[Gmod-ajax] VCF callbacks

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[Gmod-ajax] VCF callbacks

Sofia Robb
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



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Re: VCF callbacks

Colin
I think having just that would work. You might try adding "action": "defaultDialog" to see if that helps (the mouseover sort of piggybacks off the onClick behavior so in that case it kind of helps to re-specify the onClick action).

"onClick": {
    "label": "TEST",
    "action": "defaultDialog"
}


Then the mouseover label should say "TEST".



-Colin

On Tue, Feb 21, 2017 at 3:23 PM, Sofia Robb <[hidden email]> wrote:
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



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engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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Re: VCF callbacks

Sofia Robb
no clearing the cache did not help, same error

On Tue, Feb 21, 2017 at 2:10 PM, Colin <[hidden email]> wrote:
I noticed an error similar to this at one point, but adding the "action": "defaultDialog" seemed to help. Could you try clearing cache to retry?

-Colin

On Tue, Feb 21, 2017 at 4:06 PM, Sofia Robb <[hidden email]> wrote:
No :( 

That did not work. Here is the error I get with or without  "action": "defaultDialog"

Uncaught TypeError: Cannot read property 'font' of null
    at Object.<anonymous> (dojo.js:1512)
    at dojo.js:140

On Tue, Feb 21, 2017 at 1:57 PM, Colin <[hidden email]> wrote:
I think having just that would work. You might try adding "action": "defaultDialog" to see if that helps (the mouseover sort of piggybacks off the onClick behavior so in that case it kind of helps to re-specify the onClick action).

"onClick": {
    "label": "TEST",
    "action": "defaultDialog"
}


Then the mouseover label should say "TEST".



-Colin

On Tue, Feb 21, 2017 at 3:23 PM, Sofia Robb <[hidden email]> wrote:
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



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Re: VCF callbacks

Colin
Hmm.  I think I recall a similar situation that Scott Cain had where if you don't have a feature label for genes, then that causes the problem. For example, if you have features without ID/Name in GFF it causes the problem if you try to add mouseover

So, I think probably in this example, if you don't have the ID column filled out in the VCF, this might happen


-Colin

On Tue, Feb 21, 2017 at 4:19 PM, Sofia Robb <[hidden email]> wrote:
no clearing the cache did not help, same error

On Tue, Feb 21, 2017 at 2:10 PM, Colin <[hidden email]> wrote:
I noticed an error similar to this at one point, but adding the "action": "defaultDialog" seemed to help. Could you try clearing cache to retry?

-Colin

On Tue, Feb 21, 2017 at 4:06 PM, Sofia Robb <[hidden email]> wrote:
No :( 

That did not work. Here is the error I get with or without  "action": "defaultDialog"

Uncaught TypeError: Cannot read property 'font' of null
    at Object.<anonymous> (dojo.js:1512)
    at dojo.js:140

On Tue, Feb 21, 2017 at 1:57 PM, Colin <[hidden email]> wrote:
I think having just that would work. You might try adding "action": "defaultDialog" to see if that helps (the mouseover sort of piggybacks off the onClick behavior so in that case it kind of helps to re-specify the onClick action).

"onClick": {
    "label": "TEST",
    "action": "defaultDialog"
}


Then the mouseover label should say "TEST".



-Colin

On Tue, Feb 21, 2017 at 3:23 PM, Sofia Robb <[hidden email]> wrote:
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



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Re: VCF callbacks

Sofia Robb
That was it! I added IDs and it works!! Thank you Colin! 


On Tue, Feb 21, 2017 at 2:37 PM, Colin <[hidden email]> wrote:
Hmm.  I think I recall a similar situation that Scott Cain had where if you don't have a feature label for genes, then that causes the problem. For example, if you have features without ID/Name in GFF it causes the problem if you try to add mouseover

So, I think probably in this example, if you don't have the ID column filled out in the VCF, this might happen


-Colin

On Tue, Feb 21, 2017 at 4:19 PM, Sofia Robb <[hidden email]> wrote:
no clearing the cache did not help, same error

On Tue, Feb 21, 2017 at 2:10 PM, Colin <[hidden email]> wrote:
I noticed an error similar to this at one point, but adding the "action": "defaultDialog" seemed to help. Could you try clearing cache to retry?

-Colin

On Tue, Feb 21, 2017 at 4:06 PM, Sofia Robb <[hidden email]> wrote:
No :( 

That did not work. Here is the error I get with or without  "action": "defaultDialog"

Uncaught TypeError: Cannot read property 'font' of null
    at Object.<anonymous> (dojo.js:1512)
    at dojo.js:140

On Tue, Feb 21, 2017 at 1:57 PM, Colin <[hidden email]> wrote:
I think having just that would work. You might try adding "action": "defaultDialog" to see if that helps (the mouseover sort of piggybacks off the onClick behavior so in that case it kind of helps to re-specify the onClick action).

