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7 Uses of Class compbio.data.sequence.Score
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18 parent.document.title="Uses of Class compbio.data.sequence.Score";
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84 <B>Uses of Class<br>compbio.data.sequence.Score</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/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>
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94 <TD>A data model for multiple sequence alignment web services and utility methods
95 that work on the objects of this model. </TD>
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100 <A NAME="compbio.data.sequence"><!-- --></A>
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101 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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102 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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103 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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104 Uses of <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>
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110 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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111 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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112 <TH ALIGN="left" COLSPAN="2">Fields in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type parameters of type <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>
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114 <TR BGCOLOR="white" CLASS="TableRowColor">
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115 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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116 <CODE> java.util.TreeSet<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>
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117 <TD><CODE><B>ScoreManager.ScoreHolder.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#scores">scores</A></B></CODE>
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120 </TD>
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126 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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127 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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128 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>
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130 <TR BGCOLOR="white" CLASS="TableRowColor">
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131 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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132 <CODE> <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></CODE></FONT></TD>
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133 <TD><CODE><B>ScoreManager.ScoreHolder.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.Enum)">getScoreByMethod</A></B>(java.lang.Enum<?> method)</CODE>
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136 </TD>
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138 <TR BGCOLOR="white" CLASS="TableRowColor">
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139 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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140 <CODE> <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></CODE></FONT></TD>
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141 <TD><CODE><B>ScoreManager.ScoreHolder.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.String)">getScoreByMethod</A></B>(java.lang.String method)</CODE>
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144 </TD>
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150 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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151 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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152 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>
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154 <TR BGCOLOR="white" CLASS="TableRowColor">
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155 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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156 <CODE> java.util.Map<java.lang.String,java.util.TreeSet<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>></CODE></FONT></TD>
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157 <TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#asMap()">asMap</A></B>()</CODE>
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160 </TD>
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162 <TR BGCOLOR="white" CLASS="TableRowColor">
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163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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164 <CODE> java.util.Set<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>
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165 <TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#asSet()">asSet</A></B>()</CODE>
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168 </TD>
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170 <TR BGCOLOR="white" CLASS="TableRowColor">
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171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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172 <CODE>static java.util.HashSet<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>
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173 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)">readAAConResults</A></B>(java.io.InputStream results)</CODE>
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176 Read AACon result with no alignment files.</TD>
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178 <TR BGCOLOR="white" CLASS="TableRowColor">
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179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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180 <CODE>static java.util.HashMap<java.lang.String,java.util.Set<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>></CODE></FONT></TD>
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181 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readDisembl(java.io.InputStream)">readDisembl</A></B>(java.io.InputStream input)</CODE>
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184 > Foobar_dundeefriends
186 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
192 # RESIDUE COILS REM465 HOTLOOPS
194 M 0.86010 0.88512 0.37094
196 T 0.79983 0.85864 0.44331
198 >Next Sequence name</TD>
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200 <TR BGCOLOR="white" CLASS="TableRowColor">
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201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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202 <CODE>static java.util.HashMap<java.lang.String,java.util.Set<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>></CODE></FONT></TD>
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203 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readGlobPlot(java.io.InputStream)">readGlobPlot</A></B>(java.io.InputStream input)</CODE>
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206 > Foobar_dundeefriends
208 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
214 # RESIDUE COILS REM465 HOTLOOPS
216 M 0.86010 0.88512 0.37094
218 T 0.79983 0.85864 0.44331
220 >Next Sequence name</TD>
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222 <TR BGCOLOR="white" CLASS="TableRowColor">
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223 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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224 <CODE>static java.util.Map<java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>
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225 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readIUPred(java.io.File)">readIUPred</A></B>(java.io.File result)</CODE>
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228 Read IUPred output</TD>
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230 <TR BGCOLOR="white" CLASS="TableRowColor">
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231 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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232 <CODE>static java.util.Map<java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>
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233 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)">readJRonn</A></B>(java.io.File result)</CODE>
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236 </TD>
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238 <TR BGCOLOR="white" CLASS="TableRowColor">
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239 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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240 <CODE>static java.util.Map<java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>
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241 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)">readJRonn</A></B>(java.io.InputStream inStream)</CODE>
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244 Reader for JRonn horizontal file format</TD>
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250 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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251 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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252 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>
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254 <TR BGCOLOR="white" CLASS="TableRowColor">
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255 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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256 <CODE> int</CODE></FONT></TD>
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257 <TD><CODE><B>Score.</B><B><A HREF="../../../../compbio/data/sequence/Score.html#compareTo(compbio.data.sequence.Score)">compareTo</A></B>(<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A> o)</CODE>
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260 </TD>
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266 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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267 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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268 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>
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270 <TR BGCOLOR="white" CLASS="TableRowColor">
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271 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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272 <CODE>static <A HREF="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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273 <TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#newInstance(java.util.Map)">newInstance</A></B>(java.util.Map<java.lang.String,java.util.Set<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> data)</CODE>
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276 </TD>
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278 <TR BGCOLOR="white" CLASS="TableRowColor">
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279 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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280 <CODE>static <A HREF="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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281 <TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore(java.util.Map)">newInstanceSingleScore</A></B>(java.util.Map<java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> seqScoresMap)</CODE>
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284 </TD>
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286 <TR BGCOLOR="white" CLASS="TableRowColor">
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287 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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288 <CODE>static <A HREF="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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289 <TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence(java.util.Set)">newInstanceSingleSequence</A></B>(java.util.Set<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> data)</CODE>
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292 </TD>
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294 <TR BGCOLOR="white" CLASS="TableRowColor">
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295 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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296 <CODE>static void</CODE></FONT></TD>
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297 <TD><CODE><B>Score.</B><B><A HREF="../../../../compbio/data/sequence/Score.html#write(java.util.TreeSet, java.io.Writer)">write</A></B>(java.util.TreeSet<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> scores,
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298 java.io.Writer writer)</CODE>
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301 Outputs the List of Score objects into the Output stream.</TD>
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321 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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