Mussa: Master of the Universe

Mussa Development


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To Do

Last updated: Aug 5, 2002

Vague priority order: (0) = PI wanted it yesterday, no number = normal priority, (2) = waiting on another module, (3) = long term, (4) = longer term
Number of ? means uncertainy of need/desire for feature (not being worked on)

Tristan

Nora

Main & Logistics

  • Annotations:
    • Design new annotation format (more truly xml)
    • write parser for new format
    • migrate annotation data format to real class
      (methods for Nora to use to access & display)
    • This should be modular to also support 'local' or 'user' annotations?
    • (4) ?Annotation files on server as well
      (will this server be Cartwheel? Multiple server support? Nooo...)
  • (3) Cartwheel Server
    • Cartwheel server module to run seqcomp and/or mussa analyses*
    • ?Cartwheel web interface for mussa analyses
  • (3) Mussa client side
    • Get group of seqcomp analyses from cartwheel server*
    • Get mussa save file from server
* - Titus's surf student's work might allow this to be done in an easy way, so holding off on this for now

Display

  • (2) Startup/Load Interface
    • Hookup file/directory browser to load mussa save files
    • f/d browser to fiind directory of seqcomp analyses to merge
    • seqcomp analysis
      • f/d browser to find seq files to run analyses on
      • window to specify parameters of seqcomp analysis
  • Histogram
    • Nothing for now
  • Connection
    • (2) Annotations
      • Display each type of annotation in different colors
      • Independent color selection of each annotation type
      • ?mouse-over has pop-up window with some info?
  • Sequence view
    • scroll buttons getting crowded out
    • auto-update sequence shown when window resized
    • Motif finding
      • use some color effect to indicate reverse compliment matches, but can still tell "base color" - just a darkening?
      • (3) access a motif library and mark all those...
    • (3) ?Scrollbar
      • for faster movement through sequence
      • ? ability to drag each sequence separately
      • can't seem to add scroll bar to graph object
      • may need to rewrite sequence display as different type
      • holding off for a while

Analysis

  • Write function to add up all correct 2 ways from ref seq for histogram
  • (3) examine why n-way comparison same path gets added multiple times (happens with simple sequence segments)
  • (3) Recursively run n-way comparison on n-1 species to get all subpaths not 'originating' from ref sequence

Done

Tristan

Nora

Load/Save/Cartwheel Support

  • Local seqcomp batch analysis mode
    (will be modified for use on cartwheel as well)
  • Loading of simplified seqcomp data files
  • More sophisticated xml parser for loading seqcomp data files
  • Load/save first version of mussa data files
    (will be modified to store in cartwheel/postgres database)
  • Loading of simple annotation file
  • Save a chunk of sequence to a file either as new or append
    (just in fasta format)
  • Iterative function to save a batch of sequence (Nora)

Display

  • Histogram
    • Basic view migrated to class
    • Window extension
      • adjacent windows combined into 'extended windows'
      • red bars to denote full N-way ext windows
      • window size and 10x win size ref bars
    • Left mouse drag draws box right
    • Right mouse button pop-up menu
      • option to remove drawn box (done with left mouse)
      • option to spawn connection window
  • Connection
    • Basic view migrated to class, spawns as new window
    • Left mouse
      • drag draws box
      • can resize & move
      • Alignment best guess of box location on other sequences
    • Right mouse button pop-up menu
      • option to remove drawn box (done with left mouse)
      • option to spawn sequence window
      • option to save ext windows in box
      • option to save all ext windows
    • Annotations
      • Draws colored rect on seq were an annotation is
      • Color selection for each annotations
  • Sequence view
    • Sequence class made, basic display of seq, spawns as new window
    • Sequence displayed only from connection window selection
    • GUI element to interface with sequence save function
    • Horizontal scrolling of window
      • Scroll buttons - small & large jump
      • With arrow keys
    • Base pair display
      • bp matching 2+ from ref seq larger to highlight conservation
      • Dynamic coloring matching bp (handles N..1 colorizations)
    • Alignment
      • Alignment matchup lines only drawn for ext window
      • Multiple Alignments viewable at same time
      • Independ alignment location for each sequence
    • Motif search
      • finds normal & reverse compliment matches
      • the extended letter usage (N = any 4, all those others...)
      • color selection for each search pattern

Analysis

  • N-way analysis function using a ref sequence
  • Basic 2-way (FR classic) mode
  • Filter function to remove subpaths already part of larger path
  • Motif finding (Nora)