path definition pointing
to the node, starting at the root, using the column name provided. This is mainly used when the model
contains a URL or URI column, so you have both the breadcrumb path (in 'path') and the uri path.
|
|
| Returns |
Mixed, multi-dimensional array, or the current object, with added children. |
| Example |
// returns a multi-dimensional array. $tree['children'] will contain the children of Bill
$tree = $bill->dump_tree();
// returns the 'bill' object with a property 'children' containing the children of Bill
$tree = $bill->dump_tree(true);
// using $tree, this returns array($angela, $ben)
$children = $tree->children;
// and this returns array($henry, $nicola), the children of $angela
$grandchildren = reset($children)->children;
// ORM objects are always used by reference!
$bill->dump_tree(true);
// so this works fine too...
$children = $bill->children;
|
As with all ORM array's, the table's primary key is used as array index. Note that because the ORM uses objects by
reference from a single cache, if you choose to use 'as_object', children will be added to existing objects too.
The related method allows you to fetch related objects when executing a nested set command, indentical
to a normal Orm model query.
| Static |
No |
| Parameters |
| Param |
Default |
Description |
| $related |
required |
The name of the relation to include. |
| $conditions |
array() |
Any conditions you want to pass on when fetching the related objects. |
|
| Returns |
Model_Nestedset, for chaining. |
| Example |
// include related 'child' objects in the result
$tree = $bill->related('child')->dump_tree();
// get the descendants of $ben
$descendants = $ben->descendants()->related('child')->get();
// This will NOT include the child relation!
$descendants = $ben->related('child')->descendants()->get();
|
If you want to use this method on any nested set operation (like for example decendants()), make sure to setup that
operation first. If you don't, your included relations will be reset my the nested set operation method call!


In this tutorial, we will list all of the file formats supported by the current version of the library. This tutorial assumes a basic understanding of JavaScript.
This page includes examples that you can try in the developer console. Open it now by pressing ctrl + shift + C (Apple + shift + C on Mac), and clicking Console.
Currently-supported formats
You shouldn't normally deal with file formats directly. The diary objects tutorial explains how to load diaries and automatically detect formats. But it can occasionally be useful to access the list of formats. For example, your app might want to display a list of supported formats:
- (Please enable JavaScript to see the list of formats)
This list was generated by examining the sleep_diary_formats
variable. To see the variable itself, type the following command in the console:
console.log(sleep_diary_formats);
You can use this in your programs just like any other variable. For example, the list above was generated by this page's JavaScript.
Here are the meanings of each member in a format definition:
title
is the user-facing title for the formatname
is the name the code uses internally to refer to this formaturl
is a URL with more information about the formatconstructor
is the constructor used to generate files of this format - you should not need to use this


Before Change
with_IH=with_IH, safe_k=safe_k, IH_rate=IH_rate, aknn=aknn)
mode.lower()
assert Hc > 0.5
assert gamma > 0
assert mode in ["selection", "hybrid", "weighting"]
self.name = "META-des"
self.version = mode
self.kp = kp
After Change
self.meta_training_target = []
self.n_meta_features = (self.k * 2) + self.Kp + 2
self.bins = np.linspace(0.1, 1, 10)
def fit(self, X, y):
Prepare the DS model by setting the KNN algorithm and
pre-processing the information required to apply the DS


If you find more Ice Crystals, please bring them to me.


