[med-svn] [mpsqed] 07/08: Update upstream source from tag 'upstream/0.9.3'
Andreas Tille
tille at debian.org
Tue Dec 12 17:22:45 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mpsqed.
commit 1e74e3a4bec5863dccb4acea766065485d8f8294
Merge: 50f46ec 9b6edc5
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 12 18:21:34 2017 +0100
Update upstream source from tag 'upstream/0.9.3'
Update to upstream version '0.9.3'
with Debian dir 5939ee183e9a26287a52c269278a6fe6d8961006
Installer_jre.eit | Bin 0 -> 1363268 bytes
Installer_nojre.eit | Bin 0 -> 20380 bytes
RKIToolsDoc/custom-cfg/common.xsl | 24 +
RKIToolsDoc/custom-cfg/eclipse.xsl | 29 +
RKIToolsDoc/custom-cfg/fo.xsl | 26 +
RKIToolsDoc/custom-cfg/html.xsl | 29 +
RKIToolsDoc/custom-cfg/htmlhelp.xsl | 29 +
RKIToolsDoc/custom-cfg/javahelp.xsl | 29 +
RKIToolsDoc/custom-cfg/local-entities.xml | 19 +
RKIToolsDoc/custom-cfg/localbuild.properties | 22 +
RKIToolsDoc/custom-cfg/localbuild.xml | 32 +
RKIToolsDoc/custom-cfg/manpages.xsl | 29 +
RKIToolsDoc/custom-cfg/rtf.xsl | 29 +
RKIToolsDoc/custom-cfg/singlehtml.xsl | 29 +
RKIToolsDoc/custom-cfg/singlexhtml.xsl | 29 +
RKIToolsDoc/custom-cfg/slides.xsl | 29 +
RKIToolsDoc/custom-cfg/style-common.css | 453 +++++
RKIToolsDoc/custom-cfg/style-eclipse.css | 109 ++
RKIToolsDoc/custom-cfg/style-javahelp.css | 76 +
RKIToolsDoc/custom-cfg/wordml.xsl | 29 +
RKIToolsDoc/custom-cfg/xhtml.xsl | 29 +
RKIToolsDoc/input/RKIToolsDoc.xml | 64 +
RKIToolsDoc/input/book-include.xml | 30 +
RKIToolsDoc/output/javahelp/hsviewer.jar | Bin 0 -> 32193 bytes
RKIToolsDoc/output/javahelp/jh.jar | Bin 0 -> 531676 bytes
applet.policy | 3 +
build-before-profiler.xml | 69 +
build.xml | 74 +
helpSetMaker/docuData/RKIToolsExample.fasta | 32 +
helpSetMaker/docuData/analyzeMenu.png | Bin 0 -> 15287 bytes
helpSetMaker/docuData/editMenu.png | Bin 0 -> 6388 bytes
helpSetMaker/docuData/fileMenu.png | Bin 0 -> 4400 bytes
helpSetMaker/docuData/helpMenu.png | Bin 0 -> 1362 bytes
helpSetMaker/docuData/mainWindow.png | Bin 0 -> 32808 bytes
helpSetMaker/docuData/namesPane.png | Bin 0 -> 4548 bytes
helpSetMaker/docuData/primer1.png | Bin 0 -> 2453 bytes
helpSetMaker/docuData/primerProduct.png | Bin 0 -> 5071 bytes
helpSetMaker/docuData/pyrograms.png | Bin 0 -> 9796 bytes
helpSetMaker/docuData/resizingSelection.png | Bin 0 -> 3352 bytes
helpSetMaker/docuData/sequencePane.png | Bin 0 -> 6336 bytes
helpSetMaker/docuData/settings.png | Bin 0 -> 21021 bytes
helpSetMaker/docuData/toolbar.png | Bin 0 -> 3569 bytes
helpSetMaker/docuData/viewMenu.png | Bin 0 -> 3498 bytes
helpSetMaker/hs/0844fec5.html | 25 +
helpSetMaker/hs/268013c8.html | 10 +
helpSetMaker/hs/2d4d2587.html | 29 +
helpSetMaker/hs/35271893.html | 13 +
helpSetMaker/hs/3e7a5715.html | 28 +
helpSetMaker/hs/4ecd38e2.html | 34 +
helpSetMaker/hs/6036f840.html | 10 +
