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   7 Constant Field Values\r
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  84 Constant Field Values</H1>\r
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  87 <B>Contents</B><UL>\r
  88 <LI><A HREF="#compbio.data">compbio.data.*</A>\r
  89 <LI><A HREF="#compbio.metadata">compbio.metadata.*</A>\r
  90 <LI><A HREF="#compbio.ws">compbio.ws.*</A>\r
  91 </UL>\r
  92 \r
  93 <A NAME="compbio.data"><!-- --></A>\r
  94 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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  97 compbio.data.*</FONT></TH>\r
  98 </TR>\r
  99 </TABLE>\r
 100 \r
 101 <P>\r
 102 \r
 103 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 104 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 105 <TH ALIGN="left" COLSPAN="3">compbio.data.msa.<A HREF="compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A></TH>\r
 106 </TR>\r
 107 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 108 <A NAME="compbio.data.msa.Category.CATEGORY_ALIGNMENT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 109 <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
 110 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_ALIGNMENT">CATEGORY_ALIGNMENT</A></CODE></TD>\r
 111 <TD ALIGN="right"><CODE>"Alignment"</CODE></TD>\r
 112 </TR>\r
 113 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 114 <A NAME="compbio.data.msa.Category.CATEGORY_CONSERVATION"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 115 <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
 116 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_CONSERVATION">CATEGORY_CONSERVATION</A></CODE></TD>\r
 117 <TD ALIGN="right"><CODE>"Conservation"</CODE></TD>\r
 118 </TR>\r
 119 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 120 <A NAME="compbio.data.msa.Category.CATEGORY_DISORDER"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 121 <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
 122 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_DISORDER">CATEGORY_DISORDER</A></CODE></TD>\r
 123 <TD ALIGN="right"><CODE>"Protein Disorder"</CODE></TD>\r
 124 </TR>\r
 125 </FONT></TD>\r
 126 </TR>\r
 127 </TABLE>\r
 128 \r
 129 <P>\r
 130 \r
 131 <P>\r
 132 \r
 133 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 134 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 135 <TH ALIGN="left" COLSPAN="3">compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></TH>\r
 136 </TR>\r
 137 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 138 <A NAME="compbio.data.msa.JABAService.SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 139 <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
 140 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A></CODE></TD>\r
 141 <TD ALIGN="right"><CODE>"http://msa.data.compbio/01/01/2010/"</CODE></TD>\r
 142 </TR>\r
 143 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 144 <A NAME="compbio.data.msa.JABAService.V2_SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 145 <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
 146 <TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>\r
 147 <TD ALIGN="right"><CODE>"http://msa.data.compbio/01/12/2010/"</CODE></TD>\r
 148 </TR>\r
 149 </FONT></TD>\r
 150 </TR>\r
 151 </TABLE>\r
 152 \r
 153 <P>\r
 154 \r
 155 <P>\r
 156 \r
 157 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 158 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 159 <TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></TH>\r
 160 </TR>\r
 161 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 162 <A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 163 <CODE>public&nbsp;static&nbsp;final&nbsp;char</CODE></FONT></TD>\r
 164 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>\r
 165 <TD ALIGN="right"><CODE>45</CODE></TD>\r
 166 </TR>\r
 167 </FONT></TD>\r
 168 </TR>\r
 169 </TABLE>\r
 170 \r
 171 <P>\r
 172 \r
 173 <P>\r
 174 \r
 175 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 176 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 177 <TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></TH>\r
 178 </TR>\r
 179 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 180 <A NAME="compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 181 <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
 182 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</A></CODE></TD>\r
 183 <TD ALIGN="right"><CODE>"Alignment"</CODE></TD>\r
 184 </TR>\r
 185 </FONT></TD>\r
 186 </TR>\r
 187 </TABLE>\r
 188 \r
 189 <P>\r
 190 \r
 191 <P>\r
 192 \r
 193 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 194 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 195 <TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></TH>\r
 196 </TR>\r
 197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 198 <A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 199 <CODE>public&nbsp;static&nbsp;final&nbsp;double</CODE></FONT></TD>\r
 200 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</A></CODE></TD>\r
 201 <TD ALIGN="right"><CODE>0.1</CODE></TD>\r
 202 </TR>\r
 203 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 204 <A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 205 <CODE>public&nbsp;static&nbsp;final&nbsp;int</CODE></FONT></TD>\r
 206 <TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</A></CODE></TD>\r
 207 <TD ALIGN="right"><CODE>7</CODE></TD>\r
 208 </TR>\r
 209 </FONT></TD>\r
 210 </TR>\r
 211 </TABLE>\r
 212 \r
 213 <P>\r
 214 \r
 215 <P>\r
 216 <A NAME="compbio.metadata"><!-- --></A>\r
 217 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 218 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 219 <TH ALIGN="left"><FONT SIZE="+2">\r
 220 compbio.metadata.*</FONT></TH>\r
 221 </TR>\r
 222 </TABLE>\r
 223 \r
 224 <P>\r
 225 \r
 226 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 227 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 228 <TH ALIGN="left" COLSPAN="3">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;</TH>\r
 229 </TR>\r
 230 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 231 <A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 232 <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
 233 <TD ALIGN="left"><CODE><A HREF="compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></CODE></TD>\r
 234 <TD ALIGN="right"><CODE>"# LocalEngineExecutionLimit #"</CODE></TD>\r
 235 </TR>\r
 236 </FONT></TD>\r
 237 </TR>\r
 238 </TABLE>\r
 239 \r
 240 <P>\r
 241 \r
 242 <P>\r
 243 <A NAME="compbio.ws"><!-- --></A>\r
 244 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 245 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 246 <TH ALIGN="left"><FONT SIZE="+2">\r
 247 compbio.ws.*</FONT></TH>\r
 248 </TR>\r
 249 </TABLE>\r
 250 \r
 251 <P>\r
 252 \r
 253 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 254 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 255 <TH ALIGN="left" COLSPAN="3">compbio.ws.client.<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A></TH>\r
 256 </TR>\r
 257 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 258 <A NAME="compbio.ws.client.WSTester.fastaAlignment"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 259 <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
 260 <TD ALIGN="left"><CODE><A HREF="compbio/ws/client/WSTester.html#fastaAlignment">fastaAlignment</A></CODE></TD>\r
 261 <TD ALIGN="right"><CODE>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n&gt;Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>\r
 262 </TR>\r
 263 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 264 <A NAME="compbio.ws.client.WSTester.fastaInput"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
 265 <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
 266 <TD ALIGN="left"><CODE><A HREF="compbio/ws/client/WSTester.html#fastaInput">fastaInput</A></CODE></TD>\r
 267 <TD ALIGN="right"><CODE>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n&gt;Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>\r
 268 </TR>\r
 269 </FONT></TD>\r
 270 </TR>\r
 271 </TABLE>\r
 272 \r
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