Biomarkers comparer class
References
Trevisan et al 2012. Submitted to AC.
- See also
- sigfun.m
Definition at line 7 of file biocomparer.m.
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| function | go (in o, in A, in B, in WA, in WB) |
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| function | biocomparer () |
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| function | get_description (in o, in flag_short) |
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| function | setbatch (in o, in params) |
| | Sets several properties of an object at once. More...
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| function | get_methodname (in o, in flag_short) |
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| function | get_report (in o) |
| | Object reports are plain text. HTML would be cool but c'mon, we don't need that sophistication. More...
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| function | get_html (in o, in flag_stylesheet) |
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| function | get_params (in o, in data) |
| | Calls Parameters GUI. More...
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| function | extract_log (in o) |
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| function | get_ancestry (in o, in flag_title) |
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| Property | classtitle |
| | Class Title. Should have a descriptive name, as short as possible. More...
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| Property | short |
| | Short for the method name. More...
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| Property | flag_params |
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| Property | flag_ui |
| | (GUI setting) Whether to "publish" in blockmenu and datatool. Note that a class can be "published" without a GUI (set flag_params=0 in this case, at the class constructor). More...
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| Property | moreactions |
| | (GUI setting) String cell containing names of methods that may be called from the GUIs More...
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| function biocomparer::biocomparer |
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| function irobj::do_get_html |
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in |
o | ) |
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protectedinherited |
Abstract. HTML inner body.
| function irobj::do_get_report |
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in |
o | ) |
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protectedinherited |
| function irobj::extract_log |
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in |
o | ) |
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inherited |
- Parameters
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- Returns
- [o, log]
| function irobj::get_ancestry |
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in |
o, |
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in |
flag_title |
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) |
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inherited |
| function irobj::get_description |
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in |
o, |
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in |
flag_short |
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) |
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inherited |
Returns description string
Precedence according with flag_short:
- 0: title > short > classtitle
- 1: short > title > classtitle
- Parameters
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| flag_short=0 | I am sealing this to make sure that no class will try to improvise on this function. |
| function irobj::get_html |
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in |
o, |
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in |
flag_stylesheet |
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) |
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inherited |
- Parameters
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| flag_stylesheet=1 | Whether to include the stylesheet in the HTML |
| function irobj::get_methodname |
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in |
o, |
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in |
flag_short |
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) |
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inherited |
This is used only to compose sequence string e.g. xxx->yyy->zzz
- Parameters
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| function irobj::get_params |
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in |
o, |
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in |
data |
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) |
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inherited |
Calls Parameters GUI.
If flag_params, tries uip_<class>.m. If fails, tries uip_<ancestor>.m and so on
| function irobj::get_report |
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in |
o | ) |
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inherited |
Object reports are plain text. HTML would be cool but c'mon, we don't need that sophistication.
| function biocomparer::go |
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in |
o, |
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in |
A, |
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in |
B, |
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in |
WA, |
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in |
WB |
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) |
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- Parameters
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| A | First set of wavenumbers |
| B | Second set of wavenumbers |
| WA | (Optional) Weights of first set of wavenumbers. If not supplied or supplied as "[]", all weights will be considered the same. The weight scale is irrelevant. |
| WB | (Optional) Weights of second set of wavenumbers. If not supplied or supplied as "[]", all weights will be considered the same. The weight scale is irrelevant. |
- Returns
- [matches, finalindex] the "matches" structure has the following fields:
agreement*weight The "agreement" will be calculated by a logistic sigmoid function (that of shape 1/(1+exp(x)))
| static function biocomparer::internal_compare_biomarkers |
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in |
A, |
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in |
B, |
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in |
WA, |
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in |
WB, |
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in |
hh |
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) |
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staticprotected |
| function irobj::setbatch |
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in |
o, |
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in |
params |
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) |
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inherited |
Sets several properties of an object at once.
- Parameters
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| o | |
| params | Cell followint the pattern{'property1', value1, 'property2', value2, ...} |
| Property irobj::classtitle |
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protectedinherited |
Class Title. Should have a descriptive name, as short as possible.
Definition at line 50 of file irobj.m.
=[0, .8, 0]. multipurpose feature, routines may use it for different things. Major use is to change the background of objtool and blockmenu. See also classes_html.m
Definition at line 42 of file irobj.m.
| Property irobj::flag_params |
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protectedinherited |
=1. (GUI setting) Whether to call a GUI when the block is selected in blockmenu.m . If true, a routine called "uip_"<class name> will be called.
Definition at line 57 of file irobj.m.
(GUI setting) Whether to "publish" in blockmenu and datatool. Note that a class can be "published" without a GUI (set flag_params=0 in this case, at the class constructor).
Definition at line 60 of file irobj.m.
| Property biocomparer::flag_use_weights |
=1. Whether to use the weights that are passed to go()
Definition at line 17 of file biocomparer.m.
| Property biocomparer::halfheight |
=20. "half-height" distance between biomarkers. This is the distance in x-values (wavenumbers) where the degree of agreement will be considered to be 50%
Definition at line 14 of file biocomparer.m.
| Property irobj::moreactions |
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protectedinherited |
(GUI setting) String cell containing names of methods that may be called from the GUIs
Definition at line 63 of file irobj.m.
Short for the method name.
Definition at line 53 of file irobj.m.
The documentation for this class was generated from the following file:
Inheritance diagram for biocomparer:
1.8.9.1