helpSetMaker/hs/6bc41f84.html | 12 +
helpSetMaker/hs/86d0b0a1.html | 15 +
helpSetMaker/hs/87de535b.html | 14 +
helpSetMaker/hs/98c149b5.html | 15 +
helpSetMaker/hs/9d452f38.html | 13 +
helpSetMaker/hs/9ee3d3c6.html | 19 +
helpSetMaker/hs/JavaHelpSearch/DOCS | Bin 0 -> 1349 bytes
helpSetMaker/hs/JavaHelpSearch/DOCS.TAB | 7 +
helpSetMaker/hs/JavaHelpSearch/OFFSETS | 2 +
helpSetMaker/hs/JavaHelpSearch/POSITIONS | Bin 0 -> 2926 bytes
helpSetMaker/hs/JavaHelpSearch/SCHEMA | 2 +
helpSetMaker/hs/JavaHelpSearch/TMAP | Bin 0 -> 8192 bytes
helpSetMaker/hs/aa49edd7.html | 10 +
helpSetMaker/hs/ae869282.html | 10 +
helpSetMaker/hs/b139c808.html | 10 +
helpSetMaker/hs/b69463fa.html | 16 +
helpSetMaker/hs/c9e02254.html | 12 +
helpSetMaker/hs/e9fd53d0.html | 31 +
helpSetMaker/hs/ec633545.html | 10 +
helpSetMaker/hs/f19dc10a.html | 32 +
helpSetMaker/hs/main.hs | 23 +
helpSetMaker/hs/map.jhm | 25 +
helpSetMaker/hs/pics/analyzeMenu.png | Bin 0 -> 15287 bytes
helpSetMaker/hs/pics/editMenu.png | Bin 0 -> 6388 bytes
helpSetMaker/hs/pics/fileMenu.png | Bin 0 -> 4400 bytes
helpSetMaker/hs/pics/mainWindow.png | Bin 0 -> 32808 bytes
helpSetMaker/hs/pics/namesPane.png | Bin 0 -> 4548 bytes
helpSetMaker/hs/pics/primer1.png | Bin 0 -> 2453 bytes
helpSetMaker/hs/pics/primerProduct.png | Bin 0 -> 5071 bytes
helpSetMaker/hs/pics/pyrograms.png | Bin 0 -> 9796 bytes
helpSetMaker/hs/pics/resizingSelection.png | Bin 0 -> 3352 bytes
helpSetMaker/hs/pics/sequencePane.png | Bin 0 -> 6336 bytes
helpSetMaker/hs/pics/settings.png | Bin 0 -> 21021 bytes
helpSetMaker/hs/pics/toolbar.png | Bin 0 -> 3569 bytes
helpSetMaker/hs/pics/viewMenu.png | Bin 0 -> 3498 bytes
helpSetMaker/hs/toc.xml | 31 +
helpSetMaker/hsm.xml | 288 +++
helpSetMaker/html/0844fec5.html | 31 +
helpSetMaker/html/268013c8.html | 16 +
helpSetMaker/html/2d4d2587.html | 35 +
helpSetMaker/html/35271893.html | 19 +
helpSetMaker/html/3e7a5715.html | 34 +
helpSetMaker/html/4ecd38e2.html | 40 +
helpSetMaker/html/6036f840.html | 16 +
helpSetMaker/html/6bc41f84.html | 18 +
helpSetMaker/html/86d0b0a1.html | 21 +
helpSetMaker/html/87de535b.html | 20 +
helpSetMaker/html/98c149b5.html | 21 +
helpSetMaker/html/9d452f38.html | 19 +
helpSetMaker/html/9ee3d3c6.html | 25 +
helpSetMaker/html/aa49edd7.html | 16 +
helpSetMaker/html/ae869282.html | 16 +
helpSetMaker/html/b139c808.html | 16 +
helpSetMaker/html/b69463fa.html | 22 +
helpSetMaker/html/c9e02254.html | 18 +
helpSetMaker/html/e9fd53d0.html | 37 +
helpSetMaker/html/ec633545.html | 16 +
helpSetMaker/html/f19dc10a.html | 38 +
helpSetMaker/html/index.html | 10 +
helpSetMaker/html/pics/analyzeMenu.png | Bin 0 -> 15287 bytes
helpSetMaker/html/pics/editMenu.png | Bin 0 -> 6388 bytes
helpSetMaker/html/pics/fileMenu.png | Bin 0 -> 4400 bytes
helpSetMaker/html/pics/mainWindow.png | Bin 0 -> 32808 bytes