I got to speak with a group of preservice teachers this morning at the University of Evansville. Heading into the class, I was thinking about what things I would share to start them off on the right foot. This is what I came up with:
Join Twitter – If you are not involved in some sort of professional learning network, you need to find one. Now. I joined Twitter in my second year of teaching, and the last year of learning has been incredible. I want young teachers to have that network built before they start working in schools. Preparation should be relevant, and Twitter is the best way to stay up-to-date.
Start Blogging – Reflection is key to improvement. If there is no reflection in the learning process, growth cannot occur. Unfortunately, reflection usually comes when graded papers are returned. We cannot equate reflection with evaluation. Strong programs are preparing our young teachers to be writing for the sake of writing, rather than for the sake of evaluation. I was fortunate enough to have a cooperating teacher during my student teaching that understood, and instilled, the value of reflection in me and my teaching. I want to be able to do the same.
Organize Information – My first year of teaching was a whirlwind of curation. I did not have a good library built up from college (plus, it was all on paper), so I spent a great deal of time hunting for resources. Now, with tools like Diigo, Pinterest, and Scoop.it, students can curate and share information faster than ever. College students should be building this library as they plan lessons and begin practicum placements, not when they begin their first job. Sharing the information they find is also key, and each of those communities can foster that process as well.
I know one student from this morning signed up for a Twitter account. I am looking forward to going back and working with another group next semester.
Written on March 29th, 2012 by Brian Bennett Categorized in: All Teaching
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The idea for this notebook is to show how we can use a trained CNN to separate the content of an image from the style and therefore create a style transfer system, that can take 1 image and apply the style of another one.
Well, the idea here is that we can use a trained CNN as a feature extractor (VGG19) and use different layers of the net as the representation of an image and their content.
Finally, something interesting to note is that we are going to minimize a weighted sum of the losses, so we can tweak the weights to signal that we are more interested in presenting the content of on transferring as much style as possible.
# import resources
%matplotlib inline
from PIL import Image
from io import BytesIO
import matplotlib.pyplot as plt
import numpy as np
import torch
import torch.optim as optim
import requests
from torchvision import transforms, models
vgg = models.vgg19(pretrained=True).features
for param in vgg.parameters():
param.requires_grad_(False)
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
vgg.to(device)
print(vgg)
# from udacity conv
def load_image(img_path, max_size=600, shape=None):
image = Image.open(img_path).convert('RGB')
if max(image.size) > max_size:
size = max_size
else:
size = max(image.size)
if shape is not None:
size = shape
in_transform = transforms.Compose([
transforms.Resize(size),
transforms.ToTensor(),
transforms.Normalize((0.485, 0.456, 0.406),
(0.229, 0.224, 0.225))])
# ignore transparent, alpha channel and add batch
image = in_transform(image)[:3,:,:].unsqueeze(0)
return image
def im_convert(tensor):
image = tensor.to("cpu").clone().detach()
image = image.numpy().squeeze()
image = image.transpose(1,2,0)
#desnormal
image = image * np.array((0.229, 0.224, 0.225)) + np.array((0.485, 0.456, 0.406))
image = image.clip(0, 1)
return image
content = load_image('unam.jpeg').to(device)
style = load_image('cool.png', shape=content.shape[-2:]).to(device)
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(10, 5))
ax1.imshow(im_convert(content))
ax2.imshow(im_convert(style))
def get_features(image, model, layers=None) -> dict:
""" Run an image forward through a model and get the features for a set of layers. """
if layers is None:
layers = {'0': 'conv1_1',
'5': 'conv2_1',
'10': 'conv3_1',
'19': 'conv4_1',
'21': 'conv4_2', ## content representation
'28': 'conv5_1'}
features = {}
x = image
for name, layer in model._modules.items():
x = layer(x)
if name in layers:
features[layers[name]] = x
return features
def gram_matrix(tensor) -> torch.Tensor:
""" Calculate the Gram Matrix of a given tensor
Gram Matrix from :v https://en.wikipedia.org/wiki/Gramian_matrix
"""
_, d, h, w = tensor.size()
# reshape so we're multiplying the features for each channel
tensor = tensor.view(d, h * w)
gram = torch.mm(tensor, tensor.t())
return gram
content_features = get_features(content, vgg)
style_features = get_features(style, vgg)
# calculate the gram matrices for each layer of our style representation
style_grams = {layer: gram_matrix(style_features[layer]) for layer in style_features}
# create a target image and prep it for change
target = content.clone().requires_grad_(True).to(device)
style_weights = {'conv1_1': 1.,
'conv2_1': 0.85,
'conv3_1': 0.25,
'conv4_1': 0.2,
'conv5_1': 0.2}
content_weight = 1 # alpha
style_weight = 1e6 # beta
show_every = 500
optimizer = optim.Adam([target], lr=0.002)
steps = 2000
for ii in range(1, steps + 1):
target_features = get_features(target, vgg)
content_loss = torch.mean((target_features['conv4_2'] - content_features['conv4_2'])**2)
# the style loss
style_loss = 0
if ii % 50 == 0: print(f"{round(ii / steps * 100, 2)}%")
for layer in style_weights:
# get the "target" style representation for the layer
target_feature = target_features[layer]
target_gram = gram_matrix(target_feature)
_, d, h, w = target_feature.shape
style_gram = style_grams[layer]
# mean square
layer_style_loss = style_weights[layer] * torch.mean((target_gram - style_gram)**2)
style_loss += layer_style_loss / (d * h * w)
total_loss = (content_weight * content_loss) + (style_weight * style_loss)
# update target
optimizer.zero_grad()
total_loss.backward()
optimizer.step()
# display intermediate images and print the loss
if ii % show_every == 0:
print('Total loss: ', total_loss.item())
plt.imshow(im_convert(target))
plt.show()
fig, ax1 = plt.subplots(1, 1, figsize=(10, 5))
ax1.imshow(im_convert(style))
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(10, 5))
ax1.imshow(im_convert(content))
ax2.imshow(im_convert(target))


---
layout: post
title: Creamy tuna pasta
date: 2021-06-16 06:00:34 -0200
background: '/img/recipes/tuna-mate2.jpg'
categories: Recipes
---
This creamy, rich and velvety smooth bowl of pasta isn't only quick and easy to make but the ingredients are already in
most of our kitchens. Like most of my recipes, I was inspired by something I regularly ate growing up called tuna mate.
Prep time: 10 minutes
Cook time: 25 minutes
Serving: 2-4 servings
Ingredients
- 1 small garlic clove
- Handful chives (+-10g)
- 1 tbsp butter
- 1 cup cream
- ¾ cup sour cream
- 1 tbsp onion powder
- ½ cup grated cheddar cheese
- 2 cans tuna (170g)
Instructions
- Finely chop the garlic and chives. Add the butter to a medium sized pot and fry the garlic and chives on a low heat for 2 minutes
- Add the cream and sour cream to the pot and mix in the onion powder until completely combined.
- Turn up the heat (medium heat) and leave the mixture to cook for 5-10 minuntes (until it starts to thicken).
- Add the cheese to the sauce and mix thoroughly until completely melted.
- Drain the liquid from the tuna can and add the tuna to the sauce.
- Leave it to cook for another 5-10 minutes.
- Serve with your choice of low-carb pasta and fresh chives.
Tip
I use a low-carb pasta made from seed and nut flours but this recipe is just as good served with vegetable noodles.
The sauce really thickens after you mix in the cheese but the tuna adds moisture. So only consider adding extra liquid
(if it's still too thick) after you've added the tuna.
The serving suggestion is 2-4 because of the richness of the meal, some people might prefer a smaller portion.
Live long and keto-on!


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Decisions, decisions. Yurts and tipis, or converted churches and distant lighthouses? Choosing your accommodation can be the trickiest part of planning a holiday, especially if you're looking for somewhere to stay that's a little bit out of the ordinary.
If you're conscious of your carbon footprint, you can stay somewhere that likes to think green. Eco camping pods are situated in some stunning locations, from the banks of lakes to the middle of forests.
A little piece of history could be waiting for you inside the walls of somewhere that dates back centuries. These days, you can stay in an ancient broch, an abode once occupied by our prehistoric predecessors, and now fully modernised for a cosy night's slumber. Or, go a little grander with a castle stay. Many medieval fortresses now take overnight guests.
A night's sleep aboard a boat is another unique way to see the world. Wake up to the sounds of lapping water or eat al fresco on the deck, as you set sail on a yacht or see the countryside from a canal or barge. Experienced sailors can rent boats for hire, or you can choose one with a crew aboard or a vessel that doesn't require any previous boat-handling skills.


