720 lines
37 KiB
XML
720 lines
37 KiB
XML
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<title>Search tutorial</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta name="created" content="2017-02-28T16:25:02-05:00" />
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<meta name="modified" content="2017-03-10T15:53:01-05:00" />
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<meta name="publication-date" content="2017-02-28T16:22:00-05:00" />
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<meta name="subsite" content="treeviewer" />
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<meta name="path" content="treeviewer/tutorial-search" />
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<link type="text/css" rel="stylesheet" href="/core/assets/treeviewer/css/tvparams.css" />
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<link type="text/css" rel="stylesheet" href="/core/assets/treeviewer/css/codesample.css" /><meta xmlns:ncbi-portal="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="cms-edit-aux-url" content="http://cms.ncbi.nlm.nih.gov/node/3562/edit" />
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<link rel="shortcut icon" href="//www.ncbi.nlm.nih.gov/favicon.ico" /><meta name="ncbi_phid" content="CE8EA2C27C80368100000000004D003E.m_6" />
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<meta name='referrer' content='origin-when-cross-origin'/><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4148854/css/4121862/3974050/3917732/251717/3990648/14534/45193/3534283/4128070/3894326/4005757/4062871.css" /><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4148854/css/3529741/3529739.css" media="print" /></head>
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<strong>Warning:</strong>
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The NCBI web site requires JavaScript to function.
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<a href="/guide/browsers/#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a>
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<div xmlns="http://www.w3.org/1999/xhtml" id="universal_header" xml:base="http://127.0.0.1/sites/static/header_footer">
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<section class="usa-banner">
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<div class="usa-grid usa-banner-inner">
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<img src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png" alt="U.S. flag" />
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<p>An official website of the United States government</p>
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<button class="non-usa-accordion-button usa-banner-button" aria-expanded="false" aria-controls="gov-banner-top" type="button">
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<p>
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<strong>The .gov means it's official.</strong>
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<br />
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Federal government websites often end in .gov or .mil. Before
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sharing sensitive information, make sure you're on a federal
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The <strong>https://</strong> ensures that you are connecting to the
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<div class="usa-overlay"></div>
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<header class="ncbi-header" role="banner" data-section="Header">
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<div class="ncbi-header__account">
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<a id="account_login" href="https://account.ncbi.nlm.nih.gov" class="usa-button header-button" style="display:none" data-ga-action="open_menu" data-ga-label="account_menu">Log in</a>
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Logged in as:<br />
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<li><a id="account_pubs" href="/myncbi/collections/bibliography/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_pubs">Publications</a></li>
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</header>
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<div role="navigation" aria-label="access keys">
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<a id="nws_header_accesskey_0" href="https://www.ncbi.nlm.nih.gov/guide/browsers/#ncbi_accesskeys" class="usa-sr-only" accesskey="0" tabindex="-1">Access keys</a>
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<a id="nws_header_accesskey_1" href="https://www.ncbi.nlm.nih.gov" class="usa-sr-only" accesskey="1" tabindex="-1">NCBI Homepage</a>
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<!--/.header-->
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<div class="header">
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<div class="res_logo"><h1 class="res_name"><a href="/tools/treeviewer/" title="NCBI Tree Viewer home">NCBI Tree Viewer</a></h1><h2 class="res_tagline"></h2></div>
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<div class="search"><form method="get" action="/gquery/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="gquery" selected="selected">All Databases</option><option value="refseq">RefSeq</option><option value="nuccore">Nucleotide</option><option value="gene" class="last">Gene</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search All Databases" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div></form></div>
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</div>
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<div class="nav_and_browser">
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<div class="localnav"><ul class="jig-ncbilocalnav">
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<li>
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<a href="#">NCBI Tree Viewer</a>
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<ul>
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||
<li>
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<a href="/tools/treeviewer/">Tree Viewer documentation home</a></li>
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<li>
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<a href="/projects/treeview/">Tree Viewer application home</a></li>
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</ul>
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</li>
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<li>
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<a href="#">For Users</a>
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<ul>
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<li>
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<a href="/tools/treeviewer/releasenotes">Release notes</a></li>
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<li>
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<a href="/tools/treeviewer/faq">Frequently Asked Questions</a></li>
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<li>
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<a href="/tools/treeviewer/videos">Videos</a></li>
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</ul>
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</li>
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<li>
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<a href="#">User Tutorials</a>
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<ul>
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<li>
