The Madeline 2.0 Pedigree Drawing Engine (PDE) is a pedigree drawing program designed to handle large and complex pedigrees with an emphasis on readability and aesthetics. The program was designed primarily for human pedigrees.
License: GNU General Public License v2.0
Hey there,
I develop an internal web app for a genetic diagnostics company that uses your engine to draw pedigrees from our patient data. It's worked fantastically well so far.
However, a recent release has changed the feedback Madeline displays (and that my server parses to find the file Madeline creates) from using standard double quotes to typographers' quotes. If there is not a better way to locate the file Madeline creates, then is it possible to change this back, or at least know if there will be consistency in this particular line going forward?
Thanks!
I'll take a look - travis-ci is broke but the way we run the driver script it is reporting build passed - I'll update the ci to catch that error and also look at how to fix this.
I'm trying to help my wife (who works with Tasha Fingerlin) install Madeline 2 on a Windows 7 machine. We are following the instructions at http://madeline.med.umich.edu/madeline/install.php
We've hit a roadblock in the installation, and neither of us has much experience debugging this type of install. So any guidance would be appreciated (and we recognize that development has primarily happened on osx and linux).
For the cygwin installation, we downloaded the 64-bit cygwin. I think we've been able to follow the instructions quite literally. In many cases, their were multiple versions of the required packages available during cygwin installation. When that happened, we download the version with lib in the name (the other versions of those packages were under the debug, perl or python directories).
At the configure stage, when we run cmake . we get the following error:
CMake Warning at /usr/share/cmake-3.6.2/Modules/Platform/CYGWIN.cmake:15 (message):
CMake no longer defines WIN32 on Cygwin!
(1) If you are just trying to build this project, ignore this warning or
quiet it by setting CMAKE_LEGACY_CYGWIN_WIN32=0 in your environment or in
the CMake cache. If later configuration or build errors occur then this
project may have been written under the assumption that Cygwin is WIN32.
In that case, set CMAKE_LEGACY_CYGWIN_WIN32=1 instead.
(2) If you are developing this project, add the line
set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
at the top of your top-level CMakeLists.txt file or set the minimum
required version of CMake to 2.8.4 or higher. Then teach your project to
build on Cygwin without WIN32.
Call Stack (most recent call first):
/usr/share/cmake-3.6.2/Modules/CMakeSystemSpecificInformation.cmake:36 (include)
CMakeLists.txt:8 (PROJECT)
-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
-- === NOTA BENE: === Madeline will use included bzip2
CMake Error at /usr/share/cmake-3.6.2/Modules/FindPackageHandleStandardArgs.cmake:148 (message):
Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR)
Call Stack (most recent call first):
/usr/share/cmake-3.6.2/Modules/FindPackageHandleStandardArgs.cmake:388 (_FPHSA_FAILURE_MESSAGE)
/usr/share/cmake-3.6.2/Modules/FindZLIB.cmake:124 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
src/CMakeLists.txt:259 (FIND_PACKAGE)
-- Configuring incomplete, errors occurred!
See also "/home/powersju/Madeline_2.0_PDE/CMakeFiles/CMakeOutput.log".
See also "/home/powersju/Madeline_2.0_PDE/CMakeFiles/CMakeError.log".
CMakeOutput.log is quite a long file, so I've put it in this gist
Here is the content of CMakeError.log
Again, thank you so much for any suggestions or help.
Hi Ed, I've attached a sample input file that isn't generating a drawing. Looks like person 5 has children (5,10) with her nephew (9). There is nothing in the log to indicate an error (I used the flag --debug). Thanks in advance for taking a look. I'm using Madeline2 on Windows.
Hi Ed,
Is there any way to force Madeline to draw individuals not connected to anyone else?
Thanks
Grant
Hi Ed,
Is there a way to show twins with unknown zygosity without supplying the DOB? In some cases I know that 2 individuals are twins, but I do not know their DOB or zygosity, so I'd like to display the ? in the circle like it does if you do know the DOB (like it does here: https://madeline.med.umich.edu/madeline/testdata/#tw).
Many Thanks
Grant
Hi,
I tried to compile from current HEAD but I receive:
...
Resolving user defined references...
Finding anchors and sections in the documentation...
Transferring function references...
Combining using relations...
Adding members to index pages...