Contact
Thank for your visiting my site! I would love to hear from you! Please fill out the form below or email me at<EMAIL_ADDRESS>Thank for your visiting my site! I would love to hear from you! Please fill out the form below or email me at dan@danwatson.us.


tomtom [options] <query motif file>
<target motif file>+
The name of a file containing one or more motifs in MEME format or the HTML (.html
) or plain text (.txt
)
output of MEME or DREME. Each of these motifs will be searched against the
target files. If you only wish to search with a subset of these
motifs then look into the -m and
-mi options.
The names of one or more files containing MEME formatted motifs. Outputs from MEME and DREME are supported, as well as Minimal MEME Format. You can convert many other motif formats to MEME format using conversion scripts available with the MEME Suite.
Tomtom writes its output to files in a directory named
tomtom_out
, which it creates if necessary. You can change the
output directory using the -o or -oc options.
The directory will contain:
tomtom.html
-
an HTML file that provides the results in a human-readable format
tomtom.tsv
-
a TSV (tab-separated values) file that provides
the results in a format suitable for parsing by scripts and viewing with Excel
tomtom.xml
-
an XML file that provides the results in a machine-readable format
Only matches for which the significance is less than or equal to the threshold set by the -thresh option (below) will be output. By default, significance is measured by q-value of the match.
Additional outputs may be requested using the -eps and -png options, as described below.
Note: See this detailed description of the Tomtom output formats for more information.
| Option | Parameter | Description | Default Behavior | ||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Input | |||||||||||||||||||||||||||||||||
| -m | id | The name of a motif in the query file that will be used. This option may be repeated multiple times. | If both this option and the related -mi is unused then all motifs in the query file will be used. | ||||||||||||||||||||||||||||||
| -mi | index | The offset in the query file of a motif that will be used. This option may be repeated multiple times. | If both this option and the related -m is unused then all motifs in the query file will be used. | ||||||||||||||||||||||||||||||
| -bfile | file | Specify the source of a background model for converting a frequency matrix to a log-odds score matrix. The background model contains letter frequencies that can adjust for biases in the single-letter composition of the sequences in the organism from which the motif is derived. The file must be in Markov Background Model Format. The background model will be modified by averaging the frequencies of letters and their reverse complements. Note 1: The background model must be for the same alphabet as specified in the query motif file. Note 2: Not allowed with -dist ed, -dist kullback, -dist pearson, or -dist sandelin, as those distance measures are based only on the motif frequencies. | Background frequencies will be loaded from the query motif file. Note this was changed from previous versions that used the first target motif file because that design choice could not work with the -xalph option. | ||||||||||||||||||||||||||||||
| -motif-pseudo | count | This option adds the specified pseudocount to the motifs. The pseudocount is distributed taking into account the background. Note that some comparison algorithms require motif probabilities to not contain zeros. If you choose to set a pseudocount of zero with those comparison algorithms then any motifs containing a probability of zero will be discarded and a warning will be emitted. | A pseudocount of 0.1 is added to the motifs. | ||||||||||||||||||||||||||||||
| Output | |||||||||||||||||||||||||||||||||
| -png | Output motif logo alignment images in portable network graphics (PNG) format. This format is useful for display on websites. Note: Ghostscript must be installed on your computer in order to use this option. | Images are not output in PNG format. | |||||||||||||||||||||||||||||||
| -eps | Output motif logo alignment images in Encapsulated Postscript (EPS) format. This format is useful for inclusion in publications as it is a vector graphics format and can be easily scaled. | Images are not output in EPS format. | |||||||||||||||||||||||||||||||
| -no-ssc | This option causes the LOGOs in the LOGO alignments output by Tomtom not to be corrected for small-sample sizes. By default, the height of letters in the LOGOs are reduced when the number of samples on which a motif is based (nsites in the MEME motif) is small. The default setting can cause motifs based on very few sites to have "empty" LOGOs, so this switch can be used if your query or target motifs are based on few samples. | Small sample correction is used. | |||||||||||||||||||||||||||||||
| Scoring | |||||||||||||||||||||||||||||||||
| --norc | Do not score the reverse complements of target motifs. | Given and reverse complement target motifs are scored if the alphabet is complementable. | |||||||||||||||||||||||||||||||
| -incomplete-scores | Compute scores using only aligned columns. | Take into account columns that don't align. | |||||||||||||||||||||||||||||||
| -thresh | value | Only report matches with significance values ≤
value. Unless the -evalue
option is specified, this value must be smaller than or equal to
1. |
A threshold of 0.5 is used. | ||||||||||||||||||||||||||||||
| -evalue | Use the E-value of the match as the significance threshold. | Use the q-value as the significance threshold. | |||||||||||||||||||||||||||||||
| -dist | allr | ed | kullback | pearson | sandelin | blic1 | blic5 | llr1 | llr5 |
|
Pearson correlation coefficient is used by default. | ||||||||||||||||||||||||||||||
| -internal | This parameter forces the shorter motif to be completely contained in the longer motif. | The shorter motif may extend outside the longer motif. | |||||||||||||||||||||||||||||||
| -min-overlap | min overlap | Only report motif matches that overlap by min overlap positions or more. In case a query motif is smaller than min overlap, then the motif's width is used as the minimum overlap for that query. | A minimum overlap of 1 is required. | ||||||||||||||||||||||||||||||
| Miscellaneous |
If you use Tomtom in your research, please cite the following paper:
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble,
"Quantifying similarity between motifs",
Genome Biology, 8(2):R24, 2007.
[full text]


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We're onto 2020!
Starting now, make change. Start local. Make a difference.
Time, Talents, Treasure
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If you're interested, let me know!
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UI/UX Designs
Ideas for UI/UX Design
Tyrone Swinnie
Suggestive Tips For Redesign
3 Panel Design Layout
Card Based Grouping/Layout
Breadcrumb Navigation
3 Panel Design Layout
Content Grouped in 3 Key Panels
Main Panel
Hierarchy Data Display
Content Continuity
Provides a sense of intuitive design
Card Based Grouping/Layout
Organized Card Views
Menu Specific Related Content
Actionable Cards
Breadcrumb Navigation
Orientates User's Location
Intuitive Navigation
Main Menu Relative
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Adds Sub Navigation Options
Intuitive Group Options
Design in mind for application


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½d¨Òºô¶
I strove with none, for none was worth my strife. Nature I loved and , next to Nature, Art: I warmed both hands before the fire of life; It sinks, and I am ready to depart.