helpSetMaker/html/pics/namesPane.png | Bin 0 -> 4548 bytes
helpSetMaker/html/pics/primer1.png | Bin 0 -> 2453 bytes
helpSetMaker/html/pics/primerProduct.png | Bin 0 -> 5071 bytes
helpSetMaker/html/pics/pyrograms.png | Bin 0 -> 9796 bytes
helpSetMaker/html/pics/resizingSelection.png | Bin 0 -> 3352 bytes
helpSetMaker/html/pics/sequencePane.png | Bin 0 -> 6336 bytes
helpSetMaker/html/pics/settings.png | Bin 0 -> 21021 bytes
helpSetMaker/html/pics/toolbar.png | Bin 0 -> 3569 bytes
helpSetMaker/html/pics/viewMenu.png | Bin 0 -> 3498 bytes
helpSetMaker/html/toc.html | 34 +
helpSetMaker/latex/doc.aux | 13 +
helpSetMaker/latex/doc.log | 268 +++
helpSetMaker/latex/doc.pdf | Bin 0 -> 20874 bytes
helpSetMaker/latex/doc.tex | 26 +
helpSetMaker/latex/doc.toc | 3 +
helpSetMaker/presets/dabrowskiw.xml | 36 +
helpSetMaker/src/0844fec5.stml | 11 +
helpSetMaker/src/268013c8.stml | 4 +
helpSetMaker/src/2d4d2587.stml | 15 +
helpSetMaker/src/35271893.stml | 6 +
helpSetMaker/src/3e7a5715.stml | 20 +
helpSetMaker/src/4ecd38e2.stml | 17 +
helpSetMaker/src/6036f840.stml | 3 +
helpSetMaker/src/6bc41f84.stml | 5 +
helpSetMaker/src/86d0b0a1.stml | 7 +
helpSetMaker/src/87de535b.stml | 8 +
helpSetMaker/src/98c149b5.stml | 8 +
helpSetMaker/src/9d452f38.stml | 5 +
helpSetMaker/src/9ee3d3c6.stml | 12 +
helpSetMaker/src/aa49edd7.stml | 3 +
helpSetMaker/src/ae869282.stml | 3 +
helpSetMaker/src/b139c808.stml | 3 +
helpSetMaker/src/b69463fa.stml | 10 +
helpSetMaker/src/c9e02254.stml | 5 +
helpSetMaker/src/e9fd53d0.stml | 17 +
helpSetMaker/src/ec633545.stml | 3 +
helpSetMaker/src/f19dc10a.stml | 19 +
helpSetMaker/thumbnails/0e171431_100.jpg | Bin 0 -> 1834 bytes
helpSetMaker/thumbnails/0e171431_200.jpg | Bin 0 -> 4566 bytes
helpSetMaker/thumbnails/1ea36cbb_100.jpg | Bin 0 -> 1301 bytes
helpSetMaker/thumbnails/1ea36cbb_200.jpg | Bin 0 -> 3367 bytes
helpSetMaker/thumbnails/47bc4e12_100.jpg | Bin 0 -> 2043 bytes
helpSetMaker/thumbnails/47bc4e12_200.jpg | Bin 0 -> 5908 bytes
helpSetMaker/thumbnails/5031b155_100.jpg | Bin 0 -> 2460 bytes
helpSetMaker/thumbnails/5031b155_200.jpg | Bin 0 -> 7769 bytes
helpSetMaker/thumbnails/5cf69c5a_100.jpg | Bin 0 -> 1577 bytes
helpSetMaker/thumbnails/70a6cf64_100.jpg | Bin 0 -> 2787 bytes
helpSetMaker/thumbnails/70a6cf64_200.jpg | Bin 0 -> 6755 bytes
helpSetMaker/thumbnails/8ee1d6f4_100.jpg | Bin 0 -> 2004 bytes
helpSetMaker/thumbnails/90947dcc_100.jpg | Bin 0 -> 1165 bytes
helpSetMaker/thumbnails/90947dcc_200.jpg | Bin 0 -> 2872 bytes
helpSetMaker/thumbnails/99550228_100.jpg | Bin 0 -> 2235 bytes
helpSetMaker/thumbnails/99550228_200.jpg | Bin 0 -> 7777 bytes
helpSetMaker/thumbnails/b3efb285_100.jpg | Bin 0 -> 1479 bytes
helpSetMaker/thumbnails/b3efb285_200.jpg | Bin 0 -> 4472 bytes
helpSetMaker/thumbnails/c2400ae0_100.jpg | Bin 0 -> 4072 bytes