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<a href="/tools/treeviewer/tutorial-uud">User uploaded data</a></li>
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<li>
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<a href="/tools/treeviewer/tutorial-editlabels">Edit Labels Dialog</a></li>
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<li>
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<a href="/tools/treeviewer/tutorial-search">Tree View Search</a></li>
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||
</ul>
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</li>
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<li>
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<a href="#">For Developers</a>
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<ul>
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||
<li>
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<a href="/tools/treeviewer/embeddingapi">Embedding API manual</a></li>
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<li>
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<a href="/tools/treeviewer/macros">Tree Viewer Macros manual</a></li>
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<li>
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<a href="/tools/treeviewer/developerresources">Other Developer Resources</a></li>
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</ul>
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</li>
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<li>
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<a href="#">Related Resources</a>
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||
<ul>
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||
<li>
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<a href="/projects/sviewer/">Sequence Viewer</a></li>
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<li>
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<a href="/projects/msaviewer/">Multiple Sequence Alignment Viewer</a></li>
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</ul>
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||
</li>
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||
</ul></div>
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||
</div>
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<!-- was itemctrl -->
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||
<div class="container">
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||
<div id="maincontent" class="content col twelve_col last">
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||
<div class="col1">
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<h1>
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Tree View Search tutorial</h1>
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||
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<p>
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This tutorial will teach you how to edit tree labels.</p>
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||
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||
<h2 id="interface">
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Search Interface</h2>
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||
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<p>
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Search Elements are located on the toolbar.</p>
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<p>
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It has <strong>Find</strong> button, <strong>Search term</strong> combo box, and <strong>Zoom to All search results</strong> check box.</p>
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||
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<p>
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<a href="/core/assets/treeviewer/images/tv-search-toolbar-highlight.png"><img src="/core/assets/treeviewer/images/tv-search-toolbar-highlight.png" alt="tv search toolbar highlight" class="sshot" /></a></p>
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||
<h2 id="elements">
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Search Elements</h2>
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||
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<h3 id="find">
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Find button</h3>
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<p>
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||
Initiates search using search term displayed in Search term Combo box with optional zoom to results of search, if corresponding element (Zoom to All checkbox) is checked.</p>
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|
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<h3 id="term">
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Search term combo box</h3>
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<p>
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||
Allows user to type new search term or select from Most Recent Usage list (MRU). The MRU list has recent queries for the tree/ session combination. When enter is pressed search begins using the displayed search term and Zoom to All option.</p>
|
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<h3 id="zoom">
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Zoom to All search results check box</h3>
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<p>
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If checked, when search performed, the zoom level may be adjusted to ensure all results will be displayed. Checking/unchecking has no effect until search is performed.</p>
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<h3 id="substring">
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Sub-string search</h3>
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||
|
||
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||
<ol>
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||
<li>
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||
Go to <a href="/projects/treeview/tv.html?appname=ncbi_tviewer&url=ftp://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/treeviewer/tree_txt.asn&renderer=circular&featnames=*&setmidpointroot=true&treename=tree_txt.asn">https://www.ncbi.nlm.nih.gov/projects/treeview/tv.html?appname=ncbi_tviewer&url=ftp://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/treeviewer/tree_txt.asn&renderer=circular&featnames=*&setmidpointroot=true&treename=tree_txt.asn</a>.<br />
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</li>
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<li>
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Type <strong>Montevideo</strong> in search box, then hit <strong>Enter</strong><br />
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</li>
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||
<li>
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Observe search results as selection on the tree:
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<p>
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||
<a href="/core/assets/treeviewer/images/tv-sub-string-search-selection.png"><img src="/core/assets/treeviewer/images/tv-sub-string-search-selection.png" alt="tv substring search selection" class="sshot" /></a><br />
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||
</p>
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||
</li>
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||
<li>
|
||
Please note that substring search looks for the term in all tree node property strings (displayed in tootips).
