Skip to content

Commit 75968ff

Browse files
committed
Add api5.2.0
1 parent e948b09 commit 75968ff

File tree

3,913 files changed

+1418630
-1
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

3,913 files changed

+1418630
-1
lines changed

docs/api

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
api5.0.0/
1+
api5.2.0

docs/api5.2.0/allclasses-index.html

+6,771
Large diffs are not rendered by default.

docs/api5.2.0/allclasses.html

+1,185
Large diffs are not rendered by default.

docs/api5.2.0/allpackages-index.html

+702
Large diffs are not rendered by default.

docs/api5.2.0/constant-values.html

+4,544
Large diffs are not rendered by default.

docs/api5.2.0/demo/AFPFromFasta.html

+323
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,323 @@
1+
<!DOCTYPE HTML>
2+
<!-- NewPage -->
3+
<html lang="en">
4+
<head>
5+
<!-- Generated by javadoc (11.0.1) on Thu Jan 03 22:38:55 CET 2019 -->
6+
<title>AFPFromFasta (biojava 5.2.0 API)</title>
7+
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
8+
<meta name="dc.created" content="2019-01-03">
9+
<link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
10+
<link rel="stylesheet" type="text/css" href="../jquery/jquery-ui.css" title="Style">
11+
<script type="text/javascript" src="../script.js"></script>
12+
<script type="text/javascript" src="../jquery/jszip/dist/jszip.min.js"></script>
13+
<script type="text/javascript" src="../jquery/jszip-utils/dist/jszip-utils.min.js"></script>
14+
<!--[if IE]>
15+
<script type="text/javascript" src="../jquery/jszip-utils/dist/jszip-utils-ie.min.js"></script>
16+
<![endif]-->
17+
<script type="text/javascript" src="../jquery/jquery-3.3.1.js"></script>
18+
<script type="text/javascript" src="../jquery/jquery-migrate-3.0.1.js"></script>
19+
<script type="text/javascript" src="../jquery/jquery-ui.js"></script>
20+
</head>
21+
<body>
22+
<script type="text/javascript"><!--
23+
try {
24+
if (location.href.indexOf('is-external=true') == -1) {
25+
parent.document.title="AFPFromFasta (biojava 5.2.0 API)";
26+
}
27+
}
28+
catch(err) {
29+
}
30+
//-->
31+
var data = {"i0":9};
32+
var tabs = {65535:["t0","All Methods"],1:["t1","Static Methods"],8:["t4","Concrete Methods"]};
33+
var altColor = "altColor";
34+
var rowColor = "rowColor";
35+
var tableTab = "tableTab";
36+
var activeTableTab = "activeTableTab";
37+
var pathtoroot = "../";
38+
var useModuleDirectories = true;
39+
loadScripts(document, 'script');</script>
40+
<noscript>
41+
<div>JavaScript is disabled on your browser.</div>
42+
</noscript>
43+
<header role="banner">
44+
<nav role="navigation">
45+
<div class="fixedNav">
46+
<!-- ========= START OF TOP NAVBAR ======= -->
47+
<div class="topNav"><a id="navbar.top">
48+
<!-- -->
49+
</a>
50+
<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
51+
<a id="navbar.top.firstrow">
52+
<!-- -->
53+
</a>
54+
<ul class="navList" title="Navigation">
55+
<li><a href="../index.html">Overview</a></li>
56+
<li><a href="package-summary.html">Package</a></li>
57+
<li class="navBarCell1Rev">Class</li>
58+
<li><a href="class-use/AFPFromFasta.html">Use</a></li>
59+
<li><a href="package-tree.html">Tree</a></li>
60+
<li><a href="../deprecated-list.html">Deprecated</a></li>
61+
<li><a href="../index-all.html">Index</a></li>
62+
<li><a href="../help-doc.html">Help</a></li>
63+
</ul>
64+
</div>
65+
<div class="subNav">
66+
<ul class="navList" id="allclasses_navbar_top">
67+
<li><a href="../allclasses.html">All&nbsp;Classes</a></li>
68+
</ul>
69+
<ul class="navListSearch">
