Locator
The Locator, shown below, is a database browser that provides access to data sets, experiments, shim sets, commands, and other things.
The Locator is designed to enable fast access to information on all of the disk environment. The scope of the Locator’s actions is determined by the administrator who sets the scope of the Locator both globally and locally. The Locator works similar to a directory or file manager, but uses minimal filtering of the information. Rather than only showing the files that satisfy the requirements, it shows two or three lists of information. With two lists, one list shows the items (or objects) that satisfy Locator all terms of the search while the other list shows the objects that do not. Where some terms have a boolean relationship, the Locator shows three lists: • Objects that meet all criteria • Some of the boolean terms met • Remaining objects The determination of which of these lists it are shown is determined by the construction of the underlying Locator statement. Within each list, the Locator displays three attributes for each object. The displayed attributes need not necessarily be those in the Locator statement. Any one of the attributes can be designated as the sort attribute, in which case the objects in each list are sorted by the value each has for this attribute.
Locator Interface Elements The Locator interface elements are described in the following sections: • Locator Statements and Menu • Navigation in the Locator • Locator Groups • Attributes Locator Statements and Menu At the top of the Locator is a magnifying glass and the current Locator statement, as shown
Clicking on the magnifying glass opens a menu of currently available Locator statements. This menu includes both statements provided by Varian, Inc. and those customized and saved by the user. Statements are Locator sentences in which a number of words or phrases are colored and underlined, similar to links in a web page. Each link hides a menu of choices, of which the currently displayed phrase is one. The choices available vary with the types of data currently known to the Locator. Navigation in the Locator Below the Locator statement is a pair of arrows (statement navigation arrows), which enable users to move forward and back through past Locator operations, applying each to the current Locator environment. Thus a set of Locator statements can be rapidly applied in a changing environment.
Locator Groups To the right of the arrows is the tag icon for adding and removing Locator groups. Use this tool to define (tag) new user groups and apply those to existing or new objects, for example, to tag FIDs with a given project name. Clicking on this icon opens a pop-up menu. Using Locator Groups To use Locator groups, do the following steps: 1. Select a statement from the Locator statement list that sorts on groups, such as Sort NMR Data by group. 2. Select the group from the pull-down menu in the statement.
Attributes AT the right is the attribute header bar. This bar enables selection of the attributes displayed and to arrange the objects in each list in a number of ways. The padlock allows locking of an object against archival. The next three fields are the currently displayed attributes. Change any column simply by clicking on the attribute label and selecting a different attribute from the dropdown list. Below each label is its “Hot zone”. The hot zone can be either a block or a triangle. Only one attribute has a triangle and it is the attribute that serves as the sort term for each list. • Click on a block to change the sort attributes. • Click on the triangle to reverse the sort order. The boundaries between the attribute labels are adjustable. Simply place the mouse cursor on the boundary to be adjusted. At the adjust cursor, click and drag the boundary to its new position, and release. Objects in the Locator are available for a number of actions. Currently, a single click selects an object. The selected object can then be dragged to another part of VnmrJ in which case the action taken will depend on the type of object and where the object is dropped. Alternatively a double click on an object will cause the most likely action to occur. The value of an attribute might be longer than the width of the column in the Locator. When the mouse cursor rests on an attribute value, a tool tip appears for a period of time. The tool tip contains the full value of the attribute.
Attribute Lists The list of attributes in the drop-down lists are controlled by configuration files. There are three file names, for three different types of items in the locator. These are: • shuffler_param_list for 'vnmr data' and 'vnmr parameter' files • study_param_list for 'study' items • data protocol_param_list for 'protocol' items Each of these can exist for each of the appmode types and for individual users. That is, appmode types of 'imaging', 'standard' (experimental liquids & solids) and 'walkup'. The attributes visible in the drop down menu for each appmode type, will be controlled by files in the appropriate directories. If a user does not have an individual file, the file in the appropriate appmode directories will be used. If there is no file in the imaging or walkup directories listed above, then the file in /vnmr/shuffler will be used. If users have their own individual files, the attributes listed in it must also be in the appmode directory file. That is, a user's files can limit attributes shown, but cannot add to the list of attributesshown beyond the attributes in the system files.
Wildcards Wildcards can be used in attribute values, but not for the attribute name itself. For example, 'file*' does not specify the autoboot 'filename'. However select an attribute of 'filename', then edit the selection value to be 'p31*' to show all files whose names start with 'p31'. '?31*' would show all file starting with any single character followed by '31', followed by 0 or more characters. The leading '?' would allow upper or lower case 'P' as well as of course any other character. This does not apply to dates.
The following wildcards can be used: • '*' or '%' can be used to match any number of characters • '?' or '_' can be used to match any single character
Using the Locator Use the mouse to select or drag-and-drop items in the Locator interface. • Searches, • Dragging and Dropping Items from the Locator, • Editing File Names from the Locator, • Configuration Files.
Searches Clicking the magnifying glass with the left mouse button brings up a menu of searches. Selecting one changes the search sentence displayed at the top of the Locator. The results of the search is displayed in the list. Those items in the white part of the list satisfy the search sentence. Those in the gray part do not. For each item that is found by the search, three attributes are displayed. These correspond to the three columns in the list. Clicking on the attribute name at the top of the list with the left mouse button brings up a menu of attribute choices.