helpSetMaker/thumbnails/d5635043_100.jpg | Bin 0 -> 1422 bytes
helpSetMaker/thumbnails/e716f121_100.jpg | Bin 0 -> 923 bytes
helpSetMaker/thumbnails/e716f121_200.jpg | Bin 0 -> 1660 bytes
helpSetMaker/thumbnails/eab1139f_100.jpg | Bin 0 -> 1750 bytes
helpSetMaker/thumbnails/eab1139f_200.jpg | Bin 0 -> 5408 bytes
launch4j_jre.xml | 22 +
launch4j_nojre.xml | 22 +
manifest.mf | 3 +
nbproject/build-impl.xml | 1060 ++++++++++
nbproject/build-impl.xml~ | 709 +++++++
nbproject/configs/JDK_1.5.properties | 0
nbproject/genfiles.properties | 11 +
nbproject/private/config.properties | 0
nbproject/private/private.properties | 7 +
nbproject/private/private.xml | 4 +
nbproject/private/profiler/attach.xml | 12 +
nbproject/private/profiler/configurations.xml | 111 ++
.../private/profiler/snapshot-1264676579774.nps | Bin 0 -> 242666 bytes
.../private/profiler/snapshot-1264680472982.nps | Bin 0 -> 259793 bytes
.../private/profiler/snapshot-1264680536100.nps | Bin 0 -> 260686 bytes
nbproject/project.properties | 91 +
nbproject/project.xml | 18 +
resources/EditorName.png | Bin 0 -> 7647 bytes
resources/RKILogo.png | Bin 0 -> 443 bytes
resources/editor.ico | Bin 0 -> 13094 bytes
resources/icons/IUB.png | Bin 0 -> 933 bytes
resources/icons/help.png | Bin 0 -> 786 bytes
resources/icons/no_sequence_name.png | Bin 0 -> 1089 bytes
resources/icons/non-IUB.png | Bin 0 -> 894 bytes
resources/icons/primer_display.png | Bin 0 -> 914 bytes
resources/icons/primer_length_display.png | Bin 0 -> 753 bytes
resources/icons/primer_no_length_display.png | Bin 0 -> 739 bytes
resources/icons/primer_no_temperature_display.png | Bin 0 -> 698 bytes
resources/icons/primer_sequence_display.png | Bin 0 -> 923 bytes
resources/icons/primer_temperature_display.png | Bin 0 -> 727 bytes
resources/icons/sequence_name.png | Bin 0 -> 982 bytes
src/org/json/CDL.java | 261 +++
src/org/json/Cookie.java | 169 ++
src/org/json/CookieList.java | 90 +
src/org/json/HTTP.java | 163 ++
src/org/json/HTTPTokener.java | 77 +
src/org/json/JSONArray.java | 934 +++++++++
src/org/json/JSONException.java | 27 +
src/org/json/JSONML.java | 455 +++++
src/org/json/JSONObject.java | 1550 +++++++++++++++
src/org/json/JSONString.java | 18 +
src/org/json/JSONStringer.java | 78 +
src/org/json/JSONTokener.java | 422 ++++
src/org/json/JSONWriter.java | 323 +++
src/org/json/Test.java | 624 ++++++
src/org/json/XML.java | 437 +++++
src/org/json/XMLTokener.java | 365 ++++
src/org/rki/sequenceeditor/model/Alignment.java | 499 +++++
src/org/rki/sequenceeditor/model/Annotation.java | 27 +
.../rki/sequenceeditor/model/AnnotationList.java | 117 ++
src/org/rki/sequenceeditor/model/Base64.java | 2053 ++++++++++++++++++++
.../rki/sequenceeditor/model/BaseColorModel.java | 22 +
.../sequenceeditor/model/BaseColorModelMap.java | 30 +
.../sequenceeditor/model/ClientHttpRequest.java | 552 ++++++
