SampleAdapter
for
illustration:
the code for that adapter lies in the
apollo/dataadapter/sample
package. One
way of getting going quickly
would be to start by examining the code skeleton provided in the sample
dataadapter, and then modify it for your own purposes.
I assume in all the following that if you're reading this document then
you have already obtained a developer's installation of apollo - for
instance
a cvs checkout of the fully source tree and supporting files, and are
reasonably familiar with the location and basic function
of the main supporting files (apollo.cfg, the style and tiers files for
an adapter). If you haven't, then you can, via cvs or
tarball, from gmod.sourceforge.net
-
this site has all the code and instructions for downloading etc.
conf/apollo.cfg
file:
DataAdapterInstall
"apollo.dataadapter.sample.SampleAdapter"
"sample.style"
apollo.dataadapter.sample.SampleAdapter
),This is responsible for gathering data (features and sequence) from a back end, and packaging the data in terms of Apollo's datamodel. The type of data gathered and where it's gathered from is specified as state information on the adapter.
apollo.dataadapter.sample.SampleAdapterGUI
),
This is responsible for gathering the user's preferences (via a gui) for where the data should be loaded from, and what sort to gather, and setting all this information on the data adapter.
conf/sample.style
)This keeps the user's visual preferences specific to the SampleAdapter.
conf/sample.tiers)
This keeps the list of possible data "tiers" (tracks) which we expect the SampleAdapter to provide, along with their visual appearance.
When you are displaying the results of many independent analyses of a particular genome, you will need to group results of the same analysis together visually, and distinguish them from results from other analyses. You do this by putting your results in tiers (visual groupings). Tiers (visual groupings) are tied to the logical data groups via the type of the Features your adapter creates. You specify how a tier looks (data colours and glyphs) in the tiers file, and lots of other visual properties besides.
Write a nice constructor. This amounts to writing the code that creates widgets and adding them to the JPanel. Everyone has their own taste as to how to do this - the sample has a suggested style. I have a few other suggestions based on experience:
Minimise the use of direct access to instance variables in the class (the rule I use is to only directly refer to the instance when the object is created). This is generally wise rule to brutally enforce, but I think I've seen the most flagrant violations in gui-related code. So, for instance, say
getMyFavouriteDropDown().setSelectedItem(...);
instead of
myFavouriteDropDown.setSelectedItem(...)
.
If you want to remain sane, use GridBagLayout to lay your components out: Box is seductive but has weird side effects, and is basically impossible for normal humans to alter post-hoc.
Implement doOperation. This is forced on you by the DataAdapterUI interface in org.bdgp.io, and it's the call made by the DataAdapterChooser on your dataadapter when the user hits "OK". It's traditional here to have the adapter do three things in this operation:
Derive a summary of the user's choices - the "state information" - based on the GUI's current state. This summary is placed into a Properties object
Transmit this information to the DataAdapter by passing the Properties object
Call a method on the DataAdapter to fetch the CurationSet. This is where all the data gets read. Pass the CurationSet you obtain out as the return from the doOperation method.
If you intend your adapter to read and write data then you have to make a decision in the doOperation method as to what to do: each GUI instance is created with only one operation in mind, so you must check the operation inside the GUI instance, and branch based on that. See the BaseGFFAdapter or the GAMEAdapter for an example of how to do this.
get/setProperties
).
These
are explained and demonstrated in the SampleAdapter.
Your UI needs to extend org.bdgp.swing.AbstractDataAdapterUI (from the org.bdgp jar in apollos jars directory - jar created from org.bdgp on source forge). AbstractDataAdapterUI extends JPanel and implements org.bdgp.io.DataAdapterUI. The javadocs for DataAdapterUI are pretty informative so here they are:
/**
* An abstract representation of a DataAdapter user interface. These
interfaces
* are meant to be used in conjunction with a some sort of data adapter
* selection widget, like org.bdgp.swing.widget.DataAdapterChooser
*/
public interface DataAdapterUI {
/**
* Sets the data adapter for this UI. Since the UI provides it's
* own implementation of the IOOperation via the
* {link #doOperation(Object)}, the DataAdapterUI can decide whether or
* not to actually use the DataAdapter to perform the operation. However,
* a correct implementation of this interface will use the DataAdapter
* given in setDataAdapter.
*/
public void setDataAdapter(DataAdapter in);
/**
* Sets UI properties for this DataAdapterUI. The source of these
* properties is up to the widget that displays the DataAdapterUI. Most
of
* the time these properties will contain some sort of history
information
* and will be loaded from a file. The Properties object may be null if
* there are no properties to set.
*/
public void setProperties(Properties in);
/**
* Returns the UI properties for this DataAdapterUI. These properties
* may be recorded by the widget that displays the DataAdapterUI and
* provided to the setDataAdapter method of later instances of the
* DataAdapterUI. This method may return null if there are no properties
* to record.
*/
public Properties getProperties();
/**
* The method that actually performs the data adapter operation
* (presumably by delegating to a data adapter). The input and outputs
* to this method are entirely dependent on the operation the data
adapter
* is supposed to perform. The input or output of this method may be
null.
*/
public Object doOperation(Object values) throws DataAdapterException;
/**
* Set the input, if there is any. This input is the same as the Object
* passed into doOperation. A DataAdapterUI may need to get a hold of
* its input before doOperation time and this allows for it. For instance
* if the UI wants to display input related stuff it needs it before doOp
*/
public void setInput(Object input);
}
AbstractDataAdapterUI takes care of setDataAdapter so you dont need to worry about that. It also no-ops setInput, so override setInput only if you're gui needs to know about the input before doOp time.
doOperation is the most important method here, and it is described above, but heres a little more.
doOperation throws an org.bdgp.io.DataAdapterException if anything goes wrong. DataAdapterException can wrap another exception by using its constructor: DataAdapterException(Throwable nestedException,String msg), or it can just carry a message(DAE(String)).
As mentioned above what is usually done in doOperation is getCurationSet() is called on the associated data adapter, but this is not dictated by any interface. Being a subclass of AbstractDataAdapterUI, the data adapter is available as the variable "driver" of type DataAdapter. The DataAdapter interface is given below. Notice it has nothing comparable to doOperation. In other words to do anything with it at this point you have to cast it to the type of DataAdapter that you are using, that will have a getCurationSet, or whatever method you've put in there to get the data (this is a quirk with working with org.bdgp's generic data adapter chooser framework- one could argue that doOperation belongs in DataAdapter). SampleAdapterGUI has a getDataAdapter method which just returns driver as a DatAdapter. This is called and cast to a SampleAdapter in doOperation, because we happen to know its a SampleAdapter, and then getCurationSet is called on the SampleAdapter.
The history lists for the gui come from the properties, so getProperties and setProperties need to be implemented to get history.
Implement (mainly) getCurationSet. The normal pattern (not forced by
any interface) is for the DataAdapterGui to call getCurationSet on its
DataAdapter. In fact getCurationSet is in AbstractApolloAdapter, and
throws a NotImplementedException if it's not overridden. getCurationSet
returns a CurationSet (surprise surprise). This is where you need to
build your CurationSet described in the apollo datamodel below.
It is crucial that in your getCurationSet method you call
super.clearOldData() (super being AbstaractApolloAdapter which you
should be subclassing). This clears out the old data as well as sets up
the style and tiers for the new data adapter.
A data adapter needs to subclass apollo.dataadapter.AbstractApolloAdapter. AbstractApolloAdapter extends org.bdgp.io.AbstractDataAdapter (from the org.bdgp jar. org.bdgp source is on sourceforge). AbstractDataAdapter implements org.bdgp.io.VisualDataAdapter which implements org.bdgp.io.DataAdapter. DataAdapter's interface is this:
public interface DataAdapter {
/**
* Returns the type of data handled by this data adapter
*/
public String getType();
/**
* Returns a list of all operations supported by this data adapter
*/
public IOOperation [] getSupportedOperations();
/**
* For initialization, like opening files or database connections.
*/
public void init();
}
Most of those methods need to be implemented in your data adapter (the abstract classes do not implement most of them).
You should set the name that will appear in the data adapter chooser dropdown list by calling setName (which is implemented in AbstractApolloAdapter) in your constructor.
apollo.dataadpater.ApolloDataAdapterI has defined a set of org.bdgp.io.IOOperation constants that apollo uses and gets returned by getSupportedOperations:
public static final IOOperation OP_READ_DATA = new
IOOperation("Read data");
public static final IOOperation OP_WRITE_DATA = new IOOperation("Write
data");
public static final IOOperation OP_READ_SEQUENCE = new
IOOperation("Read sequence");
public static final IOOperation OP_READ_RAW_ANALYSIS = new
IOOperation("Read raw analysis results");
public static final IOOperation OP_APPEND_DATA = new IOOperation("Add
additional data");
So if your adapter is read only it should just return this array:
IOOperation[] supportedOperations = {ApolloDataAdapterI.OP_READ_DATA};
If your data adapter can read, write, and layer/append data, an
array like so should be returned:
IOOperation [] supportedOperations = {
ApolloDataAdapterI.OP_READ_DATA,
ApolloDataAdapterI.OP_WRITE_DATA,
ApolloDataAdapterI.OP_APPEND_DATA
};
init() may be a no-op if there is no initilization your data adapter needs to do (a lot of the dataadapters inits are no-ops). AbstractApolloAdapter implements this as a no-op. If you need to do initialization of your data adapter, override this.
getType() should return a String that describes the DataAdapter. GAMEAdapter returns: "GAME XML source (filename, URL, gene=cact, band=34A, or sequence=ACGT)" As far as I can tell this is actually not used anywhere by the DataAdapterChooser. Since it seems inconsequential, AbstractApiolloAdapter implements this to return the empty string. You can override this in case it does have consequence in the future (maybe it does now and I'm missing something)
From the org.bdgp.io.VisualDataAdapter interface you need to
implement the
getUI method:
/**
* Returns a user interface for the requested IOOperation. Most
* VisualDataAdapters will return a different user interface for each
* supported IOOperation.
*/
public DataAdapterUI getUI(IOOperation op);
This returns the associated DataAdapterGUI described above. (Return
null if your data adapter has no ui, like if its only used from the
command line)
CurationSet holds the annotations and results:
StrandedFeatureSetI getAnnots()
StrandedFeatureSetI getResults()
setAnnots(StrandedFeatureSetI)
setResults(StrandedFeatureSetI)
A StrandedFeatureSetI is a FeatureSetI with these added methods:
public FeatureSetI getForwardSet();
public FeatureSetI getReverseSet();
So it has a FeatureSetI for the forward and reverse strand.
A FeatureSetI is a holder of SeqFeatureIs (its also a subclass of SeqFeatureI). SeqFeatureI extends RangeI, the Range interface, which has the properties of Range mentioned above. SeqFeatureIs and FeatureSetIs are the basic building blocks of the datamodel.
