Cadixe in a Nutshell

Main Principles

Special Features



Preference Settings

Release Notes





Menu Bar of CADIXE

FILE menu

This menu gathers the commands to create, to load and to save annotated documents :

  • New Document : CADIXE initializes a new document using the current “default model” (cf. “preference settings”). A model is a file containing the name of a DTD and a list of style sheets that will be load in the new document.
  • New Document from Model : the editor asks the user for the model he/she wants to use and then builds a new document. The path to the folder containing the model files is defined in the “preference settings”.
  • Load Document : loads a document (annotated or not). When the document is a plain text file, the root tag of the DTD defined by the default model is automatically inserted. When the document is already annotated, the editor searches for the DTD and the style sheets in the directories defined in the “preference settings”.
    If the DTD used by the document is missing an error is fired. However, if there is no style sheet a new one is automatically created by CADIXE by using the name of the current DTD. Of course, this style sheet is “empty”: there is not specific graphical style associated to the tags.
  • Load recent : list of recent files loaded within the editor.
  • Insert Text … : insert a text file at the current position of the cursor.
  • Save Document : save the current annotated file with the names of the DTD and the style sheets. The meta-information (cf. menu “Documents”), cursor position, line spacing and level of zoom are also saved in the header.
  • Save As … : asks the user for the name of the annotated file to save.
  • Save Document as Model : the editor creates a new “model” file (Cf the command “new document”) from the current document. The name of this file is the DTDs name of the current document and it is stored in the folder containing the models.
  • Quit … : exits from the editor after a confirmation dialog box.

EDIT menu

In this release of CADIXE, it is possible to copy/paste an annotated area. In that case, the annotated text is stored in the clipboard as a XML string. Therefore it is possible to exchange the annotations between CADIXE and any application dealing with text.

Caution : in this release the editor doesn’t validate the content of the clipboard before pasting the tags in the document, thus if the external application sends a XML string which is wrong with respect to the DTD, the editor will fail.

  • Cut : cuts the selected text and the associated annotations and comments.
  • Copy : copies the selected text and the associated annotations and comments.
  • Paste : pastes the content of the clipboard. However, if it contains some tags, some conditions must be fulfilled in order this command succeed : the current tag in which the clipboard is pasted must be more general or identical (in that case the tags are merged) to the “root” tag in the clipboard.
  • Paste as text : pastes the plain text contained in the clipboard in the current tag.
  • Find … : searches for a string or a regular expression (when the associated check-box is activated) in the annotated document. The syntax of RG is described in the following site (among many) and here are some classical commands :
. : the “dot” corresponds to any character in the search.
^ and & : indicates the beginning and the ending of a line.
\d, \w, \s : corresponds to a number, a letter and a space character.
[ ] : list of possible characters (ie : [0-9] ; [a-z] ; [abcdef0123] …).
? : sequence of characters repeated 0 or 1 time.
+ : sequence of characters repeated 0 or several time.
* : sequence of characters repeated 1 or several time.
| : alternative (if we seek for “this” or “that”put “this|that”).
{num} : sequence of characters repeated num time exactly.
{min,max} : sequence of characters repeated between min and max time.
( ) : to delimit the sub-expression (i.e.: “[0-9\s(protein|gene)+”).

Besides, the 4 buttons placed at the bottom of the dialog : “First”, “Previous”, “Next” and “Last” allows to navigate between the occurrences.

  • Replace … : allows to replace a substring by another one in the document. To be coherent the replacement is feasible only is this substring is completely included in one or several tags. If that is not the case the replacement is impossible since the editor doesn’t know at what positions the different tags must be applied on the final substring.
  • Search Tag … : this command retrieves a tag in the document by using one or several criteria : its name, comment text and status and the value attribute. For instance the user can seeking for the <Abstract> tags which are not validated (unvalidated) and that are containing a missing attribute named ID …
  • Next Find/Search : Applies again the last find/search command performed.
  • Preferences : displays the preferences dialog box allowing to customize the software. The options are described in another section of this document.

TAG menu

This menu gathers the commands to manage the tags. In the current release some options are still missing to extend/shorten the range of a tag.

  • Delete current Tag : suppresses the current tag. This command let the included tags unchanged, for instance if we suppress the tag with red color :

It is impossible to delete the tag corresponding to the “root” of the DTD since this deletion has no meaning in the frame of CADIXE use.

