Package: jalview / 2.11.1.3+dfsg2-5

Metadata

Package Version Patches format
jalview 2.11.1.3+dfsg2-5 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
newer mime4j api.diff | (download)

src/jalview/ws/io/mime/JalviewMimeContentHandler.java | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 
 patch to use the latest version of apache mime4j
change_package_jfree.patch | (download)

src/jalview/gui/SequenceRenderer.java | 2 1 + 1 - 0 !
src/jalview/io/HtmlSvgOutput.java | 4 2 + 2 - 0 !
src/jalview/util/ImageMaker.java | 4 2 + 2 - 0 !
3 files changed, 5 insertions(+), 5 deletions(-)

 
 change the package for org.jfree, which is not the correct one
get_rid_of_quaqua.patch | (download)

src/jalview/bin/Jalview.java | 24 2 + 22 - 0 !
1 file changed, 2 insertions(+), 22 deletions(-)

 
 get rid of quaqua look and feel, only licensed for mac
using_right_json_simple_package.patch | (download)

src/jalview/io/JSONFile.java | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 
 jsonobject was wrongly invoked
 It was called with a wrong package name, "simple" being forgotten.
 Moreover it is called on an AlignmentPojo object, I added the getAppSettings
 method in the call to get a HashMap<String, Object>.
deactivate_getdown.patch | (download)

src/jalview/bin/Cache.java | 122 3 + 119 - 0 !
src/jalview/bin/Jalview.java | 20 0 + 20 - 0 !
2 files changed, 3 insertions(+), 139 deletions(-)

 
 not using getdown inside jalview
deactivate_classgraph.patch | (download)

test/jalview/bin/CommandLineOperations.java | 37 1 + 36 - 0 !
1 file changed, 1 insertion(+), 36 deletions(-)

 
 avoid using classgraph, not needed to find the debian jar
correct_last_assertion_MemorySettingTest.patch | (download)

test/jalview/bin/MemorySettingTest.java | 10 7 + 3 - 0 !
1 file changed, 7 insertions(+), 3 deletions(-)

 
 correcting the last assertion in memorysettingtest.java
deactivate_google_analytics.patch | (download)

src/jalview/bin/Jalview.java | 9 0 + 9 - 0 !
src/jalview/jbgui/GPreferences.java | 2 2 + 0 - 0 !
2 files changed, 2 insertions(+), 9 deletions(-)

 
 turn off google analytics call, relies on non-packaged software
controlling_web_services.patch | (download)

src/jalview/bin/Cache.java | 10 9 + 1 - 0 !
src/jalview/bin/Jalview.java | 9 7 + 2 - 0 !
src/jalview/gui/AlignFrame.java | 32 29 + 3 - 0 !
src/jalview/gui/BlogReader.java | 13 8 + 5 - 0 !
src/jalview/gui/Desktop.java | 61 43 + 18 - 0 !
src/jalview/ws/utils/UrlDownloadClient.java | 5 0 + 5 - 0 !
6 files changed, 96 insertions(+), 34 deletions(-)

 
 do not run web services if not allowed by the user/administrator