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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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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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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>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </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 and utility methods
103 that work on the objects of this model. </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.conservation"><B>compbio.runner.conservation</B></A></TD>
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124 <TD> </TD>
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126 <TR BGCOLOR="white" CLASS="TableRowColor">
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127 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>
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128 <TD> </TD>
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130 <TR BGCOLOR="white" CLASS="TableRowColor">
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131 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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132 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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134 <TR BGCOLOR="white" CLASS="TableRowColor">
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135 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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136 <TD> </TD>
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141 <A NAME="compbio.data.msa"><!-- --></A>
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142 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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143 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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144 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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145 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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147 <TR BGCOLOR="white" CLASS="TableRowColor">
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148 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa"><B>Alignment</B></A></B>
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151 Multiple sequence alignment.</TD>
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153 <TR BGCOLOR="white" CLASS="TableRowColor">
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154 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa"><B>FastaSequence</B></A></B>
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157 A FASTA formatted sequence.</TD>
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159 <TR BGCOLOR="white" CLASS="TableRowColor">
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160 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa"><B>ScoreManager</B></A></B>
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163 </TD>
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168 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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169 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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170 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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171 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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172 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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174 <TR BGCOLOR="white" CLASS="TableRowColor">
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175 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa.jaxws"><B>Alignment</B></A></B>
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178 Multiple sequence alignment.</TD>
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180 <TR BGCOLOR="white" CLASS="TableRowColor">
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181 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa.jaxws"><B>FastaSequence</B></A></B>
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184 A FASTA formatted sequence.</TD>
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186 <TR BGCOLOR="white" CLASS="TableRowColor">
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187 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa.jaxws"><B>ScoreManager</B></A></B>
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190 </TD>
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195 <A NAME="compbio.data.sequence"><!-- --></A>
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196 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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197 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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198 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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199 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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201 <TR BGCOLOR="white" CLASS="TableRowColor">
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202 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence"><B>Alignment</B></A></B>
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205 Multiple sequence alignment.</TD>
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207 <TR BGCOLOR="white" CLASS="TableRowColor">
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208 <TD><B><A HREF="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence"><B>AlignmentMetadata</B></A></B>
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211 Alignment metadata e.g.</TD>
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213 <TR BGCOLOR="white" CLASS="TableRowColor">
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214 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ConservationMethod.html#compbio.data.sequence"><B>ConservationMethod</B></A></B>
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217 Enumeration listing of all the supported methods.</TD>
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219 <TR BGCOLOR="white" CLASS="TableRowColor">
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220 <TD><B><A HREF="../../../compbio/data/sequence/class-use/DisorderMethod.html#compbio.data.sequence"><B>DisorderMethod</B></A></B>
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223 </TD>
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225 <TR BGCOLOR="white" CLASS="TableRowColor">
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226 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>
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229 A FASTA formatted sequence.</TD>
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231 <TR BGCOLOR="white" CLASS="TableRowColor">
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232 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>
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235 The list of programmes that can produce alignments</TD>
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237 <TR BGCOLOR="white" CLASS="TableRowColor">
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238 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Range.html#compbio.data.sequence"><B>Range</B></A></B>
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241 </TD>
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243 <TR BGCOLOR="white" CLASS="TableRowColor">
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244 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.data.sequence"><B>Score</B></A></B>
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247 A value class for AACon annotation results storage.</TD>
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249 <TR BGCOLOR="white" CLASS="TableRowColor">
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250 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.sequence"><B>ScoreManager</B></A></B>
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253 </TD>
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255 <TR BGCOLOR="white" CLASS="TableRowColor">
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256 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.ScoreHolder.html#compbio.data.sequence"><B>ScoreManager.ScoreHolder</B></A></B>
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259 </TD>
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261 <TR BGCOLOR="white" CLASS="TableRowColor">
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262 <TD><B><A HREF="../../../compbio/data/sequence/class-use/SMERFSConstraints.html#compbio.data.sequence"><B>SMERFSConstraints</B></A></B>
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265 Enumeration defining two constraints for SMERFS columns score calculation.</TD>
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267 <TR BGCOLOR="white" CLASS="TableRowColor">
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268 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>
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271 </TD>
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276 <A NAME="compbio.engine"><!-- --></A>
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277 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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278 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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279 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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280 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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282 <TR BGCOLOR="white" CLASS="TableRowColor">
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283 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.engine"><B>FastaSequence</B></A></B>
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286 A FASTA formatted sequence.</TD>
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291 <A NAME="compbio.metadata"><!-- --></A>
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292 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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293 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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294 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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295 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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297 <TR BGCOLOR="white" CLASS="TableRowColor">
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298 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>
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301 A FASTA formatted sequence.</TD>
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306 <A NAME="compbio.pipeline._jpred"><!-- --></A>
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307 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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308 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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309 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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310 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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312 <TR BGCOLOR="white" CLASS="TableRowColor">
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313 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.pipeline._jpred"><B>FastaSequence</B></A></B>
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316 A FASTA formatted sequence.</TD>
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321 <A NAME="compbio.runner"><!-- --></A>
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322 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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323 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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324 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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325 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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327 <TR BGCOLOR="white" CLASS="TableRowColor">
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328 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner"><B>Alignment</B></A></B>
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331 Multiple sequence alignment.</TD>
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333 <TR BGCOLOR="white" CLASS="TableRowColor">
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334 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.runner"><B>FastaSequence</B></A></B>
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337 A FASTA formatted sequence.</TD>
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339 <TR BGCOLOR="white" CLASS="TableRowColor">
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340 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.runner"><B>Score</B></A></B>
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343 A value class for AACon annotation results storage.</TD>
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345 <TR BGCOLOR="white" CLASS="TableRowColor">
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346 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.runner"><B>UnknownFileFormatException</B></A></B>
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349 </TD>
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354 <A NAME="compbio.runner.conservation"><!-- --></A>
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355 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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356 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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357 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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358 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>
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360 <TR BGCOLOR="white" CLASS="TableRowColor">
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361 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.runner.conservation"><B>ScoreManager</B></A></B>
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364 </TD>
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369 <A NAME="compbio.runner.disorder"><!-- --></A>
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370 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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371 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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372 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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373 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>
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375 <TR BGCOLOR="white" CLASS="TableRowColor">
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376 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.runner.disorder"><B>ScoreManager</B></A></B>
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379 </TD>
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384 <A NAME="compbio.runner.msa"><!-- --></A>
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385 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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386 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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387 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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388 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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390 <TR BGCOLOR="white" CLASS="TableRowColor">
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391 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner.msa"><B>Alignment</B></A></B>
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394 Multiple sequence alignment.</TD>
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399 <A NAME="compbio.ws.server"><!-- --></A>
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400 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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401 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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402 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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403 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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405 <TR BGCOLOR="white" CLASS="TableRowColor">
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406 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.ws.server"><B>Alignment</B></A></B>
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409 Multiple sequence alignment.</TD>
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411 <TR BGCOLOR="white" CLASS="TableRowColor">
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412 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.ws.server"><B>FastaSequence</B></A></B>
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415 A FASTA formatted sequence.</TD>
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417 <TR BGCOLOR="white" CLASS="TableRowColor">
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418 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.ws.server"><B>ScoreManager</B></A></B>
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421 </TD>
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