In file included from /scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.c:12:0:
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:118:45: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzStringFileNameCompare OF ((const char* fileName1,
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:131:32: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern unzFile ZEXPORT unzOpen OF((const char *path));
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:142:29: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzClose OF((unzFile file));
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:149:37: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzGetGlobalInfo OF((unzFile file,
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:157:40: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzGetGlobalComment OF((unzFile file,
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:170:37: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzGoToFirstFile OF((unzFile file));
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:176:36: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzGoToNextFile OF((unzFile file));
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:183:34: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzLocateFile OF((unzFile file,
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:196:42: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzGetCurrentFileInfo OF((unzFile file,
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:222:39: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzOpenCurrentFile OF((unzFile file));
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:228:40: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzCloseCurrentFile OF((unzFile file));
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:235:39: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzReadCurrentFile OF((unzFile file,
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:249:32: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern z_off_t ZEXPORT unztell OF((unzFile file));
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:254:27: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzeof OF((unzFile file));
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.h:259:42: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
extern int ZEXPORT unzGetLocalExtrafield OF((unzFile file,
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.c: In function 'unzOpen':
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.c:431:2: warning: implicit declaration of function 'unzGoToFirstFile' [-Wimplicit-function-declaration]
unzGoToFirstFile((unzFile)s);
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.c: In function 'unzClose':
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.c:450:9: warning: implicit declaration of function 'unzCloseCurrentFile' [-Wimplicit-function-declaration]
unzCloseCurrentFile(file);
^
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.c: At top level:
/scratch/var/tmp/portage/sci-biology/madeline-9999/work/madeline-9999/3rdParty/unzip/unzip.c:496:47: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'OF'
local int unzlocal_GetCurrentFileInfoInternal OF((unzFile file,
^
make[2]: *** [3rdParty/unzip/CMakeFiles/unzip.dir/build.make:63: 3rdParty/unzip/CMakeFiles/unzip.dir/unzip.c.o] Error 1
Is there a way to disable compilation of the 3rd-party stuff? I have sys-libs/zlib with minizip support installed. ;-)
Better add it to the dependencies at http://madeline.med.umich.edu/madeline/building.php and drop it from your git tree. ;-)
This is Annapoorna, from The University of Transdisciplinary Health Sciences and Technology (TDU), Bangalore, India ; wishing you a Very Happy and Healthy 2021. I write to you today asking for assistance with regard to your pedigree drawing engine Madeline 2.0
I am presently working on a project that requires using pedigrees for studying inheritance patterns of genetic traits. Madeline 2.0 seems to be an excellent choice to do this, however, I am unable to find information regarding how Madeline 2.0 is able to read data from a Mysql data table. The information brochure found online, i.e Madeline 2.0 PDE Docs, states it can do so but does not elaborate.
I request you to please guide me in this regard. Looking forward to hearing from you.
Hi there! Checking in from a gene diagnostics company. Madeline has been helpful so far.
Hope I'm not being a bother, but I've been having issues with the engine when trying to add both half-siblings and grandparents to a family. Half-siblings are well-supported, but as soon as grandparents are introduced, entire branches of the family will simply stop being drawn.
I'll add tab-delimited data files and the associated drawings to show you what I mean. Please note that the non-data .txt files are the XML drawing files, but GitHub doesn't support them with their native extension:
Working data:
data_for_working_ped.txt
Working pedigree drawing:
working_ped.txt
Data with parents newly added to rightmost father:
data_for_bad_ped.txt
Broken pedigree drawing:
bad_ped.txt
Typing make gives the following error building on CentOs7
[100%] Linking CXX executable madeline2
CMakeFiles/madeline2.dir/Network.cpp.o: In function Network::getNetworkFile(char const*)': Network.cpp:(.text+0x14a): undefined reference to curl_global_init'
Network.cpp:(.text+0x14f): undefined reference to curl_easy_init' Network.cpp:(.text+0x175): undefined reference to curl_easy_setopt'
Network.cpp:(.text+0x194): undefined reference to curl_easy_setopt' Network.cpp:(.text+0x1b3): undefined reference to curl_easy_setopt'
Network.cpp:(.text+0x1d1): undefined reference to curl_easy_setopt' Network.cpp:(.text+0x1f7): undefined reference to curl_easy_perform'
Network.cpp:(.text+0x207): undefined reference to `curl_easy_cleanup'
collect2: error: ld returned 1 exit status
make[2]: *** [src/madeline2] Error 1
make[1]: *** [src/CMakeFiles/madeline2.dir/all] Error 2
make: *** [all] Error 2
Per the NSGC recommendation on the Standardized Human Pedigree Nomenclature:
If possible, male partner should be to left of female partner on relationship line
Having issues finding out how to force drawings to always render the male partner on the left. If you have any pointers where to look in the code, would much appreciate :).
Example data:
FamilyId
IndividualId
Gender
Father
Mother
Deceased
Proband
DOB
MZTwin
DZTwin
Sampled
Test U0p100 M . . Y . . . . .
Test U0p101 F . . Y . . . . .
Test U0m100 M . . Y . . . . .
Test U0m101 F . . Y . . . . .
Test U00200 M U0p100 U0p101 Y . . . . .
Test U00201 F U0m100 U0m101 Y . . . . .
Test U00102 M . . . . . . . .
Test U00107 F U00200 U00201 . Y . . . .
