Skip to content

Commit d0cb9e3

Browse files
josemduartejosemduarte
committed
Apidocs for 7.1.4 (fixing biojava/biojava#1102)
1 parent b9104f8 commit d0cb9e3

File tree

3,620 files changed

+924482
-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.

3,620 files changed

+924482
-1
lines changed

‎docs/api

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
api6.1.0/
1+
api7.1.4

‎docs/api7.1.4/allclasses-index.html

Lines changed: 4043 additions & 0 deletions
Large diffs are not rendered by default.

‎docs/api7.1.4/allpackages-index.html

Lines changed: 365 additions & 0 deletions
Large diffs are not rendered by default.

‎docs/api7.1.4/constant-values.html

Lines changed: 2275 additions & 0 deletions
Large diffs are not rendered by default.

‎docs/api7.1.4/copy.svg

Lines changed: 33 additions & 0 deletions
Loading

‎docs/api7.1.4/demo/AFPFromFasta.html

Lines changed: 190 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,190 @@
1+
<!DOCTYPE HTML>
2+
<html lang>
3+
<head>
4+
<!-- Generated by javadoc (21) on Wed Jan 08 16:43:01 PST 2025 -->
5+
<title>AFPFromFasta (biojava 7.1.4 API)</title>
6+
<meta name="viewport" content="width=device-width, initial-scale=1">
7+
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
8+
<meta name="dc.created" content="2025-01-08">
9+
<meta name="description" content="declaration: package: demo, class: AFPFromFasta">
10+
<meta name="generator" content="javadoc/ClassWriterImpl">
11+
<link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
12+
<link rel="stylesheet" type="text/css" href="../script-dir/jquery-ui.min.css" title="Style">
13+
<script type="text/javascript" src="../script.js"></script>
14+
<script type="text/javascript" src="../script-dir/jquery-3.7.1.min.js"></script>
15+
<script type="text/javascript" src="../script-dir/jquery-ui.min.js"></script>
16+
</head>
17+
<body class="class-declaration-page">
18+
<script type="text/javascript">var pathtoroot = "../";
19+
loadScripts(document, 'script');</script>
20+
<noscript>
21+
<div>JavaScript is disabled on your browser.</div>
22+
</noscript>
23+
<div class="flex-box">
24+
<header role="banner" class="flex-header">
25+
<nav role="navigation">
26+
<!-- ========= START OF TOP NAVBAR ======= -->
27+
<div class="top-nav" id="navbar-top"><button id="navbar-toggle-button" aria-controls="navbar-top" aria-expanded="false" aria-label="Toggle navigation links"><span class="nav-bar-toggle-icon">&nbsp;</span><span class="nav-bar-toggle-icon">&nbsp;</span><span class="nav-bar-toggle-icon">&nbsp;</span></button>
28+
<div class="skip-nav"><a href="#skip-navbar-top" title="Skip navigation links">Skip navigation links</a></div>
29+
<ul id="navbar-top-firstrow" class="nav-list" title="Navigation">
30+
<li><a href="../index.html">Overview</a></li>
31+
<li><a href="package-summary.html">Package</a></li>
32+
<li class="nav-bar-cell1-rev">Class</li>
33+
<li><a href="class-use/AFPFromFasta.html">Use</a></li>
34+
<li><a href="package-tree.html">Tree</a></li>
35+
<li><a href="../deprecated-list.html">Deprecated</a></li>
36+
<li><a href="../index-all.html">Index</a></li>
37+
<li><a href="../help-doc.html#class">Help</a></li>
38+
</ul>
39+
<ul class="sub-nav-list-small">
40+
<li>
41+
<p>Summary:</p>
42+
<ul>
43+
<li>Nested</li>
44+
<li>Field</li>
45+
<li><a href="#constructor-summary">Constr</a></li>
46+
<li><a href="#method-summary">Method</a></li>
47+
</ul>
48+
</li>
49+
<li>
50+
<p>Detail:</p>
51+
<ul>
52+
<li>Field</li>
53+
<li><a href="#constructor-detail">Constr</a></li>
54+
<li><a href="#method-detail">Method</a></li>
55+
</ul>
56+
</li>
57+
</ul>
58+
</div>
59+
<div class="sub-nav">
60+
<div id="navbar-sub-list">
61+
<ul class="sub-nav-list">
62+
<li>Summary:&nbsp;</li>
63+
<li>Nested&nbsp;|&nbsp;</li>
64+
<li>Field&nbsp;|&nbsp;</li>
65+
<li><a href="#constructor-summary">Constr</a>&nbsp;|&nbsp;</li>
66+
<li><a href="#method-summary">Method</a></li>
67+
</ul>
68+
<ul class="sub-nav-list">
69+
<li>Detail:&nbsp;</li>
70+
<li>Field&nbsp;|&nbsp;</li>
71+
<li><a href="#constructor-detail">Constr</a>&nbsp;|&nbsp;</li>
72+
<li><a href="#method-detail">Method</a></li>
73+
</ul>
74+
</div>
75+
<div class="nav-list-search"><a href="../search.html">SEARCH</a>
