website/full_javadoc/compbio/data/msa/Category.html

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   5 <!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:41 GMT 2011 -->\r
   6 <TITLE>\r
   7 Category\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2011-12-07">\r
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  15 function windowTitle()\r
  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="Category";\r
  19     }\r
  20 }\r
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  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Category.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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  55 \r
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  58 &nbsp;PREV CLASS&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
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  77 <TR>\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
  80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  81 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.data.msa</FONT>\r
  92 <BR>\r
  93 Class Category</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 "><B>compbio.data.msa.Category</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public class <B>Category</B><DT>extends <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></DL>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 Class that splits <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><CODE>Services</CODE></A> to categories. Services themselves have no
 105  knowledge which category they belongs to.
 106
 107  This class is responsible for initialization of all the categories (done
 108  statically) and holds the category names as constrains.
 109
 110  Two categories considered equals if their names are equals.\r
 111 <P>\r
 112 \r
 113 <P>\r
 114 <DL>\r
 115 <DT><B>Version:</B></DT>\r
 116   <DD>1.0 September 2011</DD>\r
 117 <DT><B>Author:</B></DT>\r
 118   <DD>pvtroshin</DD>\r
 119 </DL>\r
 120 <HR>\r
 121 \r
 122 <P>\r
 123 <!-- =========== FIELD SUMMARY =========== -->\r
 124 \r
 125 <A NAME="field_summary"><!-- --></A>\r
 126 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 127 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 128 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 129 <B>Field Summary</B></FONT></TH>\r
 130 </TR>\r
 131 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 132 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 133 <CODE>static&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
 134 <TD><CODE><B><A HREF="../../../compbio/data/msa/Category.html#CATEGORY_ALIGNMENT">CATEGORY_ALIGNMENT</A></B></CODE>\r
 135 \r
 136 <BR>\r
 137 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;All of the Category names</TD>\r
 138 </TR>\r
 139 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 140 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 141 <CODE>static&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
 142 <TD><CODE><B><A HREF="../../../compbio/data/msa/Category.html#CATEGORY_CONSERVATION">CATEGORY_CONSERVATION</A></B></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 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 148 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 149 <CODE>static&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
 150 <TD><CODE><B><A HREF="../../../compbio/data/msa/Category.html#CATEGORY_DISORDER">CATEGORY_DISORDER</A></B></CODE>\r
 151 \r
 152 <BR>\r
 153 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 154 </TR>\r
 155 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 156 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 157 <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
 158 <TD><CODE><B><A HREF="../../../compbio/data/msa/Category.html#name">name</A></B></CODE>\r
 159 \r
 160 <BR>\r
 161 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 162 </TR>\r
 163 </TABLE>\r
 164 &nbsp;\r
 165 <!-- ========== METHOD SUMMARY =========== -->\r
 166 \r
 167 <A NAME="method_summary"><!-- --></A>\r
 168 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 169 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 170 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 171 <B>Method Summary</B></FONT></TH>\r
 172 </TR>\r
 173 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 174 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 175 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 176 <TD><CODE><B><A HREF="../../../compbio/data/msa/Category.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
 177 \r
 178 <BR>\r
 179 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 180 </TR>\r
 181 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 183 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>&gt;</CODE></FONT></TD>\r
 184 <TD><CODE><B><A HREF="../../../compbio/data/msa/Category.html#getCategories()">getCategories</A></B>()</CODE>\r
 185 \r
 186 <BR>\r
 187 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 188 </TR>\r
 189 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 190 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 191 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>&gt;</CODE></FONT></TD>\r
 192 <TD><CODE><B><A HREF="../../../compbio/data/msa/Category.html#getServices()">getServices</A></B>()</CODE>\r
 193 \r
 194 <BR>\r
 195 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 196 </TR>\r
