From 34d439045f483111f92b3516e71e98a0a3fbb72e Mon Sep 17 00:00:00 2001 From: haozhu233 Date: Mon, 29 Apr 2024 14:31:38 +0000 Subject: [PATCH] deploy: 28bfbbcfa238d4679670f6eb57d0e92e041e5bca --- .buildinfo | 2 +- _autosummary/regdiffusion.GRN.html | 18 +- _autosummary/regdiffusion.GRNEvaluator.html | 2 +- .../regdiffusion.RegDiffusionTrainer.html | 4 +- ...egdiffusion.data.load_atlas_microglia.html | 8 +- .../regdiffusion.data.load_beeline.html | 26 +-- ...diffusion.data.load_hammond_microglia.html | 8 +- .../regdiffusion.models.RegDiffusion.html | 33 ++-- _modules/index.html | 2 +- _modules/regdiffusion/data/beeline.html | 2 +- _modules/regdiffusion/data/microglia.html | 2 +- _modules/regdiffusion/evaluator.html | 2 +- _modules/regdiffusion/grn.html | 2 +- .../regdiffusion/models/regdiffusion.html | 2 +- _modules/regdiffusion/trainer.html | 2 +- _sources/index.rst | 13 +- _sources/quick_tour.md | 2 +- _static/basic.css | 2 +- _static/doctools.js | 2 +- _static/language_data.js | 4 +- _static/searchtools.js | 165 +++++++++++------- data_module.html | 2 +- genindex.html | 2 +- index.html | 15 +- main_api.html | 2 +- models.html | 2 +- quick_tour.html | 4 +- search.html | 2 +- searchindex.js | 2 +- supplements.html | 2 +- 30 files changed, 199 insertions(+), 137 deletions(-) diff --git a/.buildinfo b/.buildinfo index 9c9ecfa..f8373e2 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: a4ddb4b1ee677e2944e527df7fecdbe0 +config: a3784d844b5c9a0de36a926f4b21a8bb tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_autosummary/regdiffusion.GRN.html b/_autosummary/regdiffusion.GRN.html index 9603ac0..60b8ba0 100644 --- a/_autosummary/regdiffusion.GRN.html +++ b/_autosummary/regdiffusion.GRN.html @@ -38,7 +38,7 @@ - + @@ -382,12 +382,12 @@

GRN#

@@ -405,7 +405,7 @@

GRN#

  • genes (str, List(str)) – A single gene or a list of genes to inspect.

  • k (int) – Top-k edges to inspect on each node. If k=-1, export all

  • hops (str) – Number of hops to explore. We can either do a “2.5” or

    • -

  • "2.5". ("1.5" hop travesal around selected genes. Default is) –

    • +

  • "2.5". ("1.5" hop travesal around selected genes. Default is)

    • @@ -546,11 +546,11 @@

    GRN#

  • genes (str, List(str)) – A single gene or a list of genes to inspect.

  • k (int) – Top-k edges to inspect on each node. If k=-1, export all.

  • hops (str) – Number of hops of the neighborhood to explore. Default

    • -

  • "2.5". (is) –

    • +

  • "2.5". (is)

  • edge_widths (List) – The widths for edges for different edge width

    • -

  • levels. –

    • +

  • levels.

  • plot_engine (str) – Choose which network plot engine to use. Default

    • -

  • "pyvis". (is) –

    • +

  • "pyvis". (is)

  • **kwargs – Keyword arguments to be passed to plot_pyvis.

