- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/Tutorial/chapter_uniprot.html b/dev/Tutorial/chapter_uniprot.html
index 6cbe48f9..c532ae60 100644
--- a/dev/Tutorial/chapter_uniprot.html
+++ b/dev/Tutorial/chapter_uniprot.html
@@ -4,7 +4,7 @@
- Swiss-Prot and ExPASy — Biopython 1.84.dev0 documentation
+ Swiss-Prot and ExPASy — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -752,14 +752,14 @@ Scanning the Prosite database
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/Tutorial/index.html b/dev/Tutorial/index.html
index 2b772581..50ec5650 100644
--- a/dev/Tutorial/index.html
+++ b/dev/Tutorial/index.html
@@ -4,7 +4,7 @@
- Biopython Tutorial & Cookbook — Biopython 1.84.dev0 documentation
+ Biopython Tutorial & Cookbook — Biopython 1.85.dev0 documentation
@@ -16,9 +16,10 @@
-
-
+
+
+
@@ -112,7 +113,7 @@
Biopython Tutorial & Cookbook
Named authors: Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck,
Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczyński.
-This is from Biopython 1.84.dev0.
+This is from Biopython 1.85.dev0.
Table of contents:
@@ -176,14 +177,14 @@ Biopython Tutorial & Cookbook
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/_static/basic.css b/dev/_static/basic.css
index 30fee9d0..f316efcb 100644
--- a/dev/_static/basic.css
+++ b/dev/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/dev/_static/doctools.js b/dev/_static/doctools.js
index d06a71d7..4d67807d 100644
--- a/dev/_static/doctools.js
+++ b/dev/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Base JavaScript utilities for all Sphinx HTML documentation.
*
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/dev/_static/documentation_options.js b/dev/_static/documentation_options.js
index 5bb7736b..d14609fb 100644
--- a/dev/_static/documentation_options.js
+++ b/dev/_static/documentation_options.js
@@ -1,5 +1,5 @@
const DOCUMENTATION_OPTIONS = {
- VERSION: '1.84.dev0',
+ VERSION: '1.85.dev0',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/dev/_static/language_data.js b/dev/_static/language_data.js
index 250f5665..367b8ed8 100644
--- a/dev/_static/language_data.js
+++ b/dev/_static/language_data.js
@@ -5,7 +5,7 @@
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
*
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -13,7 +13,7 @@
var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
/**
* Porter Stemmer
diff --git a/dev/_static/searchtools.js b/dev/_static/searchtools.js
index 7918c3fa..92da3f8b 100644
--- a/dev/_static/searchtools.js
+++ b/dev/_static/searchtools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
.then((data) => {
if (data)
listItem.appendChild(
- Search.makeSearchSummary(data, searchTerms)
+ Search.makeSearchSummary(data, searchTerms, anchor)
);
// highlight search terms in the summary
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
@@ -116,8 +116,8 @@ const _finishSearch = (resultCount) => {
);
else
Search.status.innerText = _(
- `Search finished, found ${resultCount} page(s) matching the search query.`
- );
+ "Search finished, found ${resultCount} page(s) matching the search query."
+ ).replace('${resultCount}', resultCount);
};
const _displayNextItem = (
results,
@@ -137,6 +137,22 @@ const _displayNextItem = (
// search finished, update title and status message
else _finishSearch(resultCount);
};
+// Helper function used by query() to order search results.
+// Each input is an array of [docname, title, anchor, descr, score, filename].
+// Order the results by score (in opposite order of appearance, since the
+// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
+const _orderResultsByScoreThenName = (a, b) => {
+ const leftScore = a[4];
+ const rightScore = b[4];
+ if (leftScore === rightScore) {
+ // same score: sort alphabetically
+ const leftTitle = a[1].toLowerCase();
+ const rightTitle = b[1].toLowerCase();
+ if (leftTitle === rightTitle) return 0;
+ return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+ }
+ return leftScore > rightScore ? 1 : -1;
+};
/**
* Default splitQuery function. Can be overridden in ``sphinx.search`` with a
@@ -160,13 +176,26 @@ const Search = {
_queued_query: null,
_pulse_status: -1,
- htmlToText: (htmlString) => {
+ htmlToText: (htmlString, anchor) => {
const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
- htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
+ for (const removalQuery of [".headerlinks", "script", "style"]) {
+ htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
+ }
+ if (anchor) {
+ const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
+ if (anchorContent) return anchorContent.textContent;
+
+ console.warn(
+ `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
+ );
+ }
+
+ // if anchor not specified or not found, fall back to main content
const docContent = htmlElement.querySelector('[role="main"]');
- if (docContent !== undefined) return docContent.textContent;
+ if (docContent) return docContent.textContent;
+
console.warn(
- "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template."