Test U00108 F U00102 U00107 . . . . . .
Test U00109 F U00102 U00107 . . . . . .
Resulting drawing from example data above:
Example issues:
U00107) is drawn on left (I suspect this is because the ancestry relationships exist for this individual, if Proband was Male, he would appear on the left)U00201) on leftWould it be possible to create a tag/release here on Github?
I would like to include Madeline into Bioconda.
Hi Ed,
When I use Madeline 2 to process my data, I found one affected field in the output was not sorted by the values but by alphabetical order. It looks like:
Is there anyway can force it to be ordered by value?
Thank you!
Hi there,
I'm trying to draw some pedigree maps with madeline PDE and most of them are related to inbreeding program. I found a problem and don't know how to solve it:
parents from an inbreeding line were not stuck together, they were connected by dashed lines
it looks like this
f1_005 and f1_006 looks good, but the others are not.
How can I make the madeline to draw all parent pairs in the same manner as the f1_005Xf1_006?
Thank you.
Thank you for this wonderful program. Mother-son and father-daughter relationships are rare among humans but not so among animals and plants. Mythology is full of these cases too (I know, it'd be an unintended use of the program). Still, any chance such cases of inbreeding could become available? Consider this famous and relatively simple pedigree:
| FamilyId | IndividualId | Gender | Father | Mother |
|---|---|---|---|---|
| 1 | Oedipus | M | Laius | Jocasta |
| 1 | Polyneices | M | Oedipus | Jocasta |
| 1 | Eteocles | M | Oedipus | Jocasta |
| 1 | Ismene | F | Oedipus | Jocasta |
| 1 | Antigone | F | Oedipus | Jocasta |
If we try to run, we receive:
Unrecoverable Error: Individual::addSpouse(): Oedipus's spouse Jocasta is also his mother: Program currently cannot handle mother-son matings.
terminate called after throwing an instance of 'Exception'
Aborted (core dumped)
Thanks!
Hi,
I’m working on a multi-founder pedigree. I have something like eight founding pairs. When I get to the very last founder, I have to make virtual parents for them; otherwise I get a Segfault error. Is there a way around this?
Hi,
I recently discovered your Madeline software which is by far the best I ever saw for pedigree drawing. I look forward including your software into my own research projects.
However, I found some inconsistencies when using it to draw some test pedigree using the tab delimited format. It definitely seems to be a minimal reproducible bug, but I let you judge by yourself.
here is the pedigree (tab-separated file):
FamilyID IndividualID Gender Father Mother
3 44 M . .
3 1 M . .
3 2 F . .
3 6 M 1 2
3 7 F . .
3 15 F 6 7
3 16 F 6 7
3 17 F 44 7
Here is the command and output:
$ uname -a
Darwin GroBook.local 16.4.0 Darwin Kernel Version 16.4.0: Thu Dec 22 22:53:21 PST 2016; root:xnu-3789.41.3~3/RELEASE_X86_64 x86_64
$ ./src/madeline2 minimal_bug_pedigree.data
┌─────────────────────────────┐
│ Welcome to Madeline 2.0 PDE │
└─────────────────────────────┘
--------------------------------------------
LABELS TOTAL: 0
--------------------------------------------
--------------------------------------------
Parser::readFile(): Opening a(n) UTF-8 file ...
Reading file data in delimited format ...
Table 1 is a pedigree table.
┏ Start of addPedigreesFromDataTable ┓
Warning: Individual 17 already exists in pedigree 3: Ignoring replicated individual from data file.
Default ordering of siblings.
┗ End of addPedigreesFromDataTable ┛
┏ Start of draw ┓
Pedigree output file is “3_pedigree.svg”
┗ End of draw ┛
And here is the result (svg converted into png):
As you can see, there is clearly a problem with the output !
There is also a minor issue with the warning regarding the last entry of the file, but this is really minor since it does not seem to alter the result.
Hoping you will be able to suggest a fix. Please let me know if I can assist you in any way ...
Regards,
GN
Hello! I'm trying to build Madeline 2.0 locally on my Mac, running OSX 10.11.6. I'm having a recurrent error:
-- === NOTA BENE: === Madeline will be installed in /usr/local
CMake Error at /opt/local/share/cmake-3.9/Modules/FindDoxygen.cmake:542 (elseif):
given arguments:
"NOT" "doxygen" "IN_LIST" "Doxygen_FIND_COMPONENTS"
Unknown arguments specified
Call Stack (most recent call first):
CMakeLists.txt:57 (INCLUDE)
-- Configuring incomplete, errors occurred!
I realize that this is a CMake error, so this might not be the best place to ask, but debugging this kind of build is a bit over my head- a few hints would be appreciated!
I've installed XCode (version 7.3.1), gettext (v. 0.19.8.1), and reinstalled doxygen (1.8.13).
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