[Biojava-l] More Typos

Wed, 13 Feb 2002 10:43:45 +0000

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Some more in the documentation...

Package org.biojava.bio.seq.impl

Class AssembledSymbolList

(original)
Support class for applications which need to patch together sections of 
sequence into a single SymbolList

(suggested corrections)
either

... sections of *a* sequence into a single SymbolList

or
... sections of *multiple sequences* into a single SymbolList

(not sure if the 2nd alternative makes sense)

Class SimpleFramedFeature

Documentation doesn't quite follow other standards -

eg. Title: SimpleFramedFeature

This doesn't normally appear.

(Original)
Description: A no frills implementation of FramedFeature

(suggested correction)
A no frills implementation of FramedFeature

Package org.biojava.utils

Interface ActivityListener
(original)
Interface for object which monitor long-running activities

(suggested correction)
Interface for *objects* which monitor long-running activities

method activityProgress

(original)
Estimated progress of an activity. This indicated that current parts of the 
activity have been completed, out of a target target

(suggested correction)
Estimated progress of an activity. This *indicates* that current parts of 
the activity have been completed, out of a target target

Interface Changeable

method removeChangeListener
(original)
Remove a listener that was interested in a specific types of changes

(suggested correction)
Remove a listener that was interested in a specific *type* of *change*

Class ChangeEvent

method getChange
(original)
May return null is this is not meaningful.

(suggested correction)
May return null *if* this is not meaningful.

(ditto on getPrevious)

Class ChangeType

Field Detail

(original)
... This is the fallback for when you realy don't know what else to do

(suggested correction)
...This is the fallback for when you *really* don't know what else to do

Class NestedException

(Original)
A general perpose Exception that can wrap another exception

(suggested correction)
A general *purpose* Exception that can wrap another exception

(also)

It is common practice in BioJava to throw a NestedException or a subclass 
of it when something goes wrong. The exception can be used to catch another 
throwable, thus keeping a complete record of where the original error 
originated while adding annotation to the stack-trace. It also affords a 
neat way to avoid exception-bloat on method calls, particularly when 
objects are composed from several objects from different packages

(suggested changes)

... The exception can be used to catch another throwable, thus keeping a 
complete record of where the *error originated* while adding annotation to 
the stack-trace. It also affords a neat way to avoid exception-bloat on 
method calls, particularly when objects are composed *of* several objects 
from different packages.

Class NestedRuntimeException
(original)
A general perpose RuntimeException that can wrap another exception

(suggested correction)
A general *purpose* RuntimeException that can wrap another exception

Class ParserException

method toString
(original)
Represent this exception as a string. This includes the default exception 
toString representation, followed by details of the location where the 
error occured, if they were supplied when constructing this exception

(suggested correction)
..., followed by details of the location where the error *occurred*, if 
they were supplied ...

Hope this helps.

Cheers

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<html>
Some more in the documentation... 
Package org.biojava.bio.seq.impl 
Class AssembledSymbolList 
(original) 
Support class for applications which need to patch together sections of
sequence into a single SymbolList 
(suggested corrections) 
either 
... sections of *a* sequence into a single SymbolList 
or 
... sections of *multiple sequences* into a single SymbolList 
(not sure if the 2nd alternative makes sense) 
Class SimpleFramedFeature 
Documentation doesn't quite follow other standards - 
eg. Title: SimpleFramedFeature 
This doesn't normally appear. 
(Original) 
Description: A no frills implementation of FramedFeature 
(suggested correction) 
A no frills implementation of FramedFeature 
Package org.biojava.utils 
Interface ActivityListener 
(original) 
Interface for object which monitor long-running activities 
(suggested correction) 
Interface for *objects* which monitor long-running activities 
method activityProgress 
(original) 
Estimated progress of an activity. This indicated that
current parts of the activity
have been completed, out of
a target target 
(suggested correction) 
Estimated progress of an activity. This *indicates* that
current parts of the activity
have been completed, out of a target
target 
Interface Changeable 
method removeChangeListener 
(original) 
Remove a listener that was interested in a specific types of
changes 
(suggested correction) 
Remove a listener that was interested in a specific *type* of
*change* 
Class ChangeEvent 
method getChange 
(original) 
May return null is this is not
meaningful. 
(suggested correction) 
May return null *if* this is not
meaningful. 
(ditto on getPrevious) 
Class ChangeType 
Field Detail 
(original) 
... This is the fallback for when you realy don't know what else to
do 
(suggested correction) 
...This is the fallback for when you *really* don't know what else to
do 
Class NestedException 
(Original) 
A general perpose Exception that can wrap another exception 
(suggested correction) 
A general *purpose* Exception that can wrap another exception 
(also) 
It is common practice in BioJava to throw a NestedException or a subclass
of it when something goes wrong. The exception can be used to catch
another throwable, thus keeping a complete record of where the original
error originated while adding annotation to the stack-trace. It also
affords a neat way to avoid exception-bloat on method calls, particularly
when objects are composed from several objects from different
packages 
(suggested changes) 
... The exception can be used to catch another throwable, thus keeping a
complete record of where the *error originated* while adding annotation
to the stack-trace. It also affords a neat way to avoid exception-bloat
on method calls, particularly when objects are composed *of* several
objects from different packages. 
Class NestedRuntimeException 
(original) 
A general perpose RuntimeException that can wrap another
exception 
(suggested correction) 
A general *purpose* RuntimeException that can wrap another
exception 
Class ParserException 
method toString 
(original) 
Represent this exception as a string. This includes the default exception
toString representation, followed by details of the location where the
error occured, if they were supplied when constructing this
exception 
(suggested correction) 
..., followed by details of the location where the error *occurred*, if
they were supplied ... 
 
Hope this helps. 
Cheers 
 
 
 
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