Then different objects come into play on the result and annot side of the datamodel. The FeatureSet returned by getAnnots().getForwardSet() (or getReferseSet()) holds AnnotatedFeature objects. An AnnotatedFeature is a FeatureSet. AnnotatedFeature has things that are common to all annot model objects: comments, identifier, isProblematic, description, dbxrefs, and synonyms. An AnnotatedFeature can be a holder of other AnnotatedFeatures which may be a Transcript, if its a gene. The different annot types(e.g. gene,psuedogene,transposon...) are distinguished by the getTopLevelType() method.
A Transcript is also an AnnotatedFeature. It has a translation start and end and functions for cdna and peptide sequence. Its also a holder of Exons.
Exon extends AnnotatedFeature. An Exon has a frame. Exons are the leaves of the annot model.
On the result side, the FeatureSet from CurationSet.getResults().getForward/ReverseSet() holds a FeatureSet for each type in the strand (e.g. blastx, ESTs,...). This FeatureSet holds a FeatureSet that is the result analog to a transcript. This FeatureSet holds a bunch of SeqFeatures, which may be FeaturePairs. FeaturePair extends SeqFeature and is used for alignments. A FeaturePair holds 2 SeqFeatures: a query and a hit, which are the alignment/blast equivalents.
Here the structure from forward result set to leaves:
ForwardResultFeatureSet (isHolder = true)
|
FeatureSet For Each Type(isHolder = true)
|
FeatureSet "result transcript" (isHolder = false)
|
SeqFeature(may be FeaturePair)
Annot structure:
AnnotatedFeature (one for each strand) (isHolder = true)
|
AnnotatedFeature(previously this was Gene)(isHolder = true)
|
Transcript(isHolder = false)
|
Exon
This is the structure GAME uses. Turns out apollo is a little more flexible. FeatureSetI has a notion of being a "holder". If a feature set is not a "holder", it will be probably be getting displayed in some fashion (this admittedly is a little funny putting viewish type things in the model). So the part of the structure above where isHolder=false needs to be the same, but the part of the structure where isHolder = true can vary. You can add more layers in the holder part of the data structure if you like and apollo will not complain. In fact the ensj data adapter has more layers in here.
A CurationSet extends GenomicRange which extends Range. A GenomicRange allows you to set an organism string and a chromosome string. A Range has a name. GenomicRange sets its name to its chromosome.
Range also has a start and end to set. Your CurationSet and features need to be in the same coordinate space. Apollo does not assume the features are relative to the curation set and offset them. If your feature data is relative to the curation set, your data adapter has to do the offsetting to get your apollo features in absolute coordinates rather than relative coordinates. This is actually true of GAME XML. GAME spans(feature) are relative to its map(curation set). The GAME data adapter adds the offset of the curation set/map to all of its spans in making its SeqFeatures.
To make this clear here is an example. Lets say a data set starts at 1000, and its features are relative. A relative data feature of 100 would need to have 1000 added to it for a start of 1100.
Actually it gets even a bit more complicated. Relative coordinates might be base-oriented (counts bases themselves - start at 1) or interbase (counts between bases - start at 0). The above example assumes the coords are interbase. If they are base-oriented (as GAME is) you would have to subtract 1 to get the offset right. So if its base-oriented relative coords with cur set start at 100 and feature start at 1 then 100 + 1 would have the feature starting at 101, which is not right. Subtracting 1 to compensate for base-oriented will have it starting at 100 where it belongs.
for annots:
StrandedFeatureSet annots = new StrandedFeatureSet(new
AnnotatedFeature(), new AnnotatedFeature())
AnnotatedFeature is a FeatureSet. For CurationSets annot stranded feature set, the feature sets have to be AnnotatedFeatures.
You can then use the StrandedFeatureSet to add forward and reverse features. StrandedFeatureSet will query the features strand and add it to the appropriate feature set strand. So in practice you dont actually need to add things directly to the feature set for a strand.
So theres an apollo quirk in that it turns out a features type can
be set
in either the child (SeqFeature/FeaturePair) or parent (FeatureSet)
and it will work with the setting in tiers. Its probably best just to
set both, but minimally for interoperability with other dataadapters
(e.g. GAME)
set the FeatureSets type.
transcript.setTranslationStartAtFirstCodon()
where transcript is an instance of the Transcript class. This will set the start at the standard start codon that gives the longest peptide (none is set if no starts are found), and then sets a stop if there is one in frame with the start.
You can explicitly set a start with:
transcript.setTranslationStart(int start)
This will not explicitly set a stop.
To explicitly set a stop call:
transcript.setTranslationStop(int stop)
If you want to explicitly set a start and have the stop automatically calculated from that call:
transcript.setTranslationStart(int start, true)
where the true tells it to calculate the end. setTranslationStop with no boolean has an implicit false for this param.
You have to set the transcripts reference sequence for translation stops and starts to work properly (especially the automatic setting). This is done with:
transcript.setRefSequence(SequenceI mainGenomicSequence)
The sequence is usually (always?) the main genomic sequence. See "Sequence" below.
I noticed the GAME adapter sets its exons' ref sequence as well. Its
unclear if this is necessary but it doesn't hurt. It seems the GAME
adapter sets ref sequences for most or all of its features. (check out
source src/java/apollo/dataadapter/gamexml/GAMEAdapter setRange
method).
When the gui is retrieving the sequence that has been curated it is necessary to know where that start and end are on the reference sequence so that the correct offsets can be applied. Therefore there is a link between the annotated sequence model to the curationSet. This is initialized when curation.setRefSequence(SequenceI seq) is called. Within this method (it overrides the parent's method in Range) internally the curation calls seq.setRange(this). Then when the Sequence model's getResidues() method is call it uses the start and end of the curation set to determine the correct offset.
The needed calls in the adapter are:
1. curation.setRefSequence(SequenceI sequence)
2. curation.setStrand(int)
3. curation.setStart(int)
4. curation.setEnd(int)
A type is associated with the data. A given analysis and its results are all of a single type. Likewise a collection of annotations are organized into types (all the P-elements).
Thus, a tier describes a region of the graphic display. A type defines a collection of data.
See the Apollo
user guide for a description of the tiers file. You
will need to set up a tiers file for your datasource. Same with the
style file.
For all of your features (results and annots) you will be setting a
feature type with setFeatureType(String type). This is true of both the
leaf SeqFeatures as well as the FeatureSets up the heirarchy. In order
for your tier to be displayed, the feature type you set must correspond
to a "datatype" in the tiers file. So a gene has featureTypes gene,
transcript, and exon at its 3 levels. For the gene to be displayed
those 3 types are in the gene Type as datatypes in the tiers file as
such:
[Type]
label : gene
tiername : Annotation
datatype : gene
datatype : transcript
datatype : exon
glyph : DrawableGeneFeatureSet
.....
On the forward strand
Start = Low; End = High
on the reverse strand
Start = High; End = Low
What is stored and recorded is low/high
start/end (as Steve says) is biological and refers to what would be Start of transcription (or translation) and End of transcription.
When setStart or setEnd is called the method checks the strand and sets low/high accordingly. So, beware that if you use start/end then you must call setStrand first or else things are assumed to be forward strand.
WARNING: If you intend to use these transactions (like for jdbc writeback) the 2 files must be kept consistent! If data1.game moves so must the .tnxml file. If data1.game is renamed data2.game, data1.tnxml must be renamed data2.tnxml. If this proves problematic, I am considering an option where they are saved together in 1 file.
The Chado JDBC Adapter uses the transactions to do fine grained
write
back to the chado database. A transaction is converted into SQL
for updates, deletes, and inserts to the database.
Transactions can get very redundant. If you update the same field many
times you don't need all of those updates to go to the database.
TransactionManager has a coalesce method that tries to weed out all the
redundant transactions. The coalesce function is a work in
progress. Presently it gets most but not all redundancies. coalesce is
called by the writeback adapters at write time.
apollo.dataadapter.chadoxml.ChadoXMLTransactionAdapter converts apollo
transactions to chado xml transactions. These can be used by the chado
xort tool to update a chado database (an alternative to the jdbc
adapter). This adapter is write-only. Converting chado xml transactions
to apollo transactions is actually non-trivial.
Transactions are used for undo. Undo is currently only implemented in
the Annotation Info Editor. At some point we hope to get undo
impelemented for all of apollo.
So transactions can be used by any dataadapter that wants to do fine
grain editing. Transactions are an alternative to dumping the whole
apollo datamodel or diffing the apollo datamodel with ones datasource
to in effect create your own transactions. Transactions can be really
helpful for datasources that are not solely apollo, but are integrated
with non-apollo data. With transactions one can edit the parts of ones
datasource that apollo has changed. The alternative of dumping the
whole apollo datamodel to the datasource can mean that the data entry
gets wiped out and re-inserted, which can be tricky for integrated data.
If you want to use transactions for you dataadapter here are some
things you need to know. First get the TransactionManager with
CurationSet.getTransactionManager(). Its then a good idea to call
TransactionManager.coalesce() to get rid of redundancies.
heres a bit of sample code:
TransactionManager transactionManager =
curationSet.getTransactionManager();
transactionManager.coalesce(); // weed out redundant transactions for
writeback
for (int i=0; i < transactionManager.numberOfTransactions(); i++) {
Transaction transaction =
transactionManager.getTransaction(i);
if (transaction.isUpdate())
doUpdate(transaction);
else if (transaction.isAdd())
doAdd(transaction);
else if (transaction.isDelete())
doDelete(transaction);
}
Heres some relevant methods from Transaction:
boolean isUpdate()
boolean isAdd()
boolean isDelete()
Date getDate()
String getAuthor()
SeqFeatureI getSeqFeature() // seq feature edited
boolean hasSubpart()
-- hasSubpart returns true if transaction has a subpart. add and delete
feature have no subpart. All updates have subparts. Add and
delete may or may not have subparts. adding a whole feature has no
subpart. Adding a comment or synonym is an add with subpart. Same with
delete. apollo.editor.TransactionSubpart is basically a
controlled vocabulary of subparts.
TransactionSubpart getSubpart() // returns subpart type. see
apollo.editor.TransactionSubpart
if hasSubpart() == true then
Object getNewSubpartValue() gives new value of
subpart
Object getOldSubpartValue() gives old value of
subpart
There are also CompoundTransactions (Transaction.isComopund() == true).
For a data adapter I dont think these are of concern. They are for undo
when a bunch of transactions result from one user action/edit, so that
they can all be undone at once. coalesceTransactions actually flattens
all of the compounds (at least for now) so after a coalesce you
shouldnt see a compound transaction.
For examples of transactions being used for writeback see
apollo.dataadapter.chado.JDBCTransactionWriter,
apollo.dataadapter.gamexml.TransactionXMLAdapter, and
apollo.dataadapter.ChadoTransactionXMLWriter. The chado xml writer
writes ChadoTransactions.
apollo.dataadapter.chado.ChadoTransactionTransformer converts apollo
transaction to chado transactions.
The game adapter had an early form of these transactions. These are no
