The majority of analysis programs are set to run in interactive mode (Section 9.4.38, “Interactive”) as default. In this mode results retrieval is instant as the Saved Results window containing the data appears immediately on cessation of the program run. These results can then be saved to the local file manager (Section 188.8.131.52, “Saving Analysis Results”).
Some programs are set to run in batch mode (Section 9.4.39, “Batch”) as default. The results of these programs do not appear instantaneously on the screen, but are stored in the Jemboss Job Manager (Section 9.6.3, “Job Manager”).
The Job Manager retains a list of batch mode (Section 9.4.39, “Batch”) program runs within a single Jemboss session (Section 9.2.7, “Jemboss Session”) and keeps a tally of programs run during the session (completed) and the number of batch processes running at any one time (running) on the bar at the bottom of the central pane.
matcher by typing
mat into the
Go To Field in the left pane and hitting the enter key. Enter
uni:bgal_ecoli in the top
Sequence Filename Field and
uni:bgal1_entcl in the second one. Load sequence attributes for both sequences and alter the run mode to
batch using the drop down menu at the bottom left of the central Jemboss pane (bottom right on older versions) and hit
Access the Job Manager with a single left click from the bar at the bottom of the central Jemboss panel to the left of the tool (crossed spanners) icon.
This window appears on accessing the Job Manager and in the left hand pane lists programs in alphabetical order (and ascending time (hours and minutes) of run) from the current Jemboss session (Section 9.2.7, “Jemboss Session”). The right hand pane displays program run information when a program from the left hand list is highlighted. The program information consists of the command line for the original EMBOSS program, the date and time of run and any input files saved in the file manager.
matcher run. If the program is still running when it is accessed then the right hand pane will show that the results are Pending.
Check back to the Jemboss main window and once the Job Manager bar states that the current run is "Completed", hit the refresh (circulating arrows) button. Re-highlight the
matcher run to see the associated information. Drag the right hand edge of the Current Sessions Results window to the right to see as much of this information as possible on the screen.
EMBOSS run details information contains the name of the application and the EMBOSS command line input. The date and time of the run is also logged. Any input files associated with the run are displayed at the bottom of the information pane.
As with all other Jemboss Windows, the Current Session Results window does not close automatically and so it must be done manually when it is no longer needed.
matcher run and hit the
Save the results as the local file (Section 9.5.2, “Saved Results: Interactive mode”) naming the run
Results displayed in a Saved Results (Section 9.5.1, “Saving locally”) window may be saved to the local file manager (Section 9.3.1, “Local File Management”), and if run on a remote Jemboss installation (Section 9.2.6, “Remote Installation”) to a server file too. All features of the Saved Results Window, including alteration of font and text and background colour (Section 184.108.40.206, “Text Output”), are available.
Results may be deleted either individually or several at once. A block of results may be highlighted using the shift key whereas several separate results can be highlighted using the
CTRL key (
apple key on the Macintosh).
matcher run and hit the
For deletion of a single result no confirmation is necessary and the analysis is removed from the window. Deletion of several results must be confirmed by selecting
Yes in the Confirm Deletion window which subsequently appears. These results have only been removed from the Current Sessions Results window; they may previously have been auto-saved in either the local (Section 9.5.6, “Local Autosave”) or remote (Section 9.5.7, “Remote Autosave”) locations.
There is a refresh (circulating arrows) icon in the upper left hand corner of the Current Sessions Results window. It functions in the same manner as the
Refresh option in the local file manager (Section 9.3.12, “Refresh”). However, the Current Sessions Results window auto-refreshes after a few seconds, so unless a new list is required in a hurry, the refresh button need not be employed.
The job manager window will auto-refresh every 15 seconds and also update when a run has finished. Should the window require refreshing at a different time interval, or if the job manager update frequency has been altered (Section 9.7.4, “Job Manager Update frequency”) then the refresh icon may be used to force a refresh.
All results are returned in a Saved Results window. (Section 9.5.2, “Saved Results: Interactive mode”). This window is a text editor (Section 220.127.116.11, “Text Editors”) and may contain one or many tabs, each tab containing input or output data. The foremost tab is the active one and should default to the actual results pane. Each tab is named according to what it displays. For saved input files (Section 18.104.22.168, “Saving Analysis Results”) the file location is specified.
pepinfo by typing
pepi into the
Go To field and hitting return. Enter
uni:bgal_ecoli into the input entry field. Hit the
GO button and wait for the results. The
bgal_ecoli.pepinfo tab displays the textual results whereas the graphics are displayed in the
reset button in the
Input Section of the
pepinfo program form and this time drag the saved
bgal_ecoli.fasta file (see Section 22.214.171.124, “Saving Analysis Results” and Section 9.3.9, “Rename”) into the
Sequence Filename input field. Hit the
GO button and wait for the results. Compare the number of tabs with those retrieved above. There will be an extra one with the input file and the tab name will display the name of the file location. Close both Saved Results windows.
Results are saved in the local file manager and can be displayed in the Local File window.
Open the local file manager (if not already open) using the double arrow icon (Section 9.3.1, “Local File Management”) and double click to open the
Example folder (If this folder has not been created, please see Section 9.3.7, “New Folder Creation”). Select the
bgal_ecoli.fasta file (if this file has not been created, please see Section 126.96.36.199, “Saving Analysis Results” and Section 9.3.9, “Rename”) and double click to open the Local File window.