70+
<li><label for="search">SEARCH:</label>
71+
<input type="text" id="search" value="search" disabled="disabled">
72+
<input type="reset" id="reset" value="reset" disabled="disabled">
73+
</li>
74+
</ul>
75+
<div>
76+
<script type="text/javascript"><!--
77+
allClassesLink = document.getElementById("allclasses_navbar_top");
78+
if(window==top) {
79+
allClassesLink.style.display = "block";
80+
}
81+
else {
82+
allClassesLink.style.display = "none";
83+
}
84+
//-->
85+
</script>
86+
<noscript>
87+
<div>JavaScript is disabled on your browser.</div>
88+
</noscript>
89+
</div>
90+
<div>
91+
<ul class="subNavList">
92+
<li>Summary:&nbsp;</li>
93+
<li>Nested&nbsp;|&nbsp;</li>
94+
<li>Field&nbsp;|&nbsp;</li>
95+
<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
96+
<li><a href="#method.summary">Method</a></li>
97+
</ul>
98+
<ul class="subNavList">
99+
<li>Detail:&nbsp;</li>
100+
<li>Field&nbsp;|&nbsp;</li>
101+
<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
102+
<li><a href="#method.detail">Method</a></li>
103+
</ul>
104+
</div>
105+
<a id="skip.navbar.top">
106+
<!-- -->
107+
</a></div>
108+
<!-- ========= END OF TOP NAVBAR ========= -->
109+
</div>
110+
<div class="navPadding">&nbsp;</div>
111+
<script type="text/javascript"><!--
112+
$('.navPadding').css('padding-top', $('.fixedNav').css("height"));
113+
//-->
114+
</script>
115+
</nav>
116+
</header>
117+
<!-- ======== START OF CLASS DATA ======== -->
118+
<main role="main">
119+
<div class="header">
120+
<div class="subTitle"><span class="packageLabelInType">Package</span>&nbsp;<a href="package-summary.html">demo</a></div>
121+
<h2 title="Class AFPFromFasta" class="title">Class AFPFromFasta</h2>
122+
</div>
123+
<div class="contentContainer">
124+
<ul class="inheritance">
125+
<li><a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang" class="externalLink">java.lang.Object</a></li>
126+
<li>
127+
<ul class="inheritance">
128+
<li>demo.AFPFromFasta</li>
129+
</ul>
130+
</li>
131+
</ul>
132+
<div class="description">
133+
<ul class="blockList">
134+
<li class="blockList">
135+
<hr>
136+
<pre>public class <a href="../src-html/demo/AFPFromFasta.html#line.49">AFPFromFasta</a>
137+
extends <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang" class="externalLink">Object</a></pre>
138+
<div class="block">Demo displaying a structural alignment from a FASTA file using <a href="../org/biojava/nbio/structure/io/FastaAFPChainConverter.html" title="class in org.biojava.nbio.structure.io"><code>FastaAFPChainConverter</code></a>.</div>
139+
<dl>
140+
<dt><span class="simpleTagLabel">Author:</span></dt>
141+
<dd>dmyerstu</dd>
142+
</dl>
143+
</li>
144+
</ul>
145+
</div>
146+
<div class="summary">
147+
<ul class="blockList">
148+
<li class="blockList">
149+
<!-- ======== CONSTRUCTOR SUMMARY ======== -->
150+
<section role="region">
151+
<ul class="blockList">
152+
<li class="blockList"><a id="constructor.summary">
153+
<!-- -->
154+
</a>
155+
<h3>Constructor Summary</h3>
156+
<table class="memberSummary">
157+
<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
158+
<tr>
159+
<th class="colFirst" scope="col">Constructor</th>
160+
<th class="colLast" scope="col">Description</th>
161+
</tr>
162+
<tr class="altColor">
163+
<th class="colConstructorName" scope="row"><code><span class="memberNameLink"><a href="#%3Cinit%3E()">AFPFromFasta</a></span>()</code></th>
164+
<td class="colLast">&nbsp;</td>
165+
</tr>
166+
</table>
167+
</li>
168+
</ul>
169+
</section>
170+
