Added a dialog showing some statistics on the pedigrees and individuals in the database. These include a graph of the distribution of pedigree sizes.
Added a button to the Analyses tab of the Attributes dialog to allow any of the installed browsers to be used to run Boadicea.
Added a mechanism for reporting errors or making suggestions by email.
Modified the new pedigree dialog so that a number of the pedigree templates can be accessed easily.
Added a checkbox to the pedigree information form that allows an administrator to specify that the pedigree can be edited only by administrators. All other users can view the pedigree but not have changes recorded in the database.
Completed implementation of output for the BayesMendel web service for calculating risk. This requires a license from Kevin Hughes at Massachusetts General Hospital (see http://bcb.dfci.harvard.edu/BayesMendel/riskservice.php). The license is added from the Licensing ribbon on the Administration dialog and entry of a license adds the appropriate item to the calculations list on the Calculations ribbon in the pedigree window.
A mechanism has been provided for checking whether or not individuals in a drawing are present in an external database. The health number is used to make the comparison. The feature is accessed from the Tools ribbon and is labelled "Counselled".
The symbols for sex unknown is also used for intersex and transgender. In order to distinguish them, there being no international symbol for either, I have added an "I" to the symbol for intersex and a "T" for transgender (for which the symbol for the genetic sex should be used).
The program has had a system for defining template pedigrees for some time but this has not been widely used or particularly easy to use. I have added a small set of standard templates as follows: the family number dialog has been amended so that a pedigree can be drawn showing a symbol and its parents; a symbol and parents and maternal grandparents; a symbol and the paternal grandparents; a symbol and both sets of grandparents; and a symbol a as a result of a first cousin marriage. The program asks for the sex of the proband and the grandparental relationships for cousins.
If two symbols are selected, pressing Ctrl+K calculates the kinship coefficient between them.
The list of manifestations in the pedigree shown in a drawing is now sorted.
If the program imports a pedigree from an excel spreadsheet, a diagnosis that is not in the disease table is add if there is an entry for it in the external database diseases list.
In the print preview form, it is now possible to drag the pedigree to a new position so that in multi-page pedigrees, the alignment of the pages can be improved.
If there are multiple individuals in the database with the same health number, then a change to the disease information for one can be propagated to them all. The Attributes|Manifestations dialog page has a check box that controls this option.
Ctrl+N added the no issue symbol to a symbol. Now, if partners are selected, it adds it to the marriage.
Altered the display of current age by adding a checkbox for the display of age at death. If a person is dead, then selecting either will show the age at death as "d.xx". If only age at death is selected, the current age is not displayed for living persons. If both are checked, then either the current age or age at death are shown.
Added JSON and PDF+SON to the output options in the save on close dialog.
In the on close options, have added an option to place the pedigree number at the top left of the output drawing.
Added the ability of the administrator to change the duration which must elapse between a user logging in on one computer and then logging in on another computer.
If the program is asked to open a pedigree which is not present in the database, the user is asked if they wish to create an empty pedigree with that pedigree number. An option for curved lines descending from parents when the midpoint of children and parents does not coincide has been added.
Implemented planned adoption as defined in the pedigree standard.
Added adoption within the family. If a symbol and relative or a symbol and two partners are selected, then the "Add relatives" panel has a button "Adopted by fa..." (at the bottom of the list) that implements the standard pedigree feature.
Added a button to the layout ribbon that will centre all descent lines on parents mid-point.
I have simplified the update procedure by adding a button to the licensing tab of the administration dialog. This checks if a more recent version is available and offers to download it and run it. It also shows the list of recent changes.
Implemented pdf export – the program produces one pdf page, the size depending on the size of the pedigree.
Added the tilde "~" as a synonym for "?" to indicate uncertainty in dates.
If an administrator changes the location of analyses routines, all users get the changes automatically.
Added a bookmarks toolbar to the ribbon. This allows symbols to be bookmarked for rapid access across large pedigrees. Bookmarks are stored in the database.
Improved layout with GraphViz by excluding unattached partners from the GraphViz calculations.
Increased the speed of loading of large pedigrees. Pedigrees of 4500 members now are loaded in 5 seconds.
The updating of the layout in large pedigrees has been improved by a factor of about 30.
