Skip to content

Commit d74f3c6

Browse files
committed
Add apidocs for biojava-legacy version 1.9.5.
1 parent 586b9d2 commit d74f3c6

File tree

5,006 files changed

+1858878
-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.

5,006 files changed

+1858878
-1
lines changed

docs/api1.9.5/allclasses-index.html

+9,553
Large diffs are not rendered by default.

docs/api1.9.5/allclasses.html

+1,551
Large diffs are not rendered by default.

docs/api1.9.5/allpackages-index.html

+784
Large diffs are not rendered by default.

docs/api1.9.5/constant-values.html

+7,870
Large diffs are not rendered by default.

docs/api1.9.5/deprecated-list.html

+824
Large diffs are not rendered by default.

docs/api1.9.5/element-list

+99
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,99 @@
1+
org.biojava
2+
org.biojava.bibliography
3+
org.biojava.bio
4+
org.biojava.bio.alignment
5+
org.biojava.bio.annodb
6+
org.biojava.bio.chromatogram
7+
org.biojava.bio.chromatogram.graphic
8+
org.biojava.bio.dist
9+
org.biojava.bio.dp
10+
org.biojava.bio.dp.onehead
11+
org.biojava.bio.dp.twohead
12+
org.biojava.bio.gui
13+
org.biojava.bio.gui.glyph
14+
org.biojava.bio.gui.sequence
15+
org.biojava.bio.gui.sequence.tracklayout
16+
org.biojava.bio.molbio
17+
org.biojava.bio.program
18+
org.biojava.bio.program.abi
19+
org.biojava.bio.program.blast2html
20+
org.biojava.bio.program.fastq
21+
org.biojava.bio.program.formats
22+
org.biojava.bio.program.gff
23+
org.biojava.bio.program.gff3
24+
org.biojava.bio.program.hmmer
25+
org.biojava.bio.program.homologene
26+
org.biojava.bio.program.indexdb
27+
org.biojava.bio.program.phred
28+
org.biojava.bio.program.sax
29+
org.biojava.bio.program.sax.blastxml
30+
org.biojava.bio.program.scf
31+
org.biojava.bio.program.ssaha
32+
org.biojava.bio.program.ssbind
33+
org.biojava.bio.program.tagvalue
34+
org.biojava.bio.program.unigene
35+
org.biojava.bio.program.xff
36+
org.biojava.bio.program.xml
37+
org.biojava.bio.proteomics
38+
org.biojava.bio.proteomics.aaindex
39+
org.biojava.bio.search
40+
org.biojava.bio.seq
41+
org.biojava.bio.seq.db
42+
org.biojava.bio.seq.db.biofetch
43+
org.biojava.bio.seq.db.biosql
44+
org.biojava.bio.seq.db.emblcd
45+
org.biojava.bio.seq.db.flat
46+
org.biojava.bio.seq.distributed
47+
org.biojava.bio.seq.filter
48+
org.biojava.bio.seq.homol
49+
org.biojava.bio.seq.impl
50+
org.biojava.bio.seq.io
51+
org.biojava.bio.seq.io.agave
52+
org.biojava.bio.seq.io.filterxml
53+
org.biojava.bio.seq.io.game
54+
org.biojava.bio.seq.io.game12
55+
org.biojava.bio.seq.projection
56+
org.biojava.bio.symbol
57+
org.biojava.bio.taxa
58+
org.biojava.directory
59+
org.biojava.naming
60+
org.biojava.ontology
61+
org.biojava.ontology.io
62+
org.biojava.ontology.obo
63+
org.biojava.stats.svm
64+
org.biojava.stats.svm.tools
65+
org.biojava.utils
66+
org.biojava.utils.automata
67+
org.biojava.utils.bytecode
68+
org.biojava.utils.cache
69+
org.biojava.utils.candy
70+
org.biojava.utils.io
71+
org.biojava.utils.lsid
72+
org.biojava.utils.math
73+
org.biojava.utils.net
74+
org.biojava.utils.process
75+
org.biojava.utils.regex
76+
org.biojava.utils.stax
77+
org.biojava.utils.walker
78+
org.biojava.utils.xml
79+
org.biojavax
80+
org.biojavax.bio
81+
org.biojavax.bio.alignment
82+
org.biojavax.bio.alignment.blast
83+
org.biojavax.bio.db
84+
org.biojavax.bio.db.biosql
85+
org.biojavax.bio.db.ncbi
86+
org.biojavax.bio.phylo
87+
org.biojavax.bio.phylo.io.nexus
88+
org.biojavax.bio.phylo.io.phylip
89+
org.biojavax.bio.seq
90+
org.biojavax.bio.seq.io
91+
org.biojavax.bio.taxa
92+
org.biojavax.bio.taxa.io
93+
org.biojavax.ga
94+
org.biojavax.ga.exception
95+
org.biojavax.ga.functions
96+
org.biojavax.ga.impl
97+
org.biojavax.ga.util
98+
org.biojavax.ontology
99+
org.biojavax.utils

