[Biojava-l] What your "Gram mar" hoped she'd wrote

[Tony Watkins]

Hi again .....

Maybe I should have grabbed the whole doc tree and gone through it once 
instead of piecemeal?

(Warning - this email has been filtered through a bottle of shiraz 
cabernet! It's red and alcoholic and highly recommended for those 
pretending to be civilized. Ahem)

Here we go again ...

(When was 1.2 due out?)

Package org.biojava.bio

Interface Annotatable

(original)
Inidcates that an object has an associated annotation.

(suggested correction)
Indicates that an object has an associated annotation.

Class SimpleAnnotation

method asMap

(original)
Retern a map that contains the same key/values as this Annotation

(suggested correction)
*Return* a map that contains the same key/values as this Annotation

Class SmallAnnotation

methos asMap
(original)
Retern a map that contains the same key/values as this Annotation

(suggested correction)
*Return* a map that contains the same key/values as this Annotation

package org.biojava.bio.dist

Interface Count

method increaseCount

(original)
Set the probability or odds that Symbol s is emited by this state.

(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state.

Interface Distribution

(original)
A distribution can be implemented as a map from symbol to probability. It 
is more correct to think of them as being integrals or sums over 
probability dencity funcitons. In this world view, getWeight should look at 
the getMatches of the symbol it is given and then perform the apropreate 
sum or integral to return the probability of something within that set of 
symbols being emitted.

This interface should handle the case of emitting an ambiguity symbol. This 
should be just the sum of the probabiltiy of emitting each matching symbol. 
It is up to the code using the Distribution instance to divide out the null 
model appropreately

(suggested correction)
... It is more correct to think of them as being integrals or sums over 
probability *density functions*. In this world view, getWeight should look 
at the getMatches of the symbol it is given and then perform the 
*appropriate* sum or integral to return the probability of something within 
that set of symbols being emitted.

... This should be just the sum of the *probability* of emitting each 
matching symbol. It is up to the code using the Distribution instance to 
divide out the null model *appropriately*

method setWeight

(original)
Set the probability or odds that Symbol s is emited by this state

(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state

Interface DistributionTrainer

method getCount

(original)
This method may be called multiple times with the same symbol. Each time it 
should return the agregate of the counts added with addCount since the last 
invocation of clearCounts

(suggested correction)
... Each time it should return the *aggregate* of the counts added with 
addCount since the last invocation of clearCounts

Interface DistributionTrainerContext

(original)
A context within a group of DistributionTrainers can be trained together

(suggested change)
A context within *which* a group of DistributionTrainers can be trained

Class AbstractDistribution

method removeChangeListener

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

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

method setNullModel

(throws ...)

(original)

if this Distirbution doesn't support setting the null model, or if one of 
its listeners objects

(suggested correction)
if this *Distribution* doesn't support setting the null model, or if one of 
its listeners objects

[Aarghhh - isn't English a horrible language?  I object!  {motion denied 
says the judge}]

method getWeight

(original)
Performs the standard munge to handle ambiguity symbols. The actual weights 
for each attomic symbol should be calculated by the getWeightImpl functions

(suggested correction - and please tell me I haven't totally lost the plot 
and have fallen through the looking glass)
Performs the standard "munge" (help!!!!) to handle ambiguity symbols. The 
actual weights for each *atomic* symbol should be calculated by the 
getWeightImpl functions

Class GapDistribution

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 IgnoreCountsTrainer

method getCount

(original)
This method may be called multiple times with the same symbol. Each time it 
should return the agregate of the counts added with addCount since the last 
invocation of clearCounts.

(suggested correction)
... Each time it should return the *aggregate* of the counts ..

Class IndexedCount

method removeChangeListener

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

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

method increaseCount

(original)
Set the probability or odds that Symbol s is emited by this state.

(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state.

Class PairDistribution

method getWeight

(original)
Return the probability that Symbol s is emited by this spectrum.

If the symbol is ambiguou, then it is the sum of the probability that each 
one of the matching symbols was emitted.

(suggested correction)
Return the probability that Symbol s is *emitted* by this spectrum.

If the symbol is *ambiguous*, then it is the sum of the probability that 
each one of the matching symbols was emitted.

method setWeight

(original)
Set the probability or odds that Symbol s is emited by this state.

(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state.

Class SimpleDistributionTrainer

(original)
This requires the distribuiton being trained to have a working setWeight 
method that doesn't throw an UnsupportedOperationExcepiton

(suggested corrections)
This requires the *distribution* being trained to have a working setWeight 
method that doesn't throw an *UnsupportedOperationException*

method getCount

(original)
This method may be called multiple times with the same symbol. Each time it 
should return the agregate of the counts added with addCount since the last 
invocation of clearCounts

(suggested correction)
... Each time it should return the *aggregate* of the counts added with 
addCount since the last invocation of clearCounts

Class TranslatedDistribution

method removeChangeListener

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

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

method getWeight

(original)
Return the probability that Symbol s is emited by this spectrum.
If the symbol is ambiguou, then it is the sum of the probability that each 
one of the matching symbols was emitted

(suggested corrections)
Return the probability that Symbol s is *emitted* by this spectrum.
If the symbol is *ambiguous*, then it is the sum of the probability that 
each one of the matching symbols was emitted

method setWeight

(original)
Set the probability or odds that Symbol s is emited by this state

(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state

method setNullModel

(throws ...)

(original)
if this Distirbution doesn't support setting the null model, or if one of 
its listeners objects

(suggested correction)
if this *Distribution* doesn't support setting the null model, or if one of 
its listeners objects

Time to stop before I filter through several bottles of 1664 too.

8-)

Cheers