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7 Uses of Package compbio.data.sequence
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18 parent.document.title="Uses of Package compbio.data.sequence";
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84 <B>Uses of Package<br>compbio.data.sequence</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>
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98 <TD> </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>
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102 <TD>A data model for multiple sequence alignment web services
103 Classes in this package have no dependencies to other sources in the project. </TD>
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105 <TR BGCOLOR="white" CLASS="TableRowColor">
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106 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>
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107 <TD> </TD>
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109 <TR BGCOLOR="white" CLASS="TableRowColor">
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110 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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111 <TD>A meta-data model for multiple sequence alignment web services
112 Classes in this package have no dependencies to other sources in the project. </TD>
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114 <TR BGCOLOR="white" CLASS="TableRowColor">
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115 <TD><A HREF="#compbio.pipeline._jpred"><B>compbio.pipeline._jpred</B></A></TD>
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116 <TD> </TD>
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118 <TR BGCOLOR="white" CLASS="TableRowColor">
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119 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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120 <TD>Utilities commonly used by all runners. </TD>
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122 <TR BGCOLOR="white" CLASS="TableRowColor">
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123 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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124 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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126 <TR BGCOLOR="white" CLASS="TableRowColor">
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127 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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128 <TD> </TD>
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133 <A NAME="compbio.data.msa"><!-- --></A>
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134 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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135 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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136 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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137 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>
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139 <TR BGCOLOR="white" CLASS="TableRowColor">
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140 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa"><B>Alignment</B></A></B>
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143 Multiple sequence alignment.</TD>
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145 <TR BGCOLOR="white" CLASS="TableRowColor">
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146 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa"><B>FastaSequence</B></A></B>
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149 A FASTA formatted sequence.</TD>
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154 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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155 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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156 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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157 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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158 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>
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160 <TR BGCOLOR="white" CLASS="TableRowColor">
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161 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa.jaxws"><B>Alignment</B></A></B>
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164 Multiple sequence alignment.</TD>
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166 <TR BGCOLOR="white" CLASS="TableRowColor">
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167 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa.jaxws"><B>FastaSequence</B></A></B>
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170 A FASTA formatted sequence.</TD>
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175 <A NAME="compbio.data.sequence"><!-- --></A>
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176 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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177 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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178 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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179 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>
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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence"><B>Alignment</B></A></B>
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185 Multiple sequence alignment.</TD>
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187 <TR BGCOLOR="white" CLASS="TableRowColor">
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188 <TD><B><A HREF="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence"><B>AlignmentMetadata</B></A></B>
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191 Alignment metadata e.g.</TD>
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193 <TR BGCOLOR="white" CLASS="TableRowColor">
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194 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>
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197 A FASTA formatted sequence.</TD>
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199 <TR BGCOLOR="white" CLASS="TableRowColor">
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200 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>
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203 Programmes that can produce alignments</TD>
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205 <TR BGCOLOR="white" CLASS="TableRowColor">
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206 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>
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209 </TD>
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214 <A NAME="compbio.engine"><!-- --></A>
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215 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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216 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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217 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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218 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>
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220 <TR BGCOLOR="white" CLASS="TableRowColor">
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221 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.engine"><B>FastaSequence</B></A></B>
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224 A FASTA formatted sequence.</TD>
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229 <A NAME="compbio.metadata"><!-- --></A>
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230 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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231 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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232 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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233 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>
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235 <TR BGCOLOR="white" CLASS="TableRowColor">
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236 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>
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239 A FASTA formatted sequence.</TD>
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244 <A NAME="compbio.pipeline._jpred"><!-- --></A>
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245 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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246 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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247 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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248 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A></FONT></TH>
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250 <TR BGCOLOR="white" CLASS="TableRowColor">
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251 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.pipeline._jpred"><B>FastaSequence</B></A></B>
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254 A FASTA formatted sequence.</TD>
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259 <A NAME="compbio.runner"><!-- --></A>
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260 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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261 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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262 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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263 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
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265 <TR BGCOLOR="white" CLASS="TableRowColor">
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266 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner"><B>Alignment</B></A></B>
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269 Multiple sequence alignment.</TD>
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271 <TR BGCOLOR="white" CLASS="TableRowColor">
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272 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.runner"><B>FastaSequence</B></A></B>
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275 A FASTA formatted sequence.</TD>
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277 <TR BGCOLOR="white" CLASS="TableRowColor">
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278 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.runner"><B>UnknownFileFormatException</B></A></B>
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281 </TD>
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286 <A NAME="compbio.runner.msa"><!-- --></A>
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287 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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288 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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289 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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290 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>
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292 <TR BGCOLOR="white" CLASS="TableRowColor">
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293 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner.msa"><B>Alignment</B></A></B>
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296 Multiple sequence alignment.</TD>
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301 <A NAME="compbio.ws.server"><!-- --></A>
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302 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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303 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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304 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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305 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
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307 <TR BGCOLOR="white" CLASS="TableRowColor">
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308 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.ws.server"><B>Alignment</B></A></B>
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311 Multiple sequence alignment.</TD>
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313 <TR BGCOLOR="white" CLASS="TableRowColor">
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314 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.ws.server"><B>FastaSequence</B></A></B>
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317 A FASTA formatted sequence.</TD>
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