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notes.txt
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d3 force directed changes :
#make sure labels don't touch one another
expand 'vertical' and 'horizontal'
branch length : aestehically pleasing( how? ), or use branch length data
minor : keep labels in box
label the root( remove icon )
place the root at the bottom
differentiation ( shape or color ) of leaf nodes
after horizontal expansion, keep previous view all collapsed into one node
don't let labels touch other nodes
check out d3 tree view
check out d3 sunburst view
11/30/2011 discussion :
use plantlist, apg_taxon, and ncbi_node to populate a sunburst tree
use mutiple sunburst trees to compare
- type in a name, highlight area in all trees
- mouseover, same thing
- select different data points to highlight in each tree (support values?)
force directed tree - pin node ( zero gravity, fixed ) after it is grabbed and released
re-implement search field ( label panel )
- let user know if its collapsed
- highlight visible nodes
- let user edit searched for node
- let user navigate to node
(minor) traditional cladograms branch lengths are "split late" rather than early
- add branch length selector option
- work out a menu module for each view mode
- add option to adjeust # of max tips'
12/20/2011 discussion :
#put force directed on hold for now
svgView - cladogram changes:
#make sure sure edit node works - use a dummy tree
#source tree id = 37 has an error dealing with internal nodes
#after a collapsed node is expanded horizontally - add a collapse dialogue in place of the expand hori dialogue
#after a collapse action - scroll to collapsed node
#show a descendant taxon name and # of nodes next to the collapsed ui
#add a control panel to the left side of the tree - branch length, slider scale (mousewheel?), search bar
#the path does not look right where the lines intersect - may have to change attributes - may have to rewrite pathstring function and remove the move tos
add a circular viz layout
add a stop action to the node selector so that it stays on the node selected when a menu pops up
1/02/2011 discussion :
#internal node labels - give transparentyellow background
#vertical expansion - don't expand entire clade - just make sure not is not collapsed
future - expand multiple nodes in one column into a draggable box
1/20 : need to make 'view descendant labels ajax' - taking up too much space
1/30 discussion :
#allow slider to adjust branch length, the vertical tip buffer, and the font-size
#maxTips should be independent of window size
#when expanding vertically, maxtips should increase 50 percent ( or what we find to be aesthetically pleasing )
#label , taxa search, when a label or taxa is selected - redraw tree ( one column ) - the node's ancestors are all in the keep visible list
2/10/12 :
create column class in phylogram view
2/20/12 :
#branch lengths : smoothed, scaled (don't is broken right now)
internal labels : yellow is opaque and on top of tree, texti s on top of this
#number of tips -> control panel slider option
2/27/2012 :
bug with clipboard names having a single quote
personal clipboard - shared clipboard ?
2/29/2012 :
add to clipboard, any modal box, have automatic text selection so the user doesn't have to manually delete the text
create panel object
3/13/20120 :
add options to rotate siblings?
ladderize everything by default ?
3/14/2012 :
redirect after login still does not work =/
give notify timeout for "dotdotdot"
fix clipboard on initial open when the content overflows
3/16 :
re evaluate slider control
areThereBranchLengths should only be called once per source tree and once per gtree edit
#collapsed node ui doesn't seem to work - probably when sizes are changed ? -- unable to reproduce
3/19
#maxtips value are aribitrary list of numbers 50, 100, 150 ..
store tree data into table so one doesn't have to recurse through it each time
determine collapsed nodes : average out number of collapsed nodes across tree
4/4/2012
after tree edit - update graft history panel
4/17/2012 :
was unable to edit tree twice using clipboard - error on clip drop
5/3/2012 :
after vertical node expansion, max tips is increased - need to update the control panel when this happens
after horizontal, vertical node expansion - we add ids to the keep visible list - this needs to be reverted at some point - i think
after a vertical expand node, a popup appears next to the expanded node to notify that it is the expanded node, when scrolling, this popup is misaligned - fix this
5/23/2012 :
#after a graft on a source tree, the graft history comes to us via ajax call, need to make sure it shows up in the right spot - should probably close the clipboard if its open
collapse clade is broken
6/31/2012 :
moving item from clipboard to graft clade - dialogue comes up. user presses escape, modal dialogue box disappears, but the clade is still highlighted
6/12/12 :
on window resize: fix sidebar header width
7/12/12:
#need to create a collapsed node object
7/19/12:
#control panel hover sizing is broken - le sigh
7/24/12:
#need to figure out what to do regarding descendant labels when a user collapses a node on a tree that is un processed
7/30/12:
#when calculating node coordinates, make sure the depth of the tree reflects the actual depth of the tree being shown, not the entire tree ( collapsed nodes )
8/20/12:
save whether nodes are collapsed / expanded ( vertically, horizontally ) in session
9/5/12:
#collapse node in column that is not an ancestor of an expanded node in the same column
9/6/12:
#while vertically scrolling after a vertical expand - make sure the node selector is node being updated
9/18/12:
collapse internal node with label - refreshed, shown label is incorrect
9/24/12:
#make all? some? config settings last for the session
#switch between scaled / smooth -> don't remove columns
#save columns ( visble, collapsed ) in session
after horizontal expand, zoom out on the previous column so that it fits on the screen
#collapsed ui should push everything to the right - not the left
minimum tips per column needed
9/27/12:
#make sure collapsed node dialogue is correct when retrieving a tree with multiple columns already open
10/8/12 :
scale collapsed node ui with size of font ?
hidden hover border is on top of view descendant labels - this shouldn't be the case
11/5/12 :
testing prune node - prune entire column for source and gtree
1/11/2013 :
after a prune clade action, I viewed the tree edits, then as I was going to prune again, the prune comment modal dialogue was too tall. make a default height for the modal box, or reset the height after each use
1/15/2013 :
when attempting to replace or graft, the clipboard has some minor display issues
resizing window, change data tables
width
None is link to edit taxon
visual indication of sort order