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[CIShell-SVN] SF.net SVN: cishell:[1177] branches/tycho
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From: <fu...@us...> - 2010-11-27 03:47:35
|
Revision: 1177
http://cishell.svn.sourceforge.net/cishell/?rev=1177&view=rev
Author: fugu13
Date: 2010-11-27 03:47:24 +0000 (Sat, 27 Nov 2010)
Log Message:
-----------
committing because working copy is getting cumbersome, but stupid dependency problems with new packaging type are not yet resolved
Modified Paths:
--------------
branches/tycho/clients/gui/gui-build/pom.xml
branches/tycho/core/core-build/pom.xml
branches/tycho/deployment/deployment-parent/pom.xml
branches/tycho/deployment/org.cishell.reference.application/pom.xml
branches/tycho/deployment/org.cishell.reference.gui.feature/feature.xml
branches/tycho/deployment/org.cishell.reference.product/cishell.product
branches/tycho/deployment/org.cishell.reference.product/pom.xml
branches/tycho/lib-dependencies/pom.xml
branches/tycho/libs/org.prefuse/osgi.bnd
Added Paths:
-----------
branches/tycho/deployment/org.cishell.reference.application/
branches/tycho/deployment/org.cishell.reference.application/extra-files/
branches/tycho/deployment/org.cishell.reference.application/extra-files/configuration/
branches/tycho/deployment/org.cishell.reference.application/extra-files/configuration/config.ini.bak
branches/tycho/deployment/org.cishell.reference.application/extra-files/configuration/default_menu.xml
branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/
branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-apache-commons-collections.txt
branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-cishell.txt
branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-colt.txt
branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-jung.txt
branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-knopflerfish.txt
branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-prefuse.txt
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/isi/
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/isi/barabasi-vespignani-wasserman.isi
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/isi/savedrecs-barabasi.isi
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/isi/savedrecs-garfield.isi
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/isi/savedrecs-vespignani.isi
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/isi/savedrecs-wasserman.isi
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/TARL/
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/TARL/agingfunction.txt
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/TARL/iniscript.tarl
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/bio/
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/bio/FlyMINT.nwb
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/bio/TF_DNA_regulonDB.nwb
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/bio/WI5.nwb
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/bio/WormMint.nwb
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/bio/YeastMINT.nwb
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/conversionGraph.graphml.xml
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/florentine.nwb
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/friendster.graphml.xml
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/friendster.xgmml.xml
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/netsci06-conference.net
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/seiyu.graphml.xml
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/terror.graphml.xml
branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/network/terror.xgmml.xml
branches/tycho/deployment/org.cishell.reference.application/org.cishell.reference.application.product
branches/tycho/deployment/org.cishell.reference.application/root.properties
