Mercurial > repos > eduardo > predsi
comparison doc/jspp/SearchMatrix.html @ 0:cfd8864953c9 draft
planemo upload
| author | eduardo |
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| date | Thu, 29 Sep 2016 12:00:13 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:cfd8864953c9 |
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| 1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd"> | |
| 2 <!--NewPage--> | |
| 3 <HTML> | |
| 4 <HEAD> | |
| 5 <!-- Generated by javadoc on Fri Feb 13 17:31:23 CET 2004 --> | |
| 6 <META http-equiv="Content-Type" content="text/html; charset=windows-1252"> | |
| 7 <TITLE> | |
| 8 SearchMatrix | |
| 9 </TITLE> | |
| 10 <META NAME="keywords" CONTENT="jspp.SearchMatrix,SearchMatrix class"> | |
| 11 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style"> | |
| 12 </HEAD> | |
| 13 <SCRIPT> | |
| 14 function asd() | |
| 15 { | |
| 16 parent.document.title="SearchMatrix"; | |
| 17 } | |
| 18 </SCRIPT> | |
| 19 <BODY BGCOLOR="white" onload="asd();"> | |
| 20 | |
| 21 <!-- ========== START OF NAVBAR ========== --> | |
| 22 <A NAME="navbar_top"><!-- --></A> | |
| 23 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0"> | |
| 24 <TR> | |
| 25 <TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> | |
| 26 <A NAME="navbar_top_firstrow"><!-- --></A> | |
| 27 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3"> | |
| 28 <TR ALIGN="center" VALIGN="top"> | |
| 29 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD> | |
| 30 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD> | |
| 31 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD> | |
| 32 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD> | |
| 33 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD> | |
| 34 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD> | |
| 35 </TR> | |
| 36 </TABLE> | |
| 37 </TD> | |
| 38 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM> | |
| 39 </EM> | |
| 40 </TD> | |
| 41 </TR> | |
| 42 | |
| 43 <TR> | |
| 44 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2"> | |
| 45 <A HREF="../jspp/JSPP.html"><B>PREV CLASS</B></A> | |
| 46 <A HREF="../jspp/SignalPChecker.html"><B>NEXT CLASS</B></A></FONT></TD> | |
| 47 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2"> | |
| 48 <A HREF="../index.html" TARGET="_top"><B>FRAMES</B></A> | |
| 49 <A HREF="SearchMatrix.html" TARGET="_top"><B>NO FRAMES</B></A> | |
| 50 | |
| 51 <SCRIPT> | |
| 52 <!-- | |
| 53 if(window==top) { | |
| 54 document.writeln('<A HREF="../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>'); | |
| 55 } | |
| 56 //--> | |
| 57 </SCRIPT> | |
| 58 <NOSCRIPT> | |
| 59 <A HREF="../allclasses-noframe.html" TARGET=""><B>All Classes</B></A> | |
| 60 </NOSCRIPT> | |
| 61 </FONT></TD> | |
| 62 </TR> | |
| 63 <TR> | |
| 64 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2"> | |
| 65 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD> | |
| 66 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2"> | |
| 67 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD> | |
| 68 </TR> | |
| 69 </TABLE> | |
| 70 <!-- =========== END OF NAVBAR =========== --> | |
| 71 | |
| 72 <HR> | |
| 73 <!-- ======== START OF CLASS DATA ======== --> | |
| 74 <H2> | |
| 75 <FONT SIZE="-1"> | |
| 76 jspp</FONT> | |
| 77 <BR> | |
| 78 Class SearchMatrix</H2> | |
| 79 <PRE> | |
| 80 java.lang.Object | |
| 81 | | |
| 82 +--<B>jspp.SearchMatrix</B> | |
| 83 </PRE> | |
| 84 <DL> | |
| 85 <DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD> | |
| 86 </DL> | |
| 87 <HR> | |
| 88 <DL> | |
| 89 <DT>public class <B>SearchMatrix</B><DT>extends java.lang.Object<DT>implements java.io.Serializable</DL> | |
| 90 | |
| 91 <P> | |
| 92 <DL> | |
| 93 <DT><B>See Also:</B><DD><A HREF="../serialized-form.html" TARGET="jspp.SearchMatrix">Serialized Form</A></DL> | |