76+
<input type="text" id="search-input" disabled placeholder="Search">
77+
<input type="reset" id="reset-button" disabled value="reset">
78+
</div>
79+
</div>
80+
<!-- ========= END OF TOP NAVBAR ========= -->
81+
<span class="skip-nav" id="skip-navbar-top"></span></nav>
82+
</header>
83+
<div class="flex-content">
84+
<main role="main">
85+
<!-- ======== START OF CLASS DATA ======== -->
86+
<div class="header">
87+
<div class="sub-title"><span class="package-label-in-type">Package</span>&nbsp;<a href="package-summary.html">demo</a></div>
88+
<h1 title="Class AFPFromFasta" class="title">Class AFPFromFasta</h1>
89+
</div>
90+
<div class="inheritance" title="Inheritance Tree"><a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">java.lang.Object</a>
91+
<div class="inheritance">demo.AFPFromFasta</div>
92+
</div>
93+
<section class="class-description" id="class-description">
94+
<hr>
95+
<div class="type-signature"><span class="modifiers">public class </span><span class="element-name"><a href="../src-html/demo/AFPFromFasta.html#line-48">AFPFromFasta</a></span>
96+
<span class="extends-implements">extends <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">Object</a></span></div>
97+
<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>.
98+
See <a href="DemoAlignmentFromFasta.html" title="class in demo"><code>DemoAlignmentFromFasta</code></a> Also demonstrates the display of <a href="../org/biojava/nbio/structure/align/StructureAlignment.html" title="interface in org.biojava.nbio.structure.align"><code>StructureAlignments</code></a> from FASTA sequences, but does so using the more general
99+
<a href="../org/biojava/nbio/structure/io/FastaStructureParser.html" title="class in org.biojava.nbio.structure.io"><code>FastaStructureParser</code></a></div>
100+
<dl class="notes">
101+
<dt>Author:</dt>
102+
<dd>dmyerstu</dd>
103+
</dl>
104+
</section>
105+
<section class="summary">
106+
<ul class="summary-list">
107+
<!-- ======== CONSTRUCTOR SUMMARY ======== -->
108+
<li>
109+
<section class="constructor-summary" id="constructor-summary">
110+
<h2>Constructor Summary</h2>
111+
<div class="caption"><span>Constructors</span></div>
112+
<div class="summary-table two-column-summary">
113+
<div class="table-header col-first">Constructor</div>
114+
<div class="table-header col-last">Description</div>
115+
<div class="col-constructor-name even-row-color"><code><a href="#%3Cinit%3E()" class="member-name-link">AFPFromFasta</a>()</code></div>
116+
<div class="col-last even-row-color">&nbsp;</div>
117+
</div>
118+
</section>
119+
</li>
120+
<!-- ========== METHOD SUMMARY =========== -->
121+
<li>
122+
<section class="method-summary" id="method-summary">
123+
<h2>Method Summary</h2>
124+
<div id="method-summary-table">
125+
<div class="table-tabs" role="tablist" aria-orientation="horizontal"><button id="method-summary-table-tab0" role="tab" aria-selected="true" aria-controls="method-summary-table.tabpanel" tabindex="0" onkeydown="switchTab(event)" onclick="show('method-summary-table', 'method-summary-table', 3)" class="active-table-tab">All Methods</button><button id="method-summary-table-tab1" role="tab" aria-selected="false" aria-controls="method-summary-table.tabpanel" tabindex="-1" onkeydown="switchTab(event)" onclick="show('method-summary-table', 'method-summary-table-tab1', 3)" class="table-tab">Static Methods</button><button id="method-summary-table-tab4" role="tab" aria-selected="false" aria-controls="method-summary-table.tabpanel" tabindex="-1" onkeydown="switchTab(event)" onclick="show('method-summary-table', 'method-summary-table-tab4', 3)" class="table-tab">Concrete Methods</button></div>
126+
<div id="method-summary-table.tabpanel" role="tabpanel" aria-labelledby="method-summary-table-tab0">
127+
<div class="summary-table three-column-summary">
128+
<div class="table-header col-first">Modifier and Type</div>
129+
<div class="table-header col-second">Method</div>
130+
<div class="table-header col-last">Description</div>
131+
<div class="col-first even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code>static void</code></div>
132+
