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

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   7 Alignment\r
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  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. That is it does not guarantee that the neither the names of
 109  sequences or the sequences themselves are unique.\r
 110 <P>\r
 111 \r
 112 <P>\r
 113 <DL>\r
 114 <DT><B>Author:</B></DT>\r
 115   <DD>pvtroshin
 116
 117          Date September 2009</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;java.lang.String</CODE></FONT></TD>\r
 193 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#toString()">toString</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 </TABLE>\r
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 201 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 202 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 203 </TR>\r
 204 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 205 <TD><CODE>getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
 206 </TR>\r
 207 </TABLE>\r
 208 &nbsp;\r
 209 <P>\r
 210 \r
 211 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 212 \r
 213 <A NAME="constructor_detail"><!-- --></A>\r
 214 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 215 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 216 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 217 <B>Constructor Detail</B></FONT></TH>\r
 218 </TR>\r
 219 </TABLE>\r
 220 \r
 221 <A NAME="Alignment(java.util.List, compbio.data.sequence.Program, char)"><!-- --></A><H3>\r
 222 Alignment</H3>\r
 223 <PRE>\r
 224 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
 225                  <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
 226                  char&nbsp;gapchar)</PRE>\r
 227 <DL>\r
 228 <DL>\r
 229 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>program</CODE> - <DD><CODE>gapchar</CODE> - </DL>\r
 230 </DL>\r
 231 <HR>\r
 232 \r
 233 <A NAME="Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><!-- --></A><H3>\r
 234 Alignment</H3>\r
 235 <PRE>\r
 236 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
 237                  <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</PRE>\r
 238 <DL>\r
 239 <DL>\r
 240 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>metadata</CODE> - </DL>\r
 241 </DL>\r
 242 \r
 243 <!-- ============ METHOD DETAIL ========== -->\r
 244 \r
 245 <A NAME="method_detail"><!-- --></A>\r
 246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 247 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 248 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 249 <B>Method Detail</B></FONT></TH>\r
 250 </TR>\r
 251 </TABLE>\r
 252 \r
 253 <A NAME="getSequences()"><!-- --></A><H3>\r
 254 getSequences</H3>\r
 255 <PRE>\r
 256 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
 257 <DL>\r
 258 <DD><DL>\r
 259 \r
 260 <DT><B>Returns:</B><DD>list of FastaSequence records</DL>\r
 261 </DD>\r
 262 </DL>\r
 263 <HR>\r
 264 \r
 265 <A NAME="getSize()"><!-- --></A><H3>\r
 266 getSize</H3>\r
 267 <PRE>\r
 268 public int <B>getSize</B>()</PRE>\r
 269 <DL>\r
 270 <DD><DL>\r
 271 \r
 272 <DT><B>Returns:</B><DD>a number of sequence in the alignment</DL>\r
 273 </DD>\r
 274 </DL>\r
 275 <HR>\r
 276 \r
 277 <A NAME="getMetadata()"><!-- --></A><H3>\r
 278 getMetadata</H3>\r
 279 <PRE>\r
 280 public <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> <B>getMetadata</B>()</PRE>\r
 281 <DL>\r
 282 <DD><DL>\r
 283 \r
 284 <DT><B>Returns:</B><DD>AlignmentMetadata object</DL>\r
 285 </DD>\r
 286 </DL>\r
 287 <HR>\r
 288 \r
 289 <A NAME="toString()"><!-- --></A><H3>\r
 290 toString</H3>\r
 291 <PRE>\r
 292 public java.lang.String <B>toString</B>()</PRE>\r
 293 <DL>\r
 294 <DD><DL>\r
 295 <DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
 296 </DD>\r
 297 <DD><DL>\r
 298 </DL>\r
 299 </DD>\r
 300 </DL>\r
 301 <HR>\r
 302 \r
 303 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 304 equals</H3>\r
 305 <PRE>\r
 306 public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
 307 <DL>\r
 308 <DD>Please note that this implementation does not take the order of sequences
 309  into account!\r
 310 <P>\r
 311 <DD><DL>\r
 312 <DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
 313 </DD>\r
 314 <DD><DL>\r
 315 </DL>\r
 316 </DD>\r
 317 </DL>\r
 318 <!-- ========= END OF CLASS DATA ========= -->\r
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