Analysis Results are returned in a Saved Results window which is essentially a text editor window (Section 9.2.9.4, “Text Editors”). Results can be saved from here straight to the local (Section 9.3.1, “Local File Management”) and possibly remote (Section 9.3.14, “Remote File management”) file managers. The contents of the window may also be edited at this stage before saving, although it is recommended that a file be saved in its original state and a copy then made and edited (Section 9.3.5.2, “Re-writing a File with New Data”) where necessary.
All data created and analysed using the Jemboss interface can be saved to the local file manager (Section 9.3.1, “Local File Management”). This means that saved files will be stored on the local computer and not on the remote server. This makes sense when files need to be accessible immediately, especially if an Internet connection is not always reliable, and allows the user to manage the data directly.
For the Jemboss standalone version (Section 9.2.5, “Local Installation”), the default save directory is the home directory (Section 9.3.2, “Home Directory”) or, for mEMBOSS, a directory similar to C:/installdir/username.
For the Jemboss client/server version (Section 9.2.6, “Remote Installation”) the default save directory is typically the user home directory (Section 9.3.2, “Home Directory”).
The results of all programs run in interactive mode (Section 9.4.38, “Interactive”) appear immediately on screen and only offer the option of saving to the local file manager (Section 9.3.1, “Local File Management”). The window in which these result appear has the name Saved Results which can be seen on the left hand side of the top bar and is the name visible if the Results window is minimised.
Select charge from the left hand program category Protein and the Composition submenu. Type uni:bgal_ecoli into the Sequence Filename field and select the produce graphic option from the output section. Hit the GO button.
On the Saved Results window that appears, select the charge.1.png tab [If the Jemboss Graphics option is chosen, the tab will display charge.1.dat instead]. Select the File and then Save to Local File options. Double click on the Example folder (Section 9.3.7, “New Folder Creation”) and type bgal_ecoli_charge.png in the File Name field and hit OK. The new file will appear in the file manager pane. Minimise the Saved Results window.
Each window that displays a new set of results carries the name "Saved Results" and windows cannot currently be distinguished from each other without viewing the contents.
From the Favourites menu at the top of the central Jemboss pane select Best Local 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. Minimise the Results window.
Both sets of results have the same window name, but they appear in the bottom windows bar in chronological order, so the first Saved Results window will be the charge graphic and the second will be the alignment. Once more than a couple of analyses have been run it is important to save required results under a relevant file name to avoid confusion. This also allows windows to be closed, uncluttering the screen and freeing up computer memory.
Close both Saved Results windows.
There is an option to save all data created and analysed in batch mode (Section 9.4.39, “Batch”) to the local file manager.
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.
Access the run results by opening the Job Manager (Section 9.6.3, “Job Manager”) from the bottom of the central pane and highlighting the needle analysis run. Click on the Display button. Open the File option on the toolbar of the Saved Results window. Select the Save to Local File option, double click on the Example folder (Section 9.3.7, “New Folder Creation”) and call the new file bgal_ecoent.matcher. Hit the Save button.
The new file will not automatically be visible in the file manager.
In the local file manager pane (Section 9.3.1, “Local File Management”) of the main Jemboss window open the Example folder and highlight one of the files therein. Click once with the right hand mouse button to select the file management menu (Section 9.3.6, “File Manipulation”) and select the Refresh (Section 9.3.12, “Refresh”) option to see the new bgal_ecoent.matcher file. Close both the Saved Results and the Current Sessions Results windows.
For the client/server version of Jemboss only, the results of analyses run in batch mode (Section 9.4.39, “Batch”) can both be saved locally and also saved to the remote server. It may be advantageous to save data remotely to avoid running out of memory on the local computer (less of a problem on newer machines), or to share results with others using the same remote system. Remote results are saved to a working directory specified by the systems administrator but the user should be able to arrange folders and sub folders as they would on the local machine. There is no provision within the Jemboss remote setup for deleting files, thus data should be safe for the lifetime of the project. However, individual systems administrators may override this feature and delete data in specific folders at regular intervals. If this is not clear on the remote system, it should be checked.
Access the run results of the Global Alignments analysis (see Section 9.5.3, “Saved Results: Batch Mode”) from the Job Manager (Section 9.6.3, “Job Manager”) and open the File option on the toolbar of the Saved Results window. Select the Save Back to Project Directory option.
On selection, there is no Save window as this action is simply confirming the autosave option of every analysis run, so there is no opportunity to name a results file. To name the file, it must instead be saved to the local file manager and transferred to the remote file manager using the drag and drop technique (Section 9.3.16, “Moving Data between File Managers”).
Close Saved Results Window.
Each analysis that is run in Jemboss is automatically and permanently saved to either the local disc (standalone installations only) or remote server (see Section 9.5.4, “Saving remotely”) .
It is recommended that analysis results are periodically copied out of the auto-saved results to the user's own archive directory and deleted from auto-save.
All analysis runs conducted on a local installation of Jemboss are saved to the working directory (Section 9.3.3, “Working Directory”) and folders are listed in alphabetical order using the name of the program run. These are plain text files and can be opened with most editors. The default working directory can be altered by editing the directory locations (Section 9.7.1, “Directory location”).
(Unseen in the local file manager, but visible from the computer file manager, are .desc and a .finished files which are only used internally by Jemboss for describing the analysis and reporting that it has finished).
All analysis runs conducted on a remote installation of Jemboss are saved to a user workspace in a remote directory of the system administrator's choice. These results are accessible through the remote file manager (Section 9.3.14, “Remote File management”) and also through the Results Manager (Section 9.6.8.4, “Results in remote file manager”).