"onClick": {
    "label": "TEST",
    "action": "defaultDialog"
}


Then the mouseover label should say "TEST".



-Colin

On Tue, Feb 21, 2017 at 3:23 PM, Sofia Robb <[hidden email]> wrote:
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



------------------------------------------------------------------------------
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engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax








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Re: VCF callbacks

Sofia Robb
Uggg. Ok. Now I get the ID and description showing up under my glyph. I liked it with just the description. If  I change style->label to just name, i get the same error I was getting before. How can I keep the mouse over but not show the ID under the glyph?



On Tue, Feb 21, 2017 at 2:53 PM, Sofia Robb <[hidden email]> wrote:
That was it! I added IDs and it works!! Thank you Colin! 


On Tue, Feb 21, 2017 at 2:37 PM, Colin <[hidden email]> wrote:
Hmm.  I think I recall a similar situation that Scott Cain had where if you don't have a feature label for genes, then that causes the problem. For example, if you have features without ID/Name in GFF it causes the problem if you try to add mouseover

So, I think probably in this example, if you don't have the ID column filled out in the VCF, this might happen


-Colin

On Tue, Feb 21, 2017 at 4:19 PM, Sofia Robb <[hidden email]> wrote:
no clearing the cache did not help, same error

On Tue, Feb 21, 2017 at 2:10 PM, Colin <[hidden email]> wrote:
I noticed an error similar to this at one point, but adding the "action": "defaultDialog" seemed to help. Could you try clearing cache to retry?

-Colin

On Tue, Feb 21, 2017 at 4:06 PM, Sofia Robb <[hidden email]> wrote:
No :( 

That did not work. Here is the error I get with or without  "action": "defaultDialog"

Uncaught TypeError: Cannot read property 'font' of null
    at Object.<anonymous> (dojo.js:1512)
    at dojo.js:140

On Tue, Feb 21, 2017 at 1:57 PM, Colin <[hidden email]> wrote:
I think having just that would work. You might try adding "action": "defaultDialog" to see if that helps (the mouseover sort of piggybacks off the onClick behavior so in that case it kind of helps to re-specify the onClick action).

"onClick": {
    "label": "TEST",
    "action": "defaultDialog"
}


Then the mouseover label should say "TEST".



-Colin

On Tue, Feb 21, 2017 at 3:23 PM, Sofia Robb <[hidden email]> wrote:
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



------------------------------------------------------------------------------
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engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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Re: VCF callbacks

Colin
Does setting style->showLabels = false help? I'm suspecting it won't... Might need fixing on github!

-Colin

On Tue, Feb 21, 2017 at 5:04 PM, Sofia Robb <[hidden email]> wrote:
Uggg. Ok. Now I get the ID and description showing up under my glyph. I liked it with just the description. If  I change style->label to just name, i get the same error I was getting before. How can I keep the mouse over but not show the ID under the glyph?



On Tue, Feb 21, 2017 at 2:53 PM, Sofia Robb <[hidden email]> wrote:
That was it! I added IDs and it works!! Thank you Colin! 


On Tue, Feb 21, 2017 at 2:37 PM, Colin <[hidden email]> wrote:
Hmm.  I think I recall a similar situation that Scott Cain had where if you don't have a feature label for genes, then that causes the problem. For example, if you have features without ID/Name in GFF it causes the problem if you try to add mouseover

So, I think probably in this example, if you don't have the ID column filled out in the VCF, this might happen


-Colin

On Tue, Feb 21, 2017 at 4:19 PM, Sofia Robb <[hidden email]> wrote:
no clearing the cache did not help, same error

On Tue, Feb 21, 2017 at 2:10 PM, Colin <[hidden email]> wrote:
I noticed an error similar to this at one point, but adding the "action": "defaultDialog" seemed to help. Could you try clearing cache to retry?

-Colin

On Tue, Feb 21, 2017 at 4:06 PM, Sofia Robb <[hidden email]> wrote:
No :( 

That did not work. Here is the error I get with or without  "action": "defaultDialog"

Uncaught TypeError: Cannot read property 'font' of null
    at Object.<anonymous> (dojo.js:1512)
    at dojo.js:140

On Tue, Feb 21, 2017 at 1:57 PM, Colin <[hidden email]> wrote:
I think having just that would work. You might try adding "action": "defaultDialog" to see if that helps (the mouseover sort of piggybacks off the onClick behavior so in that case it kind of helps to re-specify the onClick action).