branches/tycho/deployment/org.cishell.reference.brand.feature/
branches/tycho/deployment/org.cishell.reference.brand.feature/build.properties
branches/tycho/deployment/org.cishell.reference.brand.feature/feature.xml
branches/tycho/deployment/org.cishell.reference.brand.feature/pom.xml
branches/tycho/deployment/org.cishell.reference.product/extra-files/
branches/tycho/deployment/org.cishell.reference.product/extra-files/configuration/
branches/tycho/deployment/org.cishell.reference.product/extra-files/configuration/config.ini
branches/tycho/deployment/org.cishell.reference.product/extra-files/configuration/default_menu.xml
branches/tycho/deployment/org.cishell.reference.product/extra-files/licenses/
branches/tycho/deployment/org.cishell.reference.product/extra-files/licenses/license-apache-commons-collections.txt
branches/tycho/deployment/org.cishell.reference.product/extra-files/licenses/license-cishell.txt
branches/tycho/deployment/org.cishell.reference.product/extra-files/licenses/license-colt.txt
branches/tycho/deployment/org.cishell.reference.product/extra-files/licenses/license-jung.txt
branches/tycho/deployment/org.cishell.reference.product/extra-files/licenses/license-knopflerfish.txt
branches/tycho/deployment/org.cishell.reference.product/extra-files/licenses/license-prefuse.txt
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/isi/
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/isi/barabasi-vespignani-wasserman.isi
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/isi/savedrecs-barabasi.isi
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/isi/savedrecs-garfield.isi
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/isi/savedrecs-vespignani.isi
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/isi/savedrecs-wasserman.isi
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/TARL/
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/TARL/agingfunction.txt
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/TARL/iniscript.tarl
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/bio/
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/bio/FlyMINT.nwb
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/bio/TF_DNA_regulonDB.nwb
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/bio/WI5.nwb
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/bio/WormMint.nwb
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/bio/YeastMINT.nwb
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/conversionGraph.graphml.xml
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/florentine.nwb
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/friendster.graphml.xml
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/friendster.xgmml.xml
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/netsci06-conference.net
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/seiyu.graphml.xml
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/terror.graphml.xml
branches/tycho/deployment/org.cishell.reference.product/extra-files/sampledata/network/terror.xgmml.xml
branches/tycho/deployment/org.cishell.reference.product/root.properties
branches/tycho/deployment/releng/
Removed Paths:
-------------
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/extra-files/
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/about.gif
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/alt16.gif
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/alt32.gif
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/alt64.gif
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.icns
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.ico
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.xpm
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/database.jpg
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/datamanager_icon.gif
