jBrowse scrolls to bottom #6

yannickwurm · 2013-12-18T18:03:09Z

When you click "Curate" from the dashboard, the loaded jBrowse scrolls down to the bottom. This is confusing to users. Like Webapollo & normal jBrowse, it should load scrolled to the top (i.e. where you cannot go any higher)

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. remove jb nav remove tracklist remove not needed dep on dijit/ indent track padding track-label tmp increase initial height of edit track do not scroll to bottom on page load #6 rework track spacing and padding Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

Launch the server and direct the browser to `/#/curate`. Login, if need be, and you will see the first curation task. Hit `Done` to save the curated gene model on the server and move to the next task. Annotation editing functionality builds on the excellent work done by JBrowse and WebApollo. JBrowse / WebApollo integration ------------------------------- JB and WA code, with several modifications, lives as a part of the source tree in app/src/JBrowse and JBrowse/WebApollo. JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA -- just one line) compiled into one styles.css. JB/WA contains upstream’s WA/js. I hacked JB’s plugin system so that loading CSS for plugins is none of it’s concern, additionally removing the dependency on lazyload. JB/main.js loads styles.css using require-css and WA using the reduced plugin architecture. This combines JB & WA into one unit. JB/main.js instantiates JB and returns a facade object. Rest of Afra inter-operates with JB through the facade. At the moment we have a single API call, `load`, to load a task into JB. We will need another API call to access contents of the annotations track. JB’s dependencies are managed through Bower. I have locked to the latest point-release of the dependencies that follow semantic versioning. While we track rolling updates from Github for the rest -- either Bower doesn’t support locking to a SHA or it just didn’t work on my Mac. It’s worth noting that these dependencies are extremely focussed and move slow: hopefully things won’t break for a while. In the near future, we should be able to remove a few more dependencies and / or lock to a working SHA using Bower. Modified default track styles for JB so it looks quite presentable. Perl sub-system of JB & WA is a part of the source tree as well. setup.sh lives as a part of `rake setup` and installs dependencies to $HOME/.extlib. Additionally, I dropped support for the deprecated legacy wiggle format and legacy bam-to-json.pl. Included for testing, MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant genome. And, * drop more than one feature * make exons resizable * trying add_exon * jbrowse refresh hack * Done button fully functional: put submission, get a new task and load it. Squashed commits ---------------- mv genome curate JB: change zoom level on scroll wheel. overlay zoom buttons over genome viewer in a horizontal orientation merge wa and jb 1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. remove jb nav remove tracklist remove not needed dep on dijit/ indent track padding track-label tmp increase initial height of edit track do not scroll to bottom on page load #6 rework track spacing and padding Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

Launch the server and direct the browser to `/#/curate`. Login, if need be, and you will see the first curation task. Hit `Done` to save the curated gene model on the server and move to the next task. Annotation editing functionality builds on the excellent work done by JBrowse and WebApollo. JBrowse / WebApollo integration ------------------------------- JB and WA code, with several modifications, lives as a part of the source tree in app/src/JBrowse and JBrowse/WebApollo. JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA -- just one line) compiled into one styles.css. JB/WA contains upstream’s WA/js. I hacked JB’s plugin system so that loading CSS for plugins is none of it’s concern, additionally removing the dependency on lazyload. JB/main.js loads styles.css using require-css and WA using the reduced plugin architecture. This combines JB & WA into one unit. JB/main.js instantiates JB and returns a facade object. Rest of Afra inter-operates with JB through the facade. At the moment we have a single API call, `load`, to load a task into JB. We will need another API call to access contents of the annotations track. JB’s dependencies are managed through Bower. I have locked to the latest point-release of the dependencies that follow semantic versioning. While we track rolling updates from Github for the rest -- either Bower doesn’t support locking to a SHA or it just didn’t work on my Mac. It’s worth noting that these dependencies are extremely focussed and move slow: hopefully things won’t break for a while. In the near future, we should be able to remove a few more dependencies and / or lock to a working SHA using Bower. Modified default track styles for JB so it looks quite presentable. Perl sub-system of JB & WA is a part of the source tree as well. setup.sh lives as a part of `rake setup` and installs dependencies to $HOME/.extlib. Additionally, I dropped support for the deprecated legacy wiggle format and legacy bam-to-json.pl. Included for testing, MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant genome. And, * drop more than one feature * make exons resizable * trying add_exon * jbrowse refresh hack * Done button fully functional: put submission, get a new task and load it. Squashed commits ---------------- mv genome curate JB: change zoom level on scroll wheel. overlay zoom buttons over genome viewer in a horizontal orientation merge wa and jb 1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. remove jb nav remove tracklist remove not needed dep on dijit/ indent track padding track-label tmp increase initial height of edit track do not scroll to bottom on page load #6 rework track spacing and padding Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> more buttons Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> make hide/show button work Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> remove horizontal scrollbar Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> remove feature right-click menu Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> lower Done button Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