The Virgin Suicides (2000) Reviewed by Eugene Novikov http://www.ultimate-movie.com/ Member: Online Film Critics Society
Starring Kirsten Dunst, James Woods, Kathleen Turner, Josh Hartnett, Hanna Hall, Chelse Swain, A.J. Cook, Leslie Hayman and the voice of Giovanni Ribisi. Directed by Sofia Coppola. Rated R.
The Lisbon sisters enchanted the boys in the neighborhood. They toyed with them, taunted them, tempted them and then just as the boys thought that they were going to score, the girls committed suicide.   Such is the difficult subject matter of Sophia Coppola's powerful, confident directing debut entitled The Virgin Suicides, a visually stunning, emotionally wrenching trip through the dark side of 70's suburbia.
There were five of them: Lux (Kirsten Dunst), Cecilia (Hanna Hall), Bonnie (Chelse Swain), Mary (A.J. Cook), Therese (Leslie Hayman). Cecilia, the youngest, was the first to go. She tried to kill herself by slitting her wrists in a bathtub; when that didn't work, she jumped out of a window and landed directly on a spiked fence.  The mother (Kathleen Turner), a devoutly Catholic woman who was paranoidly protective as it was, becomes even more cautious. The dad (James Woods), a calm, reserved schoolteacher seems to care less. In any event, the rest of the girls' lives are never the same again.
Meanwhile, the boys gather at a house across the street and spy on the Lisbon sisters through a telescope. They begin a collection of Lisbon souvenirs -- diaries, clothes, hairpins, etc. When, on prom night, Lux sleeps with the school rebel Trip Fontaine (Josh Hartnett) on the football field, mommy goes mad and shuts the girls off from the world completely. After hearing a church sermon, she makes Lux burn her rock records.
The Virgin Suicides brings a new meaning to the age-old complaint "Parents just don't understand." This is the '70's, after all -- the "ME" decade -- where, thanks to the "hippie" counterculture, teens began to be looked upon as something resembling the spawn of Satan. It's understandable, then, why Mrs. Lisbon got the idea that the best way to protect her daughters from the evils of the other teenagers was to shut them off completely. This film has been attacked by the Catholic League, who charge that the girls commit suicide because they couldn't stand their Catholic upbringing. These are misguided complaints -- Catholicism had little to do with it.
The story is told from the point of view of the boys by a sort of collective narrator (Giovanni Ribisi, who never actually appears). We see much of the events from the outside looking in. Watching the film is a little bit like putting together a jigsaw puzzle. We're told very little outright -- the boys concede that they could not even begin to understand the complexity of the Lisbon sisters -- and are expected to figure it out on our own. The film's ending, surprising despite its inevitability, leaves a lot of room for debate.
Sofia Coppola, never quite able to hit it big as an actress despite the prominence of her director father Francis Ford Coppola, shows great promise behind the camera. She has a surprising visual flair: the repeating shot of Lux's sad face translucently superimposed over a picturesque grass field with beautiful sunny skies above is hypnotic and strangely ominous. Her sparing use of camera tricks like split- screen and slow motion turn out to have a haunting effect and the film's bleak, cold color palette gives it an appropriately unrealistic, isolated, out-of-touch look, perhaps mimicking the girls' feelings.
The Virgin Suicides is a spellbinding tale of pubescent discovery, parental indifference the fundamental unfairness of the 1970's and the power that childhood memories can hold. It's rich, poignant, rewarding and ultimately unforgettable.
Grade: A
©2000 Eugene Novikov
Sent via Deja.com http://www.deja.com/ Before you buy.
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


Why git is 👌
The problem
Add people to the mix
version control system (VSC)
Why Git (and not some other VCS)?
Collisions? Well yes, but no
~3 * 10^49 change of collision
~3 * 10^23 of stars
~10^80 atoms
Hashes are unique universe-wise
Git saves snapshots of what your project was in one point in time
I'm not programmer, why should I care?
Thank you & questions
Lukasz Skotarek
@dreat_ on Twitter
dreat on Slack
mail: contact@dreat.info


