1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<!--Converted with LaTeX2HTML 2002-2-1 (1.71)
original version by: Nikos Drakos, CBLU, University of Leeds
* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
* with significant contributions from:
Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
<HTML>
<HEAD>
<TITLE>How to add new thermodynamic model</TITLE>
<META NAME="description" CONTENT="How to add new thermodynamic model">
<META NAME="keywords" CONTENT="DeveloppersGuide">
<META NAME="resource-type" CONTENT="document">
<META NAME="distribution" CONTENT="global">
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="LaTeX2HTML v2002-2-1">
<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
<LINK REL="STYLESHEET" HREF="DeveloppersGuide.css">
<LINK REL="next" HREF="node9.html">
<LINK REL="previous" HREF="node4.html">
<LINK REL="up" HREF="DeveloppersGuide.html">
<LINK REL="next" HREF="node6.html">
</HEAD>
<BODY >
<DIV CLASS="navigation"><!--Navigation Panel-->
<A NAME="tex2html111"
HREF="node6.html">
<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
SRC="/usr/share/latex2html/icons/next.png"></A>
<A NAME="tex2html107"
HREF="DeveloppersGuide.html">
<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
SRC="/usr/share/latex2html/icons/up.png"></A>
<A NAME="tex2html101"
HREF="node4.html">
<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
SRC="/usr/share/latex2html/icons/prev.png"></A>
<A NAME="tex2html109"
HREF="node1.html">
<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
SRC="/usr/share/latex2html/icons/contents.png"></A>
<BR>
<B> Next:</B> <A NAME="tex2html112"
HREF="node6.html">Thermodynamic model for Crick's</A>
<B> Up:</B> <A NAME="tex2html108"
HREF="DeveloppersGuide.html">MELTING - development guide</A>
<B> Previous:</B> <A NAME="tex2html102"
HREF="node4.html">How to add new</A>
<B> <A NAME="tex2html110"
HREF="node1.html">Contents</A></B>
<BR>
<BR></DIV>
<!--End of Navigation Panel-->
<H1><A NAME="SECTION00050000000000000000">
How to add new thermodynamic model</A>
</H1>
<P>
<SPAN CLASS="textbf">1)</SPAN> Creates a new class which implements the PatternComputationMethod interface or which extends the
PatternComputation class in the melting.patternModels package.
<BR>
<BR>
If the structure computed by the new class is already registered by the program, you can create your class
in the appropriate package (cngPatterns, cricksPair, InternalLoops, longBulge, longDanglingEnds,
secondDanglingEnds, singleBulge, singleDanglingEnds, singleMismatch, specificAcids, tandemMismatches or wobble).
<BR>
<BR>
The PatternComputation class contains all the base implementations of each PatternComputationMethod method
except for this function : <SPAN CLASS="textit">boolean isApplicable(Environment environment, int pos1, int pos2)</SPAN>.
<BR>
<BR>
You have to implement this method to compute the enthalpy and entropy of a motif in the duplex.
You also have to override the function <SPAN CLASS="textit">boolean isApplicable(Environment environment, int pos1,int pos2)</SPAN>
to define the conditions of application of the new thermodynamic model.
<BR>
<BR>
<P>
<SPAN CLASS="textbf">2)</SPAN> Always register the new model in the RegisterMethod class in the melting.configuration package.
Depending on which structure in the duplex your new model computes, you will have to add one of these
following lines :
<P>
<UL>
<LI><SPAN CLASS="textit">New model for Crick's pairs computation</SPAN>
<P>
<PRE>
private void initialiseCricksMethods(){
[...]
// To map the model name to the class which
// implements it.
cricksMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for single mismatch computation</SPAN>
<P>
<PRE>
private void initialiseSingleMismatchMethods(){
[...]
// To map the model name to the class which implements it.
singleMismatchMethod.put("model-Name", ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for tandem mismatches computation</SPAN>
<P>
<PRE>
private void initialiseTandemMismatchMethods(){
[...]
// To map the model name to the class which
// implements it.
tandemMismatchMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for GU base pairs computation</SPAN>
<P>
<PRE>
private void initialiseWobbleMismatchMethods(){
[...]
// To map the model name to the class which
// implements it.
wobbleMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for internal loop computation</SPAN>
<P>
<PRE>
private void initialiseInternalLoopMethods(){
[...]
// To map the model name to the class which
// implements it.
internalLoopMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for single bulge loop computation</SPAN>
<P>
<PRE>
private void initialiseSingleBulgeLoopMethods(){
[...]
// To map the model name to the class which
// implements it.
singleBulgeLoopMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for long bulge loop computation</SPAN>
<P>
<PRE>
private void initialiseLongBulgeLoopMethods(){
[...]
// To map the model name to the class which
// implements it.
longBulgeLoopMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for single dangling end computation</SPAN>
<P>
<PRE>
private void initialiseSingleDanglingEndMethods(){
[...]
