📄 seq__tokenizer_8h-source.html
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<a name="l00158"></a>00158 <span class="keyword">delete</span> p;<a name="l00159"></a>00159 <a name="l00160"></a>00160 }<span class="comment">//end if(vat_hmap.find())</span><a name="l00161"></a>00161 <span class="keywordflow">else</span> {<a name="l00162"></a>00162 <span class="comment">//create a new vat & insert it</span><a name="l00163"></a>00163 svat=<span class="keyword">new</span> <a class="code" href="classvat.html">VAT</a>();<a name="l00164"></a>00164 <span class="keyword">typename</span> VAT::INSTANCES new_tidlist;<a name="l00165"></a>00165 new_tidlist.push_back(<a class="code" href="classseq__instance.html">INSTANCE</a>(ts,sequence_pos));<a name="l00166"></a>00166 svat->push_back(make_pair(tid, new_tidlist));<a name="l00167"></a>00167 <span class="keywordflow">if</span>(!vat_hmap.add_vat(p, svat)) {<a name="l00168"></a>00168 cerr<<<span class="stringliteral">"tokenizer.get_length_one: add_vat failed"</span><<endl;<a name="l00169"></a>00169 <span class="keywordflow">return</span> -1;<a name="l00170"></a>00170 }<a name="l00171"></a>00171 freq_pats.push_back(p);<a name="l00172"></a>00172 }<span class="comment">//end else</span><a name="l00173"></a>00173 <a name="l00174"></a>00174 }<span class="comment">//end switch</span><a name="l00175"></a>00175 <a name="l00176"></a>00176 }<span class="comment">//end while</span><a name="l00177"></a>00177 <a name="l00178"></a>00178 }<span class="keywordflow">while</span>(<span class="keyword">true</span>);<a name="l00179"></a>00179 <a name="l00180"></a>00180 <span class="keywordflow">return</span> -1;<a name="l00181"></a>00181 }<span class="comment">//end parse_next_trans()</span><a name="l00182"></a>00182 <a name="l00183"></a>00183 <span class="keyword">private</span>:<a name="l00184"></a>00184 <span class="keywordtype">int</span> MAXLINE; <a name="l00185"></a>00185 <a class="code" href="classelement__parser.html">element_parser<V_T></a> el_prsr; <a name="l00187"></a>00187 }; <span class="comment">//end class seq_tokenizer</span><a name="l00188"></a>00188 <a name="l00189"></a>00189 <span class="keyword">template</span><<span class="keyword">class</span> PP, <span class="keyword">typename</span> MP, <span class="keyword">typename</span> TP, <span class="keyword">typename</span> PAT_ST, <span class="keyword">template</span><<span class="keyword">typename</span>, <span class="keyword">typename</span>, <span class="keyword">typename</span>, <span class="keyword">template</span> <<span class="keyword">typename</span>> <span class="keyword">class </span>> <span class="keyword">class </span>CC, <a name="l00190"></a>00190 template <typename> class ALLOC ><a name="l00191"></a>00191 class tokenizer<SEQ_PATTERN, FASTA_TKNZ_PROP, ALLOC ><a name="l00192"></a>00192 {<a name="l00193"></a>00193 <a name="l00194"></a>00194 <span class="keyword">public</span>:<a name="l00195"></a>00195 <span class="keyword">typedef</span> <a class="code" href="classpattern__support.html">pattern_support<V_Fkk_MINE_PROP></a> PAT_SUP;<a name="l00196"></a>00196 <span class="keyword">typedef</span> <a class="code" href="classvat.html">vat<SEQ_PROP, V_Fkk_MINE_PROP, ALLOC, std::vector ></a> VAT;<a name="l00197"></a>00197 <span class="keyword">typedef</span> seq_instance <V_Fkk_MINE_PROP> INSTANCE;<a name="l00198"></a>00198 <span class="keyword">typedef</span> <span class="keyword">typename</span> SEQ_PATTERN::VERTEX_T V_T;<a name="l00199"></a>00199 <span class="keyword">typedef</span> <span class="keyword">typename</span> SEQ_PATTERN::EDGE_T E_T;<a name="l00200"></a>00200 <a name="l00201"></a>00201 <a name="l00202"></a>00202 tokenizer(<span class="keywordtype">int</span> max=LINE_SZ): MAXLINE(max) {} <a name="l00210"></a>00210 <span class="keyword">template</span><<span