    • diff --git a/_autosummary/regdiffusion.GRNEvaluator.html b/_autosummary/regdiffusion.GRNEvaluator.html index 16642bc..99f5696 100644 --- a/_autosummary/regdiffusion.GRNEvaluator.html +++ b/_autosummary/regdiffusion.GRNEvaluator.html @@ -38,7 +38,7 @@ - + diff --git a/_autosummary/regdiffusion.RegDiffusionTrainer.html b/_autosummary/regdiffusion.RegDiffusionTrainer.html index 03236f0..bef48ea 100644 --- a/_autosummary/regdiffusion.RegDiffusionTrainer.html +++ b/_autosummary/regdiffusion.RegDiffusionTrainer.html @@ -38,7 +38,7 @@ - + @@ -425,7 +425,7 @@

    RegDiffusionTrainerParameters:

    • x_0 (torch.FloatTensor) – Torch tensor for expression data. Rows are

      • -

    • genes (cells and columns are) –

      • +

    • genes (cells and columns are)

    • t (torch.LongTensor) – Torch tensor for diffusion time steps.

    diff --git a/_autosummary/regdiffusion.data.load_atlas_microglia.html b/_autosummary/regdiffusion.data.load_atlas_microglia.html index 5c2c8ac..c8e40db 100644 --- a/_autosummary/regdiffusion.data.load_atlas_microglia.html +++ b/_autosummary/regdiffusion.data.load_atlas_microglia.html @@ -38,7 +38,7 @@ - + @@ -358,9 +358,9 @@

    regdiffusion.data.load_atlas_microgliaParameters:

    • data_dir (str) – Parent directory to save and load the data. If the path

      • -

    • exist (does not) –

      • -

    • a (it will be created. Data will be saved in) –

      • -

    • path. (subdirectory under the provided) –

      • +

    • exist (does not)

      • +

    • a (it will be created. Data will be saved in)

      • +

    • path. (subdirectory under the provided)

    diff --git a/_autosummary/regdiffusion.data.load_beeline.html b/_autosummary/regdiffusion.data.load_beeline.html index 3253230..3190d27 100644 --- a/_autosummary/regdiffusion.data.load_beeline.html +++ b/_autosummary/regdiffusion.data.load_beeline.html @@ -38,7 +38,7 @@ - + @@ -356,20 +356,20 @@

    regdiffusion.data.load_beelineParameters:

    • data_dir (str) – Parent directory to save and load the data. If the path

      • -

    • exist (does not) –

      • -

    • a (it will be created. Data will be saved in) –

      • -

    • path. (subdirectory under the provided) –

      • +

    • exist (does not)

      • +

    • a (it will be created. Data will be saved in)

      • +

    • path. (subdirectory under the provided)

    • benchmark_data (str) – Benchmark datasets. Choose among “hESC”, “hHep”,

      • -

    • "mDC" –

      • -

    • "mESC" –

      • -

    • "mHSC" –

      • -

    • "mHSC-GM" –

      • -

    • "mHSC-L". (and) –

      • +

    • "mDC"

      • +

    • "mESC"

      • +

    • "mHSC"

      • +

    • "mHSC-GM"

      • +

    • "mHSC-L". (and)

    • benchmark_setting (str) – Benchmark settings. Choose among “500_STRING”,

      • -

    • "1000_STRING" –

      • -

    • "500_Non-ChIP" –

      • -

    • "1000_Non-ChIP" –

      • -

    • "500_ChIP-seq" –

      • +

    • "1000_STRING"

      • +

    • "500_Non-ChIP"

      • +

    • "1000_Non-ChIP"

      • +

    • "500_ChIP-seq"

    diff --git a/_autosummary/regdiffusion.data.load_hammond_microglia.html b/_autosummary/regdiffusion.data.load_hammond_microglia.html index b29aa5a..ae469ec 100644 --- a/_autosummary/regdiffusion.data.load_hammond_microglia.html +++ b/_autosummary/regdiffusion.data.load_hammond_microglia.html @@ -38,7 +38,7 @@ - + @@ -364,9 +364,9 @@

    regdiffusion.data.load_hammond_microgliaParameters:

    • data_dir (str) – Parent directory to save and load the data. If the path

      • -

    • exist (does not) –

      • -

    • a (it will be created. Data will be saved in) –

      • -

    • path. (subdirectory under the provided) –

      • +

    • exist (does not)

      • +

    • a (it will be created. Data will be saved in)