docs/api1.9.5/help-doc.html

+282
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,282 @@
1+
<!DOCTYPE HTML>
2+
<!-- NewPage -->
3+
<html lang="en">
4+
<head>
5+
<!-- Generated by javadoc (11.0.10) on Fri Mar 12 13:02:30 CST 2021 -->
6+
<title>API Help (biojava-legacy 1.9.5 API)</title>
7+
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
8+
<meta name="dc.created" content="2021-03-12">
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-3.5.1.js"></script>
18+
<script type="text/javascript" src="jquery/jquery-ui.js"></script>
19+
</head>
20+
<body>
21+
<script type="text/javascript"><!--
22+
try {
23+
if (location.href.indexOf('is-external=true') == -1) {
24+
parent.document.title="API Help (biojava-legacy 1.9.5 API)";
25+
}
26+
}
27+
catch(err) {
28+
}
29+
//-->
30+
var pathtoroot = "./";
31+
var useModuleDirectories = true;
32+
loadScripts(document, 'script');</script>
33+
<noscript>
34+
<div>JavaScript is disabled on your browser.</div>
35+
</noscript>
36+
<header role="banner">
37+
<nav role="navigation">
38+
<div class="fixedNav">
39+
<!-- ========= START OF TOP NAVBAR ======= -->
40+
<div class="topNav"><a id="navbar.top">
41+
<!-- -->
42+
</a>
43+
<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
44+
<a id="navbar.top.firstrow">
45+
<!-- -->
46+
</a>
47+
<ul class="navList" title="Navigation">
48+
<li><a href="index.html">Overview</a></li>
49+
<li>Package</li>
50+
<li>Class</li>
51+
<li>Use</li>
52+
<li><a href="overview-tree.html">Tree</a></li>
53+
<li><a href="deprecated-list.html">Deprecated</a></li>
54+
<li><a href="index-all.html">Index</a></li>
55+
<li class="navBarCell1Rev">Help</li>
56+
</ul>
57+
</div>
58+
<div class="subNav">
59+
<ul class="navList" id="allclasses_navbar_top">
60+
<li><a href="allclasses.html">All&nbsp;Classes</a></li>
61+
</ul>
62+
<ul class="navListSearch">
63+
<li><label for="search">SEARCH:</label>
64+
<input type="text" id="search" value="search" disabled="disabled">
65+
<input type="reset" id="reset" value="reset" disabled="disabled">
66+
</li>
67+
</ul>
68+
<div>
69+
<script type="text/javascript"><!--
70+
allClassesLink = document.getElementById("allclasses_navbar_top");
71+
if(window==top) {
72+
allClassesLink.style.display = "block";
73+
}
74+
else {
75+
allClassesLink.style.display = "none";
76+
}
77+
//-->
78+
</script>
79+
<noscript>
80+
<div>JavaScript is disabled on your browser.</div>
81+
</noscript>
82+
</div>
83+
<a id="skip.navbar.top">
84+
<!-- -->
85+
</a></div>
86+
<!-- ========= END OF TOP NAVBAR ========= -->
87+
</div>
88+
<div class="navPadding">&nbsp;</div>
89+
<script type="text/javascript"><!--
90+
$('.navPadding').css('padding-top', $('.fixedNav').css("height"));
91+
//-->
92+
</script>
93+
</nav>
94+
</header>
95+
<main role="main">
96+
<div class="header">
97+
<h1 class="title">How This API Document Is Organized</h1>
98+
<div class="subTitle">This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.</div>
99+
</div>
100+
<div class="contentContainer">
101+
<ul class="blockList">
102+
<li class="blockList">
103+
<section role="region">
104+
<h2>Overview</h2>
105+
<p>The <a href="index.html">Overview</a> page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.</p>
106+
</section>
107+
</li>
108+
<li class="blockList">
109+
<section role="region">
110+