longer relevant, being supplanted by the new.
catch(Exception e) { e.printStackTrace();}
?
The JDBC chado adapter is still a work in progress(as of time of writing 3/17/05). Theres still a few bugs to be hammered out(FlyBase contig dashed lines, exons out of range... see chado-jdbc-todo), and a few bells and whistles to add (on demand retrieval of seq and descriptions, user selects which features to retrieve... todo).
The Chado adapter allows Apollo to read data directly from a Chado
database (Chado is the database schema for biological data that is
being
developed by the GMOD consortium). The default Chado database
that
Apollo reads from is the FlyBase Chado Indiana public server, which
holds
the same Drosophila melanogaster annotation data as is provided by the
GAME adapter. The Chado adapter will be most useful to groups
that are
using a Chado database for storing their sequence annotation data (in
which case you will need to modify some of the configuration files to
handle your data).
If you are setting up Apollo to read from your chado database you will
need to modify the configuration
files. To do this
you will need to add or change xml in the file conf/chado-adapter.xml
in
order to fill in two elements: "chadodb" and "chadoInstance".
chadodb element
---------------
Here is an example of the chadodb element:
<!-- Indiana public FlyBase server r3.2
-->
<chadodb>
<name>FlyBase Chado
Indiana public server r3.2</name>
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
<url>jdbc:postgresql://bugbane.bio.indiana.edu:7302/chado_r3.2</url>
<dbName>chado_r3.2</dbName>
<dbUser>flybase</dbUser>
<dbInstance>flybaseInstance</dbInstance>
<style>game.style</style>
<default-command-line-db>true</default-command-line-db>
</chadodb>
You will need to add a similar entry to chado-adapter.xml describing
your
Chado database.
"name" is the label that will appear in the dropdown list of databases.
"adapter" identifies the Apollo class to use for your database. If your
database uses Postgres, use
apollo.dataadapter.chado.jdbc.PostgresChadoAdapter; if you are using
Sybase use apollo.dataadapter.chado.jdbc.SybaseChadoAdapter. If you are
using a different database vendor, try Postgres and Sybase and see if
one
of them works. Send email to the apollo mailing list if you encounter
problems.
"url" is the URL for your database server that Apollo will connect to.
"dbName" is the database name to use on your server.
"dbUser" is the database user/login.
"dbInstance" identifies the type of Chado database (see the section on
chadoInstance).
"style" is the style file to use for this database.
"default-command-line-db" if set to true this will be the database used
when apollo is run from the command line.
chadoInstance element
---------------------
In addition to the "chadodb" xml element, chado-adapter.xml has
"chadoInstance" elements that the chadodb elements refer to.
chadoInstance captures two things: a Chado instance class to use, and a
list of annotation types in that Chado database. Here is an example of
the chadoInstance element:
<chadoInstance id="flybaseInstance">
<inheritsInstance>referenceInstance</inheritsInstance>
<sequenceTypes>
<type>
<name>chromosome_arm</name>
<useStartAndEnd>true</useStartAndEnd>
<queryForValueList>false</queryForValueList>
<values>4,2L,2R,3L,3R,X,2h,3h,4h,Xh,Yh,U</values>
</type>
<type>gene</type>
<type>golden_path_region</type>
</sequenceTypes>
<featureCV>sequence</featureCV>
<relationshipCV>relationship</relationshipCV>
<propertyTypeCV>feature_property</propertyTypeCV>
<!-- default is part_of
-->
<partOfCvTerm>part_of</partOfCvTerm>
<transProtRelationTerm>derives_from</transProtRelationTerm>
<polypeptideType>polypeptide</polypeptideType>
<retrieveAnnotations>true</retrieveAnnotations>
<genePredictionPrograms>
<program>genscan_masked</program>
<program>genie_masked</program>
</genePredictionPrograms>
<searchHitPrograms>
<program>sim4</program>
<program>%blastx%</program>
</searchHitPrograms>
<oneLevelResultPrograms>
<program>crmscan</program>
<program>crm_makeprimer</program>
</oneLevelResultPrograms>
<searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
<inheritsInstance>referenceInstance</inheritsInstance>
<writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXmlTemplateFile>
</chadoInstance>
"inheritsInstance" allows a chadoInstance to inherit all the values
from another instance (to avoid redundancy), must label a previously
described instance.
"sequenceTypes" are the database fields corresponding to top-level
entries. These are the types that you can query in the GUI to load from
chado. Each top-level controlled vocabulary term is listed as a type.
The type can optionally further be broken down. <name> is the
chado cv term for the type. <useStartAndEnd> will cause start and
end fields to appear in the gui to get a sub section of the feature,
for example a subsection of a chromosome. If <queryForValueList>
is true then the values for the type that populate the dropdown list
will be queried from chado. If queryForValueList is false then the list
values need to be provided with <values>.
"clsName" is the class name to be used for your Chado instance.
There
are currently three Chado instance classes: -
apollo.dataadapter.chado.jdbc.TigrSybilChadoInstance
- apollo.dataadapter.chado.jdbc.FlybaseChadoInstance
- apollo.dataadapter.chado.jdbc.RiceInstance
FlyInstance is the most up-to-date of the three, so you can start by
trying that with your database. If that doesn't work, please
contact the
apollo mailing list.
"oneLevelAnnotTypes" and "threeLevelAnnotTypes" list annotation types
consisting of one and three levels. (Eventually this will be figured
out
automatically.)
One level annot types substitution, nucletide_insertion, and
nucletide_deletion are treated special by apollo (though they are not
by chado). These do not show up as features in the main window, rather
they show up as sequence errors in the exon detail editor, with a base
pair turned orange. The main window just displays an orange vertical
line for these.
featureCV is the name of the feature ontology in chado,
relationshipCV is for the relationship ontology, and propertyTypeCV is
for the property type ontology.
partOfCvTerm only needs to be listed if "part_of" is not used for
this (alternate out there is "partof").
Likewise, "derives_from" is the default transcript-protein relation
term. If your chado uses something different like "produced_by", that
would need to be set here. The default polypeptide/protein type
is "polypeptide. If you are using "protein", that needs to be set.
"inheritInstance" can be used to inherit from other chado instances
already defined in the file.
"retrieveAnnotations" tells whether to query for annotations. The
default is true.
"genePredictionPrograms" list the gene prediction result programs to
query for.
"searchHitPrograms" list the programs to query for alignment/search hit
results.
"oneLevelResultPrograms" lists programs that return simple results that
are only one level deep in structure, which are often used to construct
one level annotations.
"writebackXmlTemplateFile" is the xml template configuration file to
use for writeback - more details in the next section.
If no style is set in chadodb, the style that you are using will
need to be set in apollo.cfg:
DataAdapterInstall "apollo.dataadapter.chado.ChadoAdapter"
"tigrsybil.style"
Replace tigrstybil.style with your style file. (The style param
DatabaseToStyle can be
used to have multiple chado dbs with different styles, e.g.
DatabaseToStyle "chado_r3.2 -> game.style")
ChadoInstance is where things get awkward and unsettled. TIGR stuff is outdated, FlyBase and Rice are more current, so you most likely want to try those. Unless you have mimicked the FlyBase or Rice schema exactly and have all the same kind of results in your database you will either get errors or perhaps an empty apollo (you are on unchartered territory). Currently there are TIGR, FlyBase, & Rice chado instance classes that capture all the differences between them. This is sufficient for now. When a fourth data source comes along that needs different combinations of what has been lumped into these classes, we are going to need to get a lot more fine grained about configuring this adapter, but until we get to that point, theres no urgency to finely configure this. So in other words if you are wanting to connect up your chado database, please contact us via the Apollo mailing list and we can discuss what your chado database looks like, how much it conforms to SO, and figure out where the fine grain configging will need to happen to accommodate your needs. I'm taking a config-as-we-need-it approach, as I have no idea what will be encountered in a chado database of a different species. In theory, if a chado db follows SO closely there shouldn't be that much tweaking; there still will be some of course, and I am anxious to see how it plays out in practice. So send us email if you are thinking about taking up this endeavor.
The query for CDS expects that the CDS is denoted in chado with SOFA's polypeptide and is in relationship to the transcript with "derives_from". Anything other than this, like "part_of" need to be configured as mentioned above.
Jdbc writeback uses Transactions, so read the above section on Transactions if you havent already done so.
To configure writeback you will need to modify
conf/transactionXMLTemplate so it fits your version of chado. The
template there is how rice is setup. You will minimally need to put
your organism in that file. If your cvterms vary from the standard
ontologies, that also has to be configured.
There is an "impedance mismatch" between the apollo datamodel and chado. Apollo uses unshared exons where chado uses shared exons. This is problematic for writeback, as apollo does not carry through shared exon ids (this would be non-trivial - basically a major headache). So currently the jdbc writer makes the assumption that exon names are of the form genename:start-end. So if gene xyz had start 100 and end 200 it would be named xyz:100-200.
So for the moment your chado must conform to this naming convention
for exons. If this is really problematic let us know (apollo mailing
list). One alternate solution coud be to query via the exon's
featureloc, but that is not in place at the moment.
Lincoln:
Enclosed are my informal notes on what Apollo does and does not need
[from the
XML] to correctly process and display annotations.
I found it was safer to work from the example GAME/XML file that comes with Apollo than to rely on the DTD, because there are a couple places where the reality diverges slightly from the theory.
<seq>
id yes
length yes
md5checksum no
version no
focus yes (for the main sequence)
</seq>
<map_position> need! don't need <arm> but need <span><start> & <end>
<annotation>
id and name do not have to be the same -- name is the "display_name"
<comment> internal not needed
<person> and <date> use values
symbol -- ignore
property type must be part of a controlled vocabulary, will not load
without proper controlled vocabulary
Separate step that can happen later...
<gene> -- ignore
<dbxref> -- need and should be separated from other attributes
<feature_set> is synonymous with transcript, and gene can have
multiple
<feature_set>
id -- need
produces_seq -- don't need
<feature_span>
Start codon is of type "translate offset" and coordinates are
three bases starting at codon 1.
Start can be > end for minus strand.
<seq_relationship> -- indicates coordinate system "query" usually
or "subject"
for alignments
<computational_analysis>
<database> must be there, but can say "dummy"
<result_set> is basically a hit.
id is a unique ID within the GAME file, but not critical maybe
name is a globally unique name for the hit (display_name)
The part before the first hyphen is displayed by Apollo.
<result_span> id = some number
<output> skip this section entirely
<seq_relationship>
"query" is the focus seq object
"subject" is the hit sequence
For minus strand hits, reverse the query (maybe).
Suzi's response:
For minus strands don't reverse query with subject, rather this is indicated by a start that is bigger than the end. This is true for both query and subject.
These are the four possible configurations (with pretend intervals of 100-110 on the query (genomic) and 10-20 on the subject). minus and minus is silly, but for completeness
genomic hit
100-110 10-20 (plus and plus)
110-100 10-20 (minus and plus)
100-110 20-10 (plus and minus)
110-100 20-10 (minus and minus)


