As @Orey mentionned I have wrote a bash script that contains :
#!/bin/bash
/home/me/yEd/jre/bin/java -Dswing.aatext=true \
-Dswing.plaf.metal.controlFont="Dialog-17" \
-Dswing.plaf.metal.userTextFont="Dialog-17" \
-Dswing.plaf.metal.userFont="Dialog-17"\
-Dswing.plaf.metal.menuTextFont="Dialog-17"\
-Dswing.plaf.metal.subTextFont="Dialog-17" \
-Dswing.plaf.metal.systemTextFont="Dialog-17"\
-Dswing.plaf.metal.windowTitleFont="Dialog-17" \
-Dawt.useSystemAAFontSettings=on \
-Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel \
-Dswing.crossplatformlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel \
-Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel \
-jar /home/me/yEd/yed.jar
Then create a new desktop file that calls this bash script :
#!/usr/bin/env xdg-open
[Desktop Entry]
Type=Application
Name=yEd HiFonts
Exec="/home/me/yEd/launchYed.sh"
Icon=/home/me/yEd/.install4j/yEdHiFonts.png
Categories=Application;
Name[en_GB]=yEd HiFonts.desktop
n.b : I created a new icon and call it yEdHiFonts.png