+ "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
);
return "";
},
@@ -239,16 +268,7 @@ const Search = {
else Search.deferQuery(query);
},
- /**
- * execute search (requires search index to be loaded)
- */
- query: (query) => {
- const filenames = Search._index.filenames;
- const docNames = Search._index.docnames;
- const titles = Search._index.titles;
- const allTitles = Search._index.alltitles;
- const indexEntries = Search._index.indexentries;
-
+ _parseQuery: (query) => {
// stem the search terms and add them to the correct list
const stemmer = new Stemmer();
const searchTerms = new Set();
@@ -284,16 +304,32 @@ const Search = {
// console.info("required: ", [...searchTerms]);
// console.info("excluded: ", [...excludedTerms]);
- // array of [docname, title, anchor, descr, score, filename]
- let results = [];
+ return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
+ },
+
+ /**
+ * execute search (requires search index to be loaded)
+ */
+ _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
+ const filenames = Search._index.filenames;
+ const docNames = Search._index.docnames;
+ const titles = Search._index.titles;
+ const allTitles = Search._index.alltitles;
+ const indexEntries = Search._index.indexentries;
+
+ // Collect multiple result groups to be sorted separately and then ordered.
+ // Each is an array of [docname, title, anchor, descr, score, filename].
+ const normalResults = [];
+ const nonMainIndexResults = [];
+
_removeChildren(document.getElementById("search-progress"));
- const queryLower = query.toLowerCase();
+ const queryLower = query.toLowerCase().trim();
for (const [title, foundTitles] of Object.entries(allTitles)) {
- if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) {
+ if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
for (const [file, id] of foundTitles) {
let score = Math.round(100 * queryLower.length / title.length)
- results.push([
+ normalResults.push([
docNames[file],
titles[file] !== title ? `${titles[file]} > ${title}` : title,
id !== null ? "#" + id : "",
@@ -308,46 +344,47 @@ const Search = {
// search for explicit entries in index directives
for (const [entry, foundEntries] of Object.entries(indexEntries)) {
if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
- for (const [file, id] of foundEntries) {
- let score = Math.round(100 * queryLower.length / entry.length)
- results.push([
+ for (const [file, id, isMain] of foundEntries) {
+ const score = Math.round(100 * queryLower.length / entry.length);
+ const result = [
docNames[file],
titles[file],
id ? "#" + id : "",
null,
score,
filenames[file],
- ]);
+ ];
+ if (isMain) {
+ normalResults.push(result);
+ } else {
+ nonMainIndexResults.push(result);
+ }
}
}
}
// lookup as object
objectTerms.forEach((term) =>
- results.push(...Search.performObjectSearch(term, objectTerms))
+ normalResults.push(...Search.performObjectSearch(term, objectTerms))
);
// lookup as search terms in fulltext
- results.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+ normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
// let the scorer override scores with a custom scoring function
- if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item)));
-
- // now sort the results by score (in opposite order of appearance, since the
- // display function below uses pop() to retrieve items) and then
- // alphabetically
- results.sort((a, b) => {
- const leftScore = a[4];
- const rightScore = b[4];
- if (leftScore === rightScore) {
- // same score: sort alphabetically
- const leftTitle = a[1].toLowerCase();
- const rightTitle = b[1].toLowerCase();
- if (leftTitle === rightTitle) return 0;
- return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
- }
- return leftScore > rightScore ? 1 : -1;
- });
+ if (Scorer.score) {
+ normalResults.forEach((item) => (item[4] = Scorer.score(item)));
+ nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
+ }
+
+ // Sort each group of results by score and then alphabetically by name.