A new disease list can be loaded from a text file.
Added to the administration dialog user ribbon three new features:
a button to show all the deleted users;
a button to reinstall deleted users and to reset their password to "password";
a button to reset a user's password to "password".
In the diseases edit dialog, have made more logical the way in which synchronising disease names works.
Added to the general tab of the attributes dialog an editbox to allow changes to the delay between keys when sending messages to Cyrillic.
Appending a pedigree now asks for one individual in the incoming pedigree to be matched to a particular generation in the current pedigree.
Added lists of pedigree members that can be printed and output to an xls file.
Smartened up save and restore of form positions.
Added a button to restore columns widths in the find pedigrees dialog.
Added layout revision button that uses the inbuilt method.
Added setting parents unknown to the relatives tab at left of the main form.
For csv output added "" around items and separated lines within comments with "\n".
Added password reset to administration dialog - a right click popup menu item on the users grid.
Added scrolling with Ctrl+Arrow keys (equates to the scroll bar buttons).
Changes to the letters and documents function - see the help file.
Changes to the IBIS and BayesMendel functions to facilitate use over VPN and on a laptop not attached to the network.
Added a comment to relationships as well as the name. There are now check boxes on the Drawing tab of the Administration dialog that control whether display of the name and comment is enabled. The separation between partners is automatically adjusted to accommodate the name and comment.
When checking pedigrees in and out, if the database is connected to the Shire database, a list of upcoming clinic appointments is now shown to facilitate checking out pedigrees for peripheral clinics.
Added the filled in black symbol to the list of symbol types.
Clicking on the line joining partners: Ctrl+Click changes position to the default.
Reimplemented Shift+Ctrl+'D' -> child of unknown sex in Quick Edit mode.
Added child and sibling to the Quick Edit menu (H and L respectively).
If the pedigree is small, then adding symbols to it or checking the spacing will centre the pedigree in the window.
Alt+Shift+M will change the sex of a symbol to male; Alt+Shift+F to female; and Alt+Shift+U to sex unknown. If the sex of one parent is changed, or the sex of two parents are changed, the parent attributions of the children will be swapped.
Changed to the standard setting for probands and consultands - an arrow means consultand; an arrow with a "P" indicates the proband.
Implemented the "No information about parents" symbol according to the international standard. This can be added only by using the Quick keyboard menu. This also allows a set of siblings to be shown without the parents by creating an individual with parents unknown and then adding brothers or sisters as usual.
Added to the Management ribbon a check box for controlling "semi-anonymisation" - showing only information about diagnoses; converting names to initials; and truncating dates of birth and death to years.
Converted the symbols for no issue individuals and relationships to the pedigree standard and added display of the reason for there being no issue.
Implemented output for Boadicea version 3.
Because of the need to change to FastReport , I have revised the way the ad hoc queries work. It is now possible to save queries along with page formatting information.
Due to a change in the type of edit box, pedigree finding using the NHS number did not work. This has been corrected.
The reports have been upgraded and should now be more flexible, with the actual SQL shown and page formatting can be altered before the report is run.
Added child and sibling to the left hand panel. Using the shift key in the quick edit mode is not consistent in adding individuals to the left, with rightward being the default.
Implemented copying of pedigrees to a laptop and back again. It is assumed that the laptop has an encrypted hard drive, otherwise there will be problems with information governance. There is a separate setup program that is run when a user is made able to check pedigrees in and out.
Added a new report type (Pedigree reports... on the Tools ribbon) to allow users to write their own queries. The Form lists all the tables, all their fields and all their relationships. The dialog provides help with creating joins and entering fields and conditions as well as extracting information from date and age fields. The help file has a list of tables, their relationships and fields and some pointers on how particular fields are formatted and used. Queries can be saved and reloaded and the help file contains a full list of tables, fields and their formats.
Exposed import of xml files from the Surgeon General's Family History Tool.
Simplified the output routines for Boadicea Online and BayesMendel to better allow for hidden and deleted symbols, and for individuals with only one parent in the pedigree.
Added disease codes to the manifestation description box.
Added the ability to source disease codes from an Excel spreadsheet or a .csv file.
Added several code fields to manifestations for HL7 compatibility.
