website/dm_javadoc/compbio/data/sequence/Alignment.html

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   7 Alignment\r
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  88 <!-- ======== START OF CLASS DATA ======== -->\r
  89 <H2>\r
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  91 compbio.data.sequence</FONT>\r
  92 <BR>\r
  93 Class Alignment</H2>\r
  94 <PRE>\r
  95 java.lang.Object\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Alignment</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE><FONT SIZE="-1">@Immutable\r
 101 </FONT>public final class <B>Alignment</B><DT>extends java.lang.Object</DL>\r
 102 </PRE>\r
 103 \r
 104 <P>\r
 105 Multiple sequence alignment.
 106
 107  Does not give any guarantees on the content of individual FastaSequece
 108  records. It does not guarantee neither the uniqueness of the names of
 109  sequences nor it guarantees the uniqueness of the sequences.\r
 110 <P>\r
 111 \r
 112 <P>\r
 113 <DL>\r
 114 <DT><B>Version:</B></DT>\r
 115   <DD>1.0 September 2009</DD>\r
 116 <DT><B>Author:</B></DT>\r
 117   <DD>pvtroshin</DD>\r
 118 <DT><B>See Also:</B><DD><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><CODE>FastaSequence</CODE></A>, \r
 119 <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><CODE>AlignmentMetadata</CODE></A></DL>\r
 120 <HR>\r
 121 \r
 122 <P>\r
 123 \r
 124 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 125 \r
 126 <A NAME="constructor_summary"><!-- --></A>\r
 127 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 128 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 129 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 130 <B>Constructor Summary</B></FONT></TH>\r
 131 </TR>\r
 132 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 133 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 134           <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</CODE>\r
 135 \r
 136 <BR>\r
 137 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 138 </TR>\r
 139 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 140 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 141           <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
 142           char&nbsp;gapchar)</CODE>\r
 143 \r
 144 <BR>\r
 145 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 146 </TR>\r
 147 </TABLE>\r
 148 &nbsp;\r
 149 <!-- ========== METHOD SUMMARY =========== -->\r
 150 \r
 151 <A NAME="method_summary"><!-- --></A>\r
 152 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 153 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 154 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 155 <B>Method Summary</B></FONT></TH>\r
 156 </TR>\r
 157 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 159 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 160 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
 161 \r
 162 <BR>\r
 163 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Please note that this implementation does not take the order of sequences
 164  into account!</TD>\r
 165 </TR>\r
 166 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 168 <CODE>&nbsp;<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></CODE></FONT></TD>\r
 169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getMetadata()">getMetadata</A></B>()</CODE>\r
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 176 <CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 177 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
 178 \r
 179 <BR>\r
 180 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 181 </TR>\r
 182 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 184 <CODE>&nbsp;int</CODE></FONT></TD>\r
 185 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSize()">getSize</A></B>()</CODE>\r
 186 \r
 187 <BR>\r
 188 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 189 </TR>\r
 190 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 191 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 192 <CODE>&nbsp;int</CODE></FONT></TD>\r
 193 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#hashCode()">hashCode</A></B>()</CODE>\r
 194 \r
 195 <BR>\r
 196 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 197 </TR>\r
 198 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 199 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 200 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 201 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#toString()">toString</A></B>()</CODE>\r
