jalview

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after taking a look at the rest I can see that the next step is to split this class up further. There's plenty of code that will be used by many different operations - e.g. job state management - i...

after taking a look at the rest I can see that the next step is to split this class up further. There's plenty of code that will be used by many different operations - e.g. job state management - is that the plan ?

not really the recommended way - see e.g. https://docs.oracle.com/en/java/javase/11/docs/api/java.desktop/java/beans/PropertyChangeSupport.html *do you need to expose the generic binders ? what k...

not really the recommended way - see e.g. https://docs.oracle.com/en/java/javase/11/docs/api/java.desktop/java/beans/PropertyChangeSupport.html

  • do you need to expose the generic binders ? what kind of events need to be monitored ?
is utils really the right name ? suggest the classes are used in several different places

is utils really the right name ? suggest the classes are used in several different places

this is going to get much more complex. there are plenty of additional attributes - e.g. input type (dna, protein, rna) - none of them are currently being configured on the operation.

this is going to get much more complex. there are plenty of additional attributes - e.g. input type (dna, protein, rna) - none of them are currently being configured on the operation.

this class seems to contain a bunch of hard coded stuff taken from the original web services configuration code rather than provide a way for a web services provider to configure an instance of Ali...

this class seems to contain a bunch of hard coded stuff taken from the original web services configuration code rather than provide a way for a web services provider to configure an instance of AlignmentOperation tuned to the alignment service that the provider is offering.

first review of Web Services overhaul for 2.12
first review of Web Services overhaul for 2.12
patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
remove debugging printlns

remove debugging printlns

aim is normally to avoid creating query-specific data containers on the core query response class

aim is normally to avoid creating query-specific data containers on the core query response class

? not sure this is correct

? not sure this is correct

Needs additionally: model_category created sequence_identity uniprot_start uniprot_end resolution coverage qmean_version ? model_version

Needs additionally:
model_category
created
sequence_identity
uniprot_start
uniprot_end
resolution
coverage
qmean_version ?
model_version

Evaluate 3D-Beacons dev path based on Arnaud's ERASMUS+ project code
Evaluate 3D-Beacons dev path based on Arnaud's ERASMUS+ project code
JAL-3851 start a listener with -testlistener and suggest a port with -testlistener_port. wget -S -O...
JAL-3851 start a listener with -testlistener and suggest a port with -testlistener_port. wget -S -O...
WIP
WIP
This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no sma...

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no small job) to change all dialogs to this pattern.

There are still numerous dialogs that have not been changed to either pattern (so won't work in SwingJS): see comment at https://issues.jalview.org/browse/?focusedCommentId=20525&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#JAL-3048comment-20525.

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).