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This module contains means to visualize Alignments. The most important interface is the Visualizer class. A trivial implementation (essentially just using toString()) is the StringVisualizer. A more sophisticated example that is recommended for outside use is the HTMLVisualizer. All other classes are helper classes for said HTMLVisualizer.

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# 
# TCS Alignment Toolbox Version 3
# 
# Copyright (C) 2016
# Benjamin Paa?en
# AG Theoretical Computer Science
# Centre of Excellence Cognitive Interaction Technology (CITEC)
# University of Bielefeld
# 
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
# 
# This program 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 Affero General Public License for more details.
# 
# You should have received a copy of the GNU Affero General Public License
# along with this program.  If not, see .
# 

distanceMatrix = This table contains an overview of the alignments \
visualized here. Each cell shows the total cost of the \
respective alignment (row sequence versus column sequence). \
The background color also visualizes the cost: Green is for \
costs close to zero, red for costs close to one, yellow for \
costs around 0.5.\
If you click on the cost the respective \
alignment will be visualized in detail on the bottom of the \
page.
checkboxes = Uncheck boxes to hide the respective column in the alignment \
visualization. The number in brackets behind the listed keywords shows the \
weight of the respective keyword in the alignment.
alignment = The following table visualizes an alignment path between two \
sequences. Each row of the table is one alignment operation (e.g. a \
replacement of a node in the first sequence with a node in the second \
sequence, a deletion of a node in the first sequence, an insertion of a node \
from the second sequence into the first sequence and so on).\
As a reminder: An alignment is an application of subsequent operations to \
the first sequence transform it into the second sequence. Each of those \
operations has a cost. \
This total operation cost is visualized in the column "total", an index for \
the current operation is visualized in the column "step" and the column \
"operation" informs you what kind of operation has been applied in this \
step.\
Next follow the columns for the alignment of each keyword. The \
TCSAlignmentToolbox architecture treats each operation cost as a weighted sum \
of keyword-wise comparator costs: If we have two keywords, "alpha" and "beta" \
with the weights 0.6 and 0.4 respectively and we apply a replacement operation \
in the current step then the total operation cost will be 0.6 times the \
comparator cost for replacing the value for "alpha" in the current node of the \
first sequence with the value for "alpha" in the current node of the second \
sequence plus 0.4 times the comparator cost for replacing the value for "beta" \
in the current node of the first sequence with the value for "beta" in the \
current node of the second sequence. Each column shows the value for the \
respective keyword in both sequences as well as the comparator cost for the \
respective keyword.\
Last come additional columns that users might have specified for this \
visualization.\
Again the color of cost cells is another visualization for the cost: Green \
is for costs close to zero, red for costs close to one, yellow for \
costs around 0.5.