+ normalResults.sort(_orderResultsByScoreThenName);
+ nonMainIndexResults.sort(_orderResultsByScoreThenName);
+
+ // Combine the result groups in (reverse) order.
+ // Non-main index entries are typically arbitrary cross-references,
+ // so display them after other results.
+ let results = [...nonMainIndexResults, ...normalResults];
// remove duplicate search results
// note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
@@ -361,7 +398,12 @@ const Search = {
return acc;
}, []);
- results = results.reverse();
+ return results.reverse();
+ },
+
+ query: (query) => {
+ const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
+ const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
// for debugging
//Search.lastresults = results.slice(); // a copy
@@ -466,14 +508,18 @@ const Search = {
// add support for partial matches
if (word.length > 2) {
const escapedWord = _escapeRegExp(word);
- Object.keys(terms).forEach((term) => {
- if (term.match(escapedWord) && !terms[word])
- arr.push({ files: terms[term], score: Scorer.partialTerm });
- });
- Object.keys(titleTerms).forEach((term) => {
- if (term.match(escapedWord) && !titleTerms[word])
- arr.push({ files: titleTerms[word], score: Scorer.partialTitle });
- });
+ if (!terms.hasOwnProperty(word)) {
+ Object.keys(terms).forEach((term) => {
+ if (term.match(escapedWord))
+ arr.push({ files: terms[term], score: Scorer.partialTerm });
+ });
+ }
+ if (!titleTerms.hasOwnProperty(word)) {
+ Object.keys(titleTerms).forEach((term) => {
+ if (term.match(escapedWord))
+ arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
+ });
+ }
}
// no match but word was a required one
@@ -496,9 +542,8 @@ const Search = {
// create the mapping
files.forEach((file) => {
- if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1)
- fileMap.get(file).push(word);
- else fileMap.set(file, [word]);
+ if (!fileMap.has(file)) fileMap.set(file, [word]);
+ else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
});
});
@@ -549,8 +594,8 @@ const Search = {
* search summary for a given text. keywords is a list
* of stemmed words.
*/
- makeSearchSummary: (htmlText, keywords) => {
- const text = Search.htmlToText(htmlText);
+ makeSearchSummary: (htmlText, keywords, anchor) => {
+ const text = Search.htmlToText(htmlText, anchor);
if (text === "") return null;
const textLower = text.toLowerCase();
diff --git a/dev/api/Bio.Affy.CelFile.html b/dev/api/Bio.Affy.CelFile.html
index 10354c8d..52b98447 100644
--- a/dev/api/Bio.Affy.CelFile.html
+++ b/dev/api/Bio.Affy.CelFile.html
@@ -4,7 +4,7 @@
- Bio.Affy.CelFile module — Biopython 1.84.dev0 documentation
+ Bio.Affy.CelFile module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -253,14 +253,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Affy.html b/dev/api/Bio.Affy.html
index bb21d06b..f3ca4e8b 100644
--- a/dev/api/Bio.Affy.html
+++ b/dev/api/Bio.Affy.html
@@ -4,7 +4,7 @@
- Bio.Affy package — Biopython 1.84.dev0 documentation
+ Bio.Affy package — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -187,14 +187,14 @@ Submodules
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.AlignInfo.html b/dev/api/Bio.Align.AlignInfo.html
index 6e525cc1..f24ffdaf 100644
--- a/dev/api/Bio.Align.AlignInfo.html
+++ b/dev/api/Bio.Align.AlignInfo.html
@@ -4,7 +4,7 @@
- Bio.Align.AlignInfo module — Biopython 1.84.dev0 documentation
+ Bio.Align.AlignInfo module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -390,14 +390,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.Applications.html b/dev/api/Bio.Align.Applications.html
index 59949a79..bdd19f49 100644
--- a/dev/api/Bio.Align.Applications.html
+++ b/dev/api/Bio.Align.Applications.html
@@ -4,7 +4,7 @@
- Bio.Align.Applications package — Biopython 1.84.dev0 documentation
+ Bio.Align.Applications package — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -2937,14 +2937,14 @@ Bio.Align.Applications package
