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 9.3.5.1, “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.
Select 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 GO.
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.
Highlight the 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.
The 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.
Highlight the matcher run and hit the Display button.
Save the results as the local file (Section 9.5.2, “Saved Results: Interactive mode”) naming the run bgal_ecoli_batch.
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 9.7.3.5, “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).
Highlight the matcher run and hit the Delete button.
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 9.2.9.4, “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 9.3.5.1, “Saving Analysis Results”) the file location is specified.
Select 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 pepinfo.1.png and pepinfo.2.png tabs.
Hit the reset button in the Input Section of the pepinfo program form and this time drag the saved bgal_ecoli.fasta file (see Section 9.3.5.1, “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 9.3.5.1, “Saving Analysis Results” and Section 9.3.9, “Rename”) and double click to open the Local File window.
Select the 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.
Open bgal_ecoli2 and compare with the original file. The alterations will have been stored on the local system.
There is a tab (Section 9.6.8.1, “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”)
Access the 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”).
From the 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.
Explode the 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 9.6.8.2, “Local Results”).
Save the selected file to the local file manager using the File and 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.
Explode the 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 Yes button.
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 Yes.
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 File and 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.
The Edit Notes button is located between the Delete and Display buttons and acts as a text editor enabling analysis results to be annotated.
From the 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 GO button.
Select 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 9.6.8.1, “Saved Results Window”) window and allows all the same functions.
The 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.