| 94 <HR> | |
| 95 | |
| 96 <P> | |
| 97 <!-- ======== NESTED CLASS SUMMARY ======== --> | |
| 98 | |
| 99 | |
| 100 <!-- =========== FIELD SUMMARY =========== --> | |
| 101 | |
| 102 | |
| 103 <!-- ======== CONSTRUCTOR SUMMARY ======== --> | |
| 104 | |
| 105 <A NAME="constructor_summary"><!-- --></A> | |
| 106 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> | |
| 107 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor"> | |
| 108 <TD COLSPAN=2><FONT SIZE="+2"> | |
| 109 <B>Constructor Summary</B></FONT></TD> | |
| 110 </TR> | |
| 111 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 112 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#SearchMatrix(int, int)">SearchMatrix</A></B>(int sequencelength, | |
| 113 int cleavageposition)</CODE> | |
| 114 | |
| 115 <BR> | |
| 116 constructs an empty SearchMatrix</TD> | |
| 117 </TR> | |
| 118 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 119 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#SearchMatrix(java.lang.String[], int)">SearchMatrix</A></B>(java.lang.String[] alignedsequences, | |
| 120 int cleavageposition)</CODE> | |
| 121 | |
| 122 <BR> | |
| 123 constructs a new SearchMatrix</TD> | |
| 124 </TR> | |
| 125 </TABLE> | |
| 126 | |
| 127 <!-- ========== METHOD SUMMARY =========== --> | |
| 128 | |
| 129 <A NAME="method_summary"><!-- --></A> | |
| 130 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> | |
| 131 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor"> | |
| 132 <TD COLSPAN=2><FONT SIZE="+2"> | |
| 133 <B>Method Summary</B></FONT></TD> | |
| 134 </TR> | |
| 135 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 136 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 137 <CODE> void</CODE></FONT></TD> | |
| 138 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#addSearchMatrix(jspp.SearchMatrix)">addSearchMatrix</A></B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> matrix)</CODE> | |
| 139 | |
| 140 <BR> | |
| 141 Adds a complete SearchMatrix object to this SearchMatrixThe length of both SearchMatrix must be the same, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </TD> | |
| 142 </TR> | |
| 143 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 145 <CODE> void</CODE></FONT></TD> | |
| 146 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#addSequence(java.lang.String)">addSequence</A></B>(java.lang.String sequence)</CODE> | |
| 147 | |
| 148 <BR> | |
| 149 Adds new sequences to the SearchMatrix. </TD> | |
| 150 </TR> | |
| 151 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 153 <CODE> int</CODE></FONT></TD> | |
| 154 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getCleavagePosition()">getCleavagePosition</A></B>()</CODE> | |
| 155 | |
| 156 <BR> | |
| 157 Returns the cleavage position.</TD> | |
| 158 </TR> | |
| 159 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 161 <CODE> double</CODE></FONT></TD> | |
| 162 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getCutOffScore()">getCutOffScore</A></B>()</CODE> | |
| 163 | |
| 164 <BR> | |
| 165 Returns the cutoff score</TD> | |
| 166 </TR> | |
| 167 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 169 <CODE> double</CODE></FONT></TD> | |
| 170 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getInformation(int)">getInformation</A></B>(int position)</CODE> | |
| 171 | |
| 172 <BR> | |
| 173 Returns the information contents of the specified position</TD> | |
| 174 </TR> | |
| 175 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 177 <CODE> int[][]</CODE></FONT></TD> | |
| 178 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getMatrix()">getMatrix</A></B>()</CODE> | |
| 179 | |
| 180 <BR> | |
| 181 Returns the alignment matrix</TD> | |
| 182 </TR> | |