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.a2m.html b/dev/api/Bio.Align.a2m.html
index 66e697ff..6c85430b 100644
--- a/dev/api/Bio.Align.a2m.html
+++ b/dev/api/Bio.Align.a2m.html
@@ -4,7 +4,7 @@
- Bio.Align.a2m module — Biopython 1.84.dev0 documentation
+ Bio.Align.a2m module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -221,14 +221,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.analysis.html b/dev/api/Bio.Align.analysis.html
index 7caca174..62a940bd 100644
--- a/dev/api/Bio.Align.analysis.html
+++ b/dev/api/Bio.Align.analysis.html
@@ -4,7 +4,7 @@
- Bio.Align.analysis module — Biopython 1.84.dev0 documentation
+ Bio.Align.analysis module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -222,14 +222,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.bed.html b/dev/api/Bio.Align.bed.html
index 97e6b62e..985a8270 100644
--- a/dev/api/Bio.Align.bed.html
+++ b/dev/api/Bio.Align.bed.html
@@ -4,7 +4,7 @@
- Bio.Align.bed module — Biopython 1.84.dev0 documentation
+ Bio.Align.bed module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -234,14 +234,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.bigbed.html b/dev/api/Bio.Align.bigbed.html
index 0d7a2b3a..44237fc9 100644
--- a/dev/api/Bio.Align.bigbed.html
+++ b/dev/api/Bio.Align.bigbed.html
@@ -4,7 +4,7 @@
- Bio.Align.bigbed module — Biopython 1.84.dev0 documentation
+ Bio.Align.bigbed module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -426,14 +426,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.bigmaf.html b/dev/api/Bio.Align.bigmaf.html
index 2698713f..6dd55ff0 100644
--- a/dev/api/Bio.Align.bigmaf.html
+++ b/dev/api/Bio.Align.bigmaf.html
@@ -4,7 +4,7 @@
- Bio.Align.bigmaf module — Biopython 1.84.dev0 documentation
+ Bio.Align.bigmaf module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -276,14 +276,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.bigpsl.html b/dev/api/Bio.Align.bigpsl.html
index 236a189d..6f04fa13 100644
--- a/dev/api/Bio.Align.bigpsl.html
+++ b/dev/api/Bio.Align.bigpsl.html
@@ -4,7 +4,7 @@
- Bio.Align.bigpsl module — Biopython 1.84.dev0 documentation
+ Bio.Align.bigpsl module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -279,14 +279,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.chain.html b/dev/api/Bio.Align.chain.html
index 3b78f4ca..769560d3 100644
--- a/dev/api/Bio.Align.chain.html
+++ b/dev/api/Bio.Align.chain.html
@@ -4,7 +4,7 @@
- Bio.Align.chain module — Biopython 1.84.dev0 documentation
+ Bio.Align.chain module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -218,14 +218,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.clustal.html b/dev/api/Bio.Align.clustal.html
index 98fae155..e4a36a63 100644
--- a/dev/api/Bio.Align.clustal.html
+++ b/dev/api/Bio.Align.clustal.html
@@ -4,7 +4,7 @@
- Bio.Align.clustal module — Biopython 1.84.dev0 documentation
+ Bio.Align.clustal module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -214,14 +214,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.emboss.html b/dev/api/Bio.Align.emboss.html
index 40d7632c..fdd6d29b 100644
--- a/dev/api/Bio.Align.emboss.html
+++ b/dev/api/Bio.Align.emboss.html
@@ -4,7 +4,7 @@
- Bio.Align.emboss module — Biopython 1.84.dev0 documentation
+ Bio.Align.emboss module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -187,14 +187,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.exonerate.html b/dev/api/Bio.Align.exonerate.html
index 59d6cc82..60119763 100644
--- a/dev/api/Bio.Align.exonerate.html
+++ b/dev/api/Bio.Align.exonerate.html
@@ -4,7 +4,7 @@
- Bio.Align.exonerate module — Biopython 1.84.dev0 documentation
+ Bio.Align.exonerate module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -254,14 +254,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.fasta.html b/dev/api/Bio.Align.fasta.html
index a6ef3508..2bab12c2 100644
--- a/dev/api/Bio.Align.fasta.html
