The Jemboss interface has a local file management facility which is located in the right hand pane.
Hit the double arrow button at the bottom right of the central pane to access the file manager pane.
Any files visible in this manager can be moved between folders using the drag and drop function. After initial download the file manager may remain open for subsequent Jemboss sessions.
If the file manager is left open after the Jemboss session (Section 9.2.7, “Jemboss Session”) it will remain open in the next session.
The folders and files are organised in a vertical tree-like structure with the top folder indicating whereabouts on the desktop computer everything will be stored.
For the Jemboss standalone version (Section 9.2.5, “Local Installation”), the home directory (i.e. the default directory for all your files) will typically be C:/installdir/username (using mEMBOSS as an example) where installdir is the directory where the standalone version has been installed on the desktop machine and username is the login name on the computer. It is the username that can be seen as the top folder in the local file manager.
For the Jemboss client/server version (Section 9.2.6, “Remote Installation”), the home directory of the local file manager will typically be the user space on the desktop computer, identified by the username. Thus the top folder will generally be the username.
The sequence of folder names, separated by forward slashes, is the location (or path) of a particular piece of data. Return to the home directory from anywhere using the blue up arrow at the top of the file manager.
The home directory Location can be seen using the Advanced Settings option (Section 9.7.1, “Directory location”) or on the top tab of any saved data (Section 9.6.8.1, “Saved Results Window”).
The working directory is the default save directory for all autosaved program run data (Section 9.5.6, “Local Autosave”).
For the Jemboss standalone version (Section 9.2.5, “Local Installation”), the working directory will typically be a subfolder of the home directory (Section 9.3.2, “Home Directory”) called results.
For the Jemboss client/server version (Section 9.2.6, “Remote Installation”), the working directory will be on the remote server and the program run data can be accessed using the EMBOSS Results(Section 9.6.8.4, “Results in remote file manager”) section of the remote file manager (Section 9.3.14, “Remote File management”).
Hit the wd button at the top of the file management pane. Use the blue up arrow to return to the home directory.
The green arrow button will show the directory directly above the Home Directory. This area can be written to, but requires use of the Refresh button (see Section 9.3.12, “Refresh”) to display any new data.
From the Favourites menu at the top of the central Jemboss pane select Database Sequence Retrieval. Type uni:bgal_ecoli into the Sequence Filename field and hit the GO button.
Select the File and then Save to Local File options. Type bgal_ecoli in the File Name field and hit OK. The new file will appear in the file manager pane. (Close the Saved Results (Section 9.6.8.1, “Saved Results Window”) window).
If the returned results are more complex than a single sequence then the data appears in tabs (Section 9.6.8.1, “Saved Results Window”). Each of these tabs must be saved separately to preserve the data in the local file manager.
Non-graphic results are saved in Jemboss as text files only so no filename extension is required to specify the format, however it may be included for clarity if desired.
Double click on the bgal_ecoli file (Section 9.3.5.1, “Saving Analysis Results”) to retrieve the Local File (Section 9.6.8.2, “Local Results”) and highlight the contents. Hit the <DELETE> key on the computer keyboard. In the empty field type uni:bgal_bachd ¶ uni:bgal_bacme ¶ uni:bgal_bacst (where ¶ represents one press of the <ENTER> key). Select the File and then Save to Local File option. Call the new file bgal_bacillus.list. Close the Local File window.
The Files of Type drop down menu on the Save window is set to show files with the displayed file extensions. This menu can be altered to display All Files in a particular directory.
If a file is opened and the contents manipulated, the original file will remain intact if the new file is not saved (i.e. if the window is simply closed).
If a file is to be copied, it may simply be opened and resaved using a new filename.
Use the desktop computer file manager to move files into the home directory (Section 9.3.2, “Home Directory” and Section 9.7.1, “Directory location”)
A menu allows you to create and manipulate files and folders within the file manager.
Hover the mouse over the file management pane and click once with the right hand mouse button to display the file management menu.
Those options which are not relevant for a particular operation are greyed out.
Highlight the top folder in the file manager by clicking on it once with the left hand mouse button. It is now selected. Right click to access the file management menu and select New Folder. Type Test into the folder name field and hit the OK button. The new folder will automatically appear as a sub-folder of the home directory. Create another folder, this time call it Example.
Should the new folder already have the same name as an existing folder, an error message will appear. The new folder will not be created and the process should be repeated with a different folder name.
Should the New Folder option be selected and no folder within the file manager highlighted, an error message will appear. Hit OK to remove it and select a relevant folder.