Welcome to daily dram! A site that does stuff and it is cool. Like extra cool and stuff. Stuff is cool. Scotch counts as stuff. And scotch is really good. I like really good stuff. Like Scotch.
This is the begning of the review for this awesome whiskey


ktutil - Kerberos keytab file maintenance utility
\$1 \n[an-margin] level \n[rst2man-indent-level] level margin: \n[rst2man-indent\n[rst2man-indent-level]] - \n[rst2man-indent0] \n[rst2man-indent1] \n[rst2man-indent2]
The ktutil command invokes a command interface from which an administrator can read, write, or edit entries in a keytab or Kerberos V4 srvtab file.
Displays the current keylist.
read_kt keytab
Read the Kerberos V5 keytab file keytab into the current keylist.
read_st srvtab
Read the Kerberos V4 srvtab file srvtab into the current keylist.
write_kt keytab
Write the current keylist into the Kerberos V5 keytab file keytab.
write_st srvtab
Write the current keylist into the Kerberos V4 srvtab file srvtab.
Clear the current keylist.
delete_entry slot
Delete the entry in slot number slot from the current keylist.
add_entry {-key|-password} -p principal -k kvno -e enctype
Add principal to keylist using key or password.
Displays a listing of available commands.
Quits ktutil.
ktutil: add_entry -password -p<EMAIL_ADDRESS>-k 1 -e aes128-cts-hmac-sha1-96 Password for<EMAIL_ADDRESS>ktutil: add_entry -password -p<EMAIL_ADDRESS>-k 1 -e aes256-cts-hmac-sha1-96 Password for<EMAIL_ADDRESS>ktutil: write_kt keytab ktutil:
1985-2013, MIT


