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This chapter describes the Ordalie menus. Only the entries which have not been already explained in this manual will be described in details here.
Opens an alignment file. Several file formats are recognized :
A first format checking is done using the file extension (.msf, .tfa/.fasta, .xml, .rsf, .aln or .ord recognized). Then Ordalie will check the file content. In case of incompatibility, the user will be asked for the correct file format.
Save the entire current alignment in the current file format with the current file name. The first time 'Save' is invoked, the user will be prompted to enter a file name.
Ask for a file format and a file name to save the entire current snapshot.
Save only the visible part of the snapshot in the specified file format and file name.
Close all snapshots and all dependencies (Overview, 3D Viewer ...), and set Ordalie ready to load a new file.
When the 'Print' option is invoked, a 'Setup' properties window will pop up. Several printing parameters can be set :
Guess ...
Cuts the selected sequences.
Copies the selected sequences into the memory buffer.
Pastes the sequences present in the memory buffer. The sequences are pasted just below the current selected sequence. If no sequence is selected, then no sequences are pasted. Note that in case of pasting sequences that already exist in the snapshot, their names will be suffixed by '__<n>' where '<n>' is the copy number.
Access the 'Preferences' panel. This gives acces to Ordalie internals.
Increases the font size. The Ordalie default font type and size can be defined through 'Edit' -> 'Preferences' -> 'General'.
Decreases the font size
Most of Ordalie information and computations are logged. The Log window allows to access the crude log text and to save it as a raw text file.
This will output the whole Ordalie log. A cascade menu allows to select between a HTML or Text format. The output file name is the rootname of the original alignment file suffixed by the format type.
Toggles the main window between its actual size and full screen size. This can also be achieved by hitting the <F1> key on the keyboard.
Displays or hides the Icon bar buttons frame. This is useful when a maximal window size is required, for alignment editing for example.
This turns on and off the scores frame. When displaying a conservation score, either through the Features buttons or inside the 'Conservation' tool, the global score and groups scores for each column is plotted.
Swiches on and off the Features frame. This is useful when a maximal window size is required, for alignment editing for example.
In Ordalie, there are three ways of naming a sequence :
In Macsims/Xml and Ordalie file formats, the three types of names are clearly identified. For all other formats, there is only one ID per sequence, and this one will be taken as the sequence name, accession number and bank ID.
This option allows to change the displayed name of the sequences to any of these three possibilities if available. By default, the sequence name is displayed.
Launches the Identity tool.
Launches the Search motif tool.
This option is intended to retrieve information from sequence databases. For each sequence, Ordalie will try to connect to its original database (UniProt, NCBI) and fetch information. The retrieved information will appear in the sequence contextual menu or through the Browse information menu item.
Enters the sequence information browser tool.
Enters the sequence information edit tool.
Enters the Sequence VRP tool.
If the 'Life Domain' information is available, then the sequence names will be colored accordingly. By default, Eukaryots are colored in red, Prokaryots in yellow, Archaea in blue, Viruses in black. This color scheme can be changed through the 'Preferences' panel.
For all PDB sequences present in the main window, show or hide the secondary structure information if it exists. The Helices, Strands and Turns information is extracted from the PDB file itself, and the structures are represented in red, green and cyan respectively.
Launches the Editor tool. The Editor is described in details in section 5.2..
Creates an instance of the Overview Window for the current snapshot. See “Snapshot Overview” section 5.1 for details.
Launches Conservation computation tool.
Launches the Tree tool.
Launches the 'Features Summary' tool. Sequences selected in the main window will automatically be selected in the 'Features Summary' tool.
Launches the feature editor.
Launches the snapshot annotation tool.
Creates a barcode representation of the current snapshot.
Launches the Clustering tool.
Adds a blank line separator just below the selected sequence. Be aware that only one sequence should be selected. Adding separator allow the user to create his own clusters.
Removes the separator just below the selected sequence. Be aware that only one sequence should be selected.
Removes all separators, and unselects all sequences.
Colours residues with the same mapping as in the 'Editor'.
Enters the 'Superposition' tool if several PDB structures are available in the alignment.
Launches the '3D Viewer' tool.
This tool allows coloring the secondary structures according to their sequence identity level in the snapshot. When invoked, a parameter window will pop up with the following parameters to select:
As the 3D structures may be changed using the 'Superposition' tool, this option allows to save a given 3D structure present in the alignment. It may be useful to output the superposed structures in order to render them in a more sophisticated drawing program.
When invoked, a window will pop up to ask the user for some parameters :
This menu item pops up a window giving some information about Ordalie, such as the currently used version, and the URL for the Ordalie home page.
Launches this manual on the default web browser.