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||
<p>
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||
<a href="/core/assets/treeviewer/images/tv-tooltip-strings.png"><img src="/core/assets/treeviewer/images/tv-tooltip-strings.png" alt="tv tooltip strings" class="sshot" /></a><br />
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</p>
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||
</li>
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||
<li>
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||
Please note, that sub-string search is case/quotation/space insensitive. "Montevideo", Montevideo, montevideo, and "montevideo” will give the same result, as well as serovar Montevideo or "serovar montevideo".</li>
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||
</ol>
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||
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||
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||
<h3 id="label">
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Label search</h3>
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||
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<p>
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Substring search would search labels, including custom labels.</p>
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||
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||
<ol>
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||
<li>
|
||
Go to <a href="/projects/treeview/tv.html?appname=ncbi_tviewer&url=ftp://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/treeviewer/carbohydrate_kinase_FGGY_midpoint.asn&renderer=rect&sort=distance&featnames=*&treename=carbohydrate_kinase_FGGY_midpoint.asn"> https://test.ncbi.nlm.nih.gov/projects/treeview/tv.html?appname=ncbi_tviewer&url=ftp://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/treeviewer/carbohydrate_kinase_FGGY_midpoint.asn&renderer=rect&sort=distance&featnames=*&treename=carbohydrate_kinase_FGGY_midpoint.asn<br />
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||
<br />
|
||
</a></li>
|
||
<li>
|
||
Type <strong>2.7.1.3</strong> in the search box, then hit the <strong>Find </strong>button<br />
|
||
</li>
|
||
<li>
|
||
Observe search results as selection of the tree:
|
||
<p>
|
||
<a href="/core/assets/treeviewer/images/tv-label-search.png"><img src="/core/assets/treeviewer/images/tv-label-search.png" alt="tv label search" class="sshot" /></a></p>
|
||
</li>
|
||
</ol>
|
||
|
||
|
||
<h3 id="zoom">
|
||
Zoom to selection</h3>
|
||
|
||
|
||
<p>
|
||
After search is done, Tree Viewer displays search statistics in the status bar (at the bottom). Number of selected nodes reflect search results. Tree Viewer can quickly zoom to the selected set using <strong>Zoom to Selection</strong> toolbar button or context menu item.</p>
|
||
|
||
|
||
<p>
|
||
Note: <strong>Zoom to Selection</strong> always shows ALL selected nodes/leaves, thus for big tree with many selections zoom to selection might has no effect since all selected node/leaves can be seen at 0% zoom only.</p>
|
||
|
||
|
||
<p>
|
||
<a href="/core/assets/treeviewer/images/tv-zoom-to-selection.png"><img src="/core/assets/treeviewer/images/tv-zoom-to-selection.png" alt="tv zoom to selection" class="sshot" /></a></p>
|
||
|
||
|
||
<h3 id="query">
|
||
Query search</h3>
|
||
|
||
|
||
<p>
|
||
Tree Viewer also supports queries with logical expressions as a search string.</p>
|
||
|
||
|
||
<h4>
|
||
dist>0.1</h4>
|
||
|
||
|
||
<p>
|
||
Select all nodes, which have “dist” attribute greater than 0.1</p>
|
||
|
||
|
||
<p>
|
||
<a href="/core/assets/treeviewer/images/tv-query-1.png"><img src="/core/assets/treeviewer/images/tv-query-1.png" alt="tv query 1" class="sshot" /></a></p>
|
||
|
||
|
||
<h4>
|
||
dist> 0.1 AND asm_level_txt=Contig</h4>
|
||
|
||
|
||
<p>
|
||
Select all nodes, which have dist attribute greater than 0.1 and have feature asm_level_txt with value equals to Contig.</p>
|
||
|
||
|
||
<p>
|
||