<h2>Package</h2>
111+
<p>Each package has a page that contains a list of its classes and interfaces, with a summary for each. These pages may contain six categories:</p>
112+
<ul>
113+
<li>Interfaces</li>
114+
<li>Classes</li>
115+
<li>Enums</li>
116+
<li>Exceptions</li>
117+
<li>Errors</li>
118+
<li>Annotation Types</li>
119+
</ul>
120+
</section>
121+
</li>
122+
<li class="blockList">
123+
<section role="region">
124+
<h2>Class or Interface</h2>
125+
<p>Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:</p>
126+
<ul>
127+
<li>Class Inheritance Diagram</li>
128+
<li>Direct Subclasses</li>
129+
<li>All Known Subinterfaces</li>
130+
<li>All Known Implementing Classes</li>
131+
<li>Class or Interface Declaration</li>
132+
<li>Class or Interface Description</li>
133+
</ul>
134+
<br>
135+
<ul>
136+
<li>Nested Class Summary</li>
137+
<li>Field Summary</li>
138+
<li>Property Summary</li>
139+
<li>Constructor Summary</li>
140+
<li>Method Summary</li>
141+
</ul>
142+
<br>
143+
<ul>
144+
<li>Field Detail</li>
145+
<li>Property Detail</li>
146+
<li>Constructor Detail</li>
147+
<li>Method Detail</li>
148+
</ul>
149+
<p>Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.</p>
150+
</section>
151+
</li>
152+
<li class="blockList">
153+
<section role="region">
154+
<h2>Annotation Type</h2>
155+
<p>Each annotation type has its own separate page with the following sections:</p>
156+
<ul>
157+
<li>Annotation Type Declaration</li>
158+
<li>Annotation Type Description</li>
159+
<li>Required Element Summary</li>
160+
<li>Optional Element Summary</li>
161+
<li>Element Detail</li>
162+
</ul>
163+
</section>
164+
</li>
165+
<li class="blockList">
166+
<section role="region">
167+
<h2>Enum</h2>
168+
<p>Each enum has its own separate page with the following sections:</p>
169+
<ul>
170+
<li>Enum Declaration</li>
171+
<li>Enum Description</li>
172+
<li>Enum Constant Summary</li>
173+
<li>Enum Constant Detail</li>
174+
</ul>
175+
</section>
176+
</li>
177+
<li class="blockList">
178+
<section role="region">
179+
<h2>Use</h2>
180+
<p>Each documented package, class and interface has its own Use page. This page describes what packages, classes, methods, constructors and fields use any part of the given class or package. Given a class or interface A, its "Use" page includes subclasses of A, fields declared as A, methods that return A, and methods and constructors with parameters of type A. You can access this page by first going to the package, class or interface, then clicking on the "Use" link in the navigation bar.</p>
181+
</section>
182+
</li>
183+
<li class="blockList">
184+
<section role="region">
185+
<h2>Tree (Class Hierarchy)</h2>
186+
<p>There is a <a href="overview-tree.html">Class Hierarchy</a> page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. Classes are organized by inheritance structure starting with <code>java.lang.Object</code>. Interfaces do not inherit from <code>java.lang.Object</code>.</p>
187+
<ul>
188+
<li>When viewing the Overview page, clicking on "Tree" displays the hierarchy for all packages.</li>
189+
<li>When viewing a particular package, class or interface page, clicking on "Tree" displays the hierarchy for only that package.</li>
190+
</ul>
191+
</section>
192+
</li>
193+
<li class="blockList">
194+
<section role="region">
195+
