Tree View Search tutorial
This tutorial will teach you how to edit tree labels.
Search Interface
Search Elements are located on the toolbar.
It has Find button, Search term combo box, and Zoom to All search results check box.
Search Elements
Find button
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.
Search term combo box
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.
Zoom to All search results check box
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.
Sub-string search
-
Go to https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/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.
-
Type Montevideo in search box, then hit Enter
-
Observe search results as selection on the tree:
-
Please note that substring search looks for the term in all tree node property strings (displayed in tootips).
- 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".
Label search
Substring search would search labels, including custom labels.
-
Go to 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
-
Type 2.7.1.3 in the search box, then hit the Find button
-
Observe search results as selection of the tree:
Zoom to selection
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 Zoom to Selection toolbar button or context menu item.
Note: Zoom to Selection 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.
Query search
Tree Viewer also supports queries with logical expressions as a search string.
dist>0.1
Select all nodes, which have “dist” attribute greater than 0.1
dist> 0.1 AND asm_level_txt=Contig
Select all nodes, which have dist attribute greater than 0.1 and have feature asm_level_txt with value equals to Contig.
dist > 0.0005 AND scientific_name LIKE "*Montevideo*"
Search for nodes with dist greater than 0.0005 and scientific_name that contains the string “Montevideo” (wildcard expression search).
Query based search rules and syntax
- String, numeric and boolean values (such as 5, 0.2, true, "contig")
- Node properties (such as scientific_name, dist, asm_accession, assembly_method, etc.)
- Simple comparisons: <, <=, >, >=, =, !=
- The 'Like' Comparison which allows wildcards: scientific_name like *Montevideo*
- 'Between' comparison: dist between 0.0004 and 0.01
- 'In' comparison: asm_accession in (GCF_000231645.1, GCA_000495295.1)
- Logical Operators: AND, OR, XOR, NOT
For more information please refer to:
Table of Contents
- Tree Viewer documentation home
- Tree Viewer application home
- For Users
- User Tutorials
- For Developers
- Related Resources