1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
5 <!-- Generated by javadoc (1.8.0_121) on Fri Apr 21 15:32:50 BST 2017 -->
6 <title>ScoreManager</title>
7 <meta name="date" content="2017-04-21">
8 <link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
9 <script type="text/javascript" src="../../../script.js"></script>
12 <script type="text/javascript"><!--
14 if (location.href.indexOf('is-external=true') == -1) {
15 parent.document.title="ScoreManager";
21 var methods = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10,"i5":10,"i6":9,"i7":9,"i8":9,"i9":10};
22 var tabs = {65535:["t0","All Methods"],1:["t1","Static Methods"],2:["t2","Instance Methods"],8:["t4","Concrete Methods"]};
23 var altColor = "altColor";
24 var rowColor = "rowColor";
25 var tableTab = "tableTab";
26 var activeTableTab = "activeTableTab";
29 <div>JavaScript is disabled on your browser.</div>
31 <!-- ========= START OF TOP NAVBAR ======= -->
32 <div class="topNav"><a name="navbar.top">
35 <div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
36 <a name="navbar.top.firstrow">
39 <ul class="navList" title="Navigation">
40 <li><a href="../../../overview-summary.html">Overview</a></li>
41 <li><a href="package-summary.html">Package</a></li>
42 <li class="navBarCell1Rev">Class</li>
43 <li><a href="class-use/ScoreManager.html">Use</a></li>
44 <li><a href="package-tree.html">Tree</a></li>
45 <li><a href="../../../deprecated-list.html">Deprecated</a></li>
46 <li><a href="../../../index-files/index-1.html">Index</a></li>
47 <li><a href="../../../help-doc.html">Help</a></li>
52 <li><a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><span class="typeNameLink">Prev Class</span></a></li>
53 <li><a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><span class="typeNameLink">Next Class</span></a></li>
56 <li><a href="../../../index.html?compbio/data/sequence/ScoreManager.html" target="_top">Frames</a></li>
57 <li><a href="ScoreManager.html" target="_top">No Frames</a></li>
59 <ul class="navList" id="allclasses_navbar_top">
60 <li><a href="../../../allclasses-noframe.html">All Classes</a></li>
63 <script type="text/javascript"><!--
64 allClassesLink = document.getElementById("allclasses_navbar_top");
66 allClassesLink.style.display = "block";
69 allClassesLink.style.display = "none";
75 <ul class="subNavList">
76 <li>Summary: </li>
77 <li><a href="#nested.class.summary">Nested</a> | </li>
78 <li><a href="#field.summary">Field</a> | </li>
79 <li><a href="#constructor.summary">Constr</a> | </li>
80 <li><a href="#method.summary">Method</a></li>
82 <ul class="subNavList">
83 <li>Detail: </li>
84 <li><a href="#field.detail">Field</a> | </li>
85 <li><a href="#constructor.detail">Constr</a> | </li>
86 <li><a href="#method.detail">Method</a></li>
89 <a name="skip.navbar.top">
92 <!-- ========= END OF TOP NAVBAR ========= -->
93 <!-- ======== START OF CLASS DATA ======== -->
95 <div class="subTitle">compbio.data.sequence</div>
96 <h2 title="Class ScoreManager" class="title">Class ScoreManager</h2>
98 <div class="contentContainer">
99 <ul class="inheritance">
100 <li>java.lang.Object</li>
102 <ul class="inheritance">
103 <li>compbio.data.sequence.ScoreManager</li>
107 <div class="description">
108 <ul class="blockList">
109 <li class="blockList">
111 <dt>Direct Known Subclasses:</dt>
112 <dd><a href="../../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></dd>
116 <pre>public class <span class="typeNameLabel">ScoreManager</span>
117 extends java.lang.Object</pre>
121 <div class="summary">
122 <ul class="blockList">
123 <li class="blockList">
124 <!-- ======== NESTED CLASS SUMMARY ======== -->
125 <ul class="blockList">
126 <li class="blockList"><a name="nested.class.summary">
129 <h3>Nested Class Summary</h3>
130 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Nested Class Summary table, listing nested classes, and an explanation">
131 <caption><span>Nested Classes</span><span class="tabEnd"> </span></caption>
133 <th class="colFirst" scope="col">Modifier and Type</th>
134 <th class="colLast" scope="col">Class and Description</th>
136 <tr class="altColor">
137 <td class="colFirst"><code>static class </code></td>
138 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></span></code> </td>
143 <!-- =========== FIELD SUMMARY =========== -->
144 <ul class="blockList">
145 <li class="blockList"><a name="field.summary">
148 <h3>Field Summary</h3>
149 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
150 <caption><span>Fields</span><span class="tabEnd"> </span></caption>
152 <th class="colFirst" scope="col">Modifier and Type</th>
153 <th class="colLast" scope="col">Field and Description</th>
155 <tr class="altColor">
156 <td class="colFirst"><code>protected java.util.List<<a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a>></code></td>
157 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#seqScores">seqScores</a></span></code> </td>
159 <tr class="rowColor">
160 <td class="colFirst"><code>static java.lang.String</code></td>
161 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</a></span></code> </td>
166 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
167 <ul class="blockList">
168 <li class="blockList"><a name="constructor.summary">
171 <h3>Constructor Summary</h3>
