Improvement ideas from the Backlog Grooming Meeting on 7/22/2015:
1) Allow users to select the nucleotide colors (A,C,T,G,Other) in Prot Annot's Color Preferences. Additionally, we should set Prot Annot's default nucleotide colors to match IGB's default nucleotide colors.
2) Reorder Prot Annot's Color Preferences for better organization. Place similar things together in a logical order, such as the Frame 0,1, and 2.
3) Rather than using tooltips to display the useful info on InterProScan databases we should place blue information circles next to the text for databases that have metadata that can be taken from the Rest Service. Hovering on the blue information circles will show the tooltip info and it is important to wrap this tooltip info appropriately so that it is all easily readable.
4) The InterProScan link in the InterProScan Job Configuration box should link to the "About InterProScan" page which can be found here:
https://www.ebi.ac.uk/interpro/about.html;jsessionid=580FF7F6D7FA301E3D8A719D979D89C2
5) We should move the horizontal zoom slider in the ProtAnnot plugin to the top of the plugin and the vertical zoom slider to the left. This will keep the UI more consistent with IGB's UI.
6) We should show an arrow on each intron in ProtAnnot to let users know that the direction of translation is displayed from left to right.
7) We should make the UTR blocks in ProtAnnot shorter so that the gene models look more like they do in IGB.
8) Create a new tab in ProtAnnot that will list InterProScan search results. When InterProScan is run the focus should be shifted to this tab. This will indicate to the user when the search has completed and if 0 results were found or if many results were found. In doing this we should just make sure that there is some way for the user to tell if the search is completed or if it is still running.
9) Allow mutliple ProtAnnot windows. If ProtAnnot is open and you Start ProtAnnot with a different transcript in IGB a new ProtAnnot window should open.
10) Save InterProScan enabled selections in case a user forgets to enter their email address so that they don't have to reselect all the databases they are trying to use.
Improvement
Major
Improvement ideas from the Backlog Grooming Meeting on 7/22/2015:
1) Allow users to select the nucleotide colors (A,C,T,G,Other) in Prot Annot's Color Preferences. Additionally, we should set Prot Annot's default nucleotide colors to match IGB's default nucleotide colors.
2) Reorder Prot Annot's Color Preferences for better organization. Place similar things together in a logical order, such as the Frame 0,1, and 2.
3) Rather than using tooltips to display the useful info on InterProScan databases we should place blue information circles next to the text for databases that have metadata that can be taken from the Rest Service. Hovering on the blue information circles will show the tooltip info and it is important to wrap this tooltip info appropriately so that it is all easily readable.
4) The InterProScan link in the InterProScan Job Configuration box should link to the "About InterProScan" page which can be found here:
https://www.ebi.ac.uk/interpro/about.html;jsessionid=580FF7F6D7FA301E3D8A719D979D89C2
5) We should move the horizontal zoom slider in the ProtAnnot plugin to the top of the plugin and the vertical zoom slider to the left. This will keep the UI more consistent with IGB's UI.
6) We should show an arrow on each intron in ProtAnnot to let users know that the direction of translation is displayed from left to right.
7) We should make the UTR blocks in ProtAnnot shorter so that the gene models look more like they do in IGB.
8) Create a new tab in ProtAnnot that will list InterProScan search results. When InterProScan is run the focus should be shifted to this tab. This will indicate to the user when the search has completed and if 0 results were found or if many results were found. In doing this we should just make sure that there is some way for the user to tell if the search is completed or if it is still running.
9) Allow mutliple ProtAnnot windows. If ProtAnnot is open and you Start ProtAnnot with a different transcript in IGB a new ProtAnnot window should open.
10) Save InterProScan enabled selections in case a user forgets to enter their email address so that they don't have to reselect all the databases they are trying to use.