File and then
Save to Local File options. Double click on the
Example folder and save this file under the new name
bgal_ecoli2 (see Section 9.5.1, “Saving locally” for further information on saving).
Return to the local file manager and highlight the
bgal_ecoli2 file and right click to retrieve the
file management menu (Section 9.3.6, “File Manipulation”). Select the
Open With (Section 9.3.13, “Open With”) option and then
Text Editor. This will open the exact same Local File Window as was opened above. Alter the description line to read
bgal_ecoli2 and delete a portion of the sequence from the N-terminus. Resave the file, answering
Yes to the security check.
bgal_ecoli2 and compare with the original file. The alterations will have been stored on the local system.
There is a tab (Section 188.8.131.52, “Saved Results Window”) at the top of the text within the editor which gives the location (the path) of the retrieved file. Thus the file can be located and opened with a desktop text editor using the computer file management system if necessary.
For remote client/server versions of Jemboss only (Section 9.2.7, “Jemboss Session”)
File menu on the Jemboss interface and select the
Local and Remote Files option. In the subsequent File Manager window select the
File option and
Horizontal Split. Drag the right hand side of the remote file manager screen to the right to enable a larger view.
This remote file manager window is similar to the local file manager (Section 9.3.1, “Local File Management”) attached to the main Jemboss pane. There is a slight difference with the
Refresh button function, which requires a file to be highlighted in the remote file manager before any information can be updated. Data can only be saved to the local file manager (Section 9.3.1, “Local File Management”).
REMOTE file manager on the right hand side of the window, select
EMBOSS results from the drop down menu at the bottom right of the pane.
All programs run since installation (or for a specific duration, see Section 9.5.4, “Saving remotely”) are automatically saved during the run as a series of folders bearing the name of the EMBOSS program used. These files are arranged alphabetically and in ascending order of time (although further sorted alphabetically by day). They contain the results data and any associated files (such as input files). All data for a particular analysis run is saved.
pepinfo file by clicking with the left hand mouse button on the magnifying glass icon to the left of the program name. Double click on any one of the data sub-files to retrieve a Remote File window. This window is similar to the Local File window (Section 184.108.40.206, “Local Results”).
Save the selected file to the local file manager using the
Save to Local File menus. Double click on the
Example folder and call the file
pepinfo_remote. Return to the
File Manager and open the
Example folder in the left hand
LOCAL pane (if not already open). If the file does not appear automatically, right click and select the
Refresh option from the
file management menu (Section 9.3.6, “File Manipulation”).
Drag and drop the new data file into the original program folder in the remote directory (Section 9.3.16, “Moving Data between File Managers”).
Close all Results windows opened during this section.
Should a result no longer be necessary it is possible to delete the entire results folder.
pepinfo folder (if it is not already). Left click on the first file in the folder, hold down the shift key and left click on the final file in the folder to highlight all files. Right click to retrieve the
file management menu (Section 9.3.6, “File Manipulation”) and select the
delete option. Confirm the deletion using the
The folder will still be visible but it will no longer have a magnifying glass icon to the left of it.
Left click on the now empty
pepinfo folder to highlight it and right click to retrieve the menu. Select the
delete option and confirm with
The entire information has now been permanently deleted.
Close the File Manager.
In addition to the results stored in the remote file manager, results are also available in an additional Results Manager. Run analyses are stored as folders in alphabetical and date (but not time) order in the left hand pane, and information associated with these folders is stored in the right hand pane. The information is the same as is shown in the Current Sessions Results (Section 9.6.4, “Current Sessions Results”).
From the main Jemboss window select the
Saved Results menus.
The results manager can be opened at the start of a session and results re-displayed using the
refresh button at the top left of the window. Results are not automatically updated.
Edit Notes button is located between the
Display buttons and acts as a text editor enabling analysis results to be annotated.
Favourites menu at the top of the central Jemboss pane select
Global Alignments. Type
uni:bgal_ecoli into the first
Sequence Filename field and
uni:bgal1_entcl in the second
Sequence Filename field. Hit the
LOAD SEQUENCE ATTRIBUTES button under each sequence filename entry and then the
Saved Results option from the
File menu in the main Jemboss window and highlight the
needle program run. Hit the
Edit Notes button. Place the cursor in the main text box and enter some descriptive text into the window. Select the
File menu and the option to
Save Back to Project Directory. Close the window.
The Edit Notes window functions in exactly the same way as the Saved Results (Section 220.127.116.11, “Saved Results Window”) window and allows all the same functions.
needle program run should remain highlighted, so hit the
Edit Notes button once more. The descriptive text has now been saved along with the program results. Select the
File menu again and this time
Save to Local File. Double click on the
Example folder and name the file
desc_for_needle. Hit the
Save option. Close the remote file manager window.
Open the local file manager (Section 9.3.1, “Local File Management”) and explode the
Example folder (if necessary) to see the new file. Double click to see the contents of the file. Close the window.
The disadvantage of saving to the local file manager is that the description becomes divorced from the run result and thus extra care must be taken to ensure that both the filename, and the description itself, reflects to which analysis the data pertains.
There is no autosave for
Edit Notes, so if notes are not saved directly to either the local or remote files, then the edits will be lost.