<a href="/core/assets/treeviewer/images/tv-query-2.png"><img src="/core/assets/treeviewer/images/tv-query-2.png" alt="tv query 2" class="sshot" /></a></p>
|
||
|
||
|
||
<h4>
|
||
dist > 0.0005 AND scientific_name LIKE "*Montevideo*"</h4>
|
||
|
||
|
||
<p>
|
||
Search for nodes with dist greater than 0.0005 and scientific_name that contains the string “Montevideo” (wildcard expression search).</p>
|
||
|
||
|
||
<p>
|
||
<a href="/core/assets/treeviewer/images/tv-query-3.png"><img src="/core/assets/treeviewer/images/tv-query-3.png" alt="tv query 3" class="sshot" /></a></p>
|
||
|
||
|
||
<h3 id="rules">
|
||
Query based search rules and syntax</h3>
|
||
|
||
|
||
<ul>
|
||
<li>
|
||
String, numeric and boolean values (such as 5, 0.2, true, "contig")</li>
|
||
<li>
|
||
Node properties (such as scientific_name, dist, asm_accession, assembly_method, etc.)</li>
|
||
<li>
|
||
Simple comparisons: <, <=, >, >=, =, !=</li>
|
||
<li>
|
||
The 'Like' Comparison which allows wildcards: scientific_name like *Montevideo*</li>
|
||
<li>
|
||
'Between' comparison: dist between 0.0004 and 0.01</li>
|
||
<li>
|
||
'In' comparison: asm_accession in (GCF_000231645.1, GCA_000495295.1)</li>
|
||
<li>
|
||
Logical Operators: AND, OR, XOR, NOT</li>
|
||
</ul>
|
||
|
||
|
||
<p>
|
||
<strong>For more information please refer to:</strong></p>
|
||
|
||
|
||
<ul>
|
||
<li>
|
||
<a href="/tools/treeviewer/macros/">Tree Viewer Macro manual</a></li>
|
||
<li>
|
||
<a href="/tools/treeviewer/biotreecontainer/">BioTreeContainer and its features</a></li>
|
||
<li>
|
||
<a href="/tools/gbench/manual4/">Query Syntax manual</a></li>
|
||
</ul>
|
||
|
||
</div>
|
||
<!--/.col1-->
|
||
<div class="col2">
|
||
<h2>
|
||
Table of Contents</h2><ul>
|
||
<li>
|
||
<a href="/tools/treeviewer/">Tree Viewer documentation home</a></li>
|
||
<li>
|
||
<a href="/projects/treeview/">Tree Viewer application home</a></li>
|
||
<li>
|
||
For Users
|
||
<ul>
|
||
<li>
|
||
<a href="/tools/treeviewer/releasenotes">Release notes</a></li>
|
||
<li>
|
||
<a href="/tools/treeviewer/faq">Frequently asked questions</a></li>
|
||
<li>
|
||
<a href="/tools/treeviewer/videos">Videos</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
User Tutorials
|
||
<ul>
|
||
<li>
|
||
<a href="/tools/treeviewer/tutorial-uud">User uploaded data</a></li>
|
||
<li>
|
||
<a href="/tools/treeviewer/tutorial-editlabels">Edit Labels Dialog</a></li>
|
||
|
||
|
||
<li>
|
||
<a href="/tools/treeviewer/tutorial-search">Tree View Search</a></li>
|
||
|
||
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
For Developers
|
||
<ul>
|
||
<li>
|
||
<a href="/tools/treeviewer/embeddingapi">Embedding API manual</a></li>
|
||
<li>
|
||
<a href="/tools/treeviewer/macros">Tree Viewer Macros manual</a></li>
|
||
<li>
|
||
<a href="/tools/treeviewer/developerresources">Other Developer Resources</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
Related Resources
|
||
<ul>
|
||
<li>
|
||
<a href="/projects/sviewer/">Sequence Viewer</a></li>
|
||
<li>
|
||
<a href="/projects/msaviewer/">Multiple Sequence Alignment Viewer</a></li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<!--/.col2-->
|
||
<div class="col3">
|
||
|
||
</div>
|
||
<!--/.col3-->
|
||
<div class="col4">
|
||
|
||
</div>
|
||
<!--/.col4-->
|
||
<div class="col5">
|
||
|
||
</div>
|
||
<div class="col6">
|
||
|
||
</div>
|
||
<div class="col7">
|
||
|
||
</div>
|
||
<div class="col8">
|
||
|
||
</div>
|
||
<div class="col9">
|
||
|
||
</div>
|
||
</div><!--/.content-->
|
||
</div><!--/.container-->
|
||
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|
||
<div class="breadcrumbs">You are here:
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<span id="breadcrumb_text"><a href="/guide/">NCBI</a></span></div>
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<noscript><img alt="" src="/stat?jsdisabled=true&ncbi_app=treeviewer&ncbi_db=&ncbi_pdid=static&ncbi_phid=CE8EA2C27C80368100000000004D003E" /></noscript>
|
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|
||