class="keyword">class</span> SM_T><a name="l00211"></a>00211 <span class="keywordtype">int</span> parse_next_trans(ifstream& infile, <a class="code" href="classpat__fam.html">pat_fam<SEQ_PATTERN></a>& freq_pats, <a name="l00212"></a>00212 <a class="code" href="classstorage__manager.html">storage_manager<SEQ_PATTERN, VAT, ALLOC, SM_T></a>& vat_hmap ) {<a name="l00213"></a>00213 <a name="l00214"></a>00214 <span class="keywordtype">char</span>* line=<span class="keyword">new</span> <span class="keywordtype">char</span>[MAXLINE];<a name="l00215"></a>00215 <span class="keywordtype">char</span> word[MAXLINE];<a name="l00216"></a>00216 <span class="keywordtype">char</span>* startline=line;<a name="l00217"></a>00217 <a name="l00218"></a>00218 <span class="keywordtype">int</span> i=0, len, seqlen=0;<a name="l00219"></a>00219 <span class="keyword">static</span> <span class="keywordtype">int</span> tid=-1;<a name="l00220"></a>00220 <span class="keywordtype">int</span> pos; <span class="comment">//stores starting position of input stream's get pointer</span><a name="l00221"></a>00221 VAT* svat;<a name="l00222"></a>00222 <span class="keywordtype">bool</span> first = <span class="keyword">true</span>; <span class="comment">//first line of new fasta seq in the file</span><a name="l00223"></a>00223 <a name="l00224"></a>00224 <span class="keywordflow">do</span> {<a name="l00225"></a>00225 pos=infile.tellg();<a name="l00226"></a>00226 line=startline;<a name="l00227"></a>00227 *line = <span class="charliteral">'\0'</span>;<a name="l00228"></a>00228 infile.getline(line, MAXLINE-1);<a name="l00229"></a>00229 <span class="comment">//len=infile.gcount();</span><a name="l00230"></a>00230 len = strlen(line);<a name="l00231"></a>00231 <a name="l00232"></a>00232 <span class="keywordflow">if</span>(len == 0){<a name="l00233"></a>00233 <span class="keywordflow">if</span> (infile.eof()) {<a name="l00234"></a>00234 tid= -1;<a name="l00235"></a>00235 <span class="keyword">delete</span>[] startline;<a name="l00236"></a>00236 <span class="keywordflow">return</span> tid;<a name="l00237"></a>00237 }<a name="l00238"></a>00238 <span class="keywordflow">else</span> <span class="keywordflow">continue</span>; <span class="comment">//just a blank line, skip</span><a name="l00239"></a>00239 }<a name="l00240"></a>00240 <a name="l00241"></a>00241 <a name="l00242"></a>00242 <span class="keywordflow">if</span> (line[0] == <span class="charliteral">'>'</span>){<a name="l00243"></a>00243 <span class="keywordflow">if</span> (first){<a name="l00244"></a>00244 tid++; <span class="comment">// increment the seq id</span><a name="l00245"></a>00245 first = <span class="keyword">false</span>;<a name="l00246"></a>00246 <span class="keywordflow">continue</span>; <span class="comment">//go onto next line</span><a name="l00247"></a>00247 }<a name="l00248"></a>00248 <span class="keywordflow">else</span>{<a name="l00249"></a>00249 infile.seekg(pos); <span class="comment">//reset the file pos to beginning of </span><a name="l00250"></a>00250 <span class="comment">//line for next seq</span><a name="l00251"></a>00251 <span class="keyword">delete</span>[] startline;<a name="l00252"></a>00252 <span class="keywordflow">return</span> tid;<a name="l00253"></a>00253 }<a name="l00254"></a>00254 }<a name="l00255"></a>00255 <a name="l00256"></a>00256 <span class="comment">//read the fasta seq</span><a name="l00257"></a>00257 <span class="keywordflow">for</span> (i=0; i < len; ++i, ++seqlen){<a name="l00258"></a>00258 <span class="comment">//read each char and insert into VAT</span><a name="l00259"></a>00259 <span class="comment">//this is an element, insert/append to its VAT</span><a name="l00260"></a>00260 SEQ_PATTERN* p = <span class="keyword">new</span> SEQ_PATTERN();<a name="l00261"></a>00261 V_T v = string(1,line[i]);<a name="l00262"></a>00262 <a name="l00263"></a>00263 <a name="l00264"></a>00264 <span class="comment">// Add vertex and update the canonical code.