      • +

    • path. (subdirectory under the provided)

    diff --git a/_autosummary/regdiffusion.models.RegDiffusion.html b/_autosummary/regdiffusion.models.RegDiffusion.html index 5740c07..847bb8d 100644 --- a/_autosummary/regdiffusion.models.RegDiffusion.html +++ b/_autosummary/regdiffusion.models.RegDiffusion.html @@ -38,7 +38,7 @@ - + @@ -401,16 +401,16 @@

    RegDiffusion

    Warning

    If assign is True the optimizer must be created after -the call to load_state_dict.

    +the call to load_state_dict unless +get_swap_module_params_on_conversion() is True.

    Parameters:
    @@ -844,13 +845,11 @@

    RegDiffusionstate_dict match the keys returned by this module’s state_dict() function. Default: True

    -

  • assign (bool, optional) – whether to assign items in the state -dictionary to their corresponding keys in the module instead -of copying them inplace into the module’s current parameters and buffers. -When False, the properties of the tensors in the current -module are preserved while when True, the properties of the -Tensors in the state dict are preserved. -Default: False

    • +

  • assign (bool, optional) – When False, the properties of the tensors +in the current module are preserved while when True, the +properties of the Tensors in the state dict are preserved. The only +exception is the requires_grad field of +Default: ``False`

    • Returns:
    @@ -1342,7 +1341,7 @@

    RegDiffusion
    register_state_dict_pre_hook(hook)#
    -

    Register a pre-hook for the load_state_dict() method.

    +

    Register a pre-hook for the state_dict() method.

    These hooks will be called with arguments: self, prefix, and keep_vars before calling state_dict on self. The registered hooks can be used to perform pre-processing before the state_dict @@ -1375,7 +1374,7 @@

    RegDiffusion
    -set_extra_state(state: Any)#
    +set_extra_state(state: Any) → None#

    Set extra state contained in the loaded state_dict.