Launch the server and direct the browser to `/#/curate`. Login, if need be, and you will see the first curation task. Hit `Done` to save the curated gene model on the server and move to the next task. Annotation editing functionality builds on the excellent work done by JBrowse and WebApollo. JBrowse / WebApollo integration ------------------------------- JB and WA code, with several modifications, lives as a part of the source tree in app/src/JBrowse and JBrowse/WebApollo. JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA -- just one line) compiled into one styles.css. JB/WA contains upstream’s WA/js. I hacked JB’s plugin system so that loading CSS for plugins is none of it’s concern, additionally removing the dependency on lazyload. JB/main.js loads styles.css using require-css and WA using the reduced plugin architecture. This combines JB & WA into one unit. JB/main.js instantiates JB and returns a facade object. Rest of Afra inter-operates with JB through the facade. At the moment we have a single API call, `load`, to load a task into JB. We will need another API call to access contents of the annotations track. JB’s dependencies are managed through Bower. I have locked to the latest point-release of the dependencies that follow semantic versioning. While we track rolling updates from Github for the rest -- either Bower doesn’t support locking to a SHA or it just didn’t work on my Mac. It’s worth noting that these dependencies are extremely focussed and move slow: hopefully things won’t break for a while. In the near future, we should be able to remove a few more dependencies and / or lock to a working SHA using Bower. Modified default track styles for JB so it looks quite presentable. Perl sub-system of JB & WA is a part of the source tree as well. setup.sh lives as a part of `rake setup` and installs dependencies to $HOME/.extlib. Additionally, I dropped support for the deprecated legacy wiggle format and legacy bam-to-json.pl. Included for testing, MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant genome. And, * drop more than one feature * make exons resizable * trying add_exon * jbrowse refresh hack * Done button fully functional: put submission, get a new task and load it. Squashed commits ---------------- mv genome curate JB: change zoom level on scroll wheel. overlay zoom buttons over genome viewer in a horizontal orientation merge wa and jb 1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. remove jb nav remove tracklist remove not needed dep on dijit/ indent track padding track-label tmp increase initial height of edit track do not scroll to bottom on page load #6 rework track spacing and padding Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> more buttons Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> make hide/show button work Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> remove horizontal scrollbar Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> remove feature right-click menu Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> lower Done button Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trimming annottrack.js - removed right click menu and stuff Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js -2 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js - 3 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js - 4 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js - 5 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> edit track annot css Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> clear selection after annot dropped It's causing the app to throw: Uncaught TypeError: Cannot read property 'options' of undefined at draggable.js?bust=1389699970232:659 However this error doesn't seem to affect usability. Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> use black color for edge matching Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> 4px black border for selection Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> curate.less Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

