updated javadoc
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / class-use / Score.html
1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
2 <!--NewPage-->\r
3 <HTML>\r
4 <HEAD>\r
5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:04 BST 2011 -->\r
6 <TITLE>\r
7 Uses of Class compbio.data.sequence.Score\r
8 </TITLE>\r
9 \r
10 <META NAME="date" CONTENT="2011-08-12">\r
11 \r
12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
13 \r
14 <SCRIPT type="text/javascript">\r
15 function windowTitle()\r
16 {\r
17     if (location.href.indexOf('is-external=true') == -1) {\r
18         parent.document.title="Uses of Class compbio.data.sequence.Score";\r
19     }\r
20 }\r
21 </SCRIPT>\r
22 <NOSCRIPT>\r
23 </NOSCRIPT>\r
24 \r
25 </HEAD>\r
26 \r
27 <BODY BGCOLOR="white" onload="windowTitle();">\r
28 <HR>\r
29 \r
30 \r
31 <!-- ========= START OF TOP NAVBAR ======= -->\r
32 <A NAME="navbar_top"><!-- --></A>\r
33 <A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
34 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
35 <TR>\r
36 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
37 <A NAME="navbar_top_firstrow"><!-- --></A>\r
38 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
39   <TR ALIGN="center" VALIGN="top">\r
40   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
41   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
43   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
45   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
46   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
47   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
48   </TR>\r
49 </TABLE>\r
50 </TD>\r
51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
52 </EM>\r
53 </TD>\r
54 </TR>\r
55 \r
56 <TR>\r
57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
58 &nbsp;PREV&nbsp;\r
59 &nbsp;NEXT</FONT></TD>\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
61   <A HREF="../../../../index.html?compbio/data/sequence/\class-useScore.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
62 &nbsp;<A HREF="Score.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
63 &nbsp;<SCRIPT type="text/javascript">\r
64   <!--\r
65   if(window==top) {\r
66     document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
67   }\r
68   //-->\r
69 </SCRIPT>\r
70 <NOSCRIPT>\r
71   <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
72 </NOSCRIPT>\r
73 \r
74 \r
75 </FONT></TD>\r
76 </TR>\r
77 </TABLE>\r
78 <A NAME="skip-navbar_top"></A>\r
79 <!-- ========= END OF TOP NAVBAR ========= -->\r
80 \r
81 <HR>\r
82 <CENTER>\r
83 <H2>\r
84 <B>Uses of Class<br>compbio.data.sequence.Score</B></H2>\r
85 </CENTER>\r
86 \r
87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
90 Packages that use <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>\r
91 </TR>\r
92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
93 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
94 <TD>A data model for multiple sequence alignment web services and utility methods
95  that work on the objects of this model.&nbsp;</TD>\r
96 </TR>\r
97 </TABLE>\r
98 &nbsp;\r
99 <P>\r
100 <A NAME="compbio.data.sequence"><!-- --></A>\r
101 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
102 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
103 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
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>\r
105 </TR>\r
106 </TABLE>\r
107 &nbsp;\r
108 <P>\r
109 \r
110 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
111 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
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>\r
113 </TR>\r
114 <TR BGCOLOR="white" CLASS="TableRowColor">\r
115 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
116 <CODE>&nbsp;<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>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
117 <TD><CODE><B>ScoreManager.ScoreHolder.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#scores">scores</A></B></CODE>\r
118 \r
119 <BR>\r
120 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
121 </TR>\r
122 </TABLE>\r
123 &nbsp;\r
124 <P>\r
125 \r
126 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
127 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
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>\r
129 </TR>\r
130 <TR BGCOLOR="white" CLASS="TableRowColor">\r
131 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
132 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></CODE></FONT></TD>\r
133 <TD><CODE><B>ScoreManager.ScoreHolder.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.Enum)">getScoreByMethod</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>&lt;?&gt;&nbsp;method)</CODE>\r
134 \r
135 <BR>\r
136 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
137 </TR>\r
138 <TR BGCOLOR="white" CLASS="TableRowColor">\r
139 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
140 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></CODE></FONT></TD>\r
141 <TD><CODE><B>ScoreManager.ScoreHolder.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.String)">getScoreByMethod</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>&nbsp;method)</CODE>\r
142 \r
143 <BR>\r
144 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
145 </TR>\r
146 </TABLE>\r
147 &nbsp;\r
148 <P>\r
149 \r
150 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
151 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
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>\r
153 </TR>\r
154 <TR BGCOLOR="white" CLASS="TableRowColor">\r
155 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
156 <CODE>&nbsp;<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>&lt;<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>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
157 <TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#asMap()">asMap</A></B>()</CODE>\r
158 \r
159 <BR>\r
160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
161 </TR>\r
162 <TR BGCOLOR="white" CLASS="TableRowColor">\r
163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
164 <CODE>&nbsp;<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>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
165 <TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#asSet()">asSet</A></B>()</CODE>\r
166 \r
167 <BR>\r
168 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
169 </TR>\r
170 <TR BGCOLOR="white" CLASS="TableRowColor">\r
171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
172 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
173 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)">readAAConResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;results)</CODE>\r
174 \r
175 <BR>\r
176 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read AACon result with no alignment files.</TD>\r
177 </TR>\r
178 <TR BGCOLOR="white" CLASS="TableRowColor">\r
179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
180 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashMap.html?is-external=true" title="class or interface in java.util">HashMap</A>&lt;<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>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
181 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readDisembl(java.io.InputStream)">readDisembl</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;input)</CODE>\r
182 \r
183 <BR>\r
184 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;> Foobar_dundeefriends
