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7 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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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.metadata"><B>compbio.metadata</B></A></TD>
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107 <TD>A meta-data model for multiple sequence alignment web services
108 Classes in this package have no dependencies to other sources in the project. </TD>
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113 <A NAME="compbio.data.msa"><!-- --></A>
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114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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117 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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119 <TR BGCOLOR="white" CLASS="TableRowColor">
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120 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa"><B>Alignment</B></A></B>
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123 Multiple sequence alignment.</TD>
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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa"><B>FastaSequence</B></A></B>
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129 A FASTA formatted sequence.</TD>
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131 <TR BGCOLOR="white" CLASS="TableRowColor">
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132 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa"><B>ScoreManager</B></A></B>
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135 </TD>
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140 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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141 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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143 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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144 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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146 <TR BGCOLOR="white" CLASS="TableRowColor">
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147 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa.jaxws"><B>Alignment</B></A></B>
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150 Multiple sequence alignment.</TD>
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152 <TR BGCOLOR="white" CLASS="TableRowColor">
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153 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa.jaxws"><B>FastaSequence</B></A></B>
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156 A FASTA formatted sequence.</TD>
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158 <TR BGCOLOR="white" CLASS="TableRowColor">
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159 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa.jaxws"><B>ScoreManager</B></A></B>
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162 </TD>
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167 <A NAME="compbio.data.sequence"><!-- --></A>
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168 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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170 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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171 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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173 <TR BGCOLOR="white" CLASS="TableRowColor">
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174 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence"><B>Alignment</B></A></B>
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177 Multiple sequence alignment.</TD>
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179 <TR BGCOLOR="white" CLASS="TableRowColor">
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180 <TD><B><A HREF="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence"><B>AlignmentMetadata</B></A></B>
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183 Alignment metadata e.g.</TD>
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185 <TR BGCOLOR="white" CLASS="TableRowColor">
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186 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ConservationMethod.html#compbio.data.sequence"><B>ConservationMethod</B></A></B>
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189 Enumeration listing of all the supported methods.</TD>
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191 <TR BGCOLOR="white" CLASS="TableRowColor">
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192 <TD><B><A HREF="../../../compbio/data/sequence/class-use/DisorderMethod.html#compbio.data.sequence"><B>DisorderMethod</B></A></B>
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195 </TD>
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197 <TR BGCOLOR="white" CLASS="TableRowColor">
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198 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>
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201 A FASTA formatted sequence.</TD>
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203 <TR BGCOLOR="white" CLASS="TableRowColor">
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204 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>
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207 The list of programmes that can produce alignments</TD>
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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Range.html#compbio.data.sequence"><B>Range</B></A></B>
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213 </TD>
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215 <TR BGCOLOR="white" CLASS="TableRowColor">
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216 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.data.sequence"><B>Score</B></A></B>
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219 A value class for AACon annotation results storage.</TD>
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221 <TR BGCOLOR="white" CLASS="TableRowColor">
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222 <TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.sequence"><B>ScoreManager</B></A></B>
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225 </TD>
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227 <TR BGCOLOR="white" CLASS="TableRowColor">
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228 <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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231 </TD>
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233 <TR BGCOLOR="white" CLASS="TableRowColor">
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234 <TD><B><A HREF="../../../compbio/data/sequence/class-use/SMERFSConstraints.html#compbio.data.sequence"><B>SMERFSConstraints</B></A></B>
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237 Enumeration defining two constraints for SMERFS columns score calculation.</TD>
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239 <TR BGCOLOR="white" CLASS="TableRowColor">
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240 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>
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243 </TD>
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248 <A NAME="compbio.metadata"><!-- --></A>
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249 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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252 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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254 <TR BGCOLOR="white" CLASS="TableRowColor">
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255 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>
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258 A FASTA formatted sequence.</TD>
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