ee44defec68c55c48cf35268d29bdd9392923542 hiram Wed Sep 11 13:30:48 2024 -0700 js/assemblySearch.js diff --git src/hg/htdocs/assemblySearch.html src/hg/htdocs/assemblySearch.html index a04bc55..7c0b5a2 100755 --- src/hg/htdocs/assemblySearch.html +++ src/hg/htdocs/assemblySearch.html @@ -27,77 +27,77 @@ <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> <!-- javaScript will add an extra element in debug mode to show the API reference --> </ol> </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; right:-400px;"><ul> + <legend><span class="searchTip">Assembly view/request ⓘ<span class="searchTiptext" style="width:500px; right:-400px;"><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> -</ul></span></span></legend> +</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; right:-400px;"><ul> + <legend><span class="searchTip">Assembly status ⓘ<span class="searchTiptext" style="width:600px; right:-400px;"><ol class="noBullets"> <li><b>Latest</b> - the most recent of all the versions for this assembly chain</li> <li><b>Replaced</b> - this version has been replaced by a newer version of the assembly in the same chain</li> <li><b>Suppressed</b> - this version of the assembly has been suppressed</li> <li>An assembly chain is the collection of all versions for the same assembly accession.</li> -</ul></span></span></legend> +</ol></span></span></legend> <label><input type="radio" name="asmStatus" value="latest" id="statusLatest"> Latest</label> <label><input type="radio" name="asmStatus" value="replaced" id="statusReplaced"> Replaced</label> <label><input type="radio" name="asmStatus" value="suppressed" id="statusSuppressed"> Suppressed</label> <label><input type="radio" name="asmStatus" value="statusAny" id="statusAny" checked> Any status</label> </fieldset> </div> <div class="radioGroup"> <fieldset class="colVertical" onchange="optionsChange(event)"> - <legend><span class="searchTip">RefSeq category ⓘ<span class="searchTiptext" style="width:600px; right:-400px;"<ul> + <legend><span class="searchTip">RefSeq category ⓘ<span class="searchTiptext" style="width:600px; right:-400px;"><ol class="noBullets"> <li><b>Reference</b> genome - a manually selected high quality genome assembly that NCBI and the community have identified as being important as a standard against which other data are compared</li> <li><b>Representative</b> genome - a genome computationally or manually selected as a representative from among the best genomes available for a species or clade that does not have a designated reference genome</li> <li>There are assemblies which have no RefSeq category assignment</li> <li>For more information, see also: <a href='https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/#referencegenome' target=_blank>www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/#referencegenome</a></li> -</ul></span></span></legend> +</ol></span></span></legend> <label><input type="radio" name="refSeqCategory" value="reference" id="refSeqReference"> Reference</label> <label><input type="radio" name="refSeqCategory" value="representative" id="refSeqRepresentative"> Representative</label> <label><input type="radio" name="refSeqCategory" value="refSeqAny" id="refSeqAny" checked> Any category</label> </fieldset> </div> <div class="radioGroup"> <fieldset class="colVertical" onchange="optionsChange(event)"> - <legend><span class="searchTip">Assembly level ⓘ<span class="searchTiptext" style="width:500px; right:-250px;"><ul> + <legend><span class="searchTip">Assembly level ⓘ<span class="searchTiptext" style="width:500px; right:-250px;"><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> -</ul></span></span></legend> +</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><span class="searchTip">word match control ⓘ<span class="searchTiptext" style="width:400px">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 -->