6 Menus Description

This chapter describes the Ordalie menus. Only the entries which have not been already explained in this manual will be described in details here.

6.1 The File Menu

6.1.1 Open

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.

6.1.2 Save

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.

6.1.3 Save As ...

Ask for a file format and a file name to save the entire current snapshot.

6.1.4 Save Window As

Save only the visible part of the snapshot in the specified file format and file name.

6.1.5 Close

Close all snapshots and all dependencies (Overview, 3D Viewer ...), and set Ordalie ready to load a new file.

6.1.6 Print

When the 'Print' option is invoked, a 'Setup' properties window will pop up. Several printing parameters can be set :

6.1.7 Quit Ordalie

Guess ...

6.2 The Edit Menu

6.2.1 Cut

Cuts the selected sequences.

6.2.2 Copy

Copies the selected sequences into the memory buffer.

6.2.3 Paste

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.

6.2.4 Preferences

Access the 'Preferences' panel. This gives acces to Ordalie internals.

6.3 The View Menu

6.3.1 Bigger font

Increases the font size. The Ordalie default font type and size can be defined through 'Edit' -> 'Preferences' -> 'General'.

6.3.2 Smaller font

Decreases the font size

6.3.3 Open Log Console

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.

6.3.4 Output Log as ...

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.

6.3.5 Toggle FullScreen

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.

6.3.6 Show/Hide Icon Bar

Displays or hides the Icon bar buttons frame. This is useful when a maximal window size is required, for alignment editing for example.

6.3.7 Show/Hide Scores

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.

6.3.8 Show/Hide Features frame

Swiches on and off the Features frame. This is useful when a maximal window size is required, for alignment editing for example.

6.4 The Sequence Menu

6.4.1 Names as

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.

6.4.2 Identity tool

Launches the Identity tool.

6.4.3 Search motif

Launches the Search motif tool.

6.4.4 Retrieve Seq. Info.

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.

6.4.5 Browse Info seq

Enters the sequence information browser tool.

6.4.6 Edit Info Seq

Enters the sequence information edit tool.

6.4.7 Sequence VRP

Enters the Sequence VRP tool.

6.4.8 Show/Hide Phylum

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.

6.4.9 Show/Hide Sec. Str.

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.

6.5 The Alignment Menu

6.5.1 Editor

Launches the Editor tool. The Editor is described in details in section 5.2..

6.5.2 Overview

Creates an instance of the Overview Window for the current snapshot. See ``Snapshot Overview'' section 5.1 for details.

6.5.3 Conservation

Launches Conservation computation tool.

6.5.4 Tree

Launches the Tree tool.

6.5.5 Features Summary

Launches the 'Features Summary' tool. Sequences selected in the main window will automatically be selected in the 'Features Summary' tool.

6.5.6 Features Editor

Launches the feature editor.

6.5.7 Annotate snapshot

Launches the snapshot annotation tool.

6.5.8 Barcode

Creates a barcode representation of the current snapshot.

6.5.9 Clustering

Launches the Clustering tool.

6.5.10 Add separator

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.

6.5.11 Remove Separator

Removes the separator just below the selected sequence. Be aware that only one sequence should be selected.

6.5.12 Remove All separators

Removes all separators, and unselects all sequences.

6.5.13 Toggle physicochem. col.

Colours residues with the same mapping as in the 'Editor'.

6.6 The Structure Menu

6.6.1 Superpose Structures

Enters the 'Superposition' tool if several PDB structures are available in the alignment.

6.6.2 Display Structures

Launches the '3D Viewer' tool.

6.6.3 Color Sec. Str. by identity

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:

6.6.4 Save PDB

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 :

6.7 The "?" Menu

6.7.1 About

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.

6.8 help

Launches this manual on the default web browser.

moumou 2019-03-25