 202 \r
 203 <BR>\r
 204 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 205 </TR>\r
 206 </TABLE>\r
 207 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 208 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 209 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 210 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 211 </TR>\r
 212 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 213 <TD><CODE>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
 214 </TR>\r
 215 </TABLE>\r
 216 &nbsp;\r
 217 <P>\r
 218 \r
 219 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 220 \r
 221 <A NAME="constructor_detail"><!-- --></A>\r
 222 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 223 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 224 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 225 <B>Constructor Detail</B></FONT></TH>\r
 226 </TR>\r
 227 </TABLE>\r
 228 \r
 229 <A NAME="Alignment(java.util.List, compbio.data.sequence.Program, char)"><!-- --></A><H3>\r
 230 Alignment</H3>\r
 231 <PRE>\r
 232 public <B>Alignment</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 233                  <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
 234                  char&nbsp;gapchar)</PRE>\r
 235 <DL>\r
 236 <DL>\r
 237 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>program</CODE> - <DD><CODE>gapchar</CODE> - </DL>\r
 238 </DL>\r
 239 <HR>\r
 240 \r
 241 <A NAME="Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><!-- --></A><H3>\r
 242 Alignment</H3>\r
 243 <PRE>\r
 244 public <B>Alignment</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 245                  <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</PRE>\r
 246 <DL>\r
 247 <DL>\r
 248 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>metadata</CODE> - </DL>\r
 249 </DL>\r
 250 \r
 251 <!-- ============ METHOD DETAIL ========== -->\r
 252 \r
 253 <A NAME="method_detail"><!-- --></A>\r
 254 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 255 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 256 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 257 <B>Method Detail</B></FONT></TH>\r
 258 </TR>\r
 259 </TABLE>\r
 260 \r
 261 <A NAME="getSequences()"><!-- --></A><H3>\r
 262 getSequences</H3>\r
 263 <PRE>\r
 264 public java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt; <B>getSequences</B>()</PRE>\r
 265 <DL>\r
 266 <DD><DL>\r
 267 \r
 268 <DT><B>Returns:</B><DD>list of FastaSequence records</DL>\r
 269 </DD>\r
 270 </DL>\r
 271 <HR>\r
 272 \r
 273 <A NAME="getSize()"><!-- --></A><H3>\r
 274 getSize</H3>\r
 275 <PRE>\r
 276 public int <B>getSize</B>()</PRE>\r
 277 <DL>\r
 278 <DD><DL>\r
 279 \r
 280 <DT><B>Returns:</B><DD>a number of sequence in the alignment</DL>\r
 281 </DD>\r
 282 </DL>\r
 283 <HR>\r
 284 \r
 285 <A NAME="getMetadata()"><!-- --></A><H3>\r
 286 getMetadata</H3>\r
 287 <PRE>\r
 288 public <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> <B>getMetadata</B>()</PRE>\r
 289 <DL>\r
 290 <DD><DL>\r
 291 \r
 292 <DT><B>Returns:</B><DD>AlignmentMetadata object</DL>\r
 293 </DD>\r
 294 </DL>\r
 295 <HR>\r
 296 \r
 297 <A NAME="toString()"><!-- --></A><H3>\r
 298 toString</H3>\r
 299 <PRE>\r
 300 public java.lang.String <B>toString</B>()</PRE>\r
 301 <DL>\r
 302 <DD><DL>\r
 303 <DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
 304 </DD>\r
 305 <DD><DL>\r
 306 </DL>\r
 307 </DD>\r
 308 </DL>\r
 309 <HR>\r
 310 \r
 311 <A NAME="hashCode()"><!-- --></A><H3>\r
 312 hashCode</H3>\r
 313 <PRE>\r
 314 public int <B>hashCode</B>()</PRE>\r
 315 <DL>\r
 316 <DD><DL>\r
 317 <DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
 318 </DD>\r
 319 <DD><DL>\r
 320 </DL>\r
 321 </DD>\r
 322 </DL>\r
 323 <HR>\r
 324 \r
 325 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 326 equals</H3>\r
 327 <PRE>\r
 328 public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
 329 <DL>\r
 330 <DD>Please note that this implementation does not take the order of sequences
 331  into account!\r
 332 <P>\r
 333 <DD><DL>\r
 334 <DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
 335 </DD>\r
 336 <DD><DL>\r
 337 </DL>\r
 338 </DD>\r
 339 </DL>\r
 340 <!-- ========= END OF CLASS DATA ========= -->\r
 341 <HR>\r
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