| 183 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 184 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 185 <CODE> double</CODE></FONT></TD> | |
| 186 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getRawScore(java.lang.String)">getRawScore</A></B>(java.lang.String sequence)</CODE> | |
| 187 | |
| 188 <BR> | |
| 189 Returns the raw score</TD> | |
| 190 </TR> | |
| 191 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 192 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 193 <CODE> double</CODE></FONT></TD> | |
| 194 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getScore(java.lang.String)">getScore</A></B>(java.lang.String sequence)</CODE> | |
| 195 | |
| 196 <BR> | |
| 197 Returns the normalized score.</TD> | |
| 198 </TR> | |
| 199 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 200 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 201 <CODE> int</CODE></FONT></TD> | |
| 202 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getSequenceLength()">getSequenceLength</A></B>()</CODE> | |
| 203 | |
| 204 <BR> | |
| 205 </TD> | |
| 206 </TR> | |
| 207 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 208 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 209 <CODE> double</CODE></FONT></TD> | |
| 210 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#raw2normalizedScore(double)">raw2normalizedScore</A></B>(double rawscore)</CODE> | |
| 211 | |
| 212 <BR> | |
| 213 Transfers a raw score to a normalized score</TD> | |
| 214 </TR> | |
| 215 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 216 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 217 <CODE> void</CODE></FONT></TD> | |
| 218 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#removeSequence(java.lang.String)">removeSequence</A></B>(java.lang.String sequence)</CODE> | |
| 219 | |
| 220 <BR> | |
| 221 Removes a sequence from the SearchMatrix The sequence length must be the same as the initial weight matrix size, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </TD> | |
| 222 </TR> | |
| 223 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 224 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 225 <CODE> void</CODE></FONT></TD> | |
| 226 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#setFrequencyMatrix(jspp.SearchMatrix)">setFrequencyMatrix</A></B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> sequences)</CODE> | |
| 227 | |
| 228 <BR> | |
| 229 Method for considering the amino acid background</TD> | |
| 230 </TR> | |
| 231 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 232 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 233 <CODE> void</CODE></FONT></TD> | |
| 234 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#setFrequencyMatrix(java.lang.String[])">setFrequencyMatrix</A></B>(java.lang.String[] sequences)</CODE> | |
| 235 | |
| 236 <BR> | |
| 237 Method for considering the amino acid background</TD> | |
| 238 </TR> | |
| 239 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 240 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 241 <CODE> void</CODE></FONT></TD> | |
| 242 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#setLimits(double, double)">setLimits</A></B>(double cutoff, | |
| 243 double uppercutoff)</CODE> | |
| 244 | |
| 245 <BR> | |
| 246 Sets the limits for score normalization.</TD> | |
| 247 </TR> | |
| 248 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 249 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> | |
| 250 <CODE> void</CODE></FONT></TD> | |
| 251 <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#writeMatrix(java.io.File)">writeMatrix</A></B>(java.io.File file)</CODE> | |
| 252 | |
| 253 <BR> | |
| 254 Writes the content of this object as tabulator seperated values in a file</TD> | |
| 255 </TR> | |
| 256 </TABLE> | |
| 257 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A> | |