<!-- ========== METHOD SUMMARY =========== -->
171+
<section role="region">
172+
<ul class="blockList">
173+
<li class="blockList"><a id="method.summary">
174+
<!-- -->
175+
</a>
176+
<h3>Method Summary</h3>
177+
<table class="memberSummary">
178+
<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
179+
<tr>
180+
<th class="colFirst" scope="col">Modifier and Type</th>
181+
<th class="colSecond" scope="col">Method</th>
182+
<th class="colLast" scope="col">Description</th>
183+
</tr>
184+
<tr id="i0" class="altColor">
185+
<td class="colFirst"><code>static void</code></td>
186+
<th class="colSecond" scope="row"><code><span class="memberNameLink"><a href="#main(java.lang.String%5B%5D)">main</a></span>&#8203;(<a href="https://docs.oracle.com/javase/8/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>[]&nbsp;args)</code></th>
187+
<td class="colLast">&nbsp;</td>
188+
</tr>
189+
</table>
190+
<ul class="blockList">
191+
<li class="blockList"><a id="methods.inherited.from.class.java.lang.Object">
192+
<!-- -->
193+
</a>
194+
<h3>Methods inherited from class&nbsp;java.lang.<a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang" class="externalLink">Object</a></h3>
195+
<code><a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang" class="externalLink">clone</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang" class="externalLink">equals</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang" class="externalLink">finalize</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang" class="externalLink">getClass</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang" class="externalLink">hashCode</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang" class="externalLink">notify</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang" class="externalLink">notifyAll</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang" class="externalLink">toString</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang" class="externalLink">wait</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang" class="externalLink">wait</a>, <a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html?is-external=true#wait(long,int)" title="class or interface in java.lang" class="externalLink">wait</a></code></li>
196+
</ul>
197+
</li>
198+
</ul>
199+
</section>
200+
</li>
201+
</ul>
202+
</div>
203+
<div class="details">
204+
<ul class="blockList">
205+
<li class="blockList">
206+
<!-- ========= CONSTRUCTOR DETAIL ======== -->
207+
<section role="region">
208+
<ul class="blockList">
209+
<li class="blockList"><a id="constructor.detail">
210+
<!-- -->
211+
</a>
212+
<h3>Constructor Detail</h3>
213+
<a id="&lt;init&gt;()">
214+
<!-- -->
215+
</a>
216+
<ul class="blockListLast">
217+
<li class="blockList">
218+
<h4>AFPFromFasta</h4>
219+
<pre>public&nbsp;<a href="../src-html/demo/AFPFromFasta.html#line.49">AFPFromFasta</a>()</pre>
220+
</li>
221+
</ul>
222+
</li>
223+
</ul>
224+
</section>
225+
<!-- ============ METHOD DETAIL ========== -->
226+
<section role="region">
227+
<ul class="blockList">
228+
<li class="blockList"><a id="method.detail">
229+
<!-- -->
230+
</a>
231+
<h3>Method Detail</h3>
232+
<a id="main(java.lang.String[])">
233+
<!-- -->
234+
</a>
235+
<ul class="blockListLast">
236+
<li class="blockList">
237+
<h4>main</h4>
238+
<pre class="methodSignature">public static&nbsp;void&nbsp;<a href="../src-html/demo/AFPFromFasta.html#line.51">main</a>&#8203;(<a href="https://docs.oracle.com/javase/8/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang" class="externalLink">String</a>[]&nbsp;args)