# The first commit's message is: Annotation editor. Launch the server and direct the browser to `/#/curate`. Login, if need be, and you will see the first curation task. Hit `Done` to save the curated gene model on the server and move to the next task. Annotation editing functionality builds on the excellent work done by JBrowse and WebApollo. JBrowse / WebApollo integration ------------------------------- JB and WA code, with several modifications, lives as a part of the source tree in app/src/JBrowse and JBrowse/WebApollo. JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA -- just one line) compiled into one styles.css. JB/WA contains upstream’s WA/js. I hacked JB’s plugin system so that loading CSS for plugins is none of it’s concern, additionally removing the dependency on lazyload. JB/main.js loads styles.css using require-css and WA using the reduced plugin architecture. This combines JB & WA into one unit. JB/main.js instantiates JB and returns a facade object. Rest of Afra inter-operates with JB through the facade. At the moment we have a single API call, `load`, to load a task into JB. We will need another API call to access contents of the annotations track. JB’s dependencies are managed through Bower. I have locked to the latest point-release of the dependencies that follow semantic versioning. While we track rolling updates from Github for the rest -- either Bower doesn’t support locking to a SHA or it just didn’t work on my Mac. It’s worth noting that these dependencies are extremely focussed and move slow: hopefully things won’t break for a while. In the near future, we should be able to remove a few more dependencies and / or lock to a working SHA using Bower. Modified default track styles for JB so it looks quite presentable. Perl sub-system of JB & WA is a part of the source tree as well. setup.sh lives as a part of `rake setup` and installs dependencies to $HOME/.extlib. Additionally, I dropped support for the deprecated legacy wiggle format and legacy bam-to-json.pl. Included for testing, MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant genome. And, * drop more than one feature * make exons resizable * trying add_exon * jbrowse refresh hack * Done button fully functional: put submission, get a new task and load it. Squashed commits ---------------- mv genome curate JB: change zoom level on scroll wheel. overlay zoom buttons over genome viewer in a horizontal orientation merge wa and jb 1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. remove jb nav remove tracklist remove not needed dep on dijit/ indent track padding track-label tmp increase initial height of edit track do not scroll to bottom on page load #6 rework track spacing and padding Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> more buttons Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> make hide/show button work Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> remove horizontal scrollbar Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> remove feature right-click menu Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> lower Done button Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trimming annottrack.js - removed right click menu and stuff Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js -2 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js - 3 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js - 4 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js - 5 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> edit track annot css Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> clear selection after annot dropped It's causing the app to throw: Uncaught TypeError: Cannot read property 'options' of undefined at draggable.js?bust=1389699970232:659 However this error doesn't seem to affect usability. Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> use black color for edge matching Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> 4px black border for selection Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> curate.less Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> # The 2nd commit message will be skipped: # menu # # Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> # The 3rd commit message will be skipped: # zoomToBaseLevel on base at center # # Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> # The 4th commit message will be skipped: # Reword zoom to nucleotides and zoom back out. # # Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> # The 5th commit message will be skipped: # padding on article.curate # # Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

This massive commit creates a demonstration of the concept. Launch the server and direct the browser to `/#/curate`. Login, if need be, and you will see the first curation task. Hit `Done` to save the curated gene model on the server and move to the next task. Annotation editing functionality builds on the excellent work done by JBrowse and WebApollo. JBrowse / WebApollo integration ------------------------------- JB and WA code, with several modifications, lives as a part of the source tree in app/src/JBrowse and JBrowse/WebApollo. JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA -- just one line) compiled into one styles.css. JB/WA contains upstream’s WA/js. I hacked JB’s plugin system so that loading CSS for plugins is none of it’s concern, additionally removing the dependency on lazyload. JB/main.js loads styles.css using require-css and WA using the reduced plugin architecture. This combines JB & WA into one unit. JB/main.js instantiates JB and returns a facade object. Rest of Afra inter-operates with JB through the facade. At the moment we have a single API call, `load`, to load a task into JB. We will need another API call to access contents of the annotations track. JB’s dependencies are managed through Bower. I have locked to the latest point-release of the dependencies that follow semantic versioning. While we track rolling updates from Github for the rest -- either Bower doesn’t support locking to a SHA or it just didn’t work on my Mac. It’s worth noting that these dependencies are extremely focussed and move slow: hopefully things won’t break for a while. In the near future, we should be able to remove a few more dependencies and / or lock to a working SHA using Bower. Modified default track styles for JB so it looks quite presentable. Perl sub-system of JB & WA is a part of the source tree as well. setup.sh lives as a part of `rake setup` and installs dependencies to $HOME/.extlib. Additionally, I dropped support for the deprecated legacy wiggle format and legacy bam-to-json.pl. Included for testing, MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant genome. And, * drop more than one feature * make exons resizable * trying add_exon * jbrowse refresh hack * Done button fully functional: put submission, get a new task and load it. Squashed commits ---------------- mv genome curate JB: change zoom level on scroll wheel. overlay zoom buttons over genome viewer in a horizontal orientation merge wa and jb 1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. remove jb nav remove tracklist remove not needed dep on dijit/ indent track padding track-label tmp increase initial height of edit track do not scroll to bottom on page load #6 rework track spacing and padding Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> more buttons Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> make hide/show button work Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> remove horizontal scrollbar Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> remove feature right-click menu Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> lower Done button Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trimming annottrack.js - removed right click menu and stuff Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js -2 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js - 3 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js - 4 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> trim annottrack.js - 5 Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> edit track annot css Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> clear selection after annot dropped It's causing the app to throw: Uncaught TypeError: Cannot read property 'options' of undefined at draggable.js?bust=1389699970232:659 However this error doesn't seem to affect usability. Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> use black color for edge matching Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> 4px black border for selection Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com> curate.less Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