</span><a name="l00265"></a>00265 p->add_vertex(v);<a name="l00266"></a>00266 p->init_canonical_code(v);<a name="l00267"></a>00267 <a name="l00268"></a>00268 <span class="comment">//if p contains a vat in vat_hmap, append tid/ts to the entry</span><a name="l00269"></a>00269 <span class="comment">//else create a new vat and insert it into vat_hmap, //and add p to freq_pats</span><a name="l00270"></a>00270 svat=vat_hmap.get_vat(p);<a name="l00271"></a>00271 <span class="comment">//if(vat_hmap.find(p))</span><a name="l00272"></a>00272 <span class="keywordflow">if</span>(svat != NULL) {<a name="l00273"></a>00273 <span class="comment">//vat found, check if this tid exists in it</span><a name="l00274"></a>00274 <a name="l00275"></a>00275 <span class="keyword">typename</span> VAT::IT vit=svat->end()-1;<a name="l00276"></a>00276 <span class="keywordflow">if</span>(vit->first!=tid)<a name="l00277"></a>00277 vit=svat->end(); <a name="l00278"></a>00278 <a name="l00279"></a>00279 <span class="keywordflow">if</span>(vit!=svat->end())<a name="l00280"></a>00280 <span class="comment">//tid found</span><a name="l00281"></a>00281 vit->second.push_back(INSTANCE(seqlen, seqlen));<a name="l00282"></a>00282 <span class="keywordflow">else</span> {<a name="l00283"></a>00283 <span class="comment">//tid not found</span><a name="l00284"></a>00284 <span class="keyword">typename</span> VAT::INSTANCES new_tidlist;<a name="l00285"></a>00285 new_tidlist.push_back(INSTANCE(seqlen, seqlen));<a name="l00286"></a>00286 svat->push_back(make_pair(tid, new_tidlist));<a name="l00287"></a>00287 }<a name="l00288"></a>00288 <a name="l00289"></a>00289 <span class="keyword">delete</span> p;<a name="l00290"></a>00290 <a name="l00291"></a>00291 }<span class="comment">//end if(vat_hmap.find())</span><a name="l00292"></a>00292 <span class="keywordflow">else</span> {<a name="l00293"></a>00293 <span class="comment">//create a new vat & insert it</span><a name="l00294"></a>00294 svat=<span class="keyword">new</span> VAT();<a name="l00295"></a>00295 <span class="keyword">typename</span> VAT::INSTANCES new_tidlist;<a name="l00296"></a>00296 new_tidlist.push_back(INSTANCE(seqlen, seqlen));<a name="l00297"></a>00297 svat->push_back(make_pair(tid, new_tidlist));<a name="l00298"></a>00298 <span class="keywordflow">if</span>(!vat_hmap.add_vat(p, svat)) {<a name="l00299"></a>00299 cerr<<<span class="stringliteral">"tokenizer.get_length_one: add_vat failed"</span><<endl;<a name="l00300"></a>00300 <span class="keywordflow">return</span> -1;<a name="l00301"></a>00301 }<a name="l00302"></a>00302 freq_pats.push_back(p);<a name="l00303"></a>00303 }<span class="comment">//end else</span><a name="l00304"></a>00304 }<a name="l00305"></a>00305 <a name="l00306"></a>00306 }<span class="keywordflow">while</span>(<span class="keyword">true</span>);<a name="l00307"></a>00307 <a name="l00308"></a>00308 <span class="keywordflow">return</span> -1;<a name="l00309"></a>00309 }<span class="comment">//end parse_next_trans()</span><a name="l00310"></a>00310 <a name="l00311"></a>00311 <span class="keyword">private</span>:<a name="l00312"></a>00312 <span class="keywordtype">int</span> MAXLINE; <a name="l00314"></a>00314 }; <span class="comment">//end class seq_tokenizer</span><a name="l00315"></a>00315 <a name="l00316"></a>00316 <span class="preprocessor">#endif</span><a name="l00317"></a>00317 <span class="preprocessor"></span></pre></div><hr size="1"><address style="align: right;"><small>Generated on Wed Jul 26 14:01:08 2006 for DMTL by <a href="http://www.doxygen.org/index.html"><img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.7 </small></address></body></html>⌨️ 快捷键说明
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