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18 parent.document.title="Score";
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58 <A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>
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79 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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81 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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84 <A NAME="skip-navbar_top"></A>
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.data.sequence</FONT>
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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.Score</B>
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99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></DD>
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103 <DT><PRE><FONT SIZE="-1">@Immutable
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104 </FONT>public class <B>Score</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><DT>implements <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></DL>
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108 A value class for AACon annotation results storage. The objects of this type
114 <DT><B>Author:</B></DT>
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121 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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123 <A NAME="constructor_summary"><!-- --></A>
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124 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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125 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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126 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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127 <B>Constructor Summary</B></FONT></TH>
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129 <TR BGCOLOR="white" CLASS="TableRowColor">
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130 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList)">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><?> method,
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131 <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> scores)</CODE>
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134 Instantiate the Score</TD>
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136 <TR BGCOLOR="white" CLASS="TableRowColor">
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137 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><?> method,
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138 <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> scores,
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139 <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/Range.html" title="class in compbio.data.sequence">Range</A>> ranges)</CODE>
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142 </TD>
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144 <TR BGCOLOR="white" CLASS="TableRowColor">
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145 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, float[])">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><?> method,
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146 float[] scores)</CODE>
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149 </TD>
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151 <TR BGCOLOR="white" CLASS="TableRowColor">
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152 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.TreeSet)">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><?> method,
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153 <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/Range.html" title="class in compbio.data.sequence">Range</A>> ranges)</CODE>
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156 </TD>
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160 <!-- ========== METHOD SUMMARY =========== -->
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162 <A NAME="method_summary"><!-- --></A>
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163 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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164 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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165 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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166 <B>Method Summary</B></FONT></TH>
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168 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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170 <CODE> int</CODE></FONT></TD>
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171 <TD><CODE><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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174 </TD>
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176 <TR BGCOLOR="white" CLASS="TableRowColor">
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177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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178 <CODE> boolean</CODE></FONT></TD>
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179 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.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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182 </TD>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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186 <CODE> <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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187 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getMethod()">getMethod</A></B>()</CODE>
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190 Returns the ConservationMethod</TD>
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192 <TR BGCOLOR="white" CLASS="TableRowColor">
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193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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194 <CODE> <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/Range.html" title="class in compbio.data.sequence">Range</A>></CODE></FONT></TD>
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195 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getRanges()">getRanges</A></B>()</CODE>
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198 Return Ranges if any Collections.EMPTY_SET otherwise</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> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>></CODE></FONT></TD>
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203 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getScores()">getScores</A></B>()</CODE>
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206 The column scores for the alignment</TD>
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208 <TR BGCOLOR="white" CLASS="TableRowColor">
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209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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210 <CODE> int</CODE></FONT></TD>
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211 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#hashCode()">hashCode</A></B>()</CODE>
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214 </TD>
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216 <TR BGCOLOR="white" CLASS="TableRowColor">
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217 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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218 <CODE> void</CODE></FONT></TD>
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219 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#setRanges(java.util.TreeSet)">setRanges</A></B>(<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/Range.html" title="class in compbio.data.sequence">Range</A>> ranges)</CODE>
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222 </TD>
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224 <TR BGCOLOR="white" CLASS="TableRowColor">
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225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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226 <CODE> <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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227 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#toString()">toString</A></B>()</CODE>
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230 </TD>
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232 <TR BGCOLOR="white" CLASS="TableRowColor">
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233 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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234 <CODE>static void</CODE></FONT></TD>
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235 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#write(java.util.TreeSet, java.io.Writer)">write</A></B>(<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>> scores,
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236 <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> writer)</CODE>