// To map the model name to the class which
// implements it.
singleDanglingEndMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for double dangling end computation</SPAN>
<P>
<PRE>
private void initialiseDoubleDanglingEndMethods(){
[...]
// To map the model name to the class which
// implements it.
doubleDanglingEndMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for long dangling end computation</SPAN>
<P>
<PRE>
private void initialiseLongDanglingEndMethods(){
[...]
// To map the model name to the class which
// implements it.
longDanglingEndMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for CNG repeats computation</SPAN>
<P>
<PRE>
private void initialiseCNGRepeatsMethods(){
[...]
// To map the model name to the class which
// implements it.
CNGRepeatsMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for inosine computation</SPAN>
<P>
<PRE>
private void initialiseInosineMethods(){
[...]
// To map the model name to the class
// which implements it.
inosineMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for azobenzene computation</SPAN>
<P>
<PRE>
private void initialiseAzobenzeneMethods(){
[...]
// To map the model name to the class
// which implements it.
azobenzeneMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for locked nucleic acid computation</SPAN>
<P>
<PRE>
private void initialiseLockedAcidMethods(){
[...]
// To map the model name to the class which
// implements it.
lockedAcidMethod.put("model-Name",
ClassName.class);
}
</PRE>
<P>
</LI>
<LI><SPAN CLASS="textit">New model for hydroxyadenosine computation</SPAN>
<P>
<PRE>
private void initialiseHydroxyadenosineMethods(){
[...]
// To map the model name to the class which
// implements it.
hydroxyadenosineMethod.put("model-Name",
ClassName.class);
}
</PRE>
</LI>
</UL>
<P>
<SPAN CLASS="textbf">3)</SPAN> Create a <SPAN CLASS="textit">public static String defaultFileName</SPAN> as instance variable of the class. It represents
the name of the XML file containing the thermodynamic parameters for this model. You must print it if the
user requires the verbose mode. You can create another <SPAN CLASS="textit">public static String</SPAN> which contains the
thermodynamic formula of the model and print it during the verbose mode.
<BR>
<BR>
For each message you want to print during the verbose mode, you must write this line :
<SPAN CLASS="textit">OptionManagement.meltingLogger.log(Level.FINE, "message to print");</SPAN>
<BR>
<BR>
<P>
<SPAN CLASS="textbf">4)</SPAN> You always must override or implement this function : <SPAN CLASS="textit">void initialiseFileName(String methodName)</SPAN>.
It is necessary to write that the new class can use the thermodynamic parameters of its default File or
use the thermodynamic parameters of another file required by the user.
<P>
<PRE>
@Override
public void initialiseFileName(String methodName){
super.initialiseFileName(methodName);
if (this.fileName == null){
this.fileName = defaultFileName; // The public static String
// of this class.
}
}
</PRE>
<P>
Some base implementations have been written for some non specific thermodynamic models, maybe your new
class can extend one of the following base implementations. (but you always have to do the steps 1 to 4)
<P>
<BR><HR>
<!--Table of Child-Links-->
<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
<UL CLASS="ChildLinks">
<LI><UL>
<LI><A NAME="tex2html113"
HREF="node6.html">Thermodynamic model for Crick's pairs computation</A>
<LI><A NAME="tex2html114"
HREF="node7.html">Thermodynamic model for single bulge loop computation</A>
<LI><A NAME="tex2html115"
HREF="node8.html">Thermodynamic model for inosine computation</A>
</UL></UL>
<!--End of Table of Child-Links-->
<DIV CLASS="navigation"><HR>
<!--Navigation Panel-->
<A NAME="tex2html111"
HREF="node6.html">
<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
SRC="/usr/share/latex2html/icons/next.png"></A>
<A NAME="tex2html107"
HREF="DeveloppersGuide.html">
<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
SRC="/usr/share/latex2html/icons/up.png"></A>
<A NAME="tex2html101"
HREF="node4.html">
<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
SRC="/usr/share/latex2html/icons/prev.png"></A>
<A NAME="tex2html109"
HREF="node1.html">
<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
SRC="/usr/share/latex2html/icons/contents.png"></A>
<BR>
<B> Next:</B> <A NAME="tex2html112"
HREF="node6.html">Thermodynamic model for Crick's</A>
<B> Up:</B> <A NAME="tex2html108"
HREF="DeveloppersGuide.html">MELTING - development guide</A>
<B> Previous:</B> <A NAME="tex2html102"
HREF="node4.html">How to add new</A>
<B> <A NAME="tex2html110"
HREF="node1.html">Contents</A></B> </DIV>
<!--End of Navigation Panel-->
<ADDRESS>
Computational Neurobiology
2009-08-24
</ADDRESS>
</BODY>
</HTML>
|
