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17 if (location.href.indexOf('is-external=true') == -1) {
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18 parent.document.title="ScoreManager";
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79 SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
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81 DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
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85 <!-- ========= END OF TOP NAVBAR ========= -->
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.data.sequence</FONT>
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93 Class ScoreManager</H2>
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95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.ScoreManager</B>
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100 <DT><PRE>public class <B>ScoreManager</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>
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107 <!-- ======== NESTED CLASS SUMMARY ======== -->
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111 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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112 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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113 <B>Nested Class Summary</B></FONT></TH>
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115 <TR BGCOLOR="white" CLASS="TableRowColor">
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116 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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117 <CODE>static class</CODE></FONT></TD>
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118 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A></B></CODE>
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121 </TD>
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124 <!-- =========== FIELD SUMMARY =========== -->
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126 <A NAME="field_summary"><!-- --></A>
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127 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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128 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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129 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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130 <B>Field Summary</B></FONT></TH>
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132 <TR BGCOLOR="white" CLASS="TableRowColor">
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133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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134 <CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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135 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</A></B></CODE>
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138 </TD>
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142 <!-- ========== METHOD SUMMARY =========== -->
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144 <A NAME="method_summary"><!-- --></A>
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145 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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146 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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147 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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148 <B>Method Summary</B></FONT></TH>
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150 <TR BGCOLOR="white" CLASS="TableRowColor">
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151 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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152 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/TreeSet.html?is-external=true" title="class or interface in java.util">TreeSet</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>></CODE></FONT></TD>
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153 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#asMap()">asMap</A></B>()</CODE>
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156 </TD>
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158 <TR BGCOLOR="white" CLASS="TableRowColor">
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159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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160 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>
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161 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#asSet()">asSet</A></B>()</CODE>
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164 </TD>
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166 <TR BGCOLOR="white" CLASS="TableRowColor">
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167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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168 <CODE> boolean</CODE></FONT></TD>
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169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>
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172 </TD>
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174 <TR BGCOLOR="white" CLASS="TableRowColor">
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175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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176 <CODE> <A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A></CODE></FONT></TD>
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177 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence(java.lang.String)">getAnnotationForSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> seqId)</CODE>
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180 </TD>
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182 <TR BGCOLOR="white" CLASS="TableRowColor">
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183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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184 <CODE> int</CODE></FONT></TD>
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185 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#getNumberOfSeq()">getNumberOfSeq</A></B>()</CODE>
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188 </TD>
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190 <TR BGCOLOR="white" CLASS="TableRowColor">
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191 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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192 <CODE> int</CODE></FONT></TD>
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193 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#hashCode()">hashCode</A></B>()</CODE>
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196 </TD>
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198 <TR BGCOLOR="white" CLASS="TableRowColor">
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199 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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200 <CODE>static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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201 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#newInstance(java.util.Map)">newInstance</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> data)</CODE>
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204 </TD>
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206 <TR BGCOLOR="white" CLASS="TableRowColor">
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207 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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208 <CODE>static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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209 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore(java.util.Map)">newInstanceSingleScore</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> seqScoresMap)</CODE>
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212 </TD>
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214 <TR BGCOLOR="white" CLASS="TableRowColor">
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215 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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216 <CODE>static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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217 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence(java.util.Set)">newInstanceSingleSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> data)</CODE>
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220 </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> void</CODE></FONT></TD>
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225 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#writeOut(java.io.Writer)">writeOut</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A> outStream)</CODE>
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228 </TD>
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231 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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232 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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233 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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234 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
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236 <TR BGCOLOR="white" CLASS="TableRowColor">
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237 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
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243 <!-- ============ FIELD DETAIL =========== -->
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245 <A NAME="field_detail"><!-- --></A>
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246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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247 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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248 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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249 <B>Field Detail</B></FONT></TH>
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253 <A NAME="SINGLE_ENTRY_KEY"><!-- --></A><H3>
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254 SINGLE_ENTRY_KEY</H3>
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256 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>SINGLE_ENTRY_KEY</B></PRE>
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259 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY">Constant Field Values</A></DL>
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262 <!-- ============ METHOD DETAIL ========== -->
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264 <A NAME="method_detail"><!-- --></A>
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265 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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266 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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267 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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268 <B>Method Detail</B></FONT></TH>
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272 <A NAME="newInstance(java.util.Map)"><!-- --></A><H3>
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275 public static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>newInstance</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> data)</PRE>
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283 <A NAME="newInstanceSingleScore(java.util.Map)"><!-- --></A><H3>
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284 newInstanceSingleScore</H3>
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286 public static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>newInstanceSingleScore</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> seqScoresMap)</PRE>
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294 <A NAME="newInstanceSingleSequence(java.util.Set)"><!-- --></A><H3>
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295 newInstanceSingleSequence</H3>
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297 public static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>newInstanceSingleSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> data)</PRE>
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305 <A NAME="asMap()"><!-- --></A><H3>
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308 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/TreeSet.html?is-external=true" title="class or interface in java.util">TreeSet</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> <B>asMap</B>()</PRE>
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316 <A NAME="asSet()"><!-- --></A><H3>
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319 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> <B>asSet</B>()</PRE>
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327 <A NAME="getNumberOfSeq()"><!-- --></A><H3>
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328 getNumberOfSeq</H3>
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330 public int <B>getNumberOfSeq</B>()</PRE>
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338 <A NAME="getAnnotationForSequence(java.lang.String)"><!-- --></A><H3>
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339 getAnnotationForSequence</H3>
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341 public <A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A> <B>getAnnotationForSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> seqId)</PRE>
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349 <A NAME="writeOut(java.io.Writer)"><!-- --></A><H3>
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352 public void <B>writeOut</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A> outStream)
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353 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>
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358 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>
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363 <A NAME="hashCode()"><!-- --></A><H3>
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366 public int <B>hashCode</B>()</PRE>
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369 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
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377 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
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380 public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>
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383 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
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389 <!-- ========= END OF CLASS DATA ========= -->
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393 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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394 <A NAME="navbar_bottom"><!-- --></A>
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395 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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399 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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402 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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405 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ScoreManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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407 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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408 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
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409 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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413 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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419 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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420 <A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>
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421 <A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
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423 <A HREF="../../../index.html?compbio/data/sequence/ScoreManager.html" target="_top"><B>FRAMES</B></A>
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424 <A HREF="ScoreManager.html" target="_top"><B>NO FRAMES</B></A>
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