first view of Jalview in JavaScript

hansonr · 17 July 2015 08:30

···

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

jalviewcrowdadmin · 17 July 2015 11:20

so Bob - are you doing the ‘redo’ yet or is this already the result of starting over from scratch with the overloaded constructor stuff fixed ?

···

On 17/07/2015 09:30, Robert Hanson wrote:

hansonr · 17 July 2015 12:19

I can’t figure out how the GIT business works – my version is totally corrupted, and I can’t remember how to pull it down. I probably need to start over with GIT. Don’t worry about it. For now it’s just as well if I play in my own little sandbox…

Q: what do you propose that this does? Being passed to it is Applet.getDocumentBase() or Applet.getCodeBase(), which are fully qualified URIs – with queries and such.

/**

form a complete URL given a path to a resource and a reference location on
the same server

···

On Fri, Jul 17, 2015 at 12:20 PM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

so Bob - are you doing the ‘redo’ yet or is this already the result of starting over from scratch with the overloaded constructor stuff fixed ?

On 17/07/2015 09:30, Robert Hanson wrote:
–

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

–

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

jalviewcrowdadmin · 17 July 2015 12:40

Hi Bob.

I can't figure out how the GIT business works -- my version is totally corrupted, and I can't remember how to pull it down. I probably need to start over with GIT. Don't worry about it. For now it's just as well if I play in my own little sandbox....

OK. guess that means we won't be able to help We shouldn't leave getting your git stuff working before too long, since I'm also keen on getting automated builds going for this ASAP. First thing Monday ?

Q: what do you propose that this does? Being passed to it is Applet.getDocumentBase() or Applet.getCodeBase(), which are fully qualified URIs -- with queries and such.

It's supposed to create an absolute URL given a relative URL string and fully qualified URL and a (possibly relative) URL. The applet would try both docbase and codebase (since it was never specified how relative paths were resolved in early versions of the applet) until it got something. Sometimes the codebase URL might be pointing to a specific resource, rather than a directory, so Jalview would strip off URL to the next path separator before prepending to the relative URL.

The 'debug=true' applet parameter causes Jalview to report how it's resolving file paths.. that's particularly useful when this stuff is failing to work correctly.

Jim.

···

On 17/07/2015 13:19, Robert Hanson wrote:

hansonr · 17 July 2015 14:11

Oh, SO CLOSE!!!

Loading thread started with:

file
uniref50.fa>>endfile
Loading started.
Resource ‘uniref50.fa’ was not located by classloader.
Prepended document base for resource: ‘uniref50.fa’
Protocol identified as ‘URL’
File identified as ‘FASTA’
Failed to read alignment using the ‘FASTA’ reader.
TypeError: this.alignFile is null

j_procter · 17 July 2015 15:08

Oh, SO CLOSE!!!

!! \o/ !!

Loading thread started with:

file
uniref50.fa>>endfile
Loading started.
Resource ‘uniref50.fa’ was not located by classloader.
Prepended document base for resource: ‘uniref50.fa’
Protocol identified as ‘URL’
File identified as ‘FASTA’
Failed to read alignment using the ‘FASTA’ reader.
TypeError: this.alignFile is null

hmm. it identified as FASTA - which means data should have been read (remember, jalview uses the contents to work out what format the file is, NOT the .extension. So something is broken further down ?

Jim

···

On 17/07/2015 15:11, Robert Hanson wrote:

hansonr · 18 July 2015 15:02

Mark the time – Whoo-Hooo! (note the last line)

C javax.swing.JPanel resized to java.awt.Rectangle[x=0,y=0,width=1050,height=550]
jalviewApplet_PanelUI_11_2 setBounds 0 0 1050 550 op=3
get parameter: debug = true
JalviewLite Version test
Build Date : unknown
Installation : Webstart
get parameter: externalstructureviewer = null
get parameter: nojmol = null
get parameter: separator = null
get parameter: RGB = null
get parameter: label = null
get parameter: file = uniref50.fa
get parameter: enableSplitFrame = null
get parameter: embedded = true
BYPASSING JMOL LOADING FOR NOW. THIS WILL BE DONE ANOTHER WAY
Loading thread started with:

file
uniref50.fa>>endfile
Loading started.
Resource ‘uniref50.fa’ was not located by classloader.
Prepended document base for resource: ‘uniref50.fa’
Protocol identified as ‘URL’
File identified as ‘FASTA’
Successfully loaded file.

···

On Fri, Jul 17, 2015 at 4:08 PM, James Procter <j.procter@dundee.ac.uk> wrote:

On 17/07/2015 15:11, Robert Hanson wrote:

Oh, SO CLOSE!!!

!! \o/ !!

Loading thread started with:

file
uniref50.fa>>endfile
Loading started.
Resource ‘uniref50.fa’ was not located by classloader.
Prepended document base for resource: ‘uniref50.fa’
Protocol identified as ‘URL’
File identified as ‘FASTA’
Failed to read alignment using the ‘FASTA’ reader.
TypeError: this.alignFile is null

hmm. it identified as FASTA - which means data should have been read (remember, jalview uses the contents to work out what format the file is, NOT the .extension. So something is broken further down ?