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/findandinstall.gif
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/grace.png
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/manage.gif
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/matrix.png
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/network.png
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/plot.png
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/product.ico
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/r.png
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/raster_image.jpg
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/table.png
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/text.png
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/tree.png
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/unknown.png
branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/vector_image.jpg
branches/tycho/deployment/org.cishell.reference.application/cishell.product
Modified: branches/tycho/clients/gui/gui-build/pom.xml
===================================================================
--- branches/tycho/clients/gui/gui-build/pom.xml 2010-11-22 08:29:50 UTC (rev 1176)
+++ branches/tycho/clients/gui/gui-build/pom.xml 2010-11-27 03:47:24 UTC (rev 1177)
@@ -11,6 +11,14 @@
</properties>
+ <parent>
+ <groupId>cishell</groupId>
+ <artifactId>lib-dependencies</artifactId>
+ <version>1.0.0</version>
+ <relativePath>../../../lib-dependencies/pom.xml</relativePath>
+ </parent>
+
+
<modules>
<module>../org.cishell.reference.gui.brand.cishell</module>
<module>../org.cishell.reference.gui.datamanager</module>
@@ -23,59 +31,4 @@
<module>../org.cishell.reference.gui.workspace</module>
</modules>
- <repositories>
- <repository>
- <id>ganymede</id>
- <layout>p2</layout>
- <url>http://download.eclipse.org/eclipse/updates/3.4</url>
- </repository>
- </repositories>
- <dependencies>
-<!-- <dependency>
- <groupId>org.eclipse.core</groupId>
- <artifactId>runtime</artifactId>
- <version>3.3.100-v20070530</version>
- </dependency>
- <dependency>
- <groupId>org.eclipse</groupId>
- <artifactId>ui</artifactId>
- <version>3.3.0-I20070614-0800</version>
- </dependency> -->
- <dependency>
- <groupId>cishell</groupId>
- <artifactId>org.cishell.reference</artifactId>
- <version>1.0.0</version>
- </dependency>
- <dependency>
- <groupId>cishell</groupId>
- <artifactId>org.cishell.framework</artifactId>
- <version>1.0.0</version>
- </dependency>
- </dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.sonatype.tycho</groupId>
- <artifactId>tycho-maven-plugin</artifactId>
- <version>${tycho-version}</version>
- <extensions>true</extensions>
- </plugin>
- <plugin>
- <groupId>org.sonatype.tycho</groupId>
- <artifactId>target-platform-configuration</artifactId>
- <version>${tycho-version}</version>
- <configuration>
- <resolver>p2</resolver>
- <pomDependencies>consider</pomDependencies>
- <environments>
- <environment>
- <os>linux</os>
- <ws>gtk</ws>
- <arch>x86</arch>
- </environment>
- </environments>
- </configuration>
- </plugin>
- </plugins>
- </build>
</project>
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/about.gif
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/alt16.gif
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/alt32.gif
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/alt64.gif
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.icns
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.ico
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.xpm
===================================================================
--- branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.xpm 2010-11-22 08:29:50 UTC (rev 1176)
+++ branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/cishell.xpm 2010-11-27 03:47:24 UTC (rev 1177)
@@ -1,294 +0,0 @@
-/* XPM */
