9ba1f19df30d17211ebd94e05d6feb398ebc56a9 hiram Mon Dec 9 09:33:28 2024 -0800 updated per comments from QA refs #32596 diff --git src/hg/htdocs/assemblySearch.html src/hg/htdocs/assemblySearch.html index e9ea952..ddb3cb7 100755 --- src/hg/htdocs/assemblySearch.html +++ src/hg/htdocs/assemblySearch.html @@ -10,49 +10,49 @@ <hr> <div style="border:2px solid black; padding:5px;"> <form id="searchForm"> <div class="formDiv"> <!-- the entire form element --> <div> <!-- container div for search box and submit/clear buttons --> <label for="searchBox">Enter search term(s):</label> <input type="text" id="searchBox" placeholder="e.g. white rhino* -southern" name="searchBox" style="width:20%;" required> <div class="submitContainer"> <button id="submitSearch" type="submit">Search</button> <div id="loadingSpinner" class="spinner"></div> </div> <button type="button" id="clearSearch">Clear</button> - <button type="button" id="advancedSearchButton">Show search options</button> <!-- mouse over this text to see pop-up help message --> <span class="searchTip" style="float: right;">Advanced search help ⓘ<span class="searchTiptext"> <!-- hidden span for pop-up help message --> -<ol id="searchTipList" class="noBullets"> -<li> + (plus) sign before <b>+word</b> to force included in result</li> -<li> - (minus) sign before <b>-word</b> to exclude word from result</li> -<li> * (asterisk) character at end of <b>word*</b> to make the word be a prefix search</li> -<li> enclose "words in quotes" to form a phrase for the search</li> -<li> all searches are case insensitive</li> -<li> single word searches become prefix searches if the word does not match by itself </li> +<p>All searches are case-insensitive. Single-word searches default to prefix +matching if an exact match is not found.</p> +<ul id="searchTipList" class="noBullets"> +<li> Force inclusion: Use a + sign before <b>+word</b> to ensure it appears in result.</li> +<li> Exclude words: Use a - sign before <b>-word</b> to exclude it from the search result.</li> +<li> Wildcard search: Add an * (asterisk) at end of <b>word*</b> to search for all terms starting with that prefix.</li> +<li> Phrase search: Enclose "words in quotes" to search for the exact phrase.</li> <!-- javaScript will add an extra element in debug mode to show the API reference --> -</ol> +</ul> </span> <!-- a hidden span for a pop-up help message --> </span> <!-- URL argument maxItemsOutput to html page can change this --> <input type="hidden" id="maxItemsOutput" value="500"> </div> <!-- container div for search box and submit/clear buttons --> <div id="advancedSearchOptions" class="radioGroupContainer"> <div class="radioGroup"> <fieldset class="colVertical" onchange="optionsChange(event)"> - <legend><span class="searchTip">Assembly view/request ⓘ<span class="searchTiptext" style="width:500px; left:160px;"><ol class="noBullets"> + <legend><span class="searchTip">Assembly View/Request ⓘ<span class="searchTiptext" style="width:500px; left:160px;"><ol class="noBullets"> <li><b>In available browsers</b> - the assembly exists in the UCSC browser system, the <b>view</b> link will lead to the browser</li> <li><b>Can be requested</b> - assembly is not yet in the UCSC browser system, the <b>request</b> link will open a request form to ask for the assembly to be added to the UCSC browser system</li> </ol></span></span></legend> <label><input type="checkbox" id="mustExist" onclick="atLeastOneCheckBoxOn(this)" name="mustExist" value="mustExist" checked> In available browsers </label><br> <label><input type="checkbox" id="notExist" onclick="atLeastOneCheckBoxOn(this)" name="notExist" value="notExist" checked> Can be requested </label> </fieldset> </div> <div class="radioGroup"> <fieldset class="colVertical" onchange="optionsChange(event)"> <legend><span class="searchTip">Assembly status ⓘ<span class="searchTiptext" style="width:600px; left:130px;"><ol class="noBullets"> <li><b>Latest</b> - the most recent of all the versions for this assembly chain</li> @@ -84,31 +84,31 @@ <legend><span class="searchTip">Assembly level ⓘ<span class="searchTiptext" style="width:500px; left:-510px;"><ol class="noBullets"> <li><b>Complete genome</b> - all chromosomes are gapless and have no runs of 10 or more ambiguous bases (Ns), there are no unplaced or unlocalized scaffolds, and all the expected chromosomes are present (i.e. the assembly is not noted as having partial genome representation). Plasmids and organelles may or may not be included in the assembly but if present then the sequences are gapless.</li> <li><b>Chromosome</b> - there is sequence for one or more chromosomes. This could be a completely sequenced chromosome without gaps or a chromosome containing scaffolds or contigs with gaps between them. There may also be unplaced or unlocalized scaffolds.</li> <li><b>Scaffold</b>- some sequence contigs have been connected across gaps to create scaffolds, but the scaffolds are all unplaced or unlocalized.</li> <li><b>Contig</b>- nothing is assembled beyond the level of sequence contigs</li> </ol></span></span></legend> <label><input type="radio" name="asmLevel" value="complete" id="asmLevelComplete"> Complete</label> <label><input type="radio" name="asmLevel" value="chromosome" id="asmLevelChromosome"> Chromosome</label> <label><input type="radio" name="asmLevel" value="scaffold" id="asmLevelScaffold"> Scaffold</label> <label><input type="radio" name="asmLevel" value="contig" id="asmLevelContig"> Contig</label> <label><input type="radio" name="asmLevel" value="asmLevelAny" id="asmLevelAny" checked> Any level</label> </fieldset> </div> <div class="radioGroup"> <fieldset class="colVertical" onchange="optionsChange(event)"> - <legend class="searchTip"><span>word match control ⓘ<span class="searchTiptext" style="width:400px; left:-410px">For multiple word search, <b>May match</b> will allow any combination of word matches, where <b>Must match</b> will force all words to be in the search result.</span></span></legend> + <legend class="searchTip"><span>Word match control ⓘ<span class="searchTiptext" style="width:400px; left:-410px">For multiple word search, <b>May match</b> will allow any combination of word matches, where <b>Must match</b> will force all words to be in the search result.</span></span></legend> <label><input type="radio" name="wordMatch" value="anyWord" id="anyWord"> May match any word</label> <label><input type="radio" name="wordMatch" value="allWords" id="allWords" checked> Must match all words</label> </fieldset> </div> </div> <!-- the radioGroupContainer --> </div> <!-- the entire form element --> </form> </div> <div> <!-- search results status line --> <span id="resultCounts"> </span> <span id="measureTiming">- <em>search time: </em><span id="elapsedTime">0 milliseconds</span>.</span> </div> <!-- search results status line --> <div id=urlCopyLink> <!-- copy link to share this search --> <b>Share link to this search: </b> <span id="urlText0" style="display:none">https://assemblySearch.html</span>