Skip to content

Commit baea738

Browse files
committed
Adding apidocs for 5.0.0 and linking default to it
1 parent 01c4475 commit baea738

File tree

3,994 files changed

+1273675
-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.

3,994 files changed

+1273675
-1
lines changed

docs/api

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
api4.2.9
1+
api5.0.0/

docs/api5.0.0/allclasses-frame.html

Lines changed: 1174 additions & 0 deletions
Large diffs are not rendered by default.

docs/api5.0.0/allclasses-noframe.html

Lines changed: 1174 additions & 0 deletions
Large diffs are not rendered by default.

docs/api5.0.0/constant-values.html

Lines changed: 4481 additions & 0 deletions
Large diffs are not rendered by default.

docs/api5.0.0/demo/AFPFromFasta.html

Lines changed: 291 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,291 @@
1+
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2+
<!-- NewPage -->
3+
<html lang="en">
4+
<head>
5+
<!-- Generated by javadoc (1.8.0_162) on Fri Apr 06 16:18:58 PDT 2018 -->
6+
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
7+
<title>AFPFromFasta (biojava 5.0.0 API)</title>
8+
<meta name="date" content="2018-04-06">
9+
<link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
10+
<script type="text/javascript" src="../script.js"></script>
11+
</head>
12+
<body>
13+
<script type="text/javascript"><!--
14+
try {
15+
if (location.href.indexOf('is-external=true') == -1) {
16+
parent.document.title="AFPFromFasta (biojava 5.0.0 API)";
17+
}
18+
}
19+
catch(err) {
20+
}
21+
//-->
22+
var methods = {"i0":9};
23+
var tabs = {65535:["t0","All Methods"],1:["t1","Static Methods"],8:["t4","Concrete Methods"]};
24+
var altColor = "altColor";
25+
var rowColor = "rowColor";
26+
var tableTab = "tableTab";
27+
var activeTableTab = "activeTableTab";
28+
</script>
29+
<noscript>
30+
<div>JavaScript is disabled on your browser.</div>
31+
</noscript>
32+
<!-- ========= START OF TOP NAVBAR ======= -->
33+
<div class="topNav"><a name="navbar.top">
34+
<!-- -->
35+
</a>
36+
<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
37+
<a name="navbar.top.firstrow">
38+
<!-- -->
39+
</a>
40+
<ul class="navList" title="Navigation">
41+
<li><a href="../overview-summary.html">Overview</a></li>
42+
<li><a href="package-summary.html">Package</a></li>
43+
<li class="navBarCell1Rev">Class</li>
44+
<li><a href="class-use/AFPFromFasta.html">Use</a></li>
45+
<li><a href="package-tree.html">Tree</a></li>
46+
<li><a href="../deprecated-list.html">Deprecated</a></li>
47+
<li><a href="../index-all.html">Index</a></li>
48+
<li><a href="../help-doc.html">Help</a></li>
49+
</ul>
50+
</div>
51+
<div class="subNav">
52+
<ul class="navList">
53+
<li>Prev&nbsp;Class</li>
54+
<li><a href="../demo/AlignmentGuiDemo.html" title="class in demo"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
55+
</ul>
56+
<ul class="navList">
57+
<li><a href="../index.html?demo/AFPFromFasta.html" target="_top">Frames</a></li>
58+
<li><a href="AFPFromFasta.html" target="_top">No&nbsp;Frames</a></li>
59+
</ul>
60+
<ul class="navList" id="allclasses_navbar_top">
61+
<li><a href="../allclasses-noframe.html">All&nbsp;Classes</a></li>
62+
</ul>
63+
<div>
64+
<script type="text/javascript"><!--
65+
allClassesLink = document.getElementById("allclasses_navbar_top");
66+
if(window==top) {
67+
allClassesLink.style.display = "block";
68+
}
69+
else {
70+
allClassesLink.style.display = "none";
71+
}
72+
//-->
73+
</script>
74+
</div>
75+
<div>
76+
<ul class="subNavList">
77+
<li>Summary:&nbsp;</li>
78+
<li>Nested&nbsp;|&nbsp;</li>
79+
<li>Field&nbsp;|&nbsp;</li>
80+
<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
81+
<li><a href="#method.summary">Method</a></li>
82+
</ul>
83+
<ul class="subNavList">
84+
<li>Detail:&nbsp;</li>
85+
<li>Field&nbsp;|&nbsp;</li>
86+
<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
87+
<li><a href="#method.detail">Method</a></li>
88+
</ul>
89+
</div>
90+
<a name="skip.navbar.top">
91+
<!-- -->
92+
</a></div>
93+
<!-- ========= END OF TOP NAVBAR ========= -->
94+
<!-- ======== START OF CLASS DATA ======== -->
95+
<div class="header">
96+
<div class="subTitle">demo</div>
97+
<h2 title="Class AFPFromFasta" class="title">Class AFPFromFasta</h2>
98+
</div>
99+
<div class="contentContainer">
100+
<ul class="inheritance">
101+
<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">java.lang.Object</a></li>
102+
<li>
103+
<ul class="inheritance">
104+
<li>demo.AFPFromFasta</li>
105+
</ul>
106+
</li>
107+
</ul>
108+
<div class="description">
109+
<ul class="blockList">
110+
<li class="blockList">
111+
<hr>
112+
<br>
113+
<pre>public class <a href="../src-html/demo/AFPFromFasta.html#line.49">AFPFromFasta</a>
114+
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">Object</a></pre>
115+
<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>
116+
<dl>
117+
<dt><span class="simpleTagLabel">Author:</span></dt>
118+
<dd>dmyerstu</dd>
119+
<dt><span class="seeLabel">See Also:</span></dt>
120+
<dd><code>DemoAlignmentFromFasta} Also demonstrates the display of {@link StructureAlignment StructureAlignments} from FASTA sequences, but does so using the more general
121+
{@link FastaStructureParser}</code></dd>
122+
</dl>
123+
</li>
124+
</ul>
125+
</div>
126+
<div class="summary">
127+
<ul class="blockList">
128+
<li class="blockList">
129+
<!-- ======== CONSTRUCTOR SUMMARY ======== -->
130+
<ul class="blockList">
131+
<li class="blockList"><a name="constructor.summary">
132+
<!-- -->
133+
</a>
134+
<h3>Constructor Summary</h3>
135+
<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
136+
<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
137+
<tr>
138+
<th class="colOne" scope="col">Constructor and Description</th>
139+
</tr>
140+
<tr class="altColor">
141+
<td class="colOne"><code><span class="memberNameLink"><a href="../demo/AFPFromFasta.html#AFPFromFasta--">AFPFromFasta</a></span>()</code>&nbsp;</td>
142+
</tr>
143+
</table>
144+
</li>
145+
</ul>
146+
<!-- ========== METHOD SUMMARY =========== -->
147+
<ul class="blockList">
148+
<li class="blockList"><a name="method.summary">
149+
<!-- -->
150+
</a>
151+
<h3>Method Summary</h3>
152+
<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
153+
<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>
154+
<tr>
155+
<th class="colFirst" scope="col">Modifier and Type</th>
156+
<th class="colLast" scope="col">Method and Description</th>
157+
</tr>
158+
<tr id="i0" class="altColor">
159+
<td class="colFirst"><code>static void</code></td>
160+
<td class="colLast"><code><span class="memberNameLink"><a href="../demo/AFPFromFasta.html#main-java.lang.String:A-">main</a></span>(<a href="https://docs.oracle.com/javase/8/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a>[]&nbsp;args)</code>&nbsp;</td>
161+
</tr>
162+
</table>
163+
<ul class="blockList">
164+
<li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
165+
<!-- -->
166+
</a>
167+
<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">Object</a></h3>
168+
<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">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">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">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">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">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">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">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">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">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">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">wait</a></code></li>
169+
</ul>
170+
</li>
171+
</ul>
172+
</li>
173+
</ul>
174+
</div>
175+
<div class="details">
176+
<ul class="blockList">
177+
<li class="blockList">
178+
<!-- ========= CONSTRUCTOR DETAIL ======== -->
179+
<ul class="blockList">
180+
<li class="blockList"><a name="constructor.detail">
181+
<!-- -->
182+
</a>
183+
<h3>Constructor Detail</h3>
184+
<a name="AFPFromFasta--">
185+
<!-- -->
186+
</a>
187+
<ul class="blockListLast">
188+
<li class="blockList">
189+
<h4>AFPFromFasta</h4>