ANASTASIA A film review by Steve Rhodes Copyright 1997 Steve Rhodes
RATING (0 TO ****): ***
Cartoons were originally just the opening act to whet the audience's appetite for the cinematic main course. Walt Disney changed all of that in 1937 with the first feature-length animated movie, SNOW WHITE AND THE SEVEN DWARFS.
Since then what brings people into the theaters, rather than the now ubiquitous video rental emporiums, has changed dramatically. The movies that make money these days rely heavily on star power or special effects, frequently both. Young kids are seen less and less at the multiplex because studios are ignoring them. Is it that fewer kids are coming and therefore the studio's wise marketeers are cutting back on kids' movies to match the decrease in demand? Teenagers, on the other hand, remain the mother lode for theater owners.
Yet some animated movies have been successful and a few, such as THE LION KING, have been incredibly lucrative. So what does it take to make a winning movie with cartoon characters? Although there is no sure and certain recipe, aside from having a Disney logo, some of the ingredients include color, images, music, humor, and a compelling story.
The non-Disney animated movie ANASTASIA by the directing and producing team of Don Bluth and Gary Goldman has already become a holiday hit. Its popularity comes from a combination of all of the above ingredients, but one part stands head and shoulders above the rest -- the images, which are worthy of a master painter. This film is so beautiful that, if the sound system were to go out, you would have absolutely no reason to demand your money back. Just watching the picture provides the vast majority of the enjoyment, which is not to say that the other parts have problems since they do not. Although the songs are the film's weakest element, even some of them, especially "Dancing Bear", are quite lovely.
ANASTASIA is a retelling of the legend of the missing Romanov princess. Historians would be well advised to skip the picture for it plays fast and loose with the facts, but others will not care. This is a cartoon to entertain audiences, not an instructional video.
Meg Ryan is the voice of a sassy, tough and attractive Anastasia. Ryan becomes the character rather than the other way around, unlike the Genie in ALADDIN, for example, who became Robin Williams. If your girls are looking for a good role model, look no further. Anastasia is a resourceful and self-assured young woman who is capable of saving her boyfriend rather being saved herself.
A con artist named Dimitri (John Cusack) takes a beautiful orphan named Anya (Ryan), and transforms her into a mock-Anastasia, falling in love with his creation in the process. The twist is that Anya may actually be Anastasia. Kelsey Grammer is the voice of Dimitri's companion in crime, Vladimir. If they can convince the Dowager Empress Marie (Angela Lansbury) that Anya is Anastasia, they will get a ten million ruble reward. (Anastasia has a cute little dog named Pooka, who, unlike most cartoon characters, does not get to talk.)
Along the way Dimitri and Anastasia have to fight the dastardly villain Rasputin (Christopher Lloyd), who keeps falling to pieces, literally. His hands fly off, his mouth falls down and he generally cannot keep himself together -- we've all had days like that. Rasputin's frequently not-so-willing companion is a wise-talking bat named Bartok (Hank Azaria).
The memorable parts of ANASTASIA are the visuals. Although words cannot do them justice, let me mention a few of the best. There is one sequence in a train where they show the boiler of the engine. Oranges and reds dance across the screen as the heat of the flames makes the air undulate in front of the viewers. When the train crashes down into the canyon, it explodes in a fireball both realistic and gorgeous. The characters are all drawn with life-like delicacy. And there is a scene set inside a French house with photo-accurate Impressionist and other paintings on the walls. Finally, there is a simple scene of Anya looking into the waters of a stream, which reflect with a magical luminescence. It is easy to go on, but the film is more to be seen than discussed.
ANASTASIA runs 1:34. It is rated G and would be fine for the whole family. There is some potential that the littlest munchkins might be scared by Rasputin, but I saw no evidence of it in our packed theater.
The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
The Internet Movie Database accepts no responsibility for the contents of the
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.
Broken URLs inthe reviews are the responsibility of the author.
The formatting of the review is likely to differ from the original due
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Hello and thanks for visiting my website! My name is Jay McCoy and i am a Software Developer, i been writting code for a few years now, and i absolutely love it! Now sit down, relax and see who i am and what i can do.
I was born in Mexico, Tijuna Baja California, Mexico to be more exact, and i can already hear your questions, "A fair skinned redhead like you is from Mexico?!" Yeah, yeah I am "Jay, are you related to Canelo Alvarez, can I get his autograph?!" Unfortunately we are not related, if I was I would probably be in a yatch somewhere drinking an appletini, don't judge me!.
I loved living in Mexico, there were delicious taco stand on every corner! But we also realized that it was becoming more and more dangerous living there, so we immigrated to the United States and I couldn't be happier, it's given my family and I so much and we are extremely grateful.
I will speed this along, I know you are facinated by my story but I got to code, and you have to work or sleep or watch more romantic comedies. I received my bachelor degree in biology, from California State University Channel Islands, but it wasn't up until I started working in the field that I realized that I hated it, but thankfully I already knew what to do next, programming! Besides taking biology classes in college I also took quite a few computer science classes, HTML, CSS, Javascript, Java, etc. Not only that but in my hopes to become a better programmer I enrolled in a coding bootcamp called Bloc, where I am learning a multitude of languages and perfecting the ones I already know. I code side by side with my mentor whom let's me know how I am doing.
These are some of my completed projects!
This is my first website project, it is a music player which plays 5 different songs and it served as our base for the other diffrent projects below. It was built using HTML, CSS, Javascript and JQuery. I used Buzz! as our javascript library, and it made it very easy to manage our audio files and settings.
Bloc Jams Angular is very similar to Bloc Jams, but written in all AngularJS, Javscript and JQuery. This was my first experience with dealing with AngularJS, but it was an excellent stepping stone, becuase it showed me how to play around with angular and achieve what I want. It was critical for the production of Biometrics and Bloc Chat.
Thanks to the knowledge I acquired from Bloc Jams Angular, I was able to keep track of many of the metrics related to the user's interactions with the site. The one I focused on was, how many times a song was played and organize them all using a fancy chart maker called nVd3.


{% extends 'layouts/layout-bsa-design-system.html' %} {% set active = "patterns" %} {% set activesub = "Enquiry" %} {% block pageTitle %} Check and confirm - NHSBSA design system {% endblock %} {% block beforeContent %} {% include "includes/breadcrumbs__patterns.html" %} {% endblock %} {% block content %}
Allow users to submit an enquiry to a service.
Enquiry forms should always be available to a user.
If a user submits an application, include a link to the enquiry form in follow-up communications.


- Site - the full site
- Hax - temporary sandbox for playing around with code
- Minimum Setup - just the app without any didactic details
- Game - just the game, without any communcation
- Emoji - just the emoji selection form
- Login - just the login form
- Options - just the options form
- Toolbar - just the Header and Footer toolbars
- Unit Tests


Today I decided to clean up and organise files on my windows machine at work. This process involved deleting files I no longer have use for and grouping the rest in folders. So I ended up with folders for audio, video, projects, ebooks, e.t.c.
One of the folders that I opened contained about 50 small mp3 files. Before deleting the files I had to play them just to make sure they didn't contain anything important. What do I know, turns out they are clips of a DHH(the RoR creator) interview - please don't ask me how they got to my computer. He's quite an opinionated guy so I decided to keep the files. But 50 files? Wouldn't it be nice if I could glue them together into a single file? Well, being the hacker that I am I popped open my terminal and started writing a program.
I broke down the task to two main parts.
The first part turned out to be quite easy because the files were named with a date/time stamp in the following format: Mon Jan 03 10;02;07 2011.mp3
. This meant that I could extract the time from the file names and sort them accordingly. To simplify this further I decided to rename the files with an easier format for sorting - for this I created the rename.js
file:
/*
I placed all the audio files in ./files directory
*/
var fs = require('fs'),
files = fs.readdirSync('./files');
files.forEach(function (file) {
var currentname = './files/' + file,
date = parseDate(file),
newname = './files/' + date.split(';').join('') + '.mp3';
renameFile(currentname, newname);
console.log('Renamed ' + currentname + ' to ' + newname);
});
/*
This function renames a file
@param: (String) currentname - current file name
@param: (String) newname - new file name
*/
function renameFile(currentname, newname) {
fs.renameSync(currentname, newname);
}
/*
Extracts date/time from file name string
@param: (String) filename - file name
*/
function parseDate(name) {
var date = name.substring(11, 19);
return date;
}
console.log('Done');
Up next I had to create the main program that combines the files and writes them to a single file. Streams to the rescue!
 The source of the data is a readable stream and the destination a writable stream. The file system module has 2 methods that you can use to take advantage of Node streams, fs.createReadStream
and fs.createWriteStream
. I created a new file for the main program, stream.js
var fs = require('fs'),
files = fs.readdirSync('./files'),
clips = [],
stream,
currentfile,
dhh = fs.createWriteStream('./dhh-interview.mp3');
// create an array with filenames (time)
files.forEach(function (file) {
clips.push(file.substring(0, 6));
});
// Sort
clips.sort(function (a, b) {
return a - b;
});
// recursive function
function main() {
if (!clips.length) {
dhh.end("Done");
return;
}
currentfile = './files/' + clips.shift() + '.mp3';
stream = fs.createReadStream(currentfile);
stream.pipe(dhh, {end: false});
stream.on("end", function() {
console.log(currentfile + ' appended');
main();
});
}
main();
That's it. Lastly I needed to run my programs.
node rename.js && node stream.js
Note: I have included a few files in my repo so that you can be able to try this out.