+++ b/dev/api/Bio.Align.fasta.html
@@ -4,7 +4,7 @@
- Bio.Align.fasta module — Biopython 1.84.dev0 documentation
+ Bio.Align.fasta module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -212,14 +212,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.hhr.html b/dev/api/Bio.Align.hhr.html
index 891fceef..9ff30cb6 100644
--- a/dev/api/Bio.Align.hhr.html
+++ b/dev/api/Bio.Align.hhr.html
@@ -4,7 +4,7 @@
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+ Bio.Align.hhr module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -197,14 +197,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.html b/dev/api/Bio.Align.html
index 603d9e71..d62949fd 100644
--- a/dev/api/Bio.Align.html
+++ b/dev/api/Bio.Align.html
@@ -4,7 +4,7 @@
- Bio.Align package — Biopython 1.84.dev0 documentation
+ Bio.Align package — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -3403,14 +3403,14 @@ Submodules
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.interfaces.html b/dev/api/Bio.Align.interfaces.html
index 2fe8f847..6924cb88 100644
--- a/dev/api/Bio.Align.interfaces.html
+++ b/dev/api/Bio.Align.interfaces.html
@@ -4,7 +4,7 @@
- Bio.Align.interfaces module — Biopython 1.84.dev0 documentation
+ Bio.Align.interfaces module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
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+
+
@@ -398,14 +398,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.maf.html b/dev/api/Bio.Align.maf.html
index 7675306d..0c252c78 100644
--- a/dev/api/Bio.Align.maf.html
+++ b/dev/api/Bio.Align.maf.html
@@ -4,7 +4,7 @@
- Bio.Align.maf module — Biopython 1.84.dev0 documentation
+ Bio.Align.maf module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
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+
+
@@ -246,14 +246,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.mauve.html b/dev/api/Bio.Align.mauve.html
index 4e640246..00681eaa 100644
--- a/dev/api/Bio.Align.mauve.html
+++ b/dev/api/Bio.Align.mauve.html
@@ -4,7 +4,7 @@
- Bio.Align.mauve module — Biopython 1.84.dev0 documentation
+ Bio.Align.mauve module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -246,14 +246,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.msf.html b/dev/api/Bio.Align.msf.html
index cb3f3ead..3e483749 100644
--- a/dev/api/Bio.Align.msf.html
+++ b/dev/api/Bio.Align.msf.html
@@ -4,7 +4,7 @@
- Bio.Align.msf module — Biopython 1.84.dev0 documentation
+ Bio.Align.msf module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -186,14 +186,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.nexus.html b/dev/api/Bio.Align.nexus.html
index a23d5c0f..25b0f220 100644
--- a/dev/api/Bio.Align.nexus.html
+++ b/dev/api/Bio.Align.nexus.html
@@ -4,7 +4,7 @@
- Bio.Align.nexus module — Biopython 1.84.dev0 documentation
+ Bio.Align.nexus module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -274,14 +274,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.phylip.html b/dev/api/Bio.Align.phylip.html
index 7cb851ac..73cddffc 100644
--- a/dev/api/Bio.Align.phylip.html
+++ b/dev/api/Bio.Align.phylip.html
@@ -4,7 +4,7 @@
- Bio.Align.phylip module — Biopython 1.84.dev0 documentation
+ Bio.Align.phylip module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -213,14 +213,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.psl.html b/dev/api/Bio.Align.psl.html
index 57f57f94..bb3c129e 100644
--- a/dev/api/Bio.Align.psl.html
+++ b/dev/api/Bio.Align.psl.html
@@ -4,7 +4,7 @@
- Bio.Align.psl module — Biopython 1.84.dev0 documentation
+ Bio.Align.psl module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -266,14 +266,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.sam.html b/dev/api/Bio.Align.sam.html
index 7f8d9e1e..b8d3d511 100644
--- a/dev/api/Bio.Align.sam.html
+++ b/dev/api/Bio.Align.sam.html
@@ -4,7 +4,7 @@
- Bio.Align.sam module — Biopython 1.84.dev0 documentation