-static char * cishell_xpm[] = {
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-". . . . . . . . . . . . . . . @ @ @ @ @ 0 9 a 1 1 7 b 7 6 6 6 6 c d c 5 e b 7 1 f } 9 0 @ @ ; ; @ g . . . . . . . . . . . . . . ",
-". . . . . . . . . . . . + @ @ h $ i h h j k l m 7 e 5 5 4 n o p p 6 6 6 d 5 e 7 a a a q r @ s t @ @ @ + . . . . . . . . . . . . ",
-". . . . . . . . . . . . g @ # u v $ @ = [ a 1 w x b 6 6 p y z A z z B p p c C D 7 1 f [ E h , F q > ; g . . . . . . . . . . . . ",
-". . . . . . . . . . @ @ ; G H I u ; J K L w 7 3 5 M M 6 N z O P P Q z A R M p 2 3 w l k S T @ U m 9 t @ @ + . . . . . . . . . . ",
-". . . . . . . . . + @ @ V W X Y @ h Z ` 8 .2 2 5 d R N z ........+.P O z p d 4 e 7 1 l a @.h # #.} $.%.h ; + . . . . . . . . . ",
-". . . . . . . . g @ ; &.*.=.-.;.@ = >.a } l D 6 6 n A ,.O X =.X '...I =.z B 6 d 5 7 1 } ).!.~.+ t ^ ).[ {.; @ + . . . . . . . . ",
-". . . . . . . . @ r ].^.R z u r > S /.(.a 1 2 7 M y O O ..+.X X X _.=.,.,.z B d C 2 1 a a (.S :.# U w <.[.}.# ; + . . . . . . . ",
-". . . . . . + @ @ = ~ b |.1.# r 2.3.4.} 1 1 2 b 6 B O ,.=...5.X 6.X 5...,.z R M 2 7.f 8 a ` 8.9.@ @ 0.m .[ a.; @ . . . . . . . ",
-". . . . . . @ ; ; = E $ T g @ b.c.d.4.).w 7 D 6 d A e.f...X X g.g._.I ..f.N p 6 b x w f } 3.d.h.i.r r # b.% j.@ ; @ + . . . . . ",
-". . . . . g @ @ @ @ @ @ h k.h k.9.l.a (.a 7 2 2 6 o z f.P '.X X 6._.X P O N o p b e 1 k ).4.l.m.k.@ # r @ @ r @ @ g g . . . . . ",
-". . . . . @ h , s a.2.n.o.p.q.@ h 2.[.a } 1 1 5 M p B z P ....'.X +.=.P f.y 6 c 5 3 w f L [.r.k.@ i.s.t.n.q u.s v.@ @ + . . . . ",
-". . . + @ @ s !.4.L a | f 8 m {.h @ 9.>.8 w 7 3 4 p B z Q +.+.P +.f.,.O z B 6 4 e 3 a a a j @ @ w.F l k k a k ).` u.; @ + . . . ",
-". . . . ; k.9 a k f | 7 w 7 1 x.y.r r Z . .1 2 6 4 p R z N f.,.,.f.z z A n d 5 3 7 w 8 r.> @ , z.1 1 1 1 <.f a 3.A.B.; . . . . ",
-". . . @ @ C.8 f w 7 7 b 2 b b 3 x.D.. @ E.F.f w 3 b M 6 6 z z z z N G.B R M 6 2 1 1 f s.H.r $ z.e 5 4 5 3 7 1 1 k a {.@ @ . . . ",
-". . . @ > 0.a | 7 2 e p n p p 6 6 I.J.h k.K.l m 2 e 3 d o 6 A y y 6 R 6 e C 7 7 7 l s.$ @ - L.3 b c 6 6 p 4 5 7 1 a F J ; . . . ",
-". . . @ t m .7 b 6 c R A p M M 4 4 ^ E h > 0.a 1 2 2 b c 6 c n o d c 6 2 2 1 w 1 ! 0 ; > M.6 M 6 M o o p n d 4 D .a N.@ + . . ",
-". . . @ @.l 7 e 6 n B z O O N B R 6 4 ^ : h $ ! F. .7 2 2 2 6 6 3 6 C 7 2 w w f O.t @ :.( 3 4 6 N z Q O z z p 6 6 D w ) @ g . . ",
-". . . # P.} 2 e p B Q ......+.f.N p 6 b Q., @ : O. .R.R.] x.R.C x.b b R.] ] .S.= ; k.K.e c o A f.P I =.P N A M 6 7 l O.0 + . . ",
-". . . v.S.1 3 c o z f.I X X X ..z A M 5 7 #.> @ v.~.s N.N.i i = % E E = N.%.~.T.@ @ }.C b 6 R O P ..U...V.P N p M e 1 W.E g . . ",
-". + . N.m w e 6 A z =.=._.X X '.O z n b x w q h ; g ; ; @ @ @ @ @ @ ; @ @ @ ; @ @ : m 7 2 6 z O X X _.X 6...z R 6 c 1 F.X.+ . . ",
-". . . ' .7 e 4 B Q f.X X _.6...+.z R d w ] N.@ b.X.Y._ U Z._ {._ _ Z._ _ ' a.: ; B.`.1 5 n y f.f.X X g.X ..P B c 5 D | @.g . . ",
-". + + +8 .2 c p z Q =.X X X +.O B p 6 1 .+; k.++a 8 1 1 1 2 2 @+7 1 1 } 8 (.S b.+ D.] e n R N =.X 5.X X ,.O y 6 6 1 f #++ . . ",
-". . . r.f 1 1 6 n z G.,.P P f.f.z A 5 3 ! $ @ Y.a } 1 1 7 e 3 3 2 2 e 3 1 w 8 a n.; g $+2 6 6 B z f.+.P ,.f.G.o 5 D 1 8 s.g . . ",
-". . . r.L F.w 2 c 6 z z Q O z z 6 6 5 b D.; i.F a m 3 2 5 4 6 6 c 6 5 b 5 7 | f [ ~.+ b.^ 4 6 p z z Q f.z z p 6 6 3 f a p.+ . . ",
-". . . %+3.f 1 1 6 n n R R z B R o 5 2 ( k.@ n.} | x e 4 6 p M M p n n p C e 7 l f K k.r _ b 2 n n B B B B 6 6 2 2 w 8 3.o.g . . ",
-". + + 2.d.(.a <.2 2 5 c d d d 6 e 3 &+, h = >.f w 2 4 c o y z z N N A M 6 4 e 7 l a +h @ P.2 6 5 d n M n e 2 w 7 | L 3.*++ . . ",
-". . . u.d.` ).a a 1 7 3 e e 2 7 3 w q @ J p.| .b b n p B z f.P ,.e.O z M p 4 7 7 } S.w.h = W.w 2 e 3 C 5 3 7 7 a a 3.d.q g . . ",
-". . + s l.d.d.(.8 <.1 1 1 1 w w 1 `.$ @ +a w 7 e 6 n B ,.P ..I =.'.P Q R 6 c 2 7 f a t.@ r K.a F.1 w 1 1 w f } (.a d.d.a.+ . . ",