239+
throws <a href="https://docs.oracle.com/javase/8/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io" class="externalLink">IOException</a>,
240+
<a href="../org/biojava/nbio/structure/StructureException.html" title="class in org.biojava.nbio.structure">StructureException</a>,
241+
<a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang" class="externalLink">Exception</a></pre>
242+
<dl>
243+
<dt><span class="throwsLabel">Throws:</span></dt>
244+
<dd><code><a href="https://docs.oracle.com/javase/8/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io" class="externalLink">IOException</a></code></dd>
245+
<dd><code><a href="../org/biojava/nbio/structure/StructureException.html" title="class in org.biojava.nbio.structure">StructureException</a></code></dd>
246+
<dd><code><a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang" class="externalLink">Exception</a></code></dd>
247+
</dl>
248+
</li>
249+
</ul>
250+
</li>
251+
</ul>
252+
</section>
253+
</li>
254+
</ul>
255+
</div>
256+
</div>
257+
</main>
258+
<!-- ========= END OF CLASS DATA ========= -->
259+
<footer role="contentinfo">
260+
<nav role="navigation">
261+
<!-- ======= START OF BOTTOM NAVBAR ====== -->
262+
<div class="bottomNav"><a id="navbar.bottom">
263+
<!-- -->
264+
</a>
265+
<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
266+
<a id="navbar.bottom.firstrow">
267+
<!-- -->
268+
</a>
269+
<ul class="navList" title="Navigation">
270+
<li><a href="../index.html">Overview</a></li>
271+
<li><a href="package-summary.html">Package</a></li>
272+
<li class="navBarCell1Rev">Class</li>
273+
<li><a href="class-use/AFPFromFasta.html">Use</a></li>
274+
<li><a href="package-tree.html">Tree</a></li>
275+
<li><a href="../deprecated-list.html">Deprecated</a></li>
276+
<li><a href="../index-all.html">Index</a></li>
277+
<li><a href="../help-doc.html">Help</a></li>
278+
</ul>
279+
<div class="aboutLanguage"><script src="http://www.google-analytics.com/urchin.js" type="text/javascript"></script><script type="text/javascript">_uacct = "UA-1326640-1";urchinTracker();</script></div>
280+
</div>
281+
<div class="subNav">
282+
<ul class="navList" id="allclasses_navbar_bottom">
283+
<li><a href="../allclasses.html">All&nbsp;Classes</a></li>
284+
</ul>
285+
<div>
286+
<script type="text/javascript"><!--
287+
allClassesLink = document.getElementById("allclasses_navbar_bottom");
288+
if(window==top) {
289+
allClassesLink.style.display = "block";
290+
}
291+
else {
292+
allClassesLink.style.display = "none";
293+
}
294+
//-->
295+
</script>
296+
<noscript>
297+
<div>JavaScript is disabled on your browser.</div>
298+
</noscript>
299+
</div>
300+
<div>
301+
<ul class="subNavList">
302+
<li>Summary:&nbsp;</li>
303+
<li>Nested&nbsp;|&nbsp;</li>
304+
<li>Field&nbsp;|&nbsp;</li>
305+
<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
306+
<li><a href="#method.summary">Method</a></li>
307+
</ul>
308+
<ul class="subNavList">
309+
<li>Detail:&nbsp;</li>
310+
<li>Field&nbsp;|&nbsp;</li>
311+
<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
312+
<li><a href="#method.detail">Method</a></li>
313+
</ul>
314+
</div>
315+
<a id="skip.navbar.bottom">
316+
<!-- -->
317+
</a></div>
318+
<!-- ======== END OF BOTTOM NAVBAR ======= -->
319+
</nav>
320+
<p class="legalCopy"><small>Copyright &#169; 2000&#x2013;2019 <a href="http://www.biojava.org">BioJava</a>. All rights reserved.</small></p>
321+
</footer>
322+
</body>
323+
</html>

0 commit comments

Comments
 (0)