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

Lines changed: 1 addition & 1 deletion
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

Lines changed: 6771 additions & 0 deletions
Large diffs are not rendered by default.

docs/api5.2.0/allclasses.html

Lines changed: 1185 additions & 0 deletions
Large diffs are not rendered by default.

docs/api5.2.0/allpackages-index.html

Lines changed: 702 additions & 0 deletions
Large diffs are not rendered by default.

docs/api5.2.0/constant-values.html

Lines changed: 4544 additions & 0 deletions
Large diffs are not rendered by default.

docs/api5.2.0/demo/AFPFromFasta.html

Lines changed: 323 additions & 0 deletions
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)
pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy