Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Commit 0278bd7

Browse files
committed
Adding 4.2.9 docs
1 parent 091937c commit 0278bd7

File tree

3,879 files changed

+1229564
-0
lines changed

Some content is hidden

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

3,879 files changed

+1229564
-0
lines changed

docs/api4.2.9/allclasses-frame.html

Lines changed: 1144 additions & 0 deletions
Large diffs are not rendered by default.

docs/api4.2.9/allclasses-noframe.html

Lines changed: 1144 additions & 0 deletions
Large diffs are not rendered by default.

docs/api4.2.9/constant-values.html

Lines changed: 4405 additions & 0 deletions
Large diffs are not rendered by default.
Lines changed: 290 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,290 @@
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_131) on Thu Oct 19 12:07:57 PDT 2017 -->
6+
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
7+
<title>AFPFromFasta (biojava 4.2.9 API)</title>
8+
<meta name="date" content="2017-10-19">
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 4.2.9 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="http://docs.oracle.com/javase/7/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="http://docs.oracle.com/javase/7/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="http://docs.oracle.com/javase/7/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="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</a></h3>
168+
<code><a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#clone--" title="class or interface in java.lang">clone</a>, <a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#equals-java.lang.Object-" title="class or interface in java.lang">equals</a>, <a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#finalize--" title="class or interface in java.lang">finalize</a>, <a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#getClass--" title="class or interface in java.lang">getClass</a>, <a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#hashCode--" title="class or interface in java.lang">hashCode</a>, <a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#notify--" title="class or interface in java.lang">notify</a>, <a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#notifyAll--" title="class or interface in java.lang">notifyAll</a>, <a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#toString--" title="class or interface in java.lang">toString</a>, <a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#wait--" title="class or interface in java.lang">wait</a>, <a href="http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html?is-external=true#wait-long-" title="class or interface in java.lang">wait</a>, <a href="http://docs.oracle.com/javase/7/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="http://docs.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a>[]&nbsp;args)
208+
throws <a href="http://docs.oracle.com/javase/7/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="http://docs.oracle.com/javase/7/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="http://docs.oracle.com/javase/7/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="http://docs.oracle.com/javase/7/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>
245+
<div class="subNav">
246+
<ul class="navList">
247+
<li>Prev&nbsp;Class</li>
248+
<li><a href="../demo/AlignmentGuiDemo.html" title="class in demo"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
249+
</ul>
250+
<ul class="navList">
251+
<li><a href="../index.html?demo/AFPFromFasta.html" target="_top">Frames</a></li>
252+
<li><a href="AFPFromFasta.html" target="_top">No&nbsp;Frames</a></li>
253+
</ul>
254+
<ul class="navList" id="allclasses_navbar_bottom">
255+
<li><a href="../allclasses-noframe.html">All&nbsp;Classes</a></li>
256+
</ul>
257+
<div>
258+
<script type="text/javascript"><!--
259+
allClassesLink = document.getElementById("allclasses_navbar_bottom");
260+
if(window==top) {
261+
allClassesLink.style.display = "block";
262+
}
263+
else {
264+
allClassesLink.style.display = "none";
265+
}
266+
//-->
267+
</script>
268+
</div>
269+
<div>
270+
<ul class="subNavList">
271+
<li>Summary:&nbsp;</li>
272+
<li>Nested&nbsp;|&nbsp;</li>
273+
<li>Field&nbsp;|&nbsp;</li>
274+
<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
275+
<li><a href="#method.summary">Method</a></li>
276+
</ul>
277+
<ul class="subNavList">
278+
<li>Detail:&nbsp;</li>
279+
<li>Field&nbsp;|&nbsp;</li>
280+
<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
281+
<li><a href="#method.detail">Method</a></li>
282+
</ul>
283+
</div>
284+
<a name="skip.navbar.bottom">
285+
<!-- -->
286+
</a></div>
287+
<!-- ======== END OF BOTTOM NAVBAR ======= -->
288+
<p class="legalCopy"><small>Copyright &#169; 2000&#x2013;2017 <a href="http://www.biojava.org">BioJava</a>. All rights reserved.</small></p>
289+
</body>
290+
</html>

0 commit comments

Comments
 (0)