190+
<pre>public&nbsp;<a href="../src-html/demo/AFPFromFasta.html#line.49">AFPFromFasta</a>()</pre>
191+
</li>
192+
</ul>
193+
</li>
194+
</ul>
195+
<!-- ============ METHOD DETAIL ========== -->
196+
<ul class="blockList">
197+
<li class="blockList"><a name="method.detail">
198+
<!-- -->
199+
</a>
200+
<h3>Method Detail</h3>
201+
<a name="main-java.lang.String:A-">
202+
<!-- -->
203+
</a>
204+
<ul class="blockListLast">
205+
<li class="blockList">
206+
<h4>main</h4>
207+
<pre>public static&nbsp;void&nbsp;<a href="../src-html/demo/AFPFromFasta.html#line.51">main</a>(<a href="https://docs.oracle.com/javase/8/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a>[]&nbsp;args)
208+
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">IOException</a>,
209+
<a href="../org/biojava/nbio/structure/StructureException.html" title="class in org.biojava.nbio.structure">StructureException</a>,
210+
<a href="https://docs.oracle.com/javase/8/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</a></pre>
211+
<dl>
212+
<dt><span class="throwsLabel">Throws:</span></dt>
213+
<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">IOException</a></code></dd>
214+
<dd><code><a href="../org/biojava/nbio/structure/StructureException.html" title="class in org.biojava.nbio.structure">StructureException</a></code></dd>
215+
<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">Exception</a></code></dd>
216+
</dl>
217+
</li>
218+
</ul>
219+
</li>
220+
</ul>
221+
</li>
222+
</ul>
223+
</div>
224+
</div>
225+
<!-- ========= END OF CLASS DATA ========= -->
226+
<!-- ======= START OF BOTTOM NAVBAR ====== -->
227+
<div class="bottomNav"><a name="navbar.bottom">
228+
<!-- -->
229+
</a>
230+
<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
231+
<a name="navbar.bottom.firstrow">
232+
<!-- -->
233+
</a>
234+
<ul class="navList" title="Navigation">
235+
<li><a href="../overview-summary.html">Overview</a></li>
236+
<li><a href="package-summary.html">Package</a></li>
237+
<li class="navBarCell1Rev">Class</li>
238+
<li><a href="class-use/AFPFromFasta.html">Use</a></li>
239+
<li><a href="package-tree.html">Tree</a></li>
240+
<li><a href="../deprecated-list.html">Deprecated</a></li>
241+
<li><a href="../index-all.html">Index</a></li>
242+
<li><a href="../help-doc.html">Help</a></li>
243+
</ul>
244+
<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>
245+
</div>
246+
<div class="subNav">
247+
<ul class="navList">
248+
<li>Prev&nbsp;Class</li>
249+
<li><a href="../demo/AlignmentGuiDemo.html" title="class in demo"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
250+
</ul>
251+
<ul class="navList">
252+
<li><a href="../index.html?demo/AFPFromFasta.html" target="_top">Frames</a></li>
253+
<li><a href="AFPFromFasta.html" target="_top">No&nbsp;Frames</a></li>
254+
</ul>
255+
<ul class="navList" id="allclasses_navbar_bottom">
256+
<li><a href="../allclasses-noframe.html">All&nbsp;Classes</a></li>
257+
</ul>
258+
<div>
259+
<script type="text/javascript"><!--
260+
allClassesLink = document.getElementById("allclasses_navbar_bottom");
261+
if(window==top) {
262+
allClassesLink.style.display = "block";
263+
}
264+
else {
265+
allClassesLink.style.display = "none";
266+
}
267+
//-->
268+
</script>
269+
</div>
270+
<div>
271+
<ul class="subNavList">
272+
<li>Summary:&nbsp;</li>
273+
<li>Nested&nbsp;|&nbsp;</li>
274+
<li>Field&nbsp;|&nbsp;</li>
275+
<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
276+
<li><a href="#method.summary">Method</a></li>
277+
</ul>
278+
<ul class="subNavList">
279+
<li>Detail:&nbsp;</li>
280+
<li>Field&nbsp;|&nbsp;</li>
281+
<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
282+
<li><a href="#method.detail">Method</a></li>
283+
</ul>
284+
</div>
285+
<a name="skip.navbar.bottom">
286+
<!-- -->
287+
</a></div>
288+
<!-- ======== END OF BOTTOM NAVBAR ======= -->
289+
<p class="legalCopy"><small>Copyright &#169; 2000&#x2013;2018 <a href="http://www.biojava.org">BioJava</a>. All rights reserved.</small></p>
290+
</body>
291+
</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