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<html>
<head>
<title>CaGe -- Output Options</title>
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<h1>Output Options</h1>
<p>After choosing
a generator and setting all its options, the final step is to tell CaGe
which kind(s) of embeddings you want (2D and/or 3D) and whether you want
to visually inspect results or run a background task to store the complete
result set in a file.</p>
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<p><br>
In the Output Options window
many controls are actually inivisible until you make choices that
reveal them. All you see initially are the <b>prefilter checkbox</b>,
the <b>dimension checkboxes</b>
(labelled "3D/2D representation") and, for both dimensions,
the <b>output mode radio buttons</b>, named "Viewer" and "File/Pipe".
We could have hidden these radio buttons as well, but they offer a shortcut:
Click either "Viewer" or "File/Pipe" for any dimension,
and the respective dimension checkbox will be selected automatically,
saving one click.</p>
<p>The topmost
checkbox, "Pre-filter Graphs", will activate a text input when
clicked. You are expected to enter a command here, and this command will
be connected to the generator's output using a pipe.
The command will therefore be able to read graphs on standard input as
they come from the generator (which generally will be non-embedded graphs),
and CaGe will expect to read some graphs, in one of the <a href="technical.html#formats">formats</a>
supported by CaGe, from the filter command's standard output. (Your command
can itself be a "pipeline" -- see <a href="#pipeline">below</a>
for more details.)</p>
</td>
<td><br>
<a href="Images/output.png" target="_blank" onClick="return imageWindow (this, 723, 495, 'output options -- initial state');"><img height="272" width="400" src="Images/output_small.png" border="0" alt="output options -- initial state"></a></td>
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<h2><br><a name="viewer_output"></a>Viewer output</h2>
<p>Our second
screenshot shows the Output Options window after the two "Viewer"
radio buttons for 2D and 3D have been clicked. Just below each of these
radio buttons, a row of <b>viewer checkboxes</b> has appeared. Select
any number of these checkboxes to choose one or more viewers for each
dimension. CaGe will not let you deselect all viewer checkboxes, you have
to uncheck the respective dimension checkbox instead. If one viewer is
selected and you want to switch to another, you would have to select that
other viewer first and then deselect the current one, an unintuitive clicking
sequence for many users. But there is a shortcut: You can <i>shift-click</i>
a viewer to select it "exclusively", deselecting all other viewers.</p>
<p>The "text
viewer" shows all coordinates (2D and 3D) that you have chosen to
produce, in one window. Therefore, the "text viewer" checkboxes
shown in the 3D and 2D areas refer to the same viewer window. Deselecting
the "text viewer" checkbox in one dimension will also deselect
it in the other. If the text viewer has been the only selected viewer
in that other dimension (it won't be in the dimension where CaGe has let
you deselect it), CaGe will deselect that other dimension altogether.</p>
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<td><br><a href="Images/output2.png" target="_blank" onClick="return imageWindow (this, 723, 495, 'viewer output options');"><img height="272" width="400" src="Images/output2_small.png" border="0" alt="viewer output options"></a></td>
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<h2><br><a name="file_output"></a>File output</h2>
<p>In the third
screenshot you see all the controls that appear, in place of the viewer
checkboxes, if you select the "File/Pipe" checkboxes and/or
the "Adjacency information" checkbox (which you might call the
zero dimension checkbox -- there is no zero-D viewer and therefore no
choice of viewer vs. file output for "adjacency"). Whereever
you choose file or pipe output, you are asked for the <a href="#destinations">destination</a>
and the format to use. For each generated graph, CaGe will create any
requested embeddings and write the embedded graph to the given destinations
in the selected formats. In the screenshot, the format box for 3D has
been clicked on to reveal the available 3D formats. CaGe actually uses
just a small <a href="technical.html#PDB_CML">subset</a> of both the PDB
and CML languages.</p>
<h2><a name="destinations"></a>Where your data is saved</h2>
<p>You supply
all save destinations via a text field. Normally this will be interpreted
as a filename, relative to the directory in which the generation process
is run (see <b><font face="Courier New, Courier, mono">CaGe.Generators.RunDir</font></b>
in the configuration file <font face="Courier New, Courier, mono">CaGe.ini</font>).
If you start the destination with the '|' character, it will be interpreted
as a pipeline. CaGe will start this pipeline and write to its standard
input.</p>
<p><a name="pipeline"></a>A
<b>pipeline</b> is a sequence of commands, separated by '|' characters,
with each command's standard output connected to the next command's standard
input --, but no other shell interpretation will be performed unless you
call the shell as part of the command. All pipelines are also run in the
directory given by <b><font face="Courier New, Courier, mono">CaGe.Generators.RunDir</font></b>
in <font face="Courier New, Courier, mono">CaGe.ini</font>.</p>
<h2>Either viewer output or file output</h2>
<p>You can not
select file output for some dimensions and viewer output for some others.
CaGe will disable the "Next" button if you try. Remember that
the "zero" dimension, adjacency information, only allows file
output.</p>
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<td><br>
<a href="Images/output3.png" target="_blank" onClick="return imageWindow (this, 723, 495, 'file output options');"><img height="272" width="400" src="Images/output3_small.png" border="0" alt="file output options"></a></td>
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