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

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  91 compbio.data.sequence</FONT>\r
  92 <BR>\r
  93 Class AnnotatedSequence</H2>\r
  94 <PRE>\r
  95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">compbio.data.sequence.FastaSequence</A>\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.AnnotatedSequence</B>\r
  98 </PRE>\r
  99 <HR>\r
 100 <DL>\r
 101 <DT><PRE>public class <B>AnnotatedSequence</B><DT>extends <A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></DL>\r
 102 </PRE>\r
 103 \r
 104 <P>\r
 105 <HR>\r
 106 \r
 107 <P>\r
 108 \r
 109 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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 114 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 115 <B>Constructor Summary</B></FONT></TH>\r
 116 </TR>\r
 117 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 118 <TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#AnnotatedSequence(compbio.data.sequence.FastaSequence, float[])">AnnotatedSequence</A></B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;fsequence,\r
 119                   float[]&nbsp;annotation)</CODE>\r
 120 \r
 121 <BR>\r
 122 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 123 </TR>\r
 124 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 125 <TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#AnnotatedSequence(java.lang.String, java.lang.String, float[])">AnnotatedSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;id,\r
 126                   <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence,\r
 127                   float[]&nbsp;annotation)</CODE>\r
 128 \r
 129 <BR>\r
 130 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 131 </TR>\r
 132 </TABLE>\r
 133 &nbsp;\r
 134 <!-- ========== METHOD SUMMARY =========== -->\r
 135 \r
 136 <A NAME="method_summary"><!-- --></A>\r
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 140 <B>Method Summary</B></FONT></TH>\r
 141 </TR>\r
 142 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 143 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 144 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 145 <TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</CODE>\r
 146 \r
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 149 </TR>\r
 150 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 151 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 152 <CODE>&nbsp;float[]</CODE></FONT></TD>\r
 153 <TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#getAnnotation()">getAnnotation</A></B>()</CODE>\r
 154 \r
 155 <BR>\r
 156 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 157 </TR>\r
 158 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 160 <CODE>&nbsp;int</CODE></FONT></TD>\r
 161 <TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#hashCode()">hashCode</A></B>()</CODE>\r
 162 \r
 163 <BR>\r
 164 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#toString()">toString</A></B>()</CODE>\r
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Same as oneLineFasta</TD>\r
 173 </TR>\r
 174 </TABLE>\r
 175 &nbsp;<A NAME="methods_inherited_from_class_compbio.data.sequence.FastaSequence"><!-- --></A>\r
 176 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 177 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 178 <TH ALIGN="left"><B>Methods inherited from class compbio.data.sequence.<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></B></TH>\r
 179 </TR>\r
 180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 181 <TD><CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getId()">getId</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getLength()">getLength</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getSequence()">getSequence</A></CODE></TD>\r
 182 </TR>\r
 183 </TABLE>\r
 184 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 185 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 186 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 187 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
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 191 </TR>\r
 192 </TABLE>\r
 193 &nbsp;\r
 194 <P>\r
 195 \r
 196 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 197 \r
 198 <A NAME="constructor_detail"><!-- --></A>\r
 199 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 200 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 201 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 202 <B>Constructor Detail</B></FONT></TH>\r
 203 </TR>\r
 204 </TABLE>\r
 205 \r
 206 <A NAME="AnnotatedSequence(java.lang.String, java.lang.String, float[])"><!-- --></A><H3>\r
 207 AnnotatedSequence</H3>\r
 208 <PRE>\r
 209 public <B>AnnotatedSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;id,\r
 210                          <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence,\r
 211                          float[]&nbsp;annotation)</PRE>\r
 212 <DL>\r
 213 </DL>\r
 214 <HR>\r
 215 \r
 216 <A NAME="AnnotatedSequence(compbio.data.sequence.FastaSequence, float[])"><!-- --></A><H3>\r
 217 AnnotatedSequence</H3>\r
 218 <PRE>\r
 219 public <B>AnnotatedSequence</B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;fsequence,\r
 220                          float[]&nbsp;annotation)</PRE>\r
 221 <DL>\r
 222 </DL>\r
 223 \r
 224 <!-- ============ METHOD DETAIL ========== -->\r
 225 \r
 226 <A NAME="method_detail"><!-- --></A>\r
 227 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 228 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 229 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 230 <B>Method Detail</B></FONT></TH>\r
 231 </TR>\r
 232 </TABLE>\r
 233 \r
 234 <A NAME="getAnnotation()"><!-- --></A><H3>\r
 235 getAnnotation</H3>\r
 236 <PRE>\r
 237 public float[] <B>getAnnotation</B>()</PRE>\r
 238 <DL>\r
 239 <DD><DL>\r
 240 </DL>\r
 241 </DD>\r
 242 </DL>\r
 243 <HR>\r
 244 \r
 245 <A NAME="hashCode()"><!-- --></A><H3>\r
 246 hashCode</H3>\r
 247 <PRE>\r
 248 public int <B>hashCode</B>()</PRE>\r
 249 <DL>\r
 250 <DD><DL>\r
 251 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#hashCode()">hashCode</A></CODE> in class <CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></DL>\r
 252 </DD>\r
 253 <DD><DL>\r
 254 </DL>\r
 255 </DD>\r
 256 </DL>\r
 257 <HR>\r
 258 \r
 259 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 260 equals</H3>\r
 261 <PRE>\r
 262 public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</PRE>\r
 263 <DL>\r
 264 <DD><DL>\r
 265 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></DL>\r
 266 </DD>\r
 267 <DD><DL>\r
 268 </DL>\r
 269 </DD>\r
 270 </DL>\r
 271 <HR>\r
 272 \r
 273 <A NAME="toString()"><!-- --></A><H3>\r
 274 toString</H3>\r
 275 <PRE>\r
 276 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
 277 <DL>\r
 278 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">FastaSequence</A></CODE></B></DD>\r
 279 <DD>Same as oneLineFasta\r
 280 <P>\r
 281 <DD><DL>\r
 282 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">toString</A></CODE> in class <CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></DL>\r
 283 </DD>\r
 284 <DD><DL>\r
 285 </DL>\r
 286 </DD>\r
 287 </DL>\r
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