display errors

  • I installed gap11.2 on a ubuntu machine (64 bit). At first it seemed to work but I get weired display problems. When I open the editor window I get only the tool bar. If I want to see the sequence I have to add a aa frame, then all is displayed normally. After running a find internal joins I tried to open the join editor. This yields the toolbar only without any possibility to change this and gap4 is no longer responding.
    Can anyone help me with this problem?

    Many thanks


  • James Bonfield
    James Bonfield

    Is this Gap4.11.2? I'm assuming it's one of the newer 2.0 beta releases of the package then, but it may help to know precisely which. (The version numbers of gap4 aren't so sensible.)

    The bug sounds like a window-manager incompatibility. The contig editor is a bit bizarre in that it attempts to allow user resizing in X and automatic resizing in Y, which technically should work but in practice breaks most window managers. So it's a horrible hack. Does trying to resize the window cure it?

    Which release of Ubuntu is this?
    Do you know what the name and version are of your X11 window manager?

  • Dear Dr. Bonfield,
    there is no possibility to resize the contig editor window. Only after a command like (show traces) where the aa tracks are shown the window opens completely.
    I downloaded the latest beta version of the program, hoping that it would be even more convenient. Should I go back to an earlier version or would the problem be the same? Attached are my systems settings.
    Many thanks for your help.

    Best regards


    X version:
    X.Org X Server 1.7.6
    Release Date: 2010-03-17
    Ubuntu version (comes as ubuntu10.04)
    CONFIG_VERSION_SIGNATURE="Ubuntu 2.6.32-24.39-generic"

  • The URL got mangled. Just copy the part between the "-marks.

  • James Bonfield
    James Bonfield

    The alignment looks like a font issue. In theory it picks fixed width fonts, but some seem to be mislabelled or if the exact font specified doesn't exist sometimes it gets helpfully substituted for an alternative (non-fixed) font. Try using the main Options menu to select different fonts.

    The window manager sizing problems are different. Gap4's contig editor is, not to put too fine a point on it, utterly bizarre in its usage of resizing. In theory the Y size is controlled by the program while the X size is controlled by the user. This used to work just fine, but over the years window managers have become both cleverer and dumber at the same time, often doing the wrong thing when faced with such bizarre sizing issues.

    I'd need to sit down in front of a machine to really figure out the cause, so it may be some time before I find a solution. (We have a system we can use for such purposes.)  Meanwhile there is some code in $STADENROOT/share/staden/tcl/gap/cotnig_editor.tcl that may resolve the issue by commenting it out. Look for "Any-Configure" and then comment out those 5 lines. Ie:

    #    bind $w <Any-Configure> {
    #        if {[winfo toplevel %W] == "%W"} {
    #            after 1000 {if {[winfo exists %W]} {wm geometry %W {}}}
    #        }
    #    }

    That *may* fix the problem…. or it may introduce others! This is one reason I redesigned the editor layout for gap5.