+ Bio.Align.sam module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -267,14 +267,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.stockholm.html b/dev/api/Bio.Align.stockholm.html
index 79428298..2c540300 100644
--- a/dev/api/Bio.Align.stockholm.html
+++ b/dev/api/Bio.Align.stockholm.html
@@ -4,7 +4,7 @@
- Bio.Align.stockholm module — Biopython 1.84.dev0 documentation
+ Bio.Align.stockholm module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -354,14 +354,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.substitution_matrices.html b/dev/api/Bio.Align.substitution_matrices.html
index 6f18964d..b28e1544 100644
--- a/dev/api/Bio.Align.substitution_matrices.html
+++ b/dev/api/Bio.Align.substitution_matrices.html
@@ -4,7 +4,7 @@
- Bio.Align.substitution_matrices package — Biopython 1.84.dev0 documentation
+ Bio.Align.substitution_matrices package — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -346,14 +346,14 @@ Bio.Align.substitution_matrices package
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Align.tabular.html b/dev/api/Bio.Align.tabular.html
index ebc425be..615ad409 100644
--- a/dev/api/Bio.Align.tabular.html
+++ b/dev/api/Bio.Align.tabular.html
@@ -4,7 +4,7 @@
- Bio.Align.tabular module — Biopython 1.84.dev0 documentation
+ Bio.Align.tabular module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -234,14 +234,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.ClustalIO.html b/dev/api/Bio.AlignIO.ClustalIO.html
index fdaec113..e3ca00ae 100644
--- a/dev/api/Bio.AlignIO.ClustalIO.html
+++ b/dev/api/Bio.AlignIO.ClustalIO.html
@@ -4,7 +4,7 @@
- Bio.AlignIO.ClustalIO module — Biopython 1.84.dev0 documentation
+ Bio.AlignIO.ClustalIO module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -194,14 +194,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.EmbossIO.html b/dev/api/Bio.AlignIO.EmbossIO.html
index 1c9fe7b6..d3883cf0 100644
--- a/dev/api/Bio.AlignIO.EmbossIO.html
+++ b/dev/api/Bio.AlignIO.EmbossIO.html
@@ -4,7 +4,7 @@
- Bio.AlignIO.EmbossIO module — Biopython 1.84.dev0 documentation
+ Bio.AlignIO.EmbossIO module — Biopython 1.85.dev0 documentation
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-
-
+
+
@@ -185,14 +185,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.FastaIO.html b/dev/api/Bio.AlignIO.FastaIO.html
index 01f31774..a6209eeb 100644
--- a/dev/api/Bio.AlignIO.FastaIO.html
+++ b/dev/api/Bio.AlignIO.FastaIO.html
@@ -4,7 +4,7 @@
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+ Bio.AlignIO.FastaIO module — Biopython 1.85.dev0 documentation
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-
-
+
+
@@ -208,14 +208,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.Interfaces.html b/dev/api/Bio.AlignIO.Interfaces.html
index 463684e9..e466ced7 100644
--- a/dev/api/Bio.AlignIO.Interfaces.html
+++ b/dev/api/Bio.AlignIO.Interfaces.html
@@ -4,7 +4,7 @@
- Bio.AlignIO.Interfaces module — Biopython 1.84.dev0 documentation
+ Bio.AlignIO.Interfaces module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -310,14 +310,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.MafIO.html b/dev/api/Bio.AlignIO.MafIO.html
index 3481f25b..14da93f1 100644
--- a/dev/api/Bio.AlignIO.MafIO.html
+++ b/dev/api/Bio.AlignIO.MafIO.html
@@ -4,7 +4,7 @@
- Bio.AlignIO.MafIO module — Biopython 1.84.dev0 documentation
+ Bio.AlignIO.MafIO module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -278,14 +278,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.MauveIO.html b/dev/api/Bio.AlignIO.MauveIO.html
index e512cf89..8ef1335b 100644
--- a/dev/api/Bio.AlignIO.MauveIO.html
+++ b/dev/api/Bio.AlignIO.MauveIO.html
@@ -4,7 +4,7 @@
- Bio.AlignIO.MauveIO module — Biopython 1.84.dev0 documentation
+ Bio.AlignIO.MauveIO module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
@@ -274,14 +274,14 @@
- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.MsfIO.html b/dev/api/Bio.AlignIO.MsfIO.html
index afb248dc..279a5e43 100644