| 258 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> | |
| 259 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor"> | |
| 260 <TD><B>Methods inherited from class java.lang.Object</B></TD> | |
| 261 </TR> | |
| 262 <TR BGCOLOR="white" CLASS="TableRowColor"> | |
| 263 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD> | |
| 264 </TR> | |
| 265 </TABLE> | |
| 266 | |
| 267 <P> | |
| 268 | |
| 269 <!-- ============ FIELD DETAIL =========== --> | |
| 270 | |
| 271 | |
| 272 <!-- ========= CONSTRUCTOR DETAIL ======== --> | |
| 273 | |
| 274 <A NAME="constructor_detail"><!-- --></A> | |
| 275 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> | |
| 276 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor"> | |
| 277 <TD COLSPAN=1><FONT SIZE="+2"> | |
| 278 <B>Constructor Detail</B></FONT></TD> | |
| 279 </TR> | |
| 280 </TABLE> | |
| 281 | |
| 282 <A NAME="SearchMatrix(java.lang.String[], int)"><!-- --></A><H3> | |
| 283 SearchMatrix</H3> | |
| 284 <PRE> | |
| 285 public <B>SearchMatrix</B>(java.lang.String[] alignedsequences, | |
| 286 int cleavageposition)</PRE> | |
| 287 <DL> | |
| 288 <DD>constructs a new SearchMatrix | |
| 289 <P> | |
| 290 <DT><B>Parameters:</B><DD><CODE>alignedsequences</CODE> - String-Array of aligned sequences<DD><CODE>cleavageposition</CODE> - cleavage position inside the aligned sequences</DL> | |
| 291 <HR> | |
| 292 | |
| 293 <A NAME="SearchMatrix(int, int)"><!-- --></A><H3> | |
| 294 SearchMatrix</H3> | |
| 295 <PRE> | |
| 296 public <B>SearchMatrix</B>(int sequencelength, | |
| 297 int cleavageposition)</PRE> | |
| 298 <DL> | |
| 299 <DD>constructs an empty SearchMatrix | |
| 300 <P> | |
| 301 <DT><B>Parameters:</B><DD><CODE>sequencelength</CODE> - length of sequences (signalpeptide+mature protein)<DD><CODE>cleavageposition</CODE> - cleavageposition, normally the same length as signalpeptide</DL> | |
| 302 | |
| 303 <!-- ============ METHOD DETAIL ========== --> | |
| 304 | |
| 305 <A NAME="method_detail"><!-- --></A> | |
| 306 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> | |
| 307 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor"> | |
| 308 <TD COLSPAN=1><FONT SIZE="+2"> | |
| 309 <B>Method Detail</B></FONT></TD> | |
| 310 </TR> | |
| 311 </TABLE> | |
| 312 | |
| 313 <A NAME="getSequenceLength()"><!-- --></A><H3> | |
| 314 getSequenceLength</H3> | |
| 315 <PRE> | |
| 316 public int <B>getSequenceLength</B>()</PRE> | |
| 317 <DL> | |
| 318 <DD><DL> | |
| 319 </DL> | |
| 320 </DD> | |
| 321 <DD><DL> | |
| 322 | |
| 323 <DT><B>Returns:</B><DD>the sequence length of the aligned sequences</DL> | |
| 324 </DD> | |
| 325 </DL> | |
| 326 <HR> | |
| 327 | |
| 328 <A NAME="addSequence(java.lang.String)"><!-- --></A><H3> | |
| 329 addSequence</H3> | |
| 330 <PRE> | |
| 331 public void <B>addSequence</B>(java.lang.String sequence) | |
| 332 throws jspp.SequenceLengthException</PRE> | |
| 333 <DL> | |
| 334 <DD>Adds new sequences to the SearchMatrix. <p>The sequence length must be the same as the initial weight matrix size, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </p> | |
| 335 <P> | |
| 336 <DD><DL> | |
| 337 </DL> | |
| 338 </DD> | |
| 339 <DD><DL> | |
| 340 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the sequence to add to the matrix | |
| 341 <DT><B>Throws:</B> | |
| 342 <DD><CODE>jspp.SequenceLengthException</CODE></DL> | |
| 343 </DD> | |
| 344 </DL> | |
| 345 <HR> | |
| 346 | |
| 347 <A NAME="addSearchMatrix(jspp.SearchMatrix)"><!-- --></A><H3> | |
| 348 addSearchMatrix</H3> | |
| 349 <PRE> | |
| 350 public void <B>addSearchMatrix</B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> matrix) | |
| 351 throws jspp.SequenceLengthException</PRE> | |
| 352 <DL> | |
| 353 <DD>Adds a complete SearchMatrix object to this SearchMatrix<p>The length of both SearchMatrix must be the same, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </p> | |