<h2>Deprecated API</h2>
196+
<p>The <a href="deprecated-list.html">Deprecated API</a> page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.</p>
197+
</section>
198+
</li>
199+
<li class="blockList">
200+
<section role="region">
201+
<h2>Index</h2>
202+
<p>The <a href="index-all.html">Index</a> contains an alphabetic index of all classes, interfaces, constructors, methods, and fields, as well as lists of all packages and all classes.</p>
203+
</section>
204+
</li>
205+
<li class="blockList">
206+
<section role="region">
207+
<h2>All&nbsp;Classes</h2>
208+
<p>The <a href="allclasses.html">All Classes</a> link shows all classes and interfaces except non-static nested types.</p>
209+
</section>
210+
</li>
211+
<li class="blockList">
212+
<section role="region">
213+
<h2>Serialized Form</h2>
214+
<p>Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.</p>
215+
</section>
216+
</li>
217+
<li class="blockList">
218+
<section role="region">
219+
<h2>Constant Field Values</h2>
220+
<p>The <a href="constant-values.html">Constant Field Values</a> page lists the static final fields and their values.</p>
221+
</section>
222+
</li>
223+
<li class="blockList">
224+
<section role="region">
225+
<h2>Search</h2>
226+
<p>You can search for definitions of modules, packages, types, fields, methods and other terms defined in the API, using some or all of the name. "Camel-case" abbreviations are supported: for example, "InpStr" will find "InputStream" and "InputStreamReader".</p>
227+
</section>
228+
</li>
229+
</ul>
230+
<hr>
231+
<span class="emphasizedPhrase">This help file applies to API documentation generated by the standard doclet.</span></div>
232+
</main>
233+
<footer role="contentinfo">
234+
<nav role="navigation">
235+
<!-- ======= START OF BOTTOM NAVBAR ====== -->
236+
<div class="bottomNav"><a id="navbar.bottom">
237+
<!-- -->
238+
</a>
239+
<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
240+
<a id="navbar.bottom.firstrow">
241+
<!-- -->
242+
</a>
243+
<ul class="navList" title="Navigation">
244+
<li><a href="index.html">Overview</a></li>
245+
<li>Package</li>
246+
<li>Class</li>
247+
<li>Use</li>
248+
<li><a href="overview-tree.html">Tree</a></li>
249+
<li><a href="deprecated-list.html">Deprecated</a></li>
250+
<li><a href="index-all.html">Index</a></li>
251+
<li class="navBarCell1Rev">Help</li>
252+
</ul>
253+
<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>
254+
</div>
255+
<div class="subNav">
256+
<ul class="navList" id="allclasses_navbar_bottom">
257+
<li><a href="allclasses.html">All&nbsp;Classes</a></li>
258+
</ul>
259+
<div>
260+
<script type="text/javascript"><!--
261+
allClassesLink = document.getElementById("allclasses_navbar_bottom");
262+
if(window==top) {
263+
allClassesLink.style.display = "block";
264+
}
265+
else {
266+
allClassesLink.style.display = "none";
267+
}
268+
//-->
269+
</script>
270+
<noscript>
271+
<div>JavaScript is disabled on your browser.</div>
272+
</noscript>
273+
</div>
274+
<a id="skip.navbar.bottom">
275+
<!-- -->
276+
</a></div>
277+
<!-- ======== END OF BOTTOM NAVBAR ======= -->
278+
</nav>
279+
<p class="legalCopy"><small>Copyright &#169; 2021 <a href="http://www.biojava.org">BioJava</a>. All rights reserved.</small></p>
280+
</footer>
281+
</body>
282+
</html>

0 commit comments

Comments
 (0)