This massive commit creates a demonstration of the concept. Launch the server and direct the browser to `/#/curate`. Login, if need be, and you will see the first curation task. Hit `Done` to save the curated gene model on the server and move to the next task. Annotation editing functionality builds on the excellent work done by JBrowse and WebApollo. JBrowse / WebApollo integration ------------------------------- JB and WA code, with several modifications, lives as a part of the source tree in app/src/JBrowse and JBrowse/WebApollo. JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA -- just one line) compiled into one styles.css. JB/WA contains upstream’s WA/js. I hacked JB’s plugin system so that loading CSS for plugins is none of it’s concern, additionally removing the dependency on lazyload. JB/main.js loads styles.css using require-css and WA using the reduced plugin architecture. This combines JB & WA into one unit. JB/main.js instantiates JB and returns a facade object. Rest of Afra inter-operates with JB through the facade. At the moment we have a single API call, `load`, to load a task into JB. We will need another API call to access contents of the annotations track. JB’s dependencies are managed through Bower. I have locked to the latest point-release of the dependencies that follow semantic versioning. While we track rolling updates from Github for the rest -- either Bower doesn’t support locking to a SHA or it just didn’t work on my Mac. It’s worth noting that these dependencies are extremely focussed and move slow: hopefully things won’t break for a while. In the near future, we should be able to remove a few more dependencies and / or lock to a working SHA using Bower. Modified default track styles for JB so it looks quite presentable. Perl sub-system of JB & WA is a part of the source tree as well. setup.sh lives as a part of `rake setup` and installs dependencies to $HOME/.extlib. Additionally, I dropped support for the deprecated legacy wiggle format and legacy bam-to-json.pl. Included for testing, MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant genome. And, * drop more than one feature * make exons resizable * trying add_exon * jbrowse refresh hack * Done button fully functional: put submission, get a new task and load it. Squashed commits ---------------- JB: change zoom level on scroll wheel. overlay zoom buttons over genome viewer in a horizontal orientation merge wa and jb 1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. * remove jb nav * remove tracklist * remove not needed dep on dijit/ * increase initial height of edit track * do not scroll to bottom on page load #6 * rework track spacing and padding * track padding * track-label * remove feature right-click menu * trimming annottrack.js - removed right click menu and stuff * edit track annot css * clear selection after annot dropped It's causing the app to throw: Uncaught TypeError: Cannot read property 'options' of undefined at draggable.js?bust=1389699970232:659 However this error doesn't seem to affect usability. * use black color for edge matching * 4px black border for selection * uri decode gff stream * fix anno saving * and reset feature start and end, if need be, on resize exon * try add exon again Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