Dragging and Dropping Items from the Locator
Clicking on an item in the Locator list selects that item. That item can then be dragged to the graphic area or the parameter panel area to cause the appropriate action. For example, dragging a data set to the graphic area retrieves that data set into the current workspace (experiment) and (optionally) displays the spectrum. Dragging a workspace to the graphic area selects that workspace (experiment). Dragging on an object causes the most likely action to occur. An item can be dragged from the Locator and dropped into the holding pen. The item is then available for further selection no matter what Locator statements are active. One such example might uses the Locator to inspect the available shim sets. Once the names are know select the current best set and put this into the holding pen. This set of shims is then immediately available. Dragging and dropping an item has an action appropriate to the context. In many cases the same effect can be obtained by double-clicking on an object. Some examples are: • Dragging a protocol experiment into the graphics canvas loads the experiment. 270 VnmrJ Liquids NMR • Dragging a FID from NMR data retrieves the FID. The process macro can also be invoked so that the FID is transformed. • Double-clicking a workspace joins that workspace. Dragging and dropping a workspace into the graphics area also joins the workspace (jexp). • Double-clicking a parameter set loads that set in the current workspace, as will a dragging and dropping a parameter set. • Double-clicking a shim set loads the shims. Dragging and dropping a shim set to the current shim buttons also loads the shims into acquisition. • Dragging either data or shims and dropping them in the trash can (in the lower left portion of the hardware bar) moves the item to the trash can. Retrieve an object from the trash can by double-clicking on the trash can, selecting it, and then clicking the Restore items button. Dragging either data or shims and dropping them in the trash can (in the lower left portion of the hardware bar) moves the item to the trash can. Retrieve an object from the trash can by double-clicking on the trash can, selecting it, and then clicking the Restore items button. Editing File Names from the Locator When a new file is added to the locator from within VnmrJ, the new item appears in its appropriate spot in the Locator, and it appears in green at the top of the locator window. If one of the columns in the Locator is filename, click on the green file name to changed it. After changing the file name, press Return or click on another line to remove the old name from the Locator and add the new one. The Locator redisplays to show the new name.
Configuration Files Configuration files for the locator are contained in the following directories for the differentappmode types:
Locator Statements We supply a number of Locator statements with VnmrJ. To add or edit these statements as follows: • Save the current Locator statement by clicking on Tools in the main menu, then Save Custom Locator Statement. In the Custom Locator Statement pop-up window, enter a name for the statement. • To delete a Locator statement, click on Tools, then Delete Custom Locator Statement. A Custom Locator Statement Removal window appears. Select the statement from the list in the window, then click on Delete to remove it or Cancel to exit the window without removing the statement. • Sort Protocols Entries show the know protocol experiments. Double click on the protocol to execute the associated macro. Locator statements are defined in a file named: locator_statements_default.xml. This file can reside in the system appmode directories, but not in users individual directories.
Editable Fields In the locator statements, the items shown blue and underlined can show a menu of choices by clicking the right mouse button, and can be edited by clicking on them with the left mouse button. Left-clicking puts an editing cursor on the item. Place the cursor at the point to be edited and click the left mouse button. Edit the field, then press a Return to cause a new locator search using this edited value.
Sorting Locator Statements Sort Locator items as follows: • Sort Workspaces • Sort NMR Data • Sort NMR Parameter Files • Sort Shimsets • Sort Command Macros Sort Workspaces Sort all workspaces in numeric order or selectively sort workspaces by groups. Click on the tag icon to create locator groups. Double-click on a workspace to join the workspace. Sort NMR Data Entries show the known NMR data sets, but differ in the actual format of the statement as well as the initial set of attributes shown. The most comprehensive statement is the last one, by user defined attributes and date (this is also the one that is least likely to be used, but it is discussed here to explore the scope of the data statements). The generic statement is shown at the right. There are two separate underlined choices in this statement: Std1D and on any date. Clicking on either of the underlined phrases produces a drop-down menu of the choices in this position. The menus are environment sensitive so they will not display choices that do not exist. The logic of this statement is of the form: Show attributes A and B of type C with additional limitations. First, the additional limitations phrases enable selection of the owner of the data. Currently this selection is determined by the administrator at the time a directory and it is made available to the Locator. Second, the additional limitations allows the date to be reorder. There are various dates associated with data, for example, the time started or the time saved. Specify these date fields several ways, for example, since a certain date, by changing on any date to since it can be altered either by using the left or right arrows to decrease or increase the date, by one day each click. All other statements supplied are simpler than the generic one. If there are certain statements that are in use frequently, these can be promoted to the top of the menu simply by saving them again as local variants. Sort NMR Parameter Files The statements in this category show the list of NMR parameter sets. One major category of parameter set is My Param Files. Also select the statements Test Files and by user defined attributes to do other selective searches. After selecting a category, the Locator statement changes, e.g., Test Files. Sort Shimsets The statements in this category enables access the shim sets that have been saved. Note that the shim sets can be saved with a descriptive shim name provided when using the Save Shims button in the Shim panel.
Sort Command Macros The generic statement in this category enables finding a VnmrJ command or macro based on its attributes. The Locator enables reordering of commands and macros by a number of attributes. Once located that command is executed by a double click.