WITNESS LIST Ways & Means Committee April 19, 2006-1:00P HB 1 For: Borsellino, Cynthia (Self) Schlomach, Ph.D., Byron (Texas Public Policy Foundation) Against: Grusendorf, Wm. C. (Bill) (Texas Assoc. of Rural Schools) McCown, F. Scott (Center for Public Policy Priorities) Moak, Lynn (Texas School Alliance/South Texas Association of Schools) Moorhead, Bee (Texas Impact) Pierce, Wayne (Equity Center) Thompson, David (Texas Association of School Administrators and Texas Association of School Boards) On: Anderson, David (Texas Education Agency) Keller, Harrison (Speaker Tom Craddick) Levin, Marc (Empower Texans) Milios, Danica (Office of Attorney General) HB 2 Against: Lavine, Dick (Center for Public Policy Priorities)


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Gecode::Set::Rel Namespace Reference
Standard set relation propagators. More...
Classes | |
| class | CharacteristicSets |
| Representation of the characteristic functions of two sets. More... | |
| class | Subset |
| Propagator for the subset constraint More... | |
| class | NoSubset |
| Propagator for the negated subset constraint More... | |
| class | ReSubset |
| Reified subset propagator More... | |
| class | Eq |
| Propagator for set equality More... | |
| class | ReEq |
| Reified equality propagator More... | |
| class | Lq |
| Propagator for set less than or equal More... | |
| class | ReLq |
| Reified propagator for set less than or equal More... | |
| class | Distinct |
| Propagator for negated equality More... | |
| class | DistinctDoit |
| Propagator for negated equality More... | |
Functions | |
| bool | subsumesME (ModEvent me0, ModEvent me1, ModEvent me2, ModEvent me) |
| bool | subsumesME (ModEvent me0, ModEvent me1, ModEvent me) |
| bool | subsumesME (ModEvent me0, ModEvent me) |
| bool | testSetEventLB (ModEvent me0, ModEvent me1, ModEvent me2) |
| bool | testSetEventUB (ModEvent me0, ModEvent me1, ModEvent me2) |
| bool | testSetEventAnyB (ModEvent me0, ModEvent me1, ModEvent me2) |
| bool | testSetEventCard (ModEvent me0, ModEvent me1, ModEvent me2) |
| bool | testSetEventLB (ModEvent me0, ModEvent me1) |
| bool | testSetEventUB (ModEvent me0, ModEvent me1) |
| bool | testSetEventAnyB (ModEvent me0, ModEvent me1) |
| bool | testSetEventCard (ModEvent me0, ModEvent me1) |
| bool | testSetEventLB (ModEvent me0) |
| bool | testSetEventUB (ModEvent me0) |
| bool | testSetEventAnyB (ModEvent me0) |
| bool | testSetEventCard (ModEvent me0) |
Detailed Description
Standard set relation propagators.
Function Documentation
| bool Gecode::Set::Rel::subsumesME | ( | ModEvent | me0, | |
| ModEvent | me1, | |||
| ModEvent | me2, | |||
| ModEvent | me | |||
| ) | [inline] |
Definition at line 60 of file common.hpp.
| bool Gecode::Set::Rel::subsumesME | ( | ModEvent | me0, | |
| ModEvent | me1, | |||
| ModEvent | me | |||
| ) | [inline] |
Definition at line 65 of file common.hpp.
| bool Gecode::Set::Rel::subsumesME | ( | ModEvent | me0, | |
| ModEvent | me | |||
| ) | [inline] |
Definition at line 70 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventLB | ( | ModEvent | me0, | |
| ModEvent | me1, | |||
| ModEvent | me2 | |||
| ) | [inline] |
Definition at line 75 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventUB | ( | ModEvent | me0, | |
| ModEvent | me1, | |||
| ModEvent | me2 | |||
| ) | [inline] |
Definition at line 79 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventAnyB | ( | ModEvent | me0, | |
| ModEvent | me1, | |||
| ModEvent | me2 | |||
| ) | [inline] |
Definition at line 83 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventCard | ( | ModEvent | me0, | |
| ModEvent | me1, | |||
| ModEvent | me2 | |||
| ) | [inline] |
Definition at line 87 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventLB | ( | ModEvent | me0, | |
| ModEvent | me1 | |||
| ) | [inline] |
Definition at line 91 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventUB | ( | ModEvent | me0, | |
| ModEvent | me1 | |||
| ) | [inline] |
Definition at line 95 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventAnyB | ( | ModEvent | me0, | |
| ModEvent | me1 | |||
| ) | [inline] |
Definition at line 99 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventCard | ( | ModEvent | me0, | |
| ModEvent | me1 | |||
| ) | [inline] |
Definition at line 103 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventLB | ( | ModEvent | me0 | ) | [inline] |
Definition at line 107 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventUB | ( | ModEvent | me0 | ) | [inline] |
Definition at line 111 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventAnyB | ( | ModEvent | me0 | ) | [inline] |
Definition at line 115 of file common.hpp.
| bool Gecode::Set::Rel::testSetEventCard | ( | ModEvent | me0 | ) | [inline] |
Definition at line 119 of file common.hpp.


