Bug#1142876: jalview: F2 does not toggle cursor mode (sometimes)

[Stepan]

Package: jalview
Version: 2.11.5.0+dfsg-2
Severity: normal
X-Debbugs-Cc: dabonatan at proton.me

Dear Maintainer,

F2 is supposed to toggle Cursor mode in Jalview. When I start Jalview
and open an alignment, pressing F2 does nothing and the program stays in
Normal mode. Nor does editing an alignment work: pressing up/down arrow
with a sequence selected does not move it up or down, pressing space
does not insert a gap, etc. However, if I just click around enough, the
program starts working normally: going to Tools -> Preferences -> Web
Services and deleting a service URL makes editing an alignment and
switching to Cursor mode work. So does opening and closing another view
of the alignment.

Here is the info that Jalview prints when started from the command line:

Jalview non-release Version: TEST
Jalview non-release Installation: unknown
Channel: default
Build Date: unknown
Preferences file: unknown
Log file: unknown
Java version: 25.0.4-ea
Java home: /usr/lib/jvm/java-25-openjdk-amd64
Java launch class: jalview.bin.Jalview
Java platform: Linux 7.1.3+deb14-amd64 (amd64)
Java LAF: Metal (javax.swing.plaf.metal.MetalLookAndFeel)
Java Virtual Machine PID: 10070
Using default properties file '/home/stepan/.jalview_nonrelease_properties'
Jalview non-release version: 2.11.5.0+dfsg-2 (deb)
Setting log level to INFO
Setting log level to INFO
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO - Loaded Sequence Ontology from so-xp-simple.obo.zip (107ms)
INFO - Getting messages for lang: en_US
Linux platform only! You may have the following warning next: "WARNING: An illegal reflective access operation has occurred"
This is expected and cannot be avoided, sorry about that.
INFO - JALVIEW: CREATED DESKTOP
WARN - Error when running commands
WARN - When trying to access questionnaire URL https://www.jalview.org/cgi-bin/questionnaire.pl
java.io.IOException: Server returned HTTP response code: 500 for URL: https://www.jalview.org/cgi-bin/questionnaire.pl?checkresponse=1
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1696) ~[?:?]
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1302) ~[?:?]
	at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:223) ~[?:?]
	at jalview.util.HttpUtils.openStream(HttpUtils.java:286) ~[jalview-2.11.5.0.jar:2.11.5.0]
	at jalview.util.HttpUtils.openStream(HttpUtils.java:268) ~[jalview-2.11.5.0.jar:2.11.5.0]
	at jalview.gui.UserQuestionnaireCheck.checkresponse(UserQuestionnaireCheck.java:65) ~[jalview-2.11.5.0.jar:2.11.5.0]
	at jalview.gui.UserQuestionnaireCheck.run(UserQuestionnaireCheck.java:108) ~[jalview-2.11.5.0.jar:2.11.5.0]
	at java.lang.Thread.run(Thread.java:1474) ~[?:?]
Warning - overwriting a sequenceSetId for a viewport!
INFO - ALL CLOSED
INFO - Desktop exiting.
LAUNCHER - JVM exited with value 0



-- System Information:
Debian Release: forky/sid
  APT prefers testing
  APT policy: (900, 'testing'), (800, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 7.1.3+deb14-amd64 (SMP w/8 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages jalview depends on:
ii  debconf [debconf-2.0]      1.5.92
ii  default-jre                2:1.25-77
ii  groovy                     2.4.21-10
ii  javahelp2                  2.0.05.ds1-10
ii  libandroid-json-org-java   20121204-20090211-7
ii  libapache-mime4j-java      0.8.13-1
ii  libaxis-java               1.4-29
ii  libbiojava6-java           6.1.0+dfsg-6
ii  libcommons-discovery-java  0.5-4
ii  libcommons-math3-java      3.6.1-4
ii  libhtsjdk-java             5.0.0+dfsg-1
ii  libhttpclient-java         4.5.14-1
ii  libhttpcore-java           4.4.16-1
ii  libhttpmime-java           4.5.14-1
ii  libintervalstorej-java     1.2+dfsg-5
ii  libjaba-client-java        2.2.0-2
ii  libjaxb-api-java           2.3.1-1
ii  libjaxb-java               2.3.0.1-11
ii  libjaxrs-api-java          2.1.2-2
ii  libjaxws-java              2.3.0.2-2
ii  libjersey1-client-java     1.19.3-8
ii  libjersey1-core-java       1.19.3-8
ii  libjetty9-java             9.4.58-2
ii  libjfreesvg-java           5.0.7-1
ii  libjmol-java               16.3.55+dfsg-1
ii  libjson-simple-java        2.3.0-2
ii  libjsoup-java              1.15.3-1
ii  libjswingreader-java       0.3-4
ii  liblog4j1.2-java           1.2.17-11
ii  liblog4j2-java             2.19.0-2
ii  libmiglayout-java          11.4.2+ds-2
ii  libslf4j-java              1.7.32-2
ii  libvamsas-client-java      0.2+dfsg-2
ii  varna                      3-93+ds-7

jalview recommends no packages.

Versions of packages jalview suggests:
ii  clustalw  2.1+lgpl-7
ii  kalign    1:3.5.1-1+b1
ii  t-coffee  13.45.0.4846264+really13.41.0.28bdc39+dfsg-1

-- debconf information:
  jalview/identifiersservice: true
  jalview/jws2services: true
  jalview/news: true
  jalview/questionnaire: true
  jalview/htmltemplates: true