Top ten movies
- 47 breakdown
- Small Axe: Lovers Rock
- Da 5 Bloods
- Beanpole
- Never Rarely Sometimes Always
- First Cow
- Minari
- David Byrne's American Utopia
- The Assistant
- It's Alive!: On the Many Faces of Frankenstein
My education computer science in BAU
- java
- Paython
- javascript
- css
My name is erada abdalrhman yousef ali,I am 22, i studied computer science in balqa applied university,igraduated in september of 2020 . In my childhood i had many hobbies such as i loved singing,playing sports,reading books and writing.But now, i do not feel i belong to those talens, now i like to play playstation and learn the programming language of software. I do not have any experience in the field of work.
In 2019 i trained for three mounths in the gaming industry 2d and 3d on the program unity,i really enjoyed this training. My graduation project was an application called wewe, the idea is to get an ambulance in the faster time by pressing one button,i worked hard on the project and earned a grade A, my faviortcolor is red and my faviort number is 8


Build a Dockerfile straight from your R session. 'dockerfiler' allows you to create step by step a Dockerfile, and provide convenient tools to wrap R code inside this Dockerfile.
| Version: | 0.1.1 |
| Imports: | attempt, glue, R6 |
| Suggests: | covr, testthat, knitr, rmarkdown |
| Published: | 2018-04-18 |
| Author: | Colin Fay [cre, aut] |
| Maintainer: | Colin Fay <contact at colinfay.me> |
| BugReports: | https://github.com/ColinFay/dockerfiler/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/ColinFay/dockerfiler |
| NeedsCompilation: | no |
| Materials: | NEWS |
| CRAN checks: | dockerfiler results |
| Reference manual: | dockerfiler.pdf |
| Vignettes: |
Vignette Title |
| Package source: | dockerfiler_0.1.1.tar.gz |
| Windows binaries: | r-devel: dockerfiler_0.1.1.zip, r-release: dockerfiler_0.1.1.zip, r-oldrel: dockerfiler_0.1.1.zip |
| OS X binaries: | r-release: dockerfiler_0.1.1.tgz, r-oldrel: dockerfiler_0.1.1.tgz |
| Old sources: | dockerfiler archive |
Please use the canonical form https://CRAN.R-project.org/package=dockerfiler to link to this page.


The ultimate resource for picking your Fantasy Football Team. Enter your league scoring settings on the below to get started.