Uses of Class
com.owenfeehan.pathpatternfinder.patternelements.PatternElement
| Package | Description |
|---|---|
| com.owenfeehan.pathpatternfinder |
Top-level package for all classes for finding a pattern in paths or strings in accordance to
certain rules.
|
| com.owenfeehan.pathpatternfinder.patternelements |
A pattern-element is one part of a pattern after fitting against a list of paths / strings.
|
| com.owenfeehan.pathpatternfinder.patternelements.resolved |
PatternElement s that are resolved
(cannot be broken down further). |
| com.owenfeehan.pathpatternfinder.patternelements.unresolved |
PatternElement s that are unresolved (can
possibly be broken down further into a smaller patterns). |
-
Uses of PatternElement in com.owenfeehan.pathpatternfinder
Methods in com.owenfeehan.pathpatternfinder that return PatternElement Modifier and Type Method Description PatternElement
Pattern. get(int index)
Returns true iff the element at index is unresolved.Methods in com.owenfeehan.pathpatternfinder that return types with arguments of type PatternElement Modifier and Type Method Description Iterator<PatternElement>
Pattern. iterator()
Methods in com.owenfeehan.pathpatternfinder with parameters of type PatternElement Modifier and Type Method Description void
Pattern. add(PatternElement elementToAdd)
Adds an element.Method parameters in com.owenfeehan.pathpatternfinder with type arguments of type PatternElement Modifier and Type Method Description static void
SplitDirectoriesHelper. splitStringIntoElements(String stringToParse, Consumer<PatternElement> elementConsumer)
Parses a string so that any characters matching the path separation are added separately.Constructors in com.owenfeehan.pathpatternfinder with parameters of type PatternElement Constructor Description Pattern(PatternElement element)
Create with 1 element. -
Uses of PatternElement in com.owenfeehan.pathpatternfinder.patternelements
Methods in com.owenfeehan.pathpatternfinder.patternelements that return PatternElement Modifier and Type Method Description PatternElement
PatternElement. reverseReturn()
Reverses the pattern. -
Uses of PatternElement in com.owenfeehan.pathpatternfinder.patternelements.resolved
Subclasses of PatternElement in com.owenfeehan.pathpatternfinder.patternelements.resolved Modifier and Type Class Description class
ResolvedPatternElement
APatternElement
that has been resolved.class
VariableElement
APatternElement
that is resolved and varies across the list of values.Methods in com.owenfeehan.pathpatternfinder.patternelements.resolved that return PatternElement Modifier and Type Method Description static PatternElement
ResolvedPatternElementFactory. addConstantTo(char value, Pattern pattern)
Creates a new constant element from a character, and adds topattern
.static PatternElement
ResolvedPatternElementFactory. addConstantTo(String value, Pattern pattern)
Creates a new constant element from a string, and adds topattern
.static PatternElement
ResolvedPatternElementFactory. constant(char value)
Creates constant element of a single character.static PatternElement
ResolvedPatternElementFactory. constant(String value)
Creates constant element of a string.static PatternElement
ResolvedPatternElementFactory. directorySeperator()
Creates an element representing a directory separator.static PatternElement
ResolvedPatternElementFactory. integer(int... values)
Creates a varying integer element of one or more ints.static PatternElement
ResolvedPatternElementFactory. integer(List<String> values)
Creates a varying integer element of one more strings.static PatternElement
ResolvedPatternElementFactory. string(String... values)
Creates a varying string element of one or more strings.static PatternElement
ResolvedPatternElementFactory. string(List<String> values)
Creates a varying string element from a list of strings. -
Uses of PatternElement in com.owenfeehan.pathpatternfinder.patternelements.unresolved
Methods in com.owenfeehan.pathpatternfinder.patternelements.unresolved with parameters of type PatternElement Modifier and Type Method Description Pattern
UnresolvedPatternElementFactory. createUnresolvedString(PatternElement left, List<String> right, boolean requiresPeriod)
Creates aPattern
with an element on the left, and a unresolved-string on the rightMethod parameters in com.owenfeehan.pathpatternfinder.patternelements.unresolved with type arguments of type PatternElement Modifier and Type Method Description Pattern
UnresolvedPatternElementFactory. createUnresolvedString(List<PatternElement> left, List<String> right, boolean requiresPeriod)
Creates aPattern
with an elements on the left, and a unresolved-string on the right


Manhattan Island
James Bowman Lindsay
Edison Electric Light Company
Heinrich Göbel
carbon microphone


Expected Output of EUKulele
¶
Below is what you should expect to see when you run EUKulele
. output-folder-name
is the top level directory specified by the -o/--out_dir
parameter, which defaults to a folder called “output” in the current working directory.
TransDecoder
, or protein files provided)--mets_or_mags
parameter)--mets_or_mags
parameter)Taxonomy Estimation Folders¶
Inside each of the taxonomy estimation folders (core_taxonomy_estimation
, for exclusively transcripts annotated as core genes, and taxonomy_estimation
), there are files labeled sample_name -estimated-taxonomy.out
. Each of these files has the following columns:
- transcript_name
The name of the matched transcript/contig from this sample file
- classification_level
The most specific taxonomic level that the transcript/contig was classified at
- full_classification
The full taxonomic classification for the transcript/contig, up to and including the most specific classification
- classification
Just the most specific classification obtained, at the taxonomic level specified by classification_level
- max_pid
The maximum percentage identity reported by the alignment program for the match
- counts
1 if not using
Salmon
, or the number of counts reported by the quantification program for that transcript/contig if using salmon
- ambiguous
1 if there were multiple disagreeing matches for this transcript/contig, resolved by either consensus annotation using the user-provided cutoff (defaults to 75%) or by last common ancestor (LCA) approaches, otherwise 0
Taxonomy Counts Folders¶
Inside each of the taxonomy counts folders (core_taxonomy_counts
and taxonomy_counts
), there is a file with the aggregated counts belonging to each annotation at the possible taxonomic levels. These files are derived diectly from the taxonomy estimation and used for the visualization steps. Inside this folder are comma-separated files with the following headings:
- Taxonomic Level
The taxonomic level specified by the file name
- GroupedTranscripts
A semicolon-separated list of the identification names for transcripts that matched to this taxonomic label
- NumTranscripts
The total number of transcripts (the length of the semicolon-separated list of transcripts)
- Counts
Provided if
Salmon
counts are used - the matching summed number of counts for each label
- Sample
The original metagenomic/metatranscriptomic sample that this count is from (a separate row would be provided if the match is found in multiple samples)
The taxonomic count files are named according to the convention output-folder-name _all_
taxonomic-level _counts.csv
.
Taxonomy Visualization Folders¶
Unside each of the taxonomy visualization folders (core_taxonomy_visualization
, for exclusively transcripts annotated as core genes, and taxonomy_visualization
), there are auto-generated barplots that show:
x-axis: samples
y-axis, left subplot (if using counts): relative number of transcripts
bars, left subplot (if using counts): each of the top represented taxonomic groups (must represent >= 5% of total number of transcripts)
y-axis, right subplot (if using counts): relative number of counts
bars, right subplot (if using counts): each of the top represented taxonomic groups (must represent >= 5% of total counts)
The right subplot is only generated if counts from a quantification tool (namely, Salmon
) are provided.