-". . . v.=+d.3.3.a a k l m -+] W.;+>+@ , $.k 1 7 b 4 R z ,.P X V._.I X O z A 6 e 7 <.} ` %.@ < S.f f f | <.a ).4.3.d.d.=+N.g . . ",
-". . + > %+*+m.m.2.a.a.J.%.s ~.N.,+@ r #+).k | 2 6 6 p z P =.X _._.'.X ,.O A 6 e 7 a ).3.'+:.h T.u.{.2.@.r.r.o.p.)+'+!+)+b.+ . . ",
-". . . @ @ # > @ @ @ @ + + + @ @ h r B.!.` a 1 w 2 M A O P ..6.6._.X ..P f.B d 5 7 1 a (.h.b.@ r h @ + @ . r @ @ @ @ r @ @ g . . ",
-". . . @ @ ,+T.T.s %.q.' {. +@.j }.# + u.` k 1 7 3 6 B N P X X 5.5.X =.O N R 6 e D f k [ u.h k.s %.>+= T.T.t t t i.b.b.r @ + . . ",
-". . + @ b.'+` d.` 3.a ).} f f } a U h r E.a F.w e 4 n R z f.....'.=...O B 6 c e 7 <.a %+; @ ~+l k .l F.m [ $.c.!+!+)+0 @ g . . ",
-". . g @ @ *+d.3.3.).<. .w 1 1 7 w x.q.@ > t. .1 2 c 6 R z Q +.P f.O P G.B 6 b 2 1 8 t.:.r _ R.1 w 7 7 7 .} f 3.3.d.p.> @ + . . ",
-". . . r > C.` 4.k 1 7 2 b b c 2 5 7 ~ t h $ O.1 1 e 5 6 p B z z O O B B n 4 5 1 m O.0 ; E { 2 e 4 e e 3 2 1 l } 3.a 9.h @ . . . ",
-". . + + r > S.a F.7 2 6 M n n 6 6 6 2 L.T h j.W.1 7 2 4 n A B B B R 6 p 5 e 3 w ] N.@ B.z.7 b 6 6 6 M c d e 7 f ).-+i.; + . . . ",
-". . . + @ @ 2.w 2 e d M R B B o M c e e .+k.@ }.m 1 D 7 6 6 d d 6 d d b 2 7 1 m }.; :.( 3 5 M M p N B R 6 6 5 7 1 ++@ @ . . . . ",
-". . . . ; ; : { e 6 6 B N f.f.e.N R 6 5 x.Z.; :.{+f w w 1 2 e e 5 e 2 3 7 w 1 ) H.@ {.b 6 6 p B z Q f.Q G.6 c b ]+= @ @ . . . . ",
-". . . . + @ @ .+b d A O +.P ^+=.Q z M 6 2 ] /+@ J S.f 1 w 1 7 7 7 7 w 1 <. .S.b.@ % b e e p z ,.......+.N z p 4 (+H.; . . . . . ",
-". . . . . @ + ;.6 B O P X '.X V...O p 6 4 7 ! $ @ w._ ' Y.X.y.' ' ' X.X.y.Z.w.@ i.! 1 b c y O =.X 6.6.X f.B p 6 i @ @ . . . . . ",
-". . . . + g + r _+R f.P '.X X X V.+.A n 5 7 a +r @ @ @ . ; + @ @ + g ; @ @ @ ; @.8 D 5 6 B P ..5.g.X ..=.z M :+:.@ + . . . . . ",
-". . . . . . + + : <+z +.X _.X X ..P N 6 5 D m = ; 0 s a.X.' X.X.q.X.X.X.X.%.b.@ %.R.7 e n A P ..X _._.I =.z [+>+h . . . . . . . ",
-". . . . . . . g @ }+z Q P ..5...+.z 6 4 3 7 K.k.@ #+k -+F.m m 3 m m m . .[.++@ k.) 1 3 p B z ......V.=.f.z M.r @ + . . . . . . ",
-". . . . . + + + + ;.|+z P ,.P ,.f.z p c 2 1+b.; t -+} 1 m 3 7 2 e D 7 1 1 f a ,+@ , ] 7 5 R B ,.+...f.O O <+V @ g . . . . . . . ",
-". . . . . . . . + g u y B z z z y o 4 2 3 {.; > 0.a F.7 2 e 5 4 4 d e b D F.l 0.J + 2+7 3 c p y z z z z B 3+@ ; + . . . . . . . ",
-". . . . . . + . + + # 1.6 p p n 6 6 3 7 Q.$ @ Y.F.1 w e 4 6 6 n p M d 6 e 3 f ._ ; - z.7 3 c 6 p R R 6 |+> @ + . . . . . . . . ",
-". . . . . . . . . @ ; i ^.4 c 6 2 D 7 m J.+ $ K 1 3 4 c p o A z y B p M 6 e 7 1 F 0 @ ' 1 D 3 e 4 c c |.].r @ . . . . . . . . . ",
-". . . . . . . . . + @ + 4+3 x 7 7 1 | s.k.+ j .1 3 4 n y Q ,.O O P B A p c b 1 1 j @ # 0.w w 7 7 3 2 5+h ; . . . . . . . . . . ",
-". . . . . . . . . . + g B.#.l | f l [ % @ , W.| D 4 6 R z O ....'...,.z n 6 5 2 l [ , @ = W.a l a 1 ! b.@ + + . . . . . . . . . ",
-". . . . . . . . . . + g + , F $.$.$.r.@ @ #+a 1 7 e n z P X 5.X X I X f.A o 5 2 1 k #+> @ ++$.S.S.S.6+@ @ + . . . . . . . . . . ",
-". . . . . . . . . . . + g g k.@ h @ r h = >.L 1 2 6 p z f.P X X _.5.=.,.N 6 6 3 1 a ` ~.r @ h k.k.# ; ; . . . . . . . . . . . . ",
-". . . . . . . . . . . + + @ h @ # :.k.@ w.S.l f 7 4 o z ,.=.X 6._.5...O z n c b | l $.,+h # k.# @ @ @ @ . . . . . . . . . . . . ",
-". . . . . . . . . . . . . + @ h D.P.7+> + a.8 .w 5 6 B O ,.V.X X ..X P A p 6 x 1 } u.@ # 8+9+u h @ g . . . . . . . . . . . . . ",
-". . . . . . . . . . . . . . g g # ) 3 0+k.k.#.1 7 5 d y z O =.P ^+Q z N n 4 e 7 .0.k.h 3+O :+:.; @ . . . . . . . . . . . . . . ",
-". . . . . . . . . . . . . . + @ @ T ++W.,+@ ,+W. .D 6 n R z z N O O N R p 4 3 w 1+= @ w.<+M.a+; @ . . . . . . . . . . . . . . . ",
-". . . . . . . . . . . . . . . . ; . @ q p.< + ~+7 w 2 4 p R y z z y 6 n 6 2 3 1 @.; k.( b+# @ @ + . . . . . . . . . . . . . . . ",
-". . . . . . . . . . . . . . . + + @ # k.X.~.@ > 0.1 7 3 b d n o n 6 M 6 2 D .c+$ @ %.' r @ @ . . . . . . . . . . . . . . . . . ",