Click on the bgal_ecoli file and drag it over the Example folder until this folder is highlighted. Release the mouse button to drop the file into this folder. The Example folder will explode to reveal the new file.
The Example folder will now receive a magnifying glass icon to the left of it signifying it now contains sub-files and/or folders. The vertical orientation of the icon indicates the folder is open. A horizontal orientation indicates a closed folder.
Single files can be dragged and dropped between any folders within the tree. Folders cannot be moved. Should the recipient folder not be highlighted during the drag operation then the file will not be moved. Should the file be dragged over (and thus highlight) another file instead of a folder then the original file will be dropped into the same folder as the highlighted file.
Highlight the bgal_ecoli file. Access the file manager menu and select Rename. Hit the right hand cursor button on the computer keyboard to place the cursor at the end of the current filename and then type .fasta into the field. Hit the OK button to view the newly named file.
If the filename is accidentally deleted, or a completely new one required, the new name can simply be typed into the relevant field before the OK button is selected. Folders can be renamed in the standalone version.
Should the new name be the same as the name of an existing file, an error message will appear. Hit OK to remove the message and re-select the Rename option.
Highlight the Test folder, open the menu and select Delete. Answer Yes to the security check and the file will be permanently deleted.
In the standalone version the delete option can remove folders containing other folders and files. However, on the client/server version the delete option is only available for empty folders and any files. To delete more than one file, use the <SHIFT> key to highlight a block of files, or the <CONTROL> (Mac apple) key to highlight a number of single files and select the delete option. Should an attempt be made to delete a full folder a security message will appear followed by an error message. Hit OK to remove the message and remove the files before deleting the folder.
Should several files and/or folders have been highlighted and that highlighting is no longer needed, the de-select all option from the file management menu will remove this highlighting.
When Jemboss is initiated it conducts a sweep of the local computer to display the available home directory files in the local file management pane. Once new data has been introduced (Section 9.3.5, “Creating Data Files in Jemboss”) it does not necessarily register in the file manager. The Refresh button allows the user to re-conduct that sweep of files and display any new data created since the last sweep.
In the case of the introduction of new data as a result of programs run in interactive mode (Section 9.4.38, “Interactive”), new files will be displayed automatically and there is no need to use the Refresh button. For data introduced by any other method, the Refresh option should be selected. Should a sub-folder be exploded as this option is selected, it will automatically condense and must be re-exploded to view the new file. A folder will remain open, however, if one of its sub-files has been selected (highlighted) before the Refresh option is activated (see practical Section 9.5.3, “Saved Results: Batch Mode”)
This menu option allows the selected file to be opened within one of two Jemboss utilities. The Jemboss Alignment Editor is a sequence alignment viewer and editor (Section 9.8.1, “Jemboss Alignment Editor (JAE)”) and the Text Editor is the text based Local File (Section 9.6.8.2, “Local Results”) window which can display all text files.
This option is available for the client/server version only.
Access the File option in the main Jemboss Window and select Local and Remote Files. Alter the vertical file manager to a horizontal view by selecting File and then Horizontal Split.
The local home directory (Section 9.3.2, “Home Directory”) is displayed on the left hand side, the remote home directory, and any files currently stored there, on the right.
Click with the left hand mouse button to locate the cursor in the remote file manager and then click with the right hand mouse button to access the file management menu (Section 9.3.6, “File Manipulation”). This functions in exactly the same way as for the local file manager.
It does not matter whether the preferred home directory is remote or local. Indeed, sometimes there may be limits on how much data may be saved on either one of these areas. However, it is often the case that data on a remote server is backed up daily, so it may be worthwhile moving any important files into the remote directory.
Files can be dragged and dropped between local and remote file managers (see Section 9.3.8, “Re-locating Files”). A closed folder will automatically open to reveal the new file. As the file is dragged a copy is created and it is this copy which is dropped into the folder in the recipient file manager; a file will not be deleted in the original manager and must be manually removed if so required.
Data can be moved between file managers as single files only. This option is not available for multiple files or folders.
Create an "Example" folder in the remote area. Drag the bgal_ecoli.fasta file from the local file manager into the new folder. Double click on this file to open it (it will be in a Remote File (Section 9.6.8.4, “Results in remote file manager”) window) and delete a region from the N terminal of the protein. Add the notation "(fragment)" to the description line and save to the local file manager as bgal_frag.fasta.
The save function for files within a file manager allows for saving to the local file manager only. Such files can then be transferred to the remote file manager where necessary.
Close the remote file manager.