185  
186  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
187  
188  # REM465 355-368
189  
190  # HOTLOOPS 190-204
191  
192  # RESIDUE COILS REM465 HOTLOOPS
193  
194  M 0.86010 0.88512 0.37094
195  
196  T 0.79983 0.85864 0.44331
197  
198  >Next Sequence name</TD>\r
199 </TR>\r
200 <TR BGCOLOR="white" CLASS="TableRowColor">\r
201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
202 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashMap.html?is-external=true" title="class or interface in java.util">HashMap</A>&lt;<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>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
203 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readGlobPlot(java.io.InputStream)">readGlobPlot</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;input)</CODE>\r
204 \r
205 <BR>\r
206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;> Foobar_dundeefriends
207  
208  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
209  
210  # REM465 355-368
211  
212  # HOTLOOPS 190-204
213  
214  # RESIDUE COILS REM465 HOTLOOPS
215  
216  M 0.86010 0.88512 0.37094
217  
218  T 0.79983 0.85864 0.44331
219  
220  >Next Sequence name</TD>\r
221 </TR>\r
222 <TR BGCOLOR="white" CLASS="TableRowColor">\r
223 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
224 <CODE>static&nbsp;<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>&lt;<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>&gt;</CODE></FONT></TD>\r
225 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readIUPred(java.io.File)">readIUPred</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;result)</CODE>\r
226 \r
227 <BR>\r
228 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read IUPred output</TD>\r
229 </TR>\r
230 <TR BGCOLOR="white" CLASS="TableRowColor">\r
231 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
232 <CODE>static&nbsp;<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>&lt;<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>&gt;</CODE></FONT></TD>\r
233 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)">readJRonn</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;result)</CODE>\r
234 \r
235 <BR>\r
236 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
237 </TR>\r
238 <TR BGCOLOR="white" CLASS="TableRowColor">\r
239 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
240 <CODE>static&nbsp;<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>&lt;<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>&gt;</CODE></FONT></TD>\r
241 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)">readJRonn</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;inStream)</CODE>\r
242 \r
243 <BR>\r
244 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reader for JRonn horizontal file format</TD>\r
245 </TR>\r
246 </TABLE>\r
247 &nbsp;\r
248 <P>\r
249 \r
250 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
251 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
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>\r
253 </TR>\r
254 <TR BGCOLOR="white" CLASS="TableRowColor">\r
255 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
256 <CODE>&nbsp;int</CODE></FONT></TD>\r
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>&nbsp;o)</CODE>\r
258 \r
259 <BR>\r
260 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
261 </TR>\r
262 </TABLE>\r
263 &nbsp;\r
264 <P>\r
265 \r
266 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
267 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
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>\r
269 </TR>\r
270 <TR BGCOLOR="white" CLASS="TableRowColor">\r
271 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
272 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
273 <TD><CODE><B>ScoreManager.</B><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>&lt;<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>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;&nbsp;data)</CODE>\r
274 \r
275 <BR>\r
276 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
277 </TR>\r
278 <TR BGCOLOR="white" CLASS="TableRowColor">\r
279 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
280 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
281 <TD><CODE><B>ScoreManager.</B><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>&lt;<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>&gt;&nbsp;seqScoresMap)</CODE>\r
282 \r
283 <BR>\r
284 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
285 </TR>\r
286 <TR BGCOLOR="white" CLASS="TableRowColor">\r
287 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
288 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
289 <TD><CODE><B>ScoreManager.</B><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>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;data)</CODE>\r
290 \r
291 <BR>\r
292 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
293 </TR>\r
294 <TR BGCOLOR="white" CLASS="TableRowColor">\r
295 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
296 <CODE>static&nbsp;void</CODE></FONT></TD>\r
297 <TD><CODE><B>Score.</B><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>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;scores,\r
298       <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>&nbsp;writer)</CODE>\r
299 \r
300 <BR>\r
301 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Outputs the List of Score objects into the Output stream.</TD>\r
302 </TR>\r
303 </TABLE>\r
304 &nbsp;\r
305 <P>\r
306 <HR>\r
307 \r
308 \r
309 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
310 <A NAME="navbar_bottom"><!-- --></A>\r
311 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
312 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
313 <TR>\r
314 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
315 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
316 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
317   <TR ALIGN="center" VALIGN="top">\r
318   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
319   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
320   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
321   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
322   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
323   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
324   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
325   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
326   </TR>\r
327 </TABLE>\r
328 </TD>\r
329 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
330 </EM>\r
331 </TD>\r
332 </TR>\r
333 \r
334 <TR>\r
335 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
336 &nbsp;PREV&nbsp;\r
337 &nbsp;NEXT</FONT></TD>\r
338 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
339   <A HREF="../../../../index.html?compbio/data/sequence/\class-useScore.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
340 &nbsp;<A HREF="Score.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
341 &nbsp;<SCRIPT type="text/javascript">\r
342   <!--\r
343   if(window==top) {\r
344     document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
345   }\r
346   //-->\r
347 </SCRIPT>\r
348 <NOSCRIPT>\r
349   <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
350 </NOSCRIPT>\r
351 \r
352 \r
353 </FONT></TD>\r
354 </TR>\r
355 </TABLE>\r
356 <A NAME="skip-navbar_bottom"></A>\r
357 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
358 \r
359 <HR>\r
360 \r
361 </BODY>\r
362 </HTML>\r