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Result of the recursive deconvolution of multiplet structures
The last plot of each column (no value of J) correspond to the point where no more coupling were found.


The Tale of Brownie Beaver
by Arthur Scott Bailey
Chapter 7: “A Newfangled Newspaper”
Additional Information
- Year Published: 1916
- Language: English
- Country of Origin: United States of America
- Source: Bailey, A. S. (1916). The Tale of Brownie Beaver. New York: Grosset and Dunlap.
-
Readability:
- Flesch–Kincaid Level: 5.0
- Word Count: 879
- Genre: Fantasy
- Keywords: 20th century literature, american literature, children's stories, sleepy-time tales
- ✎ Cite This
Downloads
After Mr. Crow flew back to Pleasant Valley to gather news for him, Brownie Beaver carefully counted each day that passed. Since Mr. Crow had agreed to be his newspaper, and come each Saturday afternoon to tell him everything that had happened during the week, Brownie was in a great hurry for Saturday to arrive.
In order to make no mistake, he put aside a stick in which he gnawed a notch each day. And in that way he knew exactly when Saturday came.
That was probably the longest day in Brownie Beaver’s life. At least, it seemed so to him. Whenever he saw a bird soaring above the tree-tops he couldn’t help hoping it was Mr. Crow. And whenever he heard a caw—caw far off in the distance Brownie Beaver dropped whatever he happened to be doing, expecting that Mr. Crow would flap into sight at any moment.
Brownie had many disappointments. But Mr. Crow really came at last. He lighted right on top of Brownie Beaver’s house and called “Paper!” down the chimney—just like that!
Brownie happened to be inside his house. And in a wonderfully short time his head appeared above the water and he soon crawled up beside Mr. Crow.
“Well, I am glad to see you!” he told Mr. Crow.
“Peter Mink caught a monstrous eel in the duck pond on Monday,” Mr. Crow said.  Mrs. Jeremiah Rabbit says she does not know when her husband’s relations are going home,” Mr. Crow continued to relate in a singsong voice.
“Goodness gracious!” Brownie Beaver exclaimed.
“Fatty Coon—” Mr. Crow said—“Fatty Coon was confined to his house by illness Tuesday night. He ate too many dried apples.”
“Well, well!” Brownie Beaver murmured. And he started to ask Mr. Crow a question. But Mr. Crow interrupted him with more news.
“Mrs. Bear had a birthday on Wednesday. An enjoyable time was had by all—except the pig.”
“Pig?” Brownie Beaver asked.  And he went right on talking. “On Thursday Mr. Woodchuck went to visit his cousins in the West. Mrs. Woodchuck is worried.”
“What’s she worried about?” Brownie inquired.
“She’s afraid he’s coming back again,” Mr. Crow explained.
“I have heard he was lazy,” Brownie said. “What happened on Friday?”
“Tommy Fox made a visit. But he didn’t have a good time at all,” Mr. Crow reported, “and he left faster than he came.”
Brownie Beaver wanted to know where Tommy Fox made his visit.
“At Farmer Green’s hen-house,” Mr. Crow explained.
“Why did he hurry away?” Brownie asked.
“Old dog Spot chased him,” Mr. Crow replied. “But you mustn’t ask questions,” he complained. “You can’t ask questions of a newspaper, you know.”
“Well—what happened on Saturday?”
“There you go again!” cried Mr. Crow. “Another question! I declare, I don’t believe you ever took a newspaper before—did you?”
Brownie Beaver admitted that he never had.
“Then—” said Mr. Crow—“then don’t interrupt me again, please! I’ll tell you all the news I’ve brought.  And then we can talk. But not before!” he insisted.
Brownie Beaver nodded his head. He was afraid that if he said another word Mr. Crow would grow angry and fly away without telling him any more news.
“On Saturday—this morning, to be exact”—said Mr. Crow, “there came near being a bad accident. Jimmy Rabbit almost cut off Frisky Squirrel’s tail.”
Mr. Crow paused and looked at Brownie Beaver out of the corner of his eye. He knew that Brownie would want to know what prevented the accident. But he was in no hurry to tell him.
For a few moments Brownie waited to hear the rest. But a few moments was more than he could endure.
“Why didn’t Jimmy cut off his tail?” Brownie asked eagerly.
“There!” said Mr. Crow. “You’ve done just as I told you not to. So I shall not tell you the rest until next Saturday.... You see, you have a few things to learn about taking a newspaper.” And ‘he would give Brownie no more news that day. To be sure, he was willing to talk—but only about things that had happened where Brownie Beaver lived.


This screen shows the contents of a Baptism record by each field. The purpose of the display is to show which fields of the record are in error. Errors are indicated by way of a red-backed exclamation mark alongside a field. If you hover the mouse over the icon, an error message will be displayed.
Correcting the error and pressing the OK button will eliminate that error and write the updated record back into the Workspace record list from whence the display originated. Upon return to the Workspace, the file can then be saved.


I’m a frontend developer from Donetsk, Ukraine.I enjoy creating beautiful web pages and living on the bleeding edge of the web standarts. You should write me if you have challenging projects that require range variety of skills and continuous learning


Etaoin Shrdlu translates keys to words. The more common the keys, the more common the words! Loading frequency data...