--- a/dev/api/Bio.AlignIO.MsfIO.html
+++ b/dev/api/Bio.AlignIO.MsfIO.html
@@ -4,7 +4,7 @@
- Bio.AlignIO.MsfIO module — Biopython 1.84.dev0 documentation
+ Bio.AlignIO.MsfIO module — Biopython 1.85.dev0 documentation
@@ -16,8 +16,8 @@
-
-
+
+
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.NexusIO.html b/dev/api/Bio.AlignIO.NexusIO.html
index d5bb6ac5..d36b42e1 100644
--- a/dev/api/Bio.AlignIO.NexusIO.html
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@@ -4,7 +4,7 @@
- Bio.AlignIO.NexusIO module — Biopython 1.84.dev0 documentation
+ Bio.AlignIO.NexusIO module — Biopython 1.85.dev0 documentation
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.PhylipIO.html b/dev/api/Bio.AlignIO.PhylipIO.html
index 56b7ddb7..1e74efdd 100644
--- a/dev/api/Bio.AlignIO.PhylipIO.html
+++ b/dev/api/Bio.AlignIO.PhylipIO.html
@@ -4,7 +4,7 @@
- Bio.AlignIO.PhylipIO module — Biopython 1.84.dev0 documentation
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.AlignIO.StockholmIO.html b/dev/api/Bio.AlignIO.StockholmIO.html
index e03432cc..605cb8c8 100644
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+++ b/dev/api/Bio.AlignIO.StockholmIO.html
@@ -4,7 +4,7 @@
- Bio.AlignIO.StockholmIO module — Biopython 1.84.dev0 documentation
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@@ -16,8 +16,8 @@
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
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- Latest
diff --git a/dev/api/Bio.AlignIO.html b/dev/api/Bio.AlignIO.html
index 555325d2..4043a4e9 100644
--- a/dev/api/Bio.AlignIO.html
+++ b/dev/api/Bio.AlignIO.html
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- Bio.AlignIO package — Biopython 1.84.dev0 documentation
+ Bio.AlignIO package — Biopython 1.85.dev0 documentation
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+
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Application.html b/dev/api/Bio.Application.html
index 209c2e45..dadf5378 100644
--- a/dev/api/Bio.Application.html
+++ b/dev/api/Bio.Application.html
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- Bio.Application package — Biopython 1.84.dev0 documentation
+ Bio.Application package — Biopython 1.85.dev0 documentation
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
+ - Previous
- Latest
diff --git a/dev/api/Bio.Blast.Applications.html b/dev/api/Bio.Blast.Applications.html
index f0a4bd8b..fff63a18 100644
--- a/dev/api/Bio.Blast.Applications.html
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@@ -4,7 +4,7 @@
- Bio.Blast.Applications module — Biopython 1.84.dev0 documentation
+ Bio.Blast.Applications module — Biopython 1.85.dev0 documentation
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
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- Latest
diff --git a/dev/api/Bio.Blast.NCBIWWW.html b/dev/api/Bio.Blast.NCBIWWW.html
index c09dc5bf..4fb13cb3 100644
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@@ -4,7 +4,7 @@
- Bio.Blast.NCBIWWW module — Biopython 1.84.dev0 documentation
+ Bio.Blast.NCBIWWW module — Biopython 1.85.dev0 documentation
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
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- Latest
diff --git a/dev/api/Bio.Blast.NCBIXML.html b/dev/api/Bio.Blast.NCBIXML.html
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
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- Latest
diff --git a/dev/api/Bio.Blast.html b/dev/api/Bio.Blast.html
index c000a972..62f6e738 100644
--- a/dev/api/Bio.Blast.html
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- Biopython v: 1.84.dev0
+ Biopython v: 1.85.dev0
- Versions
- - Previous
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- Latest
diff --git a/dev/api/Bio.CAPS.html b/dev/api/Bio.CAPS.html
index 884cda18..84c3b8ff 100644
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- Biopython v: 1.84.dev0
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