JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / doc / AnnotationPostAnalysis.txt

diff --git a/doc/AnnotationPostAnalysis.txt b/doc/AnnotationPostAnalysis.txt
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-##
-# Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
-# Copyright (C) $$Year-Rel$$ The Jalview Authors
-# 
-# This file is part of Jalview.
-# 
-# Jalview is free software: you can redistribute it and/or
-# modify it under the terms of the GNU General Public License 
-# as published by the Free Software Foundation, either version 3
-# of the License, or (at your option) any later version.
-#  
-# Jalview is distributed in the hope that it will be useful, but 
-# WITHOUT ANY WARRANTY; without even the implied warranty 
-# of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
-# PURPOSE.  See the GNU General Public License for more details.
-# 
-# You should have received a copy of the GNU General Public License
-# along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
-# The Jalview Authors are detailed in the 'AUTHORS' file.
-##
-Init.
-optimise rendering - use same model as alignment but with vertical binary sweep to select range of annotation to render:
-Vertical interval list
-. run length compress the sizes -> n_i * v_height_i -> label each node - total and accumulated total vertical pos (under current visibility settings ?)
---> ins/delete/hide/show of one or more contiguous individual rows causes local -> global update of position sums.
---
-. 
-indexOf(VPosition in annotation display window),
-VPositionOf(AnnotationI)
-
-0.
-i. Hide/show by whole annotation set id
-ii. move to top/bottom
-iii. 
-
-1. Summarising annotation
-{ Annotation Class ID 
-|_ { Type string } }
--> 
-
-Simple modal : 
-- Proportion of sequences with most frequent symbol
-- symbol logo
-[ option to drill down and subselect based on particular symbol or subdivide by all symbols ]
-
-3. Clustering based on annotation
-A few routes:
-use built in PCA calculation to do scalar product based analysis of one or many annotation vectors.
-Sliding window over alignment doing pca at each point. Analyse trajectories through PCA ?  (see maximum/minimum and stretches of local similarity)
-
-
-* ''' ACCESS ALL MENUS '''
--> allow context popup to show all window submenus
-{ local relevant }
-{ Parent window -> file,edit,etc }
-{ Desktop -> File, Tools, ... }
-{ other areas more distant - e.g. sequence/annotation ID popup from middle of alignment/annotation area }
- 
-