src/org/rki/sequenceeditor/model/ColorModels.java | 103 +
src/org/rki/sequenceeditor/model/Data.java | 18 +
src/org/rki/sequenceeditor/model/Flowgram.java | 143 ++
src/org/rki/sequenceeditor/model/Globals.java | 24 +
src/org/rki/sequenceeditor/model/GroupKey.java | 39 +
src/org/rki/sequenceeditor/model/Letters.java | 909 +++++++++
.../rki/sequenceeditor/model/MasterSequence.java | 33 +
src/org/rki/sequenceeditor/model/Position.java | 26 +
src/org/rki/sequenceeditor/model/Primer.java | 383 ++++
src/org/rki/sequenceeditor/model/RKIFile.java | 25 +
src/org/rki/sequenceeditor/model/RKIFolder.java | 25 +
src/org/rki/sequenceeditor/model/SNP.java | 13 +
src/org/rki/sequenceeditor/model/Sequence.java | 184 ++
src/org/rki/sequenceeditor/model/Settings.java | 191 ++
src/org/rki/sequenceeditor/model/SizeMenuItem.java | 18 +
.../rki/sequenceeditor/model/TripletMenuItem.java | 9 +
.../model/filters/BasicFastaFilter.java | 77 +
.../sequenceeditor/model/filters/FastaFilter.java | 141 ++
.../model/filters/GeneiousFilter.java | 200 ++
.../sequenceeditor/model/filters/LoadFilter.java | 18 +
.../sequenceeditor/model/filters/RSFFilter.java | 281 +++
.../sequenceeditor/model/filters/SaveFilter.java | 17 +
.../sequenceeditor/view/AnnotationTextField.java | 17 +
src/org/rki/sequenceeditor/view/BlingFilter.java | 70 +
.../sequenceeditor/view/ColorModelMenuItem.java | 18 +
src/org/rki/sequenceeditor/view/Editor.html | 35 +
src/org/rki/sequenceeditor/view/Editor.java | 1399 +++++++++++++
src/org/rki/sequenceeditor/view/EditorApp.java | 1728 ++++++++++++++++
.../rki/sequenceeditor/view/EditorInterface.java | 107 +
src/org/rki/sequenceeditor/view/EditorWindow.form | 723 +++++++
src/org/rki/sequenceeditor/view/EditorWindow.java | 871 +++++++++
src/org/rki/sequenceeditor/view/FindDialog.java | 99 +
src/org/rki/sequenceeditor/view/FlowFrame.form | 146 ++
src/org/rki/sequenceeditor/view/FlowFrame.java | 200 ++
src/org/rki/sequenceeditor/view/FlowPanel.java | 123 ++
src/org/rki/sequenceeditor/view/FlowViewer.java | 51 +
src/org/rki/sequenceeditor/view/GroupMenuItem.java | 27 +
src/org/rki/sequenceeditor/view/IntDocument.java | 29 +
src/org/rki/sequenceeditor/view/Main.java | 30 +
src/org/rki/sequenceeditor/view/NamesPane.java | 400 ++++
src/org/rki/sequenceeditor/view/OptionsFrame.form | 334 ++++
src/org/rki/sequenceeditor/view/OptionsFrame.java | 349 ++++
.../rki/sequenceeditor/view/RKIFilesDialog.java | 135 ++
.../rki/sequenceeditor/view/RecentMenuItem.java | 26 +
src/org/rki/sequenceeditor/view/SequenceInfo.java | 28 +
src/org/rki/sequenceeditor/view/SequencePane.java | 1448 ++++++++++++++
src/org/rki/sequenceeditor/view/SequenceTip.java | 32 +
src/version.properties | 2 +
276 files changed, 25833 insertions(+)
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