Added an option to save a drawing of the pedigree when closing the pedigree. This is managed from the edit ribbon of the administration dialog.
There was no update function for external disease lists. This has been added to the dialog that creates them.
Added two buttons to the Database ribbon. The first sets the current status of the pedigree to read only. The second sets it back to the normal editing mode (this reloads the pedigree from the database so that all changes are lost). This pair of actions differs from the checkpoint operations, as a record of the changes to the pedigree is not kept by the program.
Added a button to the Database ribbon of the Administration dialog that allows an administrator to delete all the relationships from a pedigree in cases where the pedigree cannot be read in and there is no error message that would allow the bug to be tracked down. The relationships will be recreated when the pedigree is loaded except for relationships without offspring.
Altered internal relationship processing a little in an attempt to avoid loops.
Added a debug output button to the Help ribbon. This outputs the user's ini file and the placement of all elements in the pedigree with not identifying information.
Added a new attribute for relationships: possible relationship shown by a dotted line (as opposed to the dashes in adoption into a family lines). This is set and reset by right clicking on the descent line or setting a checkbox in the partnership dialog.
Added check for sex of parents on output to risk calculations.
Added the new facilities in version 2.0-6. These include the use of HER2 test results and CDKN2A test results.
Command line parameters
A new parameter has been added - "/RN............" where .......... is the number of a pedigree. The program runs; asks for a password; opens and displays the pedigree; and closes when the pedigree window is closed.
This facility was supposed to allow placement of symbols as the user required, but its implementation lead to major problems in some installations. Consequently, I have changed it. If a symbol or symbols are moved with the Ctrl key held down when the mouse button is released, the program remembers this new position as a deviation from the position it expects and will apply this deviation whenever a change is made to the pedigree, such as adding new members or asking for a repositioning.
External disease lists
The implementation was over complicated and has been simplified. As long as the administrator has created an external disease list, this will be available to every user.
Added several new details - number of symbols deleted; number of generations
displaced; number of symbol moved from usual position.
On the Attributes dialog Drawing tab a button has been added to the marriage line position setting. Clicking on this sets all the relationships in the pedigree to the new setting.
Added ability to permanently move an entire generation down or up. Moving one symbol produces a dialog for this option - drag a symbol with the Shift and Ctrl keys down.
I have added a new reports button to the main menu at the lower right. This brings up the reports dialog directly. A new tab for reports about individuals has been added with an option to export the report to Excel. In this first version, the range of options is rather limited as it has been designed to meet a quite specific need, but any suggestions for improvements will be welcomed.
Number a symbol represents
*DCIS (Ductal carcinoma in situ)
The manifestations tab on the Attributes dialog provides an option set to control how DCIS is handled. It can be ignored (the default); treated as though it was breast cancer; or treated as though it was breast cancer diagnosed 10 years later than the actual age of diagnosis. This option set applies to calculations of the Manchester score, the IBIS Risk Evaluator, Boadicea and BrCaPro.
This is now set up so that no files are created in the Program files folder, conforming to the Windows standard by using the Program data folder instead. The latest version has dropped extra-colonic cancers from the MLH1/MSH2/MSH5 calculations. Changes have been made to allow for this.
Altered the sum to (the BRCA1 score with BRCA2 score -ve) plus (the BRCA2 score with BRCA1 -ve).
Implemented haplotyping using Merlin.exe to get the most likely haplotypes rather than use the marker by marker method in the main program.
*GEDCOM output (and input)
Added test results.
Allowed the Comment field to be displayed at the upper left of a symbols - controlled from the Symbol Items tab on the Attributes dialog.
Added test results output and tidied up the manifestations output to allow more control over the details.
Exposed the half left and half right symbols on the Symbols bar and added three new symbols with V, I, ? at the upper right of the symbol.
*Separation of symbols
The distance between symbols was controlled in part by the size of the symbol. Although this is still an option, the two can be made distinct by un-ticking the check-box in the Management|Attributes...|Drawing tab at the top left. As noted below, this change was made to accommodate images replacing the standard squares and circles.
Added ability to use characters and images instead of circles and squares.
These now include a wider range of attributes, including the symbol size and separation. The style labelled "Standard" is associated with the usual squares and circles, "Symbols" is associated with other types of symbol.