172 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
173 <caption><span>Constructors</span><span class="tabEnd"> </span></caption>
175 <th class="colFirst" scope="col">Modifier</th>
176 <th class="colLast" scope="col">Constructor and Description</th>
178 <tr class="altColor">
179 <td class="colFirst"><code>protected </code></td>
180 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#ScoreManager--">ScoreManager</a></span>()</code> </td>
182 <tr class="rowColor">
183 <td class="colFirst"><code>private </code></td>
184 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#ScoreManager-java.util.Map-">ScoreManager</a></span>(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> </td>
186 <tr class="altColor">
187 <td class="colFirst"><code>private </code></td>
188 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#ScoreManager-java.lang.String-java.util.Set-">ScoreManager</a></span>(java.lang.String id,
189 java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> data)</code> </td>
194 <!-- ========== METHOD SUMMARY =========== -->
195 <ul class="blockList">
196 <li class="blockList"><a name="method.summary">
199 <h3>Method Summary</h3>
200 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
201 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd"> </span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd"> </span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd"> </span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd"> </span></span></caption>
203 <th class="colFirst" scope="col">Modifier and Type</th>
204 <th class="colLast" scope="col">Method and Description</th>
206 <tr id="i0" class="altColor">
207 <td class="colFirst"><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></td>
208 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#asMap--">asMap</a></span>()</code> </td>
210 <tr id="i1" class="rowColor">
211 <td class="colFirst"><code>java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>></code></td>
212 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#asSet--">asSet</a></span>()</code> </td>
214 <tr id="i2" class="altColor">
215 <td class="colFirst"><code>boolean</code></td>
216 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#equals-java.lang.Object-">equals</a></span>(java.lang.Object obj)</code> </td>
218 <tr id="i3" class="rowColor">
219 <td class="colFirst"><code><a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></code></td>
220 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence-java.lang.String-">getAnnotationForSequence</a></span>(java.lang.String seqId)</code> </td>
222 <tr id="i4" class="altColor">
223 <td class="colFirst"><code>int</code></td>
224 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#getNumberOfSeq--">getNumberOfSeq</a></span>()</code> </td>
226 <tr id="i5" class="rowColor">
227 <td class="colFirst"><code>int</code></td>
228 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#hashCode--">hashCode</a></span>()</code> </td>
230 <tr id="i6" class="altColor">
231 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
232 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#newInstance-java.util.Map-">newInstance</a></span>(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> </td>
234 <tr id="i7" class="rowColor">
235 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
236 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore-java.util.Map-">newInstanceSingleScore</a></span>(java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> seqScoresMap)</code> </td>
238 <tr id="i8" class="altColor">
239 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
240 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence-java.util.Set-">newInstanceSingleSequence</a></span>(java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> data)</code> </td>
242 <tr id="i9" class="rowColor">
243 <td class="colFirst"><code>void</code></td>
244 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#writeOut-java.io.Writer-">writeOut</a></span>(java.io.Writer outStream)</code> </td>
247 <ul class="blockList">
248 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
251 <h3>Methods inherited from class java.lang.Object</h3>
252 <code>clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait</code></li>
259 <div class="details">
260 <ul class="blockList">
261 <li class="blockList">
262 <!-- ============ FIELD DETAIL =========== -->
263 <ul class="blockList">
264 <li class="blockList"><a name="field.detail">
267 <h3>Field Detail</h3>
268 <a name="SINGLE_ENTRY_KEY">
271 <ul class="blockList">
272 <li class="blockList">
273 <h4>SINGLE_ENTRY_KEY</h4>
274 <pre>public static final java.lang.String SINGLE_ENTRY_KEY</pre>
276 <dt><span class="seeLabel">See Also:</span></dt>
277 <dd><a href="../../../constant-values.html#compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY">Constant Field Values</a></dd>
284 <ul class="blockListLast">
285 <li class="blockList">
287 <pre>protected java.util.List<<a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a>> seqScores</pre>
292 <!-- ========= CONSTRUCTOR DETAIL ======== -->
293 <ul class="blockList">
294 <li class="blockList"><a name="constructor.detail">
297 <h3>Constructor Detail</h3>
298 <a name="ScoreManager--">
301 <ul class="blockList">
302 <li class="blockList">