Jim

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

–

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

j_procter · 18 July 2015 15:16

Looking forward to seeing this in person !

···

Sent from my Cyanogen phone

On 18 Jul 2015 16:02, Robert Hanson <hansonr@stolaf.edu> wrote:

Mark the time -- Whoo-Hooo! (note the last line)

C javax.swing.JPanel resized to java.awt.Rectangle[x=0,y=0,width=1050,height=550]
jalviewApplet_PanelUI_11_2 setBounds 0 0 1050 550 op=3
get parameter: debug = true
JalviewLite Version test
Build Date : unknown
Installation : Webstart
get parameter: externalstructureviewer = null
get parameter: nojmol = null
get parameter: separator = null
get parameter: RGB = null
get parameter: label = null
get parameter: file = uniref50.fa
get parameter: enableSplitFrame = null
get parameter: embedded = true
BYPASSING JMOL LOADING FOR NOW. THIS WILL BE DONE ANOTHER WAY
Loading thread started with:
>>file
uniref50.fa>>endfile
Loading started.
Resource 'uniref50.fa' was not located by classloader.
Prepended document base for resource: 'uniref50.fa'
Protocol identified as 'URL'
File identified as 'FASTA'
Successfully loaded file.

On Fri, Jul 17, 2015 at 4:08 PM, James Procter <j.procter@dundee.ac.uk> wrote:

On 17/07/2015 15:11, Robert Hanson wrote:

Oh, SO CLOSE!!!!

!! \o/ !!

Loading thread started with:
>>file
uniref50.fa>>endfile
Loading started.
Resource 'uniref50.fa' was not located by classloader.
Prepended document base for resource: 'uniref50.fa'
Protocol identified as 'URL'
File identified as 'FASTA'
Failed to read alignment using the 'FASTA' reader.
TypeError: this.alignFile is null

hmm. it identified as FASTA - which means data should have been read (remember, jalview uses the contents to work out what format the file is, NOT the .extension. So something is broken further down ?

Jim

_______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
Robert M. Hanson, chemistry

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

The University of Dundee is a registered Scottish Charity, No: SC015096

geoff.barton · 18 July 2015 15:22

Wow!!! More tea!!!

···

On 18/07/2015 16:02, Robert Hanson wrote:

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
College of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

The University of Dundee is registered Scottish charity: No.SC015096

hansonr · 18 July 2015 15:24

TEA??

···

On Sat, Jul 18, 2015 at 4:22 PM, Geoff Barton <gjbarton@dundee.ac.uk> wrote:

Wow!!! More tea!!!

On 18/07/2015 16:02, Robert Hanson wrote:
Mark the time – Whoo-Hooo! (note the last line)

C javax.swing.JPanel resized to java.awt.Rectangle[x=0,y=0,width=1050,height=550]
jalviewApplet_PanelUI_11_2 setBounds 0 0 1050 550 op=3
get parameter: debug = true
JalviewLite Version test
Build Date : unknown
Installation : Webstart
get parameter: externalstructureviewer = null
get parameter: nojmol = null
get parameter: separator = null
get parameter: RGB = null
get parameter: label = null
get parameter: file = uniref50.fa
get parameter: enableSplitFrame = null
get parameter: embedded = true
BYPASSING JMOL LOADING FOR NOW. THIS WILL BE DONE ANOTHER WAY
Loading thread started with:

file
uniref50.fa>>endfile
Loading started.
Resource ‘uniref50.fa’ was not located by classloader.
Prepended document base for resource: ‘uniref50.fa’
Protocol identified as ‘URL’
File identified as ‘FASTA’
Successfully loaded file.
_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)
-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
College of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

The University of Dundee is registered Scottish charity: No.SC015096 
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

–

On Fri, Jul 17, 2015 at 4:08 PM, James Procter <j.procter@dundee.ac.uk> wrote:

On 17/07/2015 15:11, Robert Hanson wrote:

Oh, SO CLOSE!!!

!! \o/ !!

Loading thread started with:

file
uniref50.fa>>endfile
Loading started.
Resource ‘uniref50.fa’ was not located by classloader.
Prepended document base for resource: ‘uniref50.fa’
Protocol identified as ‘URL’
File identified as ‘FASTA’
Failed to read alignment using the ‘FASTA’ reader.
TypeError: this.alignFile is null

hmm. it identified as FASTA - which means data should have been read (remember, jalview uses the contents to work out what format the file is, NOT the .extension. So something is broken further down ?

Jim

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

–

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

j_procter · 18 July 2015 17:14

Perhaps a G and T may now be most appropriate ?

···

On 18 Jul 2015 16:24, Robert Hanson <hansonr@stolaf.edu> wrote:

TEA??

On Sat, Jul 18, 2015 at 4:22 PM, Geoff Barton <gjbarton@dundee.ac.uk> wrote:

Wow!!! More tea???!!!