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|
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|
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|
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<div class="col-lg-3 col-12">
|
||
<p class="address_footer text-white">National Library of Medicine<br />
|
||
<a href="https://www.google.com/maps/place/8600+Rockville+Pike,+Bethesda,+MD+20894/@38.9959508,-77.101021,17z/data=!3m1!4b1!4m5!3m4!1s0x89b7c95e25765ddb:0x19156f88b27635b8!8m2!3d38.9959508!4d-77.0988323" class="text-white" target="_blank" rel="noopener noreferrer">8600 Rockville Pike<br />
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Bethesda, MD 20894</a></p>
|
||
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|
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<div class="col-lg-3 col-12 centered-lg">
|
||
<p><a href="https://www.nlm.nih.gov/web_policies.html" class="text-white">Web Policies</a><br />
|
||
<a href="https://www.nih.gov/institutes-nih/nih-office-director/office-communications-public-liaison/freedom-information-act-office" class="text-white">FOIA</a><br />
|
||
<a href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html" class="text-white" id="vdp">HHS Vulnerability Disclosure</a></p>
|
||
</div>
|
||
<div class="col-lg-3 col-12 centered-lg">
|
||
<p><a class="supportLink text-white" href="https://support.nlm.nih.gov/">Help</a><br />
|
||
<a href="https://www.nlm.nih.gov/accessibility.html" class="text-white">Accessibility</a><br />
|
||
<a href="https://www.nlm.nih.gov/careers/careers.html" class="text-white">Careers</a></p>
|
||
</div>
|
||
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|
||
<div class="row">
|
||
<div class="col-lg-12 centered-lg">
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<nav class="bottom-links">
|
||
<ul class="mt-3">
|
||
<li>
|
||
<a class="text-white" href="//www.nlm.nih.gov/">NLM</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.nih.gov/">NIH</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.hhs.gov/">HHS</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.usa.gov/">USA.gov</a>
|
||
</li>
|
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</ul>
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</nav>
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</div>
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</div>
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</div>
|
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</section>
|
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<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIConfigJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js?v=1"> </script>
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<script type="text/javascript" src="/portal/portal3rc.fcgi/static/js/hfjs2.js"> </script>
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</div>
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</div>
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<!--/.footer-->
|
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<p class="last-updated small">Last updated: 2017-03-10T15:53:01-05:00</p>
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</div>
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<!--/.page-->
|
||
</div>
|
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<!--/.wrap-->
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<span class="PAFAppResources"></span>
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||
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|
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</div><!-- /.twelve_col -->
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</div>
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<script type="text/javascript" src="//static.pubmed.gov/portal/portal3rc.fcgi/4148854/js/3879255/4121861/3989973/4087685.js" snapshot="tools"></script></body>
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</html>
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