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We implemented gchromVAR as an R
package for performing enrichment analyses of genome-wide chromatin accessibility data with summary statistics (per-variant posterior-probabilities) from common-variant associaitons.
This vignette covers the usage of gchromVAR with standard processed input data from the hematopoesis interrogation that we’ve previously described. This package was designed to provide new functionality by generalizing the chromVAR framework. Notably, while chromVAR requires binary annotations (such as the presence or absence of transcription factor binding motifs), generalized- or genetic-chromVAR relaxes this assumption and allows for continuous annotations using the computeWeightedDeviations
function. For more detailed documentation covering different options for various inputs and additional applications of the chromVAR package, see the additional vignettes on the chromVAR documentation website.
library(chromVAR)
library(gchromVAR)
library(BuenColors)
library(SummarizedExperiment)
library(data.table)
library(BiocParallel)
library(BSgenome.Hsapiens.UCSC.hg19)
set.seed(123)
register(MulticoreParam(2))
After loading the required packages as shown in the preceding code chunk, note also that the time-consuming functionality in gchromVAR can be parallelized to the number of available cores on your machine. The rest of this vignette will involve using these imported functions and packages to score GWAS enrichments for 16 traits in 18 cell types.
Below is an overview highlighting the cell types with the corresponding colors used throughout this vignette available through BuenColors. Under our schematic of the differentation hierarchy, the 16 terminal blood cell traits that we analyzed with common variant associations are shown.
Figure 1. Overview of hematopoesis with cell types (top; note colors) and GWAS traits (bottom) explored thus far with gchromVAR.
Also, note that the traits are positioned under the hierarchy in accordance with our current understanding of where these cell traits manifest after differentiating. One might hypothesize that the terminal cell types may be the most enriched for those particular traits (e.g. erythroblasts should be enriched for GWAS signal for traits like red blood cell count). One may also expect late-stage progenitors (i.e. the cell types that occur before terminal differentation that may be multi-potent like CMPs or MEPs). With this in mind, we are ready to explore the gchromVAR results.
For using ATAC-seq or other chromatin accessibility data for gchromVAR, we recommend using the proatac pipeline to generate 1 set of consensus, equal-wdith peaks spanning the cellular phenotypes and synthesizing a singular counts table. These data for hematopoesis are already available in the extdata
of gchromVAR. The format of the quantitative chromatin data for the key functionality is a RangedSummarizedExperiment, which we construct using the counts matrix and peak definitions. The last line of code also adds the GC content per peak, which is used in the background model.
countsFile <- paste0(system.file('extdata/paper',package='gchromVAR'), "/hemeCounts.tsv.gz")
peaksFile<- paste0(system.file('extdata/paper',package='gchromVAR'), "/hemePeaks.bed.gz")
peaksdf <- data.frame(fread(paste0("zcat < ", peaksFile)))
peaks <- makeGRangesFromDataFrame(peaksdf, seqnames = "V1", start.field = "V2", end.field = "V3")
counts <- data.matrix(fread(paste0("zcat < ", countsFile)))
SE <- SummarizedExperiment(assays = list(counts = counts),
rowData = peaks,
colData = DataFrame(names = colnames(counts)))
SE <- addGCBias(SE, genome = BSgenome.Hsapiens.UCSC.hg19)
Next, we want to overlap the GWAS summary statistics with our accessibility peaks. To facilitate this, we’ve created the importBedScore
function, which will iteratively build another RangedSummarizedExperiment where the same peaks define the row space and the columns are defined as various GWAS annotations.
## .. .. .. .. ..@
## ..@ NAMES : NULL
## ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
## .. .. ..@ rownames : NULL
## .. .. ..@ nrows : int 451283
## .. .. ..@ listData : Named list()
## .. .. ..@ elementType : chr "ANY"
## .. .. ..@ elementMetadata: NULL
## .. .. ..@ metadata : list()
## ..@ metadata : list()
With these two RSE
objects created (SE
for chromatin counts and ukbb
for GWAS data), we can now run the core gchromVAR function, computeWeightedDeviations
.
The functional execution having followed the previous steps is straight forward–
ukbb_wDEV <- computeWeightedDeviations(SE, ukbb)
zdf <- reshape2::melt(t(assays(ukbb_wDEV)[["z"]]))
zdf[,2] <- gsub("_PP001", "", zdf[,2])
colnames(zdf) <- c("ct", "tr", "Zscore")
head(zdf)
## ct tr Zscore
## 1 B BASO_COUNT 0.54028791
## 2 CD4 BASO_COUNT -0.08351059
## 3 CD8 BASO_COUNT -0.66325644
## 4 CLP BASO_COUNT 0.49815087
## 5 CMP BASO_COUNT 1.70456014
## 6 Ery BASO_COUNT -0.68111180
The later steps just show re-formatted output for convenience. The last table, zdf
provides a data frame of the Cell type (ct
), trait (tr
) and enrichment z-score for each of the 16x18 combinations.
A statistical way of determining how our results faired is to determine the relative positioning of lineage-specific enrichments. For each trait, we define the appropriate set of lineage-specific tissues (from Figure 1), and then annotate the results data frame. First, we define the four major lineages in hematopoesis:
Ery <- c("HSC", "MPP", "CMP", "MEP", "Ery")
Meg <- c("HSC", "MPP", "CMP", "MEP", "Mega")
Mye <- c("HSC", "MPP", "CMP", "LMPP", "GMP-A", "GMP-B", "GMP-C", "Mono", "mDC")
Lymph <- c("HSC", "MPP", "LMPP", "CLP", "NK", "pDC", "CD4", "CD8", "B")
Next, we annotate the data frame work lineage-specific (“LS”) enrichments:
zdf$LS <-
(zdf$tr == "BASO_COUNT" & zdf$ct %in% Mye) +
(zdf$tr == "EO_COUNT" & zdf$ct %in% Mye) +
(zdf$tr == "NEUTRO_COUNT" & zdf$ct %in% Mye) +
(zdf$tr == "MONO_COUNT" & zdf$ct %in% Mye) +
(zdf$tr == "WBC_COUNT" & zdf$ct %in% c(Mye, Lymph)) +
(zdf$tr == "LYMPH_COUNT" & zdf$ct %in% Lymph) +
(zdf$tr == "PLT_COUNT" & zdf$ct %in% Meg) +
(zdf$tr == "MPV" & zdf$ct %in% Meg) +
(zdf$tr == "MEAN_RETIC_VOL" & zdf$ct %in% Ery) +
(zdf$tr == "HGB" & zdf$ct %in% Ery) +
(zdf$tr == "HCT" & zdf$ct %in% Ery) +
(zdf$tr == "MCH" & zdf$ct %in% Ery) +
(zdf$tr == "MCV" & zdf$ct %in% Ery) +
(zdf$tr == "MCHC" & zdf$ct %in% Ery) +
(zdf$tr == "RBC_COUNT" & zdf$ct %in% Ery) +
(zdf$tr == "RETIC_COUNT" & zdf$ct %in% Ery)
Finally, we can compute a Mann-Whitney Rank-sum statistic to determine the relative enrichment of the gchromVAR results compared to the non-lineage specific measures:
zdf$gchromVAR_pvalue <- pnorm(zdf$Zscore, lower.tail = FALSE)
gchromVAR_ranksum <- sum(1:dim(zdf)[1]*zdf[order(zdf$gchromVAR_pvalue, decreasing = FALSE), "LS"])
permuted <- sapply(1:10000, function(i) sum(1:dim(zdf)[1] * sample(zdf$LS, length(zdf$LS))))
pnorm((mean(permuted) - gchromVAR_ranksum)/sd(permuted), lower.tail = FALSE)
## [1] 5.075067e-15
From this statistic, we can see that lineage-specific enrichments for much stronger for gchromVAR than we’d expect by chance. We quantified this for several related methods on the initial landing page, demonstrating the utility of our approach.
Finally, we can do a simple Bonferonni-correction threshold to see that nearly all of the enrichments from gchromVAR are lineage specific.


public interface SerializerVisitor extends Visitor
ResourceConfigSortComparator
.
See Delivery Overview.| Modifier and Type | Method and Description |
|---|---|
void |
writeCharacterData(Node node,
Writer writer,
ExecutionContext executionContext)
Write element text.
|
boolean |
writeChildElements()
Write the child elements of the element this SerializationUnit is being applied to.
|
void |
writeElementCDATA(CDATASection cdata,
Writer writer,
ExecutionContext executionContext)
Write element CDATA section.
|
void |
writeElementComment(Comment comment,
Writer writer,
ExecutionContext executionContext)
Write element comment.
|
void |
writeElementEntityRef(EntityReference entityRef,
Writer writer,
ExecutionContext executionContext)
Write element entity reference object.
|
void |
writeElementNode(Node node,
Writer writer,
ExecutionContext executionContext)
Write element Node object.
|
void |
writeEndElement(Element element,
Writer writer,
ExecutionContext executionContext)
Write the element end portion; close the element.
|
void |
writeStartElement(Element element,
Writer writer,
ExecutionContext executionContext)
Write the element start portion; the element name and it's
attributes.
|
void writeStartElement(Element element, Writer writer, ExecutionContext executionContext) throws IOException
element
- The element start to write.writer
- The writer to be written to.executionContext
- ExecutionContext instance for the delivery context.IOException
- Exception writing output.void writeEndElement(Element element, Writer writer, ExecutionContext executionContext) throws IOException
element
- The element end to write.writer
- The writer to be written to.executionContext
- ExecutionContext instance for the delivery context.IOException
- Exception writing output.void writeCharacterData(Node node, Writer writer, ExecutionContext executionContext) throws IOException
node
- The Text object to write.writer
- The writer to be written to.executionContext
- ExecutionContext instance for the delivery context.IOException
- Exception writing output.void writeElementComment(Comment comment, Writer writer, ExecutionContext executionContext) throws IOException
comment
- The comment o write.writer
- The writer to be written to.executionContext
- ExecutionContext instance for the delivery context.IOException
- Exception writing output.void writeElementEntityRef(EntityReference entityRef, Writer writer, ExecutionContext executionContext) throws IOException
entityRef
- The entity reference to write.writer
- The writer to be written to.executionContext
- ExecutionContext instance for the delivery context.IOException
- Exception writing output.void writeElementCDATA(CDATASection cdata, Writer writer, ExecutionContext executionContext) throws IOException
cdata
- The CDATA section to write.writer
- The writer to be written to.executionContext
- ExecutionContext instance for the delivery context.IOException
- Exception writing output.void writeElementNode(Node node, Writer writer, ExecutionContext executionContext) throws IOException
node
- The node to write.writer
- The writer to be written to.executionContext
- ExecutionContext instance for the delivery context.IOException
- Exception writing output.boolean writeChildElements()
Copyright © 2020. All rights reserved.


Ballerina Cloud Performance Stats
Daily Performance Tests
Language Comparison
Test Scenario
HTTP1->HTTP1 Passthrough
HTTP1 Transformation
HTTP1 Client->HTTP1 Client Passthrough
HTTP1 Client Transformation
Observability Enabled
MySQL Insert
MySQL Delete
MySQL Update
MySQL Select
60 Users 50b
60 Users 1024b
200 Users 50b
200 Users 1024b
From:
To:
Throughput (Req/sec)
Average Response Time (ms)
Standard Deviation of Response Time
99th Percentile of Response Time
Error Percentage


The Connection
Welcome to my dating website! Create a profile with your interests. We generate matches by interest and location. This site has successfully matched many couples. Take a moment to find out if your special someone is out there!
Hear what users have to say about us...
Finally! I'm super stoked that there is a dating site dedicated to Stormtroopers
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Met my partner, who is also my best friend, on this site.