On 18/07/2015 16:02, Robert Hanson wrote:

Mark the time -- Whoo-Hooo! (note the last line)

C javax.swing.JPanel resized to java.awt.Rectangle[x=0,y=0,width=1050,height=550]
jalviewApplet_PanelUI_11_2 setBounds 0 0 1050 550 op=3
get parameter: debug = true
JalviewLite Version test
Build Date : unknown
Installation : Webstart
get parameter: externalstructureviewer = null
get parameter: nojmol = null
get parameter: separator = null
get parameter: RGB = null
get parameter: label = null
get parameter: file = uniref50.fa
get parameter: enableSplitFrame = null
get parameter: embedded = true
BYPASSING JMOL LOADING FOR NOW. THIS WILL BE DONE ANOTHER WAY
Loading thread started with:
>>file
uniref50.fa>>endfile
Loading started.
Resource 'uniref50.fa' was not located by classloader.
Prepended document base for resource: 'uniref50.fa'
Protocol identified as 'URL'
File identified as 'FASTA'
Successfully loaded file.

On Fri, Jul 17, 2015 at 4:08 PM, James Procter <j.procter@dundee.ac.uk> wrote:

On 17/07/2015 15:11, Robert Hanson wrote:

Oh, SO CLOSE!!!!

!! \o/ !!

Loading thread started with:
>>file
uniref50.fa>>endfile
Loading started.
Resource 'uniref50.fa' was not located by classloader.
Prepended document base for resource: 'uniref50.fa'
Protocol identified as 'URL'
File identified as 'FASTA'
Failed to read alignment using the 'FASTA' reader.
TypeError: this.alignFile is null

hmm. it identified as FASTA - which means data should have been read (remember, jalview uses the contents to work out what format the file is, NOT the .extension. So something is broken further down ?

Jim

_______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
Robert M. Hanson, chemistry

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

_______________________________________________

Jalview-dev mailing list

Jalview-dev@jalview.org

http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

--

Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology

College of Life Sciences | University of Dundee, Scotland, UK | g.j.barton@dundee.ac.uk

Tel: +44 1382 385860 | www.compbio.dundee.ac.uk | twitter: @gjbarton

The University of Dundee is registered Scottish charity: No.SC015096

_______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
Robert M. Hanson, chemistry

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

The University of Dundee is a registered Scottish Charity, No: SC015096

hansonr · 18 July 2015 17:44

not quite yet, perhaps. Aspirin, though…

And Julia’s fantastic dinner…

We are not out of the woods yet.

···

On Sat, Jul 18, 2015 at 6:14 PM, Jim Procter <j.procter@dundee.ac.uk> wrote:

Perhaps a G and T may now be most appropriate ?

On 18 Jul 2015 16:24, Robert Hanson <hansonr@stolaf.edu> wrote:

TEA??

On Sat, Jul 18, 2015 at 4:22 PM, Geoff Barton <gjbarton@dundee.ac.uk> wrote:

Wow!!! More tea!!!

On 18/07/2015 16:02, Robert Hanson wrote:

Mark the time – Whoo-Hooo! (note the last line)

C javax.swing.JPanel resized to java.awt.Rectangle[x=0,y=0,width=1050,height=550]
jalviewApplet_PanelUI_11_2 setBounds 0 0 1050 550 op=3
get parameter: debug = true
JalviewLite Version test
Build Date : unknown
Installation : Webstart
get parameter: externalstructureviewer = null
get parameter: nojmol = null
get parameter: separator = null
get parameter: RGB = null
get parameter: label = null
get parameter: file = uniref50.fa
get parameter: enableSplitFrame = null
get parameter: embedded = true
BYPASSING JMOL LOADING FOR NOW. THIS WILL BE DONE ANOTHER WAY
Loading thread started with:

file
uniref50.fa>>endfile
Loading started.
Resource ‘uniref50.fa’ was not located by classloader.
Prepended document base for resource: ‘uniref50.fa’
Protocol identified as ‘URL’
File identified as ‘FASTA’
Successfully loaded file.

On Fri, Jul 17, 2015 at 4:08 PM, James Procter <j.procter@dundee.ac.uk> wrote:

On 17/07/2015 15:11, Robert Hanson wrote:

Oh, SO CLOSE!!!

!! \o/ !!

Loading thread started with:

file
uniref50.fa>>endfile
Loading started.
Resource ‘uniref50.fa’ was not located by classloader.
Prepended document base for resource: ‘uniref50.fa’
Protocol identified as ‘URL’
File identified as ‘FASTA’
Failed to read alignment using the ‘FASTA’ reader.
TypeError: this.alignFile is null

hmm. it identified as FASTA - which means data should have been read (remember, jalview uses the contents to work out what format the file is, NOT the .extension. So something is broken further down ?

Jim

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

–
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Jalview-dev mailing list

Jalview-dev@jalview.org

http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

–

Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology

College of Life Sciences | University of Dundee, Scotland, UK | g.j.barton@dundee.ac.uk

Tel: +44 1382 385860 | www.compbio.dundee.ac.uk | twitter: @gjbarton

The University of Dundee is registered Scottish charity: No.SC015096

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

–
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

The University of Dundee is a registered Scottish Charity, No: SC015096

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

–

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900