| 354 <P> | |
| 355 <DD><DL> | |
| 356 </DL> | |
| 357 </DD> | |
| 358 <DD><DL> | |
| 359 <DT><B>Parameters:</B><DD><CODE>matrix</CODE> - SearchMatrix to add to this SearchMatrix | |
| 360 <DT><B>Throws:</B> | |
| 361 <DD><CODE>jspp.SequenceLengthException</CODE></DL> | |
| 362 </DD> | |
| 363 </DL> | |
| 364 <HR> | |
| 365 | |
| 366 <A NAME="removeSequence(java.lang.String)"><!-- --></A><H3> | |
| 367 removeSequence</H3> | |
| 368 <PRE> | |
| 369 public void <B>removeSequence</B>(java.lang.String sequence) | |
| 370 throws jspp.SequenceLengthException</PRE> | |
| 371 <DL> | |
| 372 <DD>Removes a sequence from the SearchMatrix <p>The sequence length must be the same as the initial weight matrix size, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </p> | |
| 373 <P> | |
| 374 <DD><DL> | |
| 375 </DL> | |
| 376 </DD> | |
| 377 <DD><DL> | |
| 378 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - Sequence to remove from the SearchMatrix | |
| 379 <DT><B>Throws:</B> | |
| 380 <DD><CODE>jspp.SequenceLengthException</CODE></DL> | |
| 381 </DD> | |
| 382 </DL> | |
| 383 <HR> | |
| 384 | |
| 385 <A NAME="getCleavagePosition()"><!-- --></A><H3> | |
| 386 getCleavagePosition</H3> | |
| 387 <PRE> | |
| 388 public int <B>getCleavagePosition</B>()</PRE> | |
| 389 <DL> | |
| 390 <DD>Returns the cleavage position. | |
| 391 <P> | |
| 392 <DD><DL> | |
| 393 </DL> | |
| 394 </DD> | |
| 395 <DD><DL> | |
| 396 | |
| 397 <DT><B>Returns:</B><DD>the cleavage position.</DL> | |
| 398 </DD> | |
| 399 </DL> | |
| 400 <HR> | |
| 401 | |
| 402 <A NAME="setLimits(double, double)"><!-- --></A><H3> | |
| 403 setLimits</H3> | |
| 404 <PRE> | |
| 405 public void <B>setLimits</B>(double cutoff, | |
| 406 double uppercutoff)</PRE> | |
| 407 <DL> | |
| 408 <DD>Sets the limits for score normalization.<p>Scores are normalized in a linear manner, where cutoff is normalized to 0.5 and uppercuttoff is normalized to 1.0.</p> | |
| 409 <P> | |
| 410 <DD><DL> | |
| 411 </DL> | |
| 412 </DD> | |
| 413 <DD><DL> | |
| 414 <DT><B>Parameters:</B><DD><CODE>cutoff</CODE> - cutoff-score will be normalized to 0.5.<DD><CODE>uppercutoff</CODE> - upper-limit will be normalized to 1.0.</DL> | |
| 415 </DD> | |
| 416 </DL> | |
| 417 <HR> | |
| 418 | |
| 419 <A NAME="getScore(java.lang.String)"><!-- --></A><H3> | |
| 420 getScore</H3> | |
| 421 <PRE> | |
| 422 public double <B>getScore</B>(java.lang.String sequence) | |
| 423 throws jspp.SequenceLengthException</PRE> | |
| 424 <DL> | |
| 425 <DD>Returns the normalized score.<p>Method <A HREF="../jspp/SearchMatrix.html#setLimits(double, double)"><CODE>setLimits()</CODE></A> should be called before.</p> | |
| 426 <P> | |
| 427 <DD><DL> | |
| 428 </DL> | |
| 429 </DD> | |
| 430 <DD><DL> | |
| 431 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - sequence for score calculation | |
| 432 <DT><B>Returns:</B><DD>a normalized score for <CODE>sequence</CODE> | |
| 433 <DT><B>Throws:</B> | |
| 434 <DD><CODE>jspp.SequenceLengthException</CODE></DL> | |
| 435 </DD> | |
| 436 </DL> | |
| 437 <HR> | |
| 438 | |
| 439 <A NAME="getRawScore(java.lang.String)"><!-- --></A><H3> | |
| 440 getRawScore</H3> | |
| 441 <PRE> | |
| 442 public double <B>getRawScore</B>(java.lang.String sequence) | |
| 443 throws jspp.SequenceLengthException</PRE> | |
| 444 <DL> | |
| 445 <DD>Returns the raw score | |
| 446 <P> | |
| 447 <DD><DL> | |
| 448 </DL> | |
| 449 </DD> | |
| 450 <DD><DL> | |
| 451 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - sequence for score calculation | |
| 452 <DT><B>Returns:</B><DD>the raw score | |
| 453 <DT><B>Throws:</B> | |
| 454 <DD><CODE>jspp.SequenceLengthException</CODE></DL> | |
| 455 </DD> | |
| 456 </DL> | |
| 457 <HR> | |
| 458 | |
| 459 <A NAME="getCutOffScore()"><!-- --></A><H3> | |