 197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 199 <CODE>&nbsp;int</CODE></FONT></TD>\r
 200 <TD><CODE><B><A HREF="../../../compbio/data/msa/Category.html#hashCode()">hashCode</A></B>()</CODE>\r
 201 \r
 202 <BR>\r
 203 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 204 </TR>\r
 205 </TABLE>\r
 206 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 207 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 208 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 209 <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
 210 </TR>\r
 211 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 212 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
 213 </TR>\r
 214 </TABLE>\r
 215 &nbsp;\r
 216 <P>\r
 217 \r
 218 <!-- ============ FIELD DETAIL =========== -->\r
 219 \r
 220 <A NAME="field_detail"><!-- --></A>\r
 221 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 222 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 223 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 224 <B>Field Detail</B></FONT></TH>\r
 225 </TR>\r
 226 </TABLE>\r
 227 \r
 228 <A NAME="CATEGORY_ALIGNMENT"><!-- --></A><H3>\r
 229 CATEGORY_ALIGNMENT</H3>\r
 230 <PRE>\r
 231 public static final <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>CATEGORY_ALIGNMENT</B></PRE>\r
 232 <DL>\r
 233 <DD>All of the Category names\r
 234 <P>\r
 235 <DL>\r
 236 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.msa.Category.CATEGORY_ALIGNMENT">Constant Field Values</A></DL>\r
 237 </DL>\r
 238 <HR>\r
 239 \r
 240 <A NAME="CATEGORY_DISORDER"><!-- --></A><H3>\r
 241 CATEGORY_DISORDER</H3>\r
 242 <PRE>\r
 243 public static final <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>CATEGORY_DISORDER</B></PRE>\r
 244 <DL>\r
 245 <DL>\r
 246 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.msa.Category.CATEGORY_DISORDER">Constant Field Values</A></DL>\r
 247 </DL>\r
 248 <HR>\r
 249 \r
 250 <A NAME="CATEGORY_CONSERVATION"><!-- --></A><H3>\r
 251 CATEGORY_CONSERVATION</H3>\r
 252 <PRE>\r
 253 public static final <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>CATEGORY_CONSERVATION</B></PRE>\r
 254 <DL>\r
 255 <DL>\r
 256 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.msa.Category.CATEGORY_CONSERVATION">Constant Field Values</A></DL>\r
 257 </DL>\r
 258 <HR>\r
 259 \r
 260 <A NAME="name"><!-- --></A><H3>\r
 261 name</H3>\r
 262 <PRE>\r
 263 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>name</B></PRE>\r
 264 <DL>\r
 265 <DL>\r
 266 </DL>\r
 267 </DL>\r
 268 \r
 269 <!-- ============ METHOD DETAIL ========== -->\r
 270 \r
 271 <A NAME="method_detail"><!-- --></A>\r
 272 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 273 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 274 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 275 <B>Method Detail</B></FONT></TH>\r
 276 </TR>\r
 277 </TABLE>\r
 278 \r
 279 <A NAME="getServices()"><!-- --></A><H3>\r
 280 getServices</H3>\r
 281 <PRE>\r
 282 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>&gt; <B>getServices</B>()</PRE>\r
 283 <DL>\r
 284 <DD><DL>\r
 285 </DL>\r
 286 </DD>\r
 287 </DL>\r
 288 <HR>\r
 289 \r
 290 <A NAME="getCategories()"><!-- --></A><H3>\r
 291 getCategories</H3>\r
 292 <PRE>\r
 293 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>&gt; <B>getCategories</B>()</PRE>\r
 294 <DL>\r
 295 <DD><DL>\r
 296 </DL>\r
 297 </DD>\r
 298 </DL>\r
 299 <HR>\r
 300 \r
 301 <A NAME="hashCode()"><!-- --></A><H3>\r
 302 hashCode</H3>\r
 303 <PRE>\r
 304 public int <B>hashCode</B>()</PRE>\r
 305 <DL>\r
 306 <DD><DL>\r
 307 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><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></CODE></DL>\r
 308 </DD>\r
 309 <DD><DL>\r
 310 </DL>\r
 311 </DD>\r
 312 </DL>\r
 313 <HR>\r
 314 \r
 315 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 316 equals</H3>\r
 317 <PRE>\r
 318 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
 319 <DL>\r
 320 <DD><DL>\r
 321 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><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></CODE></DL>\r
 322 </DD>\r
 323 <DD><DL>\r
 324 </DL>\r
 325 </DD>\r
 326 </DL>\r
 327 <!-- ========= END OF CLASS DATA ========= -->\r
 328 <HR>\r
 329 \r
 330 \r
 331 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 332 <A NAME="navbar_bottom"><!-- --></A>\r
 333 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 334 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 335 <TR>\r
 336 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 337 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 338 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 339   <TR ALIGN="center" VALIGN="top">\r
 340   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 341   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 342   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 343   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Category.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 344   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 345   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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 347   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 348   </TR>\r
 349 </TABLE>\r
 350 </TD>\r
 351 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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