303 <h4>ScoreManager</h4>
304 <pre>protected ScoreManager()</pre>
307 <a name="ScoreManager-java.lang.String-java.util.Set-">
310 <ul class="blockList">
311 <li class="blockList">
312 <h4>ScoreManager</h4>
313 <pre>private ScoreManager(java.lang.String id,
314 java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> data)</pre>
317 <a name="ScoreManager-java.util.Map-">
320 <ul class="blockListLast">
321 <li class="blockList">
322 <h4>ScoreManager</h4>
323 <pre>private ScoreManager(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)</pre>
328 <!-- ============ METHOD DETAIL ========== -->
329 <ul class="blockList">
330 <li class="blockList"><a name="method.detail">
333 <h3>Method Detail</h3>
334 <a name="newInstance-java.util.Map-">
337 <ul class="blockList">
338 <li class="blockList">
340 <pre>public static <a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a> newInstance(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)</pre>
343 <a name="newInstanceSingleScore-java.util.Map-">
346 <ul class="blockList">
347 <li class="blockList">
348 <h4>newInstanceSingleScore</h4>
349 <pre>public static <a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a> newInstanceSingleScore(java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> seqScoresMap)</pre>
352 <a name="newInstanceSingleSequence-java.util.Set-">
355 <ul class="blockList">
356 <li class="blockList">
357 <h4>newInstanceSingleSequence</h4>
358 <pre>public static <a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a> newInstanceSingleSequence(java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> data)</pre>
364 <ul class="blockList">
365 <li class="blockList">
367 <pre>public java.util.Map<java.lang.String,java.util.TreeSet<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>>> asMap()</pre>
373 <ul class="blockList">
374 <li class="blockList">
376 <pre>public java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> asSet()</pre>
379 <a name="getNumberOfSeq--">
382 <ul class="blockList">
383 <li class="blockList">
384 <h4>getNumberOfSeq</h4>
385 <pre>public int getNumberOfSeq()</pre>
388 <a name="getAnnotationForSequence-java.lang.String-">
391 <ul class="blockList">
392 <li class="blockList">
393 <h4>getAnnotationForSequence</h4>
394 <pre>public <a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a> getAnnotationForSequence(java.lang.String seqId)</pre>
397 <a name="writeOut-java.io.Writer-">
400 <ul class="blockList">
401 <li class="blockList">
403 <pre>public void writeOut(java.io.Writer outStream)
404 throws java.io.IOException</pre>
406 <dt><span class="throwsLabel">Throws:</span></dt>
407 <dd><code>java.io.IOException</code></dd>
411 <a name="hashCode--">
414 <ul class="blockList">
415 <li class="blockList">
417 <pre>public int hashCode()</pre>
419 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
420 <dd><code>hashCode</code> in class <code>java.lang.Object</code></dd>
424 <a name="equals-java.lang.Object-">
427 <ul class="blockListLast">
428 <li class="blockList">
430 <pre>public boolean equals(java.lang.Object obj)</pre>
432 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
433 <dd><code>equals</code> in class <code>java.lang.Object</code></dd>
443 <!-- ========= END OF CLASS DATA ========= -->
444 <!-- ======= START OF BOTTOM NAVBAR ====== -->
445 <div class="bottomNav"><a name="navbar.bottom">
448 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
449 <a name="navbar.bottom.firstrow">
452 <ul class="navList" title="Navigation">
453 <li><a href="../../../overview-summary.html">Overview</a></li>
454 <li><a href="package-summary.html">Package</a></li>
455 <li class="navBarCell1Rev">Class</li>
456 <li><a href="class-use/ScoreManager.html">Use</a></li>
457 <li><a href="package-tree.html">Tree</a></li>
458 <li><a href="../../../deprecated-list.html">Deprecated</a></li>
459 <li><a href="../../../index-files/index-1.html">Index</a></li>
460 <li><a href="../../../help-doc.html">Help</a></li>
465 <li><a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><span class="typeNameLink">Prev Class</span></a></li>
466 <li><a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><span class="typeNameLink">Next Class</span></a></li>
469 <li><a href="../../../index.html?compbio/data/sequence/ScoreManager.html" target="_top">Frames</a></li>
470 <li><a href="ScoreManager.html" target="_top">No Frames</a></li>
472 <ul class="navList" id="allclasses_navbar_bottom">
473 <li><a href="../../../allclasses-noframe.html">All Classes</a></li>
476 <script type="text/javascript"><!--
477 allClassesLink = document.getElementById("allclasses_navbar_bottom");
479 allClassesLink.style.display = "block";
482 allClassesLink.style.display = "none";
488 <ul class="subNavList">
489 <li>Summary: </li>
490 <li><a href="#nested.class.summary">Nested</a> | </li>
491 <li><a href="#field.summary">Field</a> | </li>
492 <li><a href="#constructor.summary">Constr</a> | </li>
493 <li><a href="#method.summary">Method</a></li>
495 <ul class="subNavList">
496 <li>Detail: </li>
497 <li><a href="#field.detail">Field</a> | </li>
498 <li><a href="#constructor.detail">Constr</a> | </li>
499 <li><a href="#method.detail">Method</a></li>
502 <a name="skip.navbar.bottom">
505 <!-- ======== END OF BOTTOM NAVBAR ======= -->