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239 Outputs the List of Score objects into the Output stream.</TD>
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242 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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243 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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244 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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245 <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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247 <TR BGCOLOR="white" CLASS="TableRowColor">
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248 <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#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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254 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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256 <A NAME="constructor_detail"><!-- --></A>
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257 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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258 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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259 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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260 <B>Constructor Detail</B></FONT></TH>
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264 <A NAME="Score(java.lang.Enum, java.util.ArrayList)"><!-- --></A><H3>
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267 public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><?> method,
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268 <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> scores)</PRE>
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270 <DD>Instantiate the Score
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273 <DT><B>Parameters:</B><DD><CODE>method</CODE> - the ConservationMethod with which <code>scores</code> were
274 calculated<DD><CODE>scores</CODE> - the actual conservation values for each column of the
279 <A NAME="Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)"><!-- --></A><H3>
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282 public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><?> method,
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283 <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> scores,
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284 <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/Range.html" title="class in compbio.data.sequence">Range</A>> ranges)</PRE>
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287 <DT><B>Parameters:</B><DD><CODE>method</CODE> - the ConservationMethod with which <code>scores</code> were
288 calculated<DD><CODE>scores</CODE> - the actual conservation values for each column of the
289 alignment<DD><CODE>ranges</CODE> - The set of ranges i.e. parts of the sequence with specific
290 function, usually can be calculated based on scores</DL>
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294 <A NAME="Score(java.lang.Enum, java.util.TreeSet)"><!-- --></A><H3>
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297 public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><?> method,
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298 <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/Range.html" title="class in compbio.data.sequence">Range</A>> ranges)</PRE>
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303 <A NAME="Score(java.lang.Enum, float[])"><!-- --></A><H3>
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306 public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><?> method,
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307 float[] scores)</PRE>
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311 <!-- ============ METHOD DETAIL ========== -->
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313 <A NAME="method_detail"><!-- --></A>
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314 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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315 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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316 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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317 <B>Method Detail</B></FONT></TH>
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321 <A NAME="getMethod()"><!-- --></A><H3>
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324 public <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>getMethod</B>()</PRE>
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326 <DD>Returns the ConservationMethod
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333 <DT><B>Returns:</B><DD>the ConservationMethod</DL>
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338 <A NAME="getScores()"><!-- --></A><H3>
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341 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> <B>getScores</B>()</PRE>
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343 <DD>The column scores for the alignment
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350 <DT><B>Returns:</B><DD>the column scores for the alignment</DL>
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355 <A NAME="getRanges()"><!-- --></A><H3>
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358 public <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/Range.html" title="class in compbio.data.sequence">Range</A>> <B>getRanges</B>()</PRE>
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360 <DD>Return Ranges if any Collections.EMPTY_SET otherwise
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367 <DT><B>Returns:</B><DD>ordered set of Range</DL>
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372 <A NAME="setRanges(java.util.TreeSet)"><!-- --></A><H3>
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375 public void <B>setRanges</B>(<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/Range.html" title="class in compbio.data.sequence">Range</A>> ranges)</PRE>
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386 <A NAME="toString()"><!-- --></A><H3>
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389 public <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>toString</B>()</PRE>
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392 <DT><B>Overrides:</B><DD><CODE><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></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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400 <A NAME="hashCode()"><!-- --></A><H3>
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403 public int <B>hashCode</B>()</PRE>
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406 <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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414 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
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417 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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420 <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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428 <A NAME="write(java.util.TreeSet, java.io.Writer)"><!-- --></A><H3>
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431 public static void <B>write</B>(<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>> scores,
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432 <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> writer)
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433 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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435 <DD>Outputs the List of Score objects into the Output stream. The output
436 format is as follows:
439 <code>#MethodName <space separated list of values>
443 #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
444 #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
448 The maximum precision for values is 3 digits, but can be less.
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454 <DT><B>Parameters:</B><DD><CODE>scores</CODE> - the list of scores to output<DD><CODE>writer</CODE> -
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456 <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> - if the OutputStream cannot be written into
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457 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the output stream is null</DL>
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462 <A NAME="compareTo(compbio.data.sequence.Score)"><!-- --></A><H3>
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465 public int <B>compareTo</B>(<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A> o)</PRE>
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468 <DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true#compareTo(T)" title="class or interface in java.lang">compareTo</A></CODE> in interface <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></DL>
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