| 460 getCutOffScore</H3> | |
| 461 <PRE> | |
| 462 public double <B>getCutOffScore</B>()</PRE> | |
| 463 <DL> | |
| 464 <DD>Returns the cutoff score | |
| 465 <P> | |
| 466 <DD><DL> | |
| 467 </DL> | |
| 468 </DD> | |
| 469 <DD><DL> | |
| 470 | |
| 471 <DT><B>Returns:</B><DD>the cutoff score</DL> | |
| 472 </DD> | |
| 473 </DL> | |
| 474 <HR> | |
| 475 | |
| 476 <A NAME="raw2normalizedScore(double)"><!-- --></A><H3> | |
| 477 raw2normalizedScore</H3> | |
| 478 <PRE> | |
| 479 public double <B>raw2normalizedScore</B>(double rawscore)</PRE> | |
| 480 <DL> | |
| 481 <DD>Transfers a raw score to a normalized score | |
| 482 <P> | |
| 483 <DD><DL> | |
| 484 </DL> | |
| 485 </DD> | |
| 486 <DD><DL> | |
| 487 <DT><B>Parameters:</B><DD><CODE>rawscore</CODE> - the raw score | |
| 488 <DT><B>Returns:</B><DD>the normalized score</DL> | |
| 489 </DD> | |
| 490 </DL> | |
| 491 <HR> | |
| 492 | |
| 493 <A NAME="getInformation(int)"><!-- --></A><H3> | |
| 494 getInformation</H3> | |
| 495 <PRE> | |
| 496 public double <B>getInformation</B>(int position) | |
| 497 throws jspp.SequenceLengthException</PRE> | |
| 498 <DL> | |
| 499 <DD>Returns the information contents of the specified position | |
| 500 <P> | |
| 501 <DD><DL> | |
| 502 </DL> | |
| 503 </DD> | |
| 504 <DD><DL> | |
| 505 <DT><B>Parameters:</B><DD><CODE>position</CODE> - the weight matrix position | |
| 506 <DT><B>Returns:</B><DD>the information content of specified weight matrix position | |
| 507 <DT><B>Throws:</B> | |
| 508 <DD><CODE>jspp.SequenceLengthException</CODE></DL> | |
| 509 </DD> | |
| 510 </DL> | |
| 511 <HR> | |
| 512 | |
| 513 <A NAME="getMatrix()"><!-- --></A><H3> | |
| 514 getMatrix</H3> | |
| 515 <PRE> | |
| 516 public int[][] <B>getMatrix</B>()</PRE> | |
| 517 <DL> | |
| 518 <DD>Returns the alignment matrix | |
| 519 <P> | |
| 520 <DD><DL> | |
| 521 </DL> | |
| 522 </DD> | |
| 523 <DD><DL> | |
| 524 | |
| 525 <DT><B>Returns:</B><DD>the alignment matrix</DL> | |
| 526 </DD> | |
| 527 </DL> | |
| 528 <HR> | |
| 529 | |
| 530 <A NAME="setFrequencyMatrix(java.lang.String[])"><!-- --></A><H3> | |
| 531 setFrequencyMatrix</H3> | |
| 532 <PRE> | |
| 533 public void <B>setFrequencyMatrix</B>(java.lang.String[] sequences)</PRE> | |
| 534 <DL> | |
| 535 <DD>Method for considering the amino acid background | |
| 536 <P> | |
| 537 <DD><DL> | |
| 538 </DL> | |
| 539 </DD> | |
| 540 <DD><DL> | |
| 541 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - array of Strings containing sequences of dependent organism / group</DL> | |
| 542 </DD> | |
| 543 </DL> | |
| 544 <HR> | |
| 545 | |
| 546 <A NAME="setFrequencyMatrix(jspp.SearchMatrix)"><!-- --></A><H3> | |
| 547 setFrequencyMatrix</H3> | |
| 548 <PRE> | |
| 549 public void <B>setFrequencyMatrix</B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> sequences)</PRE> | |
| 550 <DL> | |
| 551 <DD>Method for considering the amino acid background | |
| 552 <P> | |
| 553 <DD><DL> | |
| 554 </DL> | |
| 555 </DD> | |
| 556 <DD><DL> | |
| 557 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - sequences stored in a SearchMatrix object</DL> | |
| 558 </DD> | |
| 559 </DL> | |
| 560 <HR> | |
| 561 | |
| 562 <A NAME="writeMatrix(java.io.File)"><!-- --></A><H3> | |
| 563 writeMatrix</H3> | |
| 564 <PRE> | |
| 565 public void <B>writeMatrix</B>(java.io.File file) | |
| 566 throws java.io.IOException</PRE> | |
| 567 <DL> | |
| 568 <DD>Writes the content of this object as tabulator seperated values in a file | |
| 569 <P> | |
| 570 <DD><DL> | |
| 571 </DL> | |
| 572 </DD> | |
| 573 <DD><DL> | |
| 574 <DT><B>Parameters:</B><DD><CODE>file</CODE> - the output file | |
| 575 <DT><B>Throws:</B> | |
| 576 <DD><CODE>java.io.IOException</CODE></DL> | |
| 577 </DD> | |
| 578 </DL> | |
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