buildcore.xml

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I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

JAL-3560 better build xml names

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JAL-3559 temporary branch adding JS files complete

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Revert "JAL-3210 Moving j2s components around"

This reverts commit ea88f37133ba49aca6cd7bf0cc4242c0594cebf1.

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JAL-3210 Moving j2s components around

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JAL-3210 Moving j2s components around

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I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit ...

I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit with the issue.

This reset also needs to happen in copyAlignPanel() (which also calls loadViewport() where the flag is set on).

This reset also needs to happen in copyAlignPanel() (which also calls loadViewport() where the flag is set on).

JAL-3210 Barebones gradle/buildship/eclipse. See README

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JAL-3253 updated _j2sclasslist.txt, SwingJS-site.zip

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Can't reproduce this now (can't "bring desktop to front"). Will resolve and reopen if it recurs.

Can't reproduce this now (can't "bring desktop to front"). Will resolve and reopen if it recurs.

Jalview-JS/JAL-3253-applet fix for original desktop, centralizing regex and loadStaticResource

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Jalview-JS/JAL-3253-applet also comments relating to JAL-3268

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No proprietary format files please! Is this meant to be a temporary working record or a permanent one. If the latter, can it be in csv or tsv format?

No proprietary format files please! Is this meant to be a temporary working record or a permanent one. If the latter, can it be in csv or tsv format?

No problem, the call to ScoreModels.getInstance() is unchanged, only how it is implemented.

No problem, the call to ScoreModels.getInstance() is unchanged, only how it is implemented.

Deferred to JAL-3265

Deferred to JAL-3265

Failing test getValidSourceDBRefExceptionXTest() (Network not Functional test). Now throws NullPointerException but coded only to expect SiftsException. Traced to uninitialized field DBRefEntry.ucv...

Failing test getValidSourceDBRefExceptionXTest() (Network not Functional test).
Now throws NullPointerException but coded only to expect SiftsException.
Traced to uninitialized field DBRefEntry.ucversion. Initialising this to "" (like version) resolves this.

I am nervous of doing much processing in a static block in case of errors giving ExceptionInInitializerError. Also possible dependency on order of classloading if one class's static codes reference...

I am nervous of doing much processing in a static block in case of errors giving ExceptionInInitializerError.
Also possible dependency on order of classloading if one class's static codes references another's.
Maybe move back to inside constructor?
In fact, was there any need to change this class from the 'standard' singleton pattern, if we don't want it "per applet"?

? there are no tests that call this getInstance() for this class. And if there were they would normally be in the same package so the method could be either package private, or called by reflection.

? there are no tests that call this getInstance() for this class. And if there were they would normally be in the same package so the method could be either package private, or called by reflection.

I am seeing some odd z-plane behaviour, not sure if it is specific to this branch. If the desktop is brought to front, I can't then bring any other panel to front.

I am seeing some odd z-plane behaviour, not sure if it is specific to this branch. If the desktop is brought to front, I can't then bring any other panel to front.

Too much change around ASequenceFetcher, DbRoot etc to be able to review from the diffs. They seem to work when testing! (The code here may now be overcomplicated for the simplified (post-DAS) world.)

Too much change around ASequenceFetcher, DbRoot etc to be able to review from the diffs. They seem to work when testing!
(The code here may now be overcomplicated for the simplified (post-DAS) world.)

So what if anything used to access this? Why I hate public fields!

So what if anything used to access this? Why I hate public fields!

Could write file.contains("/") rather than file.indexOf('/') >= 0, for simplicity and readability. This is buggy - also in the original. Fetching from URL "https://www.ebi.ac.uk/Tools/dbfetch/dbfet...

Could write file.contains("/") rather than file.indexOf('/') >= 0, for simplicity and readability.
This is buggy - also in the original. Fetching from URL "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/1a70/pdb" results in file.substring(52, 18).
Issue JAL-3272 raised for that.

I have restored member variables to the top of the class declaration to keep standard source code ordering.

I have restored member variables to the top of the class declaration to keep standard source code ordering.

We have Platform.openURL() calling BrowserLauncher.openURL() and and vice versa, confusing. Suggest we make BrowserLauncher a package private class and route all calls via Platform.

We have Platform.openURL() calling BrowserLauncher.openURL() and and vice versa, confusing.
Suggest we make BrowserLauncher a package private class and route all calls via Platform.

Possibly the most strangely designed class in Jalview, but this version of it seems to work as well as any other!

Possibly the most strangely designed class in Jalview, but this version of it seems to work as well as any other!

This goes back to 2005...but it would be tidier to overload Cache.setProperty() to take a boolean value, and apply Boolean.toString() there...oh well.

This goes back to 2005...but it would be tidier to overload Cache.setProperty() to take a boolean value, and apply Boolean.toString() there...oh well.

Is this still 'TODO'? I just tried it and it worked fine (uniref50.fa + exampleFeatures.txt, popup menu on FER_CAPAA, Link sub-menu, Pfam family target).

Is this still 'TODO'? I just tried it and it worked fine (uniref50.fa + exampleFeatures.txt, popup menu on FER_CAPAA, Link sub-menu, Pfam family target).

We will need clarity on behaviour of copy and paste. Jalview uses both Toolkit.getDefaultToolkit().getSystemClipboard() // this has global scope and Desktop.getInstance().jalviewClipboard // this h...

We will need clarity on behaviour of copy and paste. Jalview uses both
Toolkit.getDefaultToolkit().getSystemClipboard() // this has global scope
and
Desktop.getInstance().jalviewClipboard // this has per-applet scope
with the latter 'overriding' the former.
This may be fine as is, or may create some puzzling behaviour e.g. a "rich paste" (sequence + features) within an applet and a "text paste" (sequence only) across applications.

Jalview-JS/JAL-3253-applet JAL-3192 secondary core files

buildcore now creates core_stevesoft (350K uncompressed) and core_jvjmol

(2.9M uncompressed)

Still needs some tweaking, but the process is relatively

straightforward:

1) To know what files to include, make sure you are using the core

version of the html file, and, after exercizing the program, issue:

J2S._saveFile('_j2sclasslist.txt',

Clazz.ClassFilesLoaded.sort().join('\n'))

(Sorry, I could make that simpler, I know.)

2) add a section in buildcore.xml that concatenates the desired file set

and turns that into a core file.

3) in the FIRST class loaded for this option, add something like this

static block:

static

{

/**

* This is the entry class. Load the core file directly, if it

exists. See

* buildcore.xml.

*

*

* @j2sNative

*

* swingjs.JSUtil.loadStaticResource$S("core/core_stevesoft.z.js");

*/

}

3) run buildcore.xml

2)

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