    This function is called from load_state_dict() to handle any extra state found within the state_dict. Implement this function and a corresponding diff --git a/_modules/index.html b/_modules/index.html index 24c3b99..17e6326 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -37,7 +37,7 @@ - + diff --git a/_modules/regdiffusion/data/beeline.html b/_modules/regdiffusion/data/beeline.html index 85569b0..b1a0233 100644 --- a/_modules/regdiffusion/data/beeline.html +++ b/_modules/regdiffusion/data/beeline.html @@ -37,7 +37,7 @@ - + diff --git a/_modules/regdiffusion/data/microglia.html b/_modules/regdiffusion/data/microglia.html index 6d621fe..3a0e659 100644 --- a/_modules/regdiffusion/data/microglia.html +++ b/_modules/regdiffusion/data/microglia.html @@ -37,7 +37,7 @@ - + diff --git a/_modules/regdiffusion/evaluator.html b/_modules/regdiffusion/evaluator.html index 29a99ff..c7516e7 100644 --- a/_modules/regdiffusion/evaluator.html +++ b/_modules/regdiffusion/evaluator.html @@ -37,7 +37,7 @@ - + diff --git a/_modules/regdiffusion/grn.html b/_modules/regdiffusion/grn.html index b2dc4be..b8f9c86 100644 --- a/_modules/regdiffusion/grn.html +++ b/_modules/regdiffusion/grn.html @@ -37,7 +37,7 @@ - + diff --git a/_modules/regdiffusion/models/regdiffusion.html b/_modules/regdiffusion/models/regdiffusion.html index cdbc502..c7b14b7 100644 --- a/_modules/regdiffusion/models/regdiffusion.html +++ b/_modules/regdiffusion/models/regdiffusion.html @@ -37,7 +37,7 @@ - + diff --git a/_modules/regdiffusion/trainer.html b/_modules/regdiffusion/trainer.html index 5d8d850..ab23ab0 100644 --- a/_modules/regdiffusion/trainer.html +++ b/_modules/regdiffusion/trainer.html @@ -37,7 +37,7 @@ - + diff --git a/_sources/index.rst b/_sources/index.rst index 0ad1576..5f46e20 100644 --- a/_sources/index.rst +++ b/_sources/index.rst @@ -35,7 +35,7 @@ consists of 4 components: the ``RegDiffusionTrainer`` class, the ``GRN`` class, export or visualize local regions. For example, you can use the ``.visualize_local_neighborhood()`` to generate a similar plot as used in the RegDiffusion paper. You can also extract the underlying adjacency list - using the ``.extract_node_2hop_neighborhood()`` method. + using the ``.extract_local_neighborhood()`` method. - ``GRNEvaluator``: The ground truth of regulatory relationship often exist as list of edges but the values to be evaluated are often in adjacency matrix. The ``GRNEvaluator`` class is designed to fill the gap. Right now it supports @@ -43,6 +43,15 @@ consists of 4 components: the ``RegDiffusionTrainer`` class, the ``GRN`` class, - ``data`` module: Right now, the ``data`` module includes quick access to BEELINE benchmarks and our preprocessed single cell datasets on mouse microglia. +Model Structure +--------------- + +RegDiffusion includes an innovative model structure to estimate the added noise. Here is an high level illustraction. Please refer to our paper for details. + +.. image:: https://github.com/TuftsBCB/RegDiffusion/blob/master/resources/regdiffusion_structure.png?raw=true + :width: 700 + :alt: RegDiffusion Structure + Understanding the Inferred Networks ----------------------------------- After the ``RegDiffusion`` model converges, what you get is simply an @@ -53,7 +62,7 @@ the most. Check out the tutorials on the left side for how to perform a similar network analysis like the one we did in the paper. We are also working on an interactive tool to analyze saved GRN object. -.. image:: https://github.com/TuftsBCB/RegDiffusion/blob/master/resources/apoe_reg.png?raw=true +.. image:: https://github.com/TuftsBCB/RegDiffusion/blob/master/resources/apoe_net.png?raw=true :width: 700 :alt: Inferred network around ApoE diff --git a/_sources/quick_tour.md b/_sources/quick_tour.md index b7cb1ba..be162ee 100644 --- a/_sources/quick_tour.md +++ b/_sources/quick_tour.md @@ -134,7 +134,7 @@ Here we have a fairly obvious bipartisan graph. It also makes sense to use some >>> from sklearn.cluster import KMeans >>> from node2vec import Node2Vec >>> ->>> adj_table = grn.extract_node_2hop_neighborhood('HIST1H1D', 40) +>>> adj_table = grn.extract_local_neighborhood('HIST1H1D', 40) >>> nxg = nx.from_pandas_edgelist(adj_table) >>> >>> node2vec = Node2Vec(nxg, dimensions=64, walk_length=30, num_walks=200, diff --git a/_static/basic.css b/_static/basic.css index e760386..2af6139 100644 --- a/_static/basic.css +++ b/_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/_static/doctools.js b/_static/doctools.js index d06a71d..4d67807 100644 --- a/_static/doctools.js +++ b/_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/_static/language_data.js b/_static/language_data.js index 250f566..367b8ed 100644 --- a/_static/language_data.js +++ b/_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/_static/searchtools.js b/_static/searchtools.js index 7918c3f..92da3f8 100644 --- a/_static/searchtools.js +++ b/_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/data_module.html b/data_module.html index 7575ab4..6fd1615 100644 --- a/data_module.html +++ b/data_module.html @@ -38,7 +38,7 @@ - + diff --git a/genindex.html b/genindex.html index a22c5fc..5d4dfdf 100644 --- a/genindex.html +++ b/genindex.html @@ -37,7 +37,7 @@ - + diff --git a/index.html b/index.html index 30fd41a..8f59d2e 100644 --- a/index.html +++ b/index.html @@ -38,7 +38,7 @@ - + @@ -331,6 +331,7 @@

    Contents