* proof of concept * IE10 and above only. * Annotation editor. Launch the server and direct the browser to `/#/curate`. Login, if need be, and you will see the first curation task. Hit `Done` to save the curated gene model on the server and move to the next task. Annotation editing functionality builds on the excellent work done by JBrowse and WebApollo. JBrowse / WebApollo integration ------------------------------- JB and WA code, with several modifications, lives as a part of the source tree in app/src/JBrowse and JBrowse/WebApollo. JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA -- just one line) compiled into one styles.css. JB/WA contains upstream’s WA/js. I hacked JB’s plugin system so that loading CSS for plugins is none of it’s concern, additionally removing the dependency on lazyload. JB/main.js loads styles.css using require-css and WA using the reduced plugin architecture. This combines JB & WA into one unit. JB/main.js instantiates JB and returns a facade object. Rest of Afra inter-operates with JB through the facade. At the moment we have a single API call, `load`, to load a task into JB. We will need another API call to access contents of the annotations track. JB’s dependencies are managed through Bower. I have locked to the latest point-release of the dependencies that follow semantic versioning. While we track rolling updates from Github for the rest -- either Bower doesn’t support locking to a SHA or it just didn’t work on my Mac. It’s worth noting that these dependencies are extremely focussed and move slow: hopefully things won’t break for a while. In the near future, we should be able to remove a few more dependencies and / or lock to a working SHA using Bower. Modified default track styles for JB so it looks quite presentable. Perl sub-system of JB & WA is a part of the source tree as well. setup.sh lives as a part of `rake setup` and installs dependencies to $HOME/.extlib. Additionally, I dropped support for the deprecated legacy wiggle format and legacy bam-to-json.pl. Included for testing, MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant genome. And, * drop more than one feature * make exons resizable * trying add_exon * jbrowse refresh hack * Done button fully functional: put submission, get a new task and load it. Squashed commits ---------------- JB: change zoom level on scroll wheel. overlay zoom buttons over genome viewer in a horizontal orientation merge wa and jb 1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. * remove jb nav * remove tracklist * remove not needed dep on dijit/ * increase initial height of edit track * do not scroll to bottom on page load #6 * rework track spacing and padding * track padding * track-label * remove feature right-click menu * trimming annottrack.js - removed right click menu and stuff * edit track annot css * clear selection after annot dropped It's causing the app to throw: Uncaught TypeError: Cannot read property 'options' of undefined at draggable.js?bust=1389699970232:659 However this error doesn't seem to affect usability. * use black color for edge matching * 4px black border for selection * uri decode gff stream * fix anno saving * and reset feature start and end, if need be, on resize exon * try add exon again * Mention we support Google Chrome only at the moment on #signin. * daemonize * fb popup * package.json Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

* proof of concept * IE10 and above only. * Annotation editor. Launch the server and direct the browser to `/#/curate`. Login, if need be, and you will see the first curation task. Hit `Done` to save the curated gene model on the server and move to the next task. Annotation editing functionality builds on the excellent work done by JBrowse and WebApollo. JBrowse / WebApollo integration ------------------------------- JB and WA code, with several modifications, lives as a part of the source tree in app/src/JBrowse and JBrowse/WebApollo. JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA -- just one line) compiled into one styles.css. JB/WA contains upstream’s WA/js. I hacked JB’s plugin system so that loading CSS for plugins is none of it’s concern, additionally removing the dependency on lazyload. JB/main.js loads styles.css using require-css and WA using the reduced plugin architecture. This combines JB & WA into one unit. JB/main.js instantiates JB and returns a facade object. Rest of Afra inter-operates with JB through the facade. At the moment we have a single API call, `load`, to load a task into JB. We will need another API call to access contents of the annotations track. JB’s dependencies are managed through Bower. I have locked to the latest point-release of the dependencies that follow semantic versioning. While we track rolling updates from Github for the rest -- either Bower doesn’t support locking to a SHA or it just didn’t work on my Mac. It’s worth noting that these dependencies are extremely focussed and move slow: hopefully things won’t break for a while. In the near future, we should be able to remove a few more dependencies and / or lock to a working SHA using Bower. Modified default track styles for JB so it looks quite presentable. Perl sub-system of JB & WA is a part of the source tree as well. setup.sh lives as a part of `rake setup` and installs dependencies to $HOME/.extlib. Additionally, I dropped support for the deprecated legacy wiggle format and legacy bam-to-json.pl. Included for testing, MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant genome. And, * drop more than one feature * make exons resizable * trying add_exon * jbrowse refresh hack * Done button fully functional: put submission, get a new task and load it. Squashed commits ---------------- JB: change zoom level on scroll wheel. overlay zoom buttons over genome viewer in a horizontal orientation merge wa and jb 1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. * remove jb nav * remove tracklist * remove not needed dep on dijit/ * increase initial height of edit track * do not scroll to bottom on page load #6 * rework track spacing and padding * track padding * track-label * remove feature right-click menu * trimming annottrack.js - removed right click menu and stuff * edit track annot css * clear selection after annot dropped It's causing the app to throw: Uncaught TypeError: Cannot read property 'options' of undefined at draggable.js?bust=1389699970232:659 However this error doesn't seem to affect usability. * use black color for edge matching * 4px black border for selection * uri decode gff stream * fix anno saving * and reset feature start and end, if need be, on resize exon * try add exon again * Mention we support Google Chrome only at the moment on #signin. * fb popup * package.json Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