  • Delete Tree Tags : suppresses recursively all the tags contained in the current tag. As this command could be dangerous (you can delete a large amount of tags) a confirmation dialog box is displayed before the deletion. If we tag back the previous example, here is the effect of this command :

  • Add comment … : adds a comment to the current tag, the notion of “comment” is describe in a previous section of this document. We can also add a new comment by double-clicking in the column “comment” of the XML zone.


This menu gathers the commands allowing to manage the documents that have been loaded in the editor.

  • Document Information … : this command allows to display some information about the document (DTD used, saving date) and to edit some “meta information” associated to the document. These information are stored in the header of the document as XML comments <-- … -->. We can provide :
    • The (long) title of the document,
    • The names of the annotators,
    • The references to the genuine document,
    • Some comments about the history of the annotation …
  • Zoom : to modify the zoom level, this information is stored (by default 100%).
  • Spacing : spacing (in number of points) between the lines of the document.
  • Window organisation : this command allows to switch between the mono/multi-documents modes and to set the way these documents are organized : horizontally or vertically. The maximum number of documents that can be displayed can be modified in the CADIXE preference settings. Of course these possibilities are interesting to use in order to compare two or several annotated documents.
  • Load Style … : loads a new styles file in the current document. This new style becomes the current one.
  • Reload Style : reloads the current style from its file. This command is very useful when the user is “finalizing” a style sheet with an external CSS editor (cf. “Style sheet”) to display rapidly the effect of a modification. In this way he/she doesn’t have to close and reload the document to take into account the new style.
  • Remove Style : removes the current style from the document (the file is not deleted). If there is just one style in the document this command do nothing.
  • Styles : this sub-menu contains the list of styles loaded in the current document and allows to select a given style.
  • Close document : close the current document (the document having the focus). If it has not been already saved a confirmation dialog box is displayed.
  • Document list : the menu DOCUMENTS finishes by the list of all the documents currently loaded in CADIXE. By selecting one of these items the user can change the document associated to the current window.

TOOLS menu

  • The five first items provide the list and the state (“show/hide”) of the palette tools that can be displayed at the top/right part of the interface. When the user changes this display his/her choices are automatically stored in the preferences of the editor and reused at the next run. Let’s notice that the relative positions of the palettes can be changed thanks to the preference dialog box. The tools are the following :
    • The toolbar containing the icons of the most common commands
    • The list of possible tags (with respect to the cursor position)
    • The attributes of the current tag
    • The comment tool (can be also a dialog box, menu EDIT)
    • The search tool. (can be also a dialog box, menu TAG)

According the current task, the user can use one or several palettes. For instance, during the annotation (s)he mainly uses the tools “tags” and “attributes”, but when verifying an existing annotation (s)he mainly uses the tools “search” and “comments”.

  • XML Validation of the Document : this command runs the XML validation of the annotated document. The errors are displayed in the panel “Validation result”.
    When the user clicks on an error, CADIXE automatically sets the cursor on the corresponding part in the document. Furthermore, by double-clicking on an error the editor also selects the panel “XML code”. In the XML code, the faulty tags have a red bullet. By double-clicking on this bullet the editor switches back to the list of error (panel “Validation result”). There are three kind of validation error :
    • Warning : these errors generally point out a problem in the attributes of the tag : missing value, erroneous value, … If this error frequently occurs the user should activate the flag “Display a dialog to fill the attributes “ (cf in preferences, Attribute options) which forces the user to enter a value in the attributes of the inserted tag.
    • Simple error : this is the most frequent error corresponding in CADIXE to a missing tag in the document with respect to the DTD. If this error frequently occurs the user should activate the mode “Allows to insert the most specific tag” (cf in preferences, Tag options) which forces the user to enter the tags in the same order they are defined in the DTD. In this way it becomes difficult to forget the intermediary level of tagging.
    • Fatal error : this kind of error stops the validation process. It can occur for instance when an ending tag is missing. In principle, this kind of error should not appear in CADIXE due to the controls made during tag insertion.

HELP menu

In this release, this menu just allows to display the presentation screen of the application with the current release number.

Last Modification : 11/03/05, gb