Enter Your API Key:
Enter The Feed Number:
Enter your start date (must be in format YYYY-MM-DD HH:MM:SS):
Enter your end date (must be in format YYYY-MM-DD HH:MM:SS):
Enter your increment in seconds:
Output will appear here


Growing Together
This site was put together in early 2018 by a group of students from the Seattle area taking the "challenge course" portion of Udacity's Front End Web Development Nanodegree, as part of the Grow with Google scholarship program.
We are ecstatic to continue our learning journies in tech.
Building this site inspired us to push our capacities as developers and effective team members to the next level. We hope it might help you find and share opportunities for inspiration and for learning, for growth, and for community, too.
Code on.
Meet the Team
- Click a team member's profile to learn more about them.
Jacki Bostow
- Organized group meetings
- Event calendar creation
- Responsive layout
Jinjin Ge
- Event data extraction
- Event list view creation
- Event filter functionality
Robert Grunau
Ming Ho
- Sign Up page
- Login page
- Submit Event page
Yuka Mullen
- Event Details page
- Color scheme
Jacob Olson
- About page
Alex Tran
- UX Advisor


BECOMING
Crevecoeur illustrates that an American is made by people from all backgrounds and of all religions. America is a melting pot of all religions in his case, but in the future this will become all races, all genders. He may not mention the future conflicts that may be in store, but this is the root of all out identities, accepting everyone is the core of writing our own identity.


I’m afraid that Civil Legal Advice does not provide advice about the issue that you are calling about. But our service is not your only option and I can direct you to solicitors whom may be able to help.
I can’t guarantee that these organisations/this organisation will take on your case under legal aid so please check with them to see whether they are able to help you. If you do not qualify for legal aid you may have to pay for their service.
Before I can provide you with your details, we need to complete a short financial assessment to see if you can get Legal Aid. Do you have financial information to hand?
You may need details of:
From the information you have given today we may be able to put you through to a specialist provider/or a legally aided Education provider who could help you with this area of law.
Before I can transfer you, we need to complete a short financial assessment to see if you can get Legal Aid. Do you have financial information to hand?
You may need details of:
From the information you have given me today, you may be able to get free advice from a legal adviser in your area. Please enquire with the provider as there may be a charge for this service.
Before I can provide you with the contact details for providers that are local to you, we need to complete a short financial assessment to see if you can get Legal Aid.
From the information you have given today we may be able to put you through to a specialist provider who could help you with this area of law.
Before I can transfer you we need to complete a short financial assessment to see if you can get Legal Aid. Do you have financial information to hand?
You may need details of:
From the information you have given today we may be able to put you through to a specialist provider who could help you with this area of law.
Before I can transfer you we need to complete a short financial assessment to see if you can get Legal Aid. Do you have financial information to hand?
You may need details of:
Are you aged 17 or under?
Do you receive any money on a regular basis?
Do you have any savings, items of value or investments totalling £2500 or more?
Do you have a partner?
Are you or your partner aged 60 or over?
I am now going to read through a list of benefits. Could you please tell me if you or your partner receive any of these.
{{ ::opt.text }}
I am now going to read through a list of benefits. Could you please tell me if you or your partner receive any of these:


Using the Post'Em tool, you can upload a comma delimited (CSV) spreadsheet to present feedback to site participants. More...


Kekropus:
But the Star of Destiny you have brought makes me question...
This world can only be shaped by the woman in the blue dress and the ones guided by her, the ones who bear her proofs...
If that is indeed you, then you know of our fate, don't you?

Tell him that you are ready.


--- title: (BFDataPackage) BFDataPackage keywords: documentation theme, jekyll, technical writers, help authoring tools, hat replacements last_updated: July 3, 2016 tags: [getting_started] sidebar: matlab_docs_sidebar permalink: bfdatapackage_bfdatapackage.html folder: mydoc ---
BFDataPackage Constructor for BFDataPackage OBJ = BFDataPackage(SESSION, 'id', 'name', 'type') creates a BFDataPackage instance where SESSION is an instance of BFSESSION, 'id' is the id of the package, 'name' is the name of the package and 'type' is the type of the package.


The goal of this activity is to identify two organizations that you can connect with after your program to help them potentially with their technology needs.
Research two organizations. Preferably one for-profit company and one not-for-profit organization. Then, see if you have mutual connection there, utilized LinkedIn and your network.
Fill out this online survey once for each organization
Survey Monkey Form to fill outReach out a person that works there and ask for an “Informational Interview”


#include <TraCIServer.h>
◆ TraCIServer()
| traci_api::TraCIServer::TraCIServer |
( |
int |
port | ) |
|
Standard constructor.
- Parameters
-
| port | The port on which the server should listen for incoming requests. |
◆ ~TraCIServer()
| traci_api::TraCIServer::~TraCIServer |
( |
| ) |
|
◆ close()
| void traci_api::TraCIServer::close |
( |
| ) |
|
Closes the socket, severing all connections.
◆ postStep()
| void traci_api::TraCIServer::postStep |
( |
| ) |
|
◆ preStep()
| void traci_api::TraCIServer::preStep |
( |
| ) |
|
◆ waitForConnection()
| void traci_api::TraCIServer::waitForConnection |
( |
| ) |
|
Starts this instance, binding it to a port and awaiting connections.
The documentation for this class was generated from the following files:
- C:/Users/Public/paramics/programmer/plugins/pveins/src/TraCIAPI/TraCIServer.h
- C:/Users/Public/paramics/programmer/plugins/pveins/src/TraCIAPI/TraCIServer.cpp