* proof of concept * IE10 and above only. * Annotation editor. Launch the server and direct the browser to `/#/curate`. Login, if need be, and you will see the first curation task. Hit `Done` to save the curated gene model on the server and move to the next task. Annotation editing functionality builds on the excellent work done by JBrowse and WebApollo. JBrowse / WebApollo integration ------------------------------- JB and WA code, with several modifications, lives as a part of the source tree in app/src/JBrowse and JBrowse/WebApollo. JB contains upstream’s src/JBrowse, img, and all CSS (including that of WA -- just one line) compiled into one styles.css. JB/WA contains upstream’s WA/js. I hacked JB’s plugin system so that loading CSS for plugins is none of it’s concern, additionally removing the dependency on lazyload. JB/main.js loads styles.css using require-css and WA using the reduced plugin architecture. This combines JB & WA into one unit. JB/main.js instantiates JB and returns a facade object. Rest of Afra inter-operates with JB through the facade. At the moment we have a single API call, `load`, to load a task into JB. We will need another API call to access contents of the annotations track. JB’s dependencies are managed through Bower. I have locked to the latest point-release of the dependencies that follow semantic versioning. While we track rolling updates from Github for the rest -- either Bower doesn’t support locking to a SHA or it just didn’t work on my Mac. It’s worth noting that these dependencies are extremely focussed and move slow: hopefully things won’t break for a while. In the near future, we should be able to remove a few more dependencies and / or lock to a working SHA using Bower. Modified default track styles for JB so it looks quite presentable. Perl sub-system of JB & WA is a part of the source tree as well. setup.sh lives as a part of `rake setup` and installs dependencies to $HOME/.extlib. Additionally, I dropped support for the deprecated legacy wiggle format and legacy bam-to-json.pl. Included for testing, MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant genome. And, * drop more than one feature * make exons resizable * trying add_exon * jbrowse refresh hack * Done button fully functional: put submission, get a new task and load it. Squashed commits ---------------- JB: change zoom level on scroll wheel. overlay zoom buttons over genome viewer in a horizontal orientation merge wa and jb 1. Removed TrackTransformer stuff - DraggableHTMLFeatures now the default for FeatureTrack. 2. Merge permission.js and annottrack.js - will eventually remove permission stuff. * remove jb nav * remove tracklist * remove not needed dep on dijit/ * increase initial height of edit track * do not scroll to bottom on page load #6 * rework track spacing and padding * track padding * track-label * remove feature right-click menu * trimming annottrack.js - removed right click menu and stuff * edit track annot css DnD: * If the annotation wasn't dropped on edit track, bring it back to * clear selection after annot dropped * use black color for edge matching * 4px black border for selection * uri decode gff stream * fix anno saving * and reset feature start and end, if need be, on resize exon * try add exon again * Mention we support Google Chrome only at the moment on #signin. * fb popup * package.json Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

yeban added a commit that referenced this issue Jan 13, 2014

do not scroll to bottom on page load #6

234f9d0

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

yeban closed this as completed Jan 28, 2014

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jBrowse scrolls to bottom #6

jBrowse scrolls to bottom #6

yannickwurm commented Dec 18, 2013

jBrowse scrolls to bottom #6

jBrowse scrolls to bottom #6

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yannickwurm commented Dec 18, 2013