"onClick": {
    "label": "TEST",
    "action": "defaultDialog"
}


Then the mouseover label should say "TEST".



-Colin

On Tue, Feb 21, 2017 at 3:23 PM, Sofia Robb <[hidden email]> wrote:
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



------------------------------------------------------------------------------
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engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax










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Re: VCF callbacks

Sofia Robb
Hi Colin,

using style->showLabels results in both the name and description not being displayed, but the popup works.

If I use style→label with just id, the name is not displayed but the popup goes away. 

I even tried changing the label font to 0px, this changes the font in the popup too.


On Wed, Feb 22, 2017 at 10:27 AM, Colin <[hidden email]> wrote:
Does setting style->showLabels = false help? I'm suspecting it won't... Might need fixing on github!

-Colin

On Tue, Feb 21, 2017 at 5:04 PM, Sofia Robb <[hidden email]> wrote:
Uggg. Ok. Now I get the ID and description showing up under my glyph. I liked it with just the description. If  I change style->label to just name, i get the same error I was getting before. How can I keep the mouse over but not show the ID under the glyph?



On Tue, Feb 21, 2017 at 2:53 PM, Sofia Robb <[hidden email]> wrote:
That was it! I added IDs and it works!! Thank you Colin! 


On Tue, Feb 21, 2017 at 2:37 PM, Colin <[hidden email]> wrote:
Hmm.  I think I recall a similar situation that Scott Cain had where if you don't have a feature label for genes, then that causes the problem. For example, if you have features without ID/Name in GFF it causes the problem if you try to add mouseover

So, I think probably in this example, if you don't have the ID column filled out in the VCF, this might happen


-Colin

On Tue, Feb 21, 2017 at 4:19 PM, Sofia Robb <[hidden email]> wrote:
no clearing the cache did not help, same error

On Tue, Feb 21, 2017 at 2:10 PM, Colin <[hidden email]> wrote:
I noticed an error similar to this at one point, but adding the "action": "defaultDialog" seemed to help. Could you try clearing cache to retry?

-Colin

On Tue, Feb 21, 2017 at 4:06 PM, Sofia Robb <[hidden email]> wrote:
No :( 

That did not work. Here is the error I get with or without  "action": "defaultDialog"

Uncaught TypeError: Cannot read property 'font' of null
    at Object.<anonymous> (dojo.js:1512)
    at dojo.js:140

On Tue, Feb 21, 2017 at 1:57 PM, Colin <[hidden email]> wrote:
I think having just that would work. You might try adding "action": "defaultDialog" to see if that helps (the mouseover sort of piggybacks off the onClick behavior so in that case it kind of helps to re-specify the onClick action).

"onClick": {
    "label": "TEST",
    "action": "defaultDialog"
}


Then the mouseover label should say "TEST".



-Colin

On Tue, Feb 21, 2017 at 3:23 PM, Sofia Robb <[hidden email]> wrote:
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
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Re: VCF callbacks

Colin
Oh darn. Maybe you sort of "move the description onto the label" and make style->label into whatever the style->description was, and then make textColor blue to make the label look like a description :)


-Colin

On Wed, Feb 22, 2017 at 12:39 PM, Sofia Robb <[hidden email]> wrote:
Hi Colin,

using style->showLabels results in both the name and description not being displayed, but the popup works.

If I use style→label with just id, the name is not displayed but the popup goes away. 

I even tried changing the label font to 0px, this changes the font in the popup too.


On Wed, Feb 22, 2017 at 10:27 AM, Colin <[hidden email]> wrote:
Does setting style->showLabels = false help? I'm suspecting it won't... Might need fixing on github!

-Colin

On Tue, Feb 21, 2017 at 5:04 PM, Sofia Robb <[hidden email]> wrote:
Uggg. Ok. Now I get the ID and description showing up under my glyph. I liked it with just the description. If  I change style->label to just name, i get the same error I was getting before. How can I keep the mouse over but not show the ID under the glyph?



On Tue, Feb 21, 2017 at 2:53 PM, Sofia Robb <[hidden email]> wrote:
That was it! I added IDs and it works!! Thank you Colin! 


On Tue, Feb 21, 2017 at 2:37 PM, Colin <[hidden email]> wrote:
Hmm.  I think I recall a similar situation that Scott Cain had where if you don't have a feature label for genes, then that causes the problem. For example, if you have features without ID/Name in GFF it causes the problem if you try to add mouseover

So, I think probably in this example, if you don't have the ID column filled out in the VCF, this might happen


-Colin

On Tue, Feb 21, 2017 at 4:19 PM, Sofia Robb <[hidden email]> wrote:
no clearing the cache did not help, same error

On Tue, Feb 21, 2017 at 2:10 PM, Colin <[hidden email]> wrote:
I noticed an error similar to this at one point, but adding the "action": "defaultDialog" seemed to help. Could you try clearing cache to retry?