Helper class that resolves connection and credential parameters, validates them and generates connection options.
More...
|
| void | Configure (ConfigParams config) |
| | Configures component by passing configuration parameters. More...
|
| |
| void | SetReferences (IReferences references) |
| | Sets references to dependent components. More...
|
| |
| async Task< ConfigParams > | ResolveAsync (string correlationId) |
| | Resolves connection options from connection and credential parameters. More...
|
| |
| ConfigParams | Compose (string correlationId, IList< ConnectionParams > connections, CredentialParams credential, ConfigParams parameters) |
| | Composes Composite connection options from connection and credential parameters. More...
|
| |
|
| void | ValidateConnection (string correlationId, ConnectionParams connection) |
| | Validates connection parameters. This method can be overriden in child classes. Throw error if validation failed. More...
|
| |
| void | ValidateCredential (string correlationId, CredentialParams credential) |
| | Validates credential parameters. This method can be overriden in child classes. Throw error if validation failed. More...
|
| |
| ConfigParams | ComposeOptions (IList< ConnectionParams > connections, CredentialParams credential, ConfigParams parameters) |
| | Composes connection and credential parameters into connection options. This method can be overriden in child classes. More...
|
| |
| ConfigParams | MergeConnection (ConfigParams options, ConnectionParams connection) |
| | Merges connection options with connection parameters This method can be overriden in child classes. More...
|
| |
| ConfigParams | MergeCredential (ConfigParams options, CredentialParams credential) |
| | Merges connection options with credential parameters This method can be overriden in child classes. More...
|
| |
| ConfigParams | MergeOptional (ConfigParams options, ConfigParams parameters) |
| | Merges connection options with optional parameters This method can be overriden in child classes. More...
|
| |
| ConfigParams | FinalizeOptions (ConfigParams options) |
| | Finalize merged options This method can be overriden in child classes. More...
|
| |
Helper class that resolves connection and credential parameters, validates them and generates connection options.
- connection(s):
- discovery_key: (optional) a key to retrieve the connection from IDiscovery
- protocol: communication protocol
- host: host name or IP address
- port: port number
- uri: resource URI or connection string with all parameters in it
- credential(s):
- store_key: (optional) a key to retrieve the credentials from ICredentialStore
- username: user name
- password: user password
- *:discovery:*:*:1.0 (optional) IDiscovery services to resolve connections
- *:credential-store:*:*:1.0 (optional) Credential stores to resolve credentials
◆ Compose()
| ConfigParams PipServices3.Components.Connect.CompositeConnectionResolver.Compose |
( |
string |
correlationId, |
|
|
IList< ConnectionParams > |
connections, |
|
|
CredentialParams |
credential, |
|
|
ConfigParams |
parameters |
|
) |
| |
Composes Composite connection options from connection and credential parameters.
- Parameters
-
| correlationId | (optional) transaction id to trace execution through call chain. |
| connections | connection parameters |
| credential | credential parameters |
| parameters | optional parameters |
- Returns
- resolved options or throw error
◆ ComposeOptions()
| ConfigParams PipServices3.Components.Connect.CompositeConnectionResolver.ComposeOptions |
( |
IList< ConnectionParams > |
connections, |
|
|
CredentialParams |
credential, |
|
|
ConfigParams |
parameters |
|
) |
| |
|
protected |
Composes connection and credential parameters into connection options. This method can be overriden in child classes.
- Parameters
-
| connections | a list of connection parameters |
| credential | credential parameters |
| parameters | optional parameters |
- Returns
- a composed connection options.
◆ Configure()
| void PipServices3.Components.Connect.CompositeConnectionResolver.Configure |
( |
ConfigParams |
config | ) |
|
Configures component by passing configuration parameters.
- Parameters
-
| config | configuration parameters to be set. |
◆ FinalizeOptions()
| ConfigParams PipServices3.Components.Connect.CompositeConnectionResolver.FinalizeOptions |
( |
ConfigParams |
options | ) |
|
|
protected |
Finalize merged options This method can be overriden in child classes.
- Parameters
-
| options | connection options |
- Returns
- finalized connection options
◆ MergeConnection()
| ConfigParams PipServices3.Components.Connect.CompositeConnectionResolver.MergeConnection |
( |
ConfigParams |
options, |
|
|
ConnectionParams |
connection |
|
) |
| |
|
protected |
Merges connection options with connection parameters This method can be overriden in child classes.
- Parameters
-
| options | connection options |
| connection | connection parameters to be merged |
- Returns
- merged connection options.
◆ MergeCredential()
| ConfigParams PipServices3.Components.Connect.CompositeConnectionResolver.MergeCredential |
( |
ConfigParams |
options, |
|
|
CredentialParams |
credential |
|
) |
| |
|
protected |
Merges connection options with credential parameters This method can be overriden in child classes.
- Parameters
-
| options | connection options |
| credential | credential parameters to be merged |
- Returns
- merged connection options.
◆ MergeOptional()
| ConfigParams PipServices3.Components.Connect.CompositeConnectionResolver.MergeOptional |
( |
ConfigParams |
options, |
|
|
ConfigParams |
parameters |
|
) |
| |
|
protected |
Merges connection options with optional parameters This method can be overriden in child classes.
- Parameters
-
| options | connection options |
| parameters | optional parameters to be merged |
- Returns
- merged connection options.
◆ ResolveAsync()
| async Task<ConfigParams> PipServices3.Components.Connect.CompositeConnectionResolver.ResolveAsync |
( |
string |
correlationId | ) |
|
Resolves connection options from connection and credential parameters.
- Parameters
-
| correlationId | (optional) transaction id to trace execution through call chain. |
- Returns
- resolved options or throw error
◆ SetReferences()
| void PipServices3.Components.Connect.CompositeConnectionResolver.SetReferences |
( |
IReferences |
references | ) |
|
Sets references to dependent components.
- Parameters
-
| references | references to locate the component dependencies. |
◆ ValidateConnection()
| void PipServices3.Components.Connect.CompositeConnectionResolver.ValidateConnection |
( |
string |
correlationId, |
|
|
ConnectionParams |
connection |
|
) |
| |
|
protected |
Validates connection parameters. This method can be overriden in child classes. Throw error if validation failed.
- Parameters
-
| correlationId | (optional) transaction id to trace execution through call chain. |
| connection | connection parameters to be validated |
◆ ValidateCredential()
| void PipServices3.Components.Connect.CompositeConnectionResolver.ValidateCredential |
( |
string |
correlationId, |
|
|
CredentialParams |
credential |
|
) |
| |
|
protected |
Validates credential parameters. This method can be overriden in child classes. Throw error if validation failed.
- Parameters
-
| correlationId | (optional) transaction id to trace execution through call chain. |
| credential | credential parameters to be validated |
◆ _clusterSupported
| bool PipServices3.Components.Connect.CompositeConnectionResolver._clusterSupported = true |
|
protected |
The cluster support (multiple connections)
◆ _connectionResolver
The connections resolver.
◆ _credentialResolver
The credentials resolver.
◆ _defaultPort
| int PipServices3.Components.Connect.CompositeConnectionResolver._defaultPort = 0 |
|
protected |
◆ _defaultProtocol
| string PipServices3.Components.Connect.CompositeConnectionResolver._defaultProtocol = null |
|
protected |
◆ _options
| ConfigParams PipServices3.Components.Connect.CompositeConnectionResolver._options |
|
protected |
◆ _supportedProtocols
| IList<string> PipServices3.Components.Connect.CompositeConnectionResolver._supportedProtocols = null |
|
protected |
The list of supported protocols
The documentation for this class was generated from the following file:
- src/Connect/CompositeConnectionResolver.cs


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Justin Stockton
@poorgeek
- how were these decision going to effect page load times below 2 seconds?
- what are non-funcitonal requirements?
- how do work a11y into those decisions?
What are non-functional requirements?
- they define the size of the box
- the canvas decides how big the picture will base
- those constraints define how we’re going to build
- as an artist you work within the scope of the canvas
- don’t think of constaints as limiting, think of them..
Non-funcitonal Requirements
see image
a11y vs. other non-functional requirements
- a11y is context oriented
Accessibility & Security
- Security is usually the loudest voice in the room
- Both have legal and financial ramifications
Common Conflicts
- Timing Adjustments (2.2.1)
- Error Identification (3.3.1)
- Error Suggestion (3.3.3)
Accessibility & Performance
- Page load and rendering time cascade down to the a11y tree
- Utilize native components where possible
Common conflicts
- Meaningful Sequence (1.3.2)
- Keyboard (2.1.1)
Accessibility & Usability
- Two sides of the same coin
- Possible to make something usable, but not accessible and vice-versa
Common Conflicts
- On Focus (3.2.1)
- On Input (3.2.2)
- Error Identification (3.3.1)
Make sure you’re aware what is happening to gauge the a11y requirements. It may help some users but could harm a11y.
Accessibility & Maintainability
- Plan for tomorrow today because your time is money
- Document the why not just the what
- Invest in pattern and component library
- Automate as many test as you can
Developers want to try new things. They want to push the limits of technology. We can’t hold them back so we have to rely on what we know to apply those to the technologies.
The more you can invest in components, the easier it is to maintain a11y. This helps lower the bar for successful.
Use different tools to test your site. Examine the difference.
Workopolis
- a11yenhancer.js
- a11y modal
- we need to create more standardized components!
One more thing…
Get the definition of ready. And get the definition of done.
definition of done - acceptance criteria - concept of minimum viable product - a way of managing the risk associated with the project. Limiting the investment in a product that may never work.
How does the relate to a11y? You want to focus on making sure all of those constrains are baked in the from the start. Use prototypes - especially for really complex things. If we can identify that one of our constraints will effect it. See how it might work. Test it outside of the system.
Test it with assistive technology. Test it with an expert in assistive technology.
The Definition Done reflects back on the definition of ready.
Think about the consequences.


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#You can install the released version of pal:
install.packages("pal")
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devtools::install_github('csaybar/pal')
pal
has been designed to be the most intuitive as possible. You can access to any color palette using pal_search
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.
pal_search
initializes a S3 object that stores the databases and globals params (See pal_search). Additionally, its have four methods:
pal_n
: filter by color palette complexity.pal_colors
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