Sec edit crashes when saving secondary structure

[fog]

-------------------- ARB-backtrace for 'received signal 11':
/arb/software/arbsvn_5766M_tum64/lib/libARBDB.so(GBK_dump_backtrace+0x2e)[0x2b286e5e2f5e]
/arb/software/arbsvn_5766M_tum64/lib/libARBDB.so(sigsegv_handler_dump+0x33)[0x2b286e5e5f73]
/megx/chroot/amd64_hardy/lib/libc.so.6[0x2b28705fb100]
/megx/chroot/amd64_hardy/lib/libc.so.6(strlen+0x30)[0x2b2870644080]
/arb/software/arbsvn_5766M_tum64/lib/libARBDB.so(GBS_strcat+0x21)[0x2b286e5e2781]
arb_edit4[0x4628ad]
arb_edit4[0x47801a]
/arb/software/arbsvn_5766M_tum64/lib/libAW.so(_Z18AW_server_callbackP10_WidgetRecPvS1_+0xb6)[0x2b286e8d6b76]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtCallCallbackList+0x12f)[0x2b286f6c9a8f]
/megx/chroot/amd64_hardy/usr/lib/libXm.so.3[0x2b286eec9dc5]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6[0x2b286f6ff1ae]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(_XtTranslateEvent+0x337)[0x2b286f6ff927]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtDispatchEventToWidget+0x43e)[0x2b286f6d756e]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6[0x2b286f6d7c70]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtDispatchEvent+0xdb)[0x2b286f6d6d1b]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtAppMainLoop+0x45)[0x2b286f6d6e95]
arb_edit4[0x4342d8]
/megx/chroot/amd64_hardy/lib/libc.so.6(__libc_start_main+0xf4)[0x2b28705e71c4]
arb_edit4[0x414ec9]
-------------------- End of backtrace
[Terminating with signal 11]
ARB_DB_SERVER: a client died abnormally

[westram]

• works perfectly for me. Please test again and in case reopen ticket and provide more info here.

[fog]

I selected some sequences in e.g. the Living dataset, or in Silva 94/98, opened ARB Edit 4, clicked on one of the sequences and opened Sec Edit. Go to file→save structure, left name to noname.ass and clicked on EXPORT: Result: Sec Edit and the Editor crashed: ARB Version 5766, but its the same for 071207 (original Munich). Maybe something happens in combination with our machines??

-------------------- ARB-backtrace for 'received signal 11':
/arb/software/arbsvn_5766M_tum64_sina/lib/libARBDB.so(GBK_dump_backtrace+0x2e)[0x2b28cd9d7f5e]
/arb/software/arbsvn_5766M_tum64_sina/lib/libARBDB.so(sigsegv_handler_dump+0x33)[0x2b28cd9daf73]
/megx/chroot/amd64_hardy/lib/libc.so.6[0x2b28cf9f1100]
/megx/chroot/amd64_hardy/lib/libc.so.6(strlen+0x30)[0x2b28cfa3a080]
/arb/software/arbsvn_5766M_tum64_sina/lib/libARBDB.so(GBS_strcat+0x21)[0x2b28cd9d7781]
arb_edit4[0x4628ad]
arb_edit4[0x47801a]
/arb/software/arbsvn_5766M_tum64_sina/lib/libAW.so(_Z18AW_server_callbackP10_WidgetRecPvS1_+0xb6)[0x2b28cdccbb76]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtCallCallbackList+0x12f)[0x2b28ceabfa8f]
/megx/chroot/amd64_hardy/usr/lib/libXm.so.3[0x2b28ce2bfdc5]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6[0x2b28ceaf51ae]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(_XtTranslateEvent+0x337)[0x2b28ceaf5927]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtDispatchEventToWidget+0x43e)[0x2b28ceacd56e]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6[0x2b28ceacdc70]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtDispatchEvent+0xdb)[0x2b28ceaccd1b]
/megx/chroot/amd64_hardy/usr/lib/libXt.so.6(XtAppMainLoop+0x45)[0x2b28ceacce95]
arb_edit4[0x4342d8]
/megx/chroot/amd64_hardy/lib/libc.so.6(__libc_start_main+0xf4)[0x2b28cf9dd1c4]
arb_edit4[0x414ec9]
-------------------- End of backtrace
[Terminating with signal 11]
ARB_DB_SERVER: a client died abnormally

[meierh]

Confirmed for SVN 5990 on OpenSuse? 10.3 (64_bit !) tested with SSURef_98.

Structure is saved correctly, but arb_edit4 crashes (attached "bt_secstr_save").

[westram]

• related to #100
• x-string and HELIX get out of sync (by inserting columns)

[westram]

• assertion fails with 32bit version as well
• xstring (aka _REF) is broken in SILVA_98 (most likely by inserting columns). 'x' at position 420 should be at position 370 (behind end of left helix 6)

[westram]

• dont fix for upcoming release

[westram]

• x-string design sucks, will easily break when inserting/deleting columns
  • needs some kind of re-design:
    • 'x' at helix start is at same position as '/'
    • 'x' at helix end is one position behind '/' - this one gets out of sync!

[westram]

what i really meant was:

• 'x' at helix start is at same position as '[' / ']'
• 'x' at helix end is one position behind '[' / ']' - this one gets out of sync!