Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview pinging www.jalview.org/services/identifiers to get a list of URL link templates for viewing database crossreferences

  1. … 2 more files in changeset.
Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work! Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this m...

Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work!
Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this method seems to be trying to do two different things.

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called). So what is it there for?

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called).
So what is it there for?

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

Needs proper Javadoc

Needs proper Javadoc

JAL-3446 unused imports removed

  1. … 36 more files in changeset.
Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide...

Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide documentation.
e.g. http://source.jalview.org/gitweb/?p=jalview.git;a=blob;f=doc/JalviewJS-startupParams.md;h=9ff33529b2dbc2da34d2a573ccf5d042194fbb0d;hb=refs/heads/Jalview-JS/develop

Due to the number of changes this is likely to be a 'best efforts' review.

Due to the number of changes this is likely to be a 'best efforts' review.

Commits to JS-develop from 2nd to 25th June 2020
Commits to JS-develop from 2nd to 25th June 2020
JAL-3446 UrlDownloadClient and Test

- moving download to Platform

- trivializing JavaScript method

- expanding SwingJS to allow for nio methods

Note: SwingJS preserves byte[] in the File, Path, or FileOutputStream

objects as well as in J2S._javaFileCache. Because of that, one thing you

have to look out for is stale references. In this case, we have:

temp = new Path(...);

fos = new FileOutputStream(temp.toString);

now two independent pointers both refer to the tmp file.

rbc = new

ReadableByteChannel(url.openStream());

fos.getChannel().transferFrom(rbc);

Now the bytes are in fos's channel, but they are not associated yet with

"tmp".

Files.copy(tmp, outfile);

This wasn't working in JavaScript, because Path tmp was out of date, and

so no bytes were being copied.

Working now, but still far to complicated for the simple operation of

transferring bytes from an InputStream to a File in JavaScript.

  1. … 2 more files in changeset.
consolidation of Platform isJS calls

  1. … 9 more files in changeset.
j2sNative references moved to Platform

  1. … 38 more files in changeset.
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>

  1. … 52 more files in changeset.

changeset discussion

  1. Mungo Carstairs: why are loops in removeAlreadyRetrievedSeqs now backwards?
JAL-3026 GD#107,128,130,139 build-site.xml

JInternalFrame z-order issues resolved

EBIFeching via server proxy as no access-control-origin:*

Temp file creation by File.createTempFile

Jmol app fixes for virtual key issues and starting to display now. Still

not dynamic, though. (No mouse action)

URL downloads now allow checking of status code (actually a hack, just

200 or 404, but we can get access to the real code.

  1. … 9 more files in changeset.
JAL-2738 copy to spikes/mungo

  1. … 568 more files in changeset.
JAL-2418 source formatting

  1. … 464 more files in changeset.
JAL-2446 merged to spike branch

    • -0
    • +110
    ./UrlDownloadClient.java
  1. … 493 more files in changeset.
JAL-2520 improvement to download and update structure files loaded via URL to a local file before parsing the file

  1. … 1 more file in changeset.
JAL-2316 Changes following review.

    • -0
    • +109
    ./UrlDownloadClient.java
  1. … 25 more files in changeset.