-Colin

On Tue, Feb 21, 2017 at 4:06 PM, Sofia Robb <[hidden email]> wrote:
No :( 

That did not work. Here is the error I get with or without  "action": "defaultDialog"

Uncaught TypeError: Cannot read property 'font' of null
    at Object.<anonymous> (dojo.js:1512)
    at dojo.js:140

On Tue, Feb 21, 2017 at 1:57 PM, Colin <[hidden email]> wrote:
I think having just that would work. You might try adding "action": "defaultDialog" to see if that helps (the mouseover sort of piggybacks off the onClick behavior so in that case it kind of helps to re-specify the onClick action).

"onClick": {
    "label": "TEST",
    "action": "defaultDialog"
}


Then the mouseover label should say "TEST".



-Colin

On Tue, Feb 21, 2017 at 3:23 PM, Sofia Robb <[hidden email]> wrote:
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax












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Re: VCF callbacks

Sofia Robb
Ill try that!

On Wed, Feb 22, 2017 at 11:01 AM, Colin <[hidden email]> wrote:
Oh darn. Maybe you sort of "move the description onto the label" and make style->label into whatever the style->description was, and then make textColor blue to make the label look like a description :)


-Colin

On Wed, Feb 22, 2017 at 12:39 PM, Sofia Robb <[hidden email]> wrote:
Hi Colin,

using style->showLabels results in both the name and description not being displayed, but the popup works.

If I use style→label with just id, the name is not displayed but the popup goes away. 

I even tried changing the label font to 0px, this changes the font in the popup too.


On Wed, Feb 22, 2017 at 10:27 AM, Colin <[hidden email]> wrote:
Does setting style->showLabels = false help? I'm suspecting it won't... Might need fixing on github!

-Colin

On Tue, Feb 21, 2017 at 5:04 PM, Sofia Robb <[hidden email]> wrote:
Uggg. Ok. Now I get the ID and description showing up under my glyph. I liked it with just the description. If  I change style->label to just name, i get the same error I was getting before. How can I keep the mouse over but not show the ID under the glyph?



On Tue, Feb 21, 2017 at 2:53 PM, Sofia Robb <[hidden email]> wrote:
That was it! I added IDs and it works!! Thank you Colin! 


On Tue, Feb 21, 2017 at 2:37 PM, Colin <[hidden email]> wrote:
Hmm.  I think I recall a similar situation that Scott Cain had where if you don't have a feature label for genes, then that causes the problem. For example, if you have features without ID/Name in GFF it causes the problem if you try to add mouseover

So, I think probably in this example, if you don't have the ID column filled out in the VCF, this might happen


-Colin

On Tue, Feb 21, 2017 at 4:19 PM, Sofia Robb <[hidden email]> wrote:
no clearing the cache did not help, same error

On Tue, Feb 21, 2017 at 2:10 PM, Colin <[hidden email]> wrote:
I noticed an error similar to this at one point, but adding the "action": "defaultDialog" seemed to help. Could you try clearing cache to retry?

-Colin

On Tue, Feb 21, 2017 at 4:06 PM, Sofia Robb <[hidden email]> wrote:
No :( 

That did not work. Here is the error I get with or without  "action": "defaultDialog"

Uncaught TypeError: Cannot read property 'font' of null
    at Object.<anonymous> (dojo.js:1512)
    at dojo.js:140

On Tue, Feb 21, 2017 at 1:57 PM, Colin <[hidden email]> wrote:
I think having just that would work. You might try adding "action": "defaultDialog" to see if that helps (the mouseover sort of piggybacks off the onClick behavior so in that case it kind of helps to re-specify the onClick action).

"onClick": {
    "label": "TEST",
    "action": "defaultDialog"
}


Then the mouseover label should say "TEST".



-Colin

On Tue, Feb 21, 2017 at 3:23 PM, Sofia Robb <[hidden email]> wrote:
Hi,

I am trying to customize the display of my SNPs (JBrowse/Store/SeqFeature/VCFTabix). I figured out how to reformat SNPEff annotations. Now I would like to add some info from the SNPEff annotations to the box that pops up when you hoover over the glyph.

I tried adding this to my track config but I get an empty box.

          "onClick"  : {
             "label": "TEST",
         }

Thanks!
Sofia



------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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