<div class="col-second even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code><a href="#main(java.lang.String%5B%5D)" class="member-name-link">main</a><wbr>(<a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a>[]&nbsp;args)</code></div>
133+
<div class="col-last even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4">&nbsp;</div>
134+
</div>
135+
</div>
136+
</div>
137+
<div class="inherited-list">
138+
<h3 id="methods-inherited-from-class-java.lang.Object">Methods inherited from class&nbsp;java.lang.<a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">Object</a></h3>
139+
<code><a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#clone()" title="class or interface in java.lang" class="external-link">clone</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#equals(java.lang.Object)" title="class or interface in java.lang" class="external-link">equals</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#finalize()" title="class or interface in java.lang" class="external-link">finalize</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#getClass()" title="class or interface in java.lang" class="external-link">getClass</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#hashCode()" title="class or interface in java.lang" class="external-link">hashCode</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#notify()" title="class or interface in java.lang" class="external-link">notify</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#notifyAll()" title="class or interface in java.lang" class="external-link">notifyAll</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#toString()" title="class or interface in java.lang" class="external-link">toString</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#wait()" title="class or interface in java.lang" class="external-link">wait</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#wait(long)" title="class or interface in java.lang" class="external-link">wait</a>, <a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Object.html#wait(long,int)" title="class or interface in java.lang" class="external-link">wait</a></code></div>
140+
</section>
141+
</li>
142+
</ul>
143+
</section>
144+
<section class="details">
145+
<ul class="details-list">
146+
<!-- ========= CONSTRUCTOR DETAIL ======== -->
147+
<li>
148+
<section class="constructor-details" id="constructor-detail">
149+
<h2>Constructor Details</h2>
150+
<ul class="member-list">
151+
<li>
152+
<section class="detail" id="&lt;init&gt;()">
153+
<h3>AFPFromFasta</h3>
154+
<div class="member-signature"><span class="modifiers">public</span>&nbsp;<span class="element-name"><a href="../src-html/demo/AFPFromFasta.html#line-48">AFPFromFasta</a></span>()</div>
155+
</section>
156+
</li>
157+
</ul>
158+
</section>
159+
</li>
160+
<!-- ============ METHOD DETAIL ========== -->
161+
<li>
162+
<section class="method-details" id="method-detail">
163+
<h2>Method Details</h2>
164+
<ul class="member-list">
165+
<li>
166+
<section class="detail" id="main(java.lang.String[])">
167+
<h3>main</h3>
168+
<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type">void</span>&nbsp;<span class="element-name"><a href="../src-html/demo/AFPFromFasta.html#line-50">main</a></span><wbr><span class="parameters">(<a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a>[]&nbsp;args)</span>
169+
throws <span class="exceptions"><a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Exception.html" title="class or interface in java.lang" class="external-link">Exception</a></span></div>
170+
<dl class="notes">
171+
<dt>Throws:</dt>
172+
<dd><code><a href="https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/lang/Exception.html" title="class or interface in java.lang" class="external-link">Exception</a></code></dd>
173+
</dl>
174+
</section>
175+
</li>
176+
</ul>
177+
</section>
178+
</li>
179+
</ul>
180+
</section>
181+
<!-- ========= END OF CLASS DATA ========= -->
182+
</main>
183+
<footer role="contentinfo">
184+
<hr>
185+
<p class="legal-copy"><small>Copyright &#169; 2000&#x2013;2025 <a href="https://www.biojava.org">BioJava</a>. All rights reserved.</small></p>
186+
</footer>
187+
</div>
188+
</div>
189+
</body>
190+
</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