-". . . . . . . . . . . . . . . . . + + + @ > r @ = .1 D 2 e C c 5 3 2 1 7 w a = @ ; b.h ; g + . . . . . . . . . . . . . . . . . ",
-". . . . . . . . . . . . . . . . + . + + @ h @ r @ n.a 1 .f 2 7 D 2 w w f a d+@ ; @ + @ + . . . . . . . . . . . . . . . . . . . ",
-". . . . . . . . . . . . . . . . . . . . + + @ @ h a+j `.S.1+] W.W.W.W.1+O.K.i.@ @ ; g + . . . . . . . . . . . . . . . . . . . . ",
-". . . . . . . . . . . . . . . . . . . . . . . g @ + r k.% = = E = E = t > @ @ @ g + + . . . . . . . . . . . . . . . . . . . . . "};
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/database.jpg
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/datamanager_icon.gif
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/findandinstall.gif
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/grace.png
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/manage.gif
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/matrix.png
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/network.png
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/plot.png
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/product.ico
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/r.png
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/raster_image.jpg
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/table.png
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/text.png
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/tree.png
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/unknown.png
===================================================================
(Binary files differ)
Deleted: branches/tycho/clients/gui/org.cishell.reference.gui.brand.cishell/icons/vector_image.jpg
===================================================================
(Binary files differ)
Modified: branches/tycho/core/core-build/pom.xml
===================================================================
--- branches/tycho/core/core-build/pom.xml 2010-11-22 08:29:50 UTC (rev 1176)
+++ branches/tycho/core/core-build/pom.xml 2010-11-27 03:47:24 UTC (rev 1177)
@@ -20,10 +20,10 @@
</parent>
- <scm>
+<!-- <scm>
<connection>scm:svn:http://cishell.svn.sourceforge.net/svnroot/cishell/branches/tycho/core</connection>
<developerConnection>scm:svn:https://cishell.svn.sourceforge.net/svnroot/cishell/branches/tycho/core</developerConnection>
- </scm>
+ </scm> -->
<properties>
<tycho-version>0.10.0</tycho-version>
@@ -68,14 +68,6 @@
</dependencies> -->
- <repositories>
- <repository>
- <id>ganymede</id>
- <layout>p2</layout>
- <url>http://download.eclipse.org/eclipse/updates/3.4</url>
- </repository>
- </repositories>
-
<build>
<plugins>
<plugin>
Modified: branches/tycho/deployment/deployment-parent/pom.xml
===================================================================
--- branches/tycho/deployment/deployment-parent/pom.xml 2010-11-22 08:29:50 UTC (rev 1176)
+++ branches/tycho/deployment/deployment-parent/pom.xml 2010-11-27 03:47:24 UTC (rev 1177)
@@ -26,20 +26,13 @@
<modules>
<module>../org.cishell.feature</module>
<module>../org.cishell.reference.gui.feature</module>
- <module>../org.cishell.reference.product</module>
+ <module>../org.cishell.reference.brand.feature</module>
+ <module>../org.cishell.reference.application</module>
<module>../../clients/gui/gui-build</module>
<module>../../core/core-build</module>
</modules>
- <repositories>
- <repository>
- <id>ganymede</id>
- <layout>p2</layout>
- <url>http://download.eclipse.org/eclipse/updates/3.4</url>
- </repository>
- </repositories>
-
<build>
<plugins>
<plugin>
Deleted: branches/tycho/deployment/org.cishell.reference.application/cishell.product
===================================================================
--- branches/tycho/deployment/org.cishell.reference.product/cishell.product 2010-11-22 06:03:33 UTC (rev 1175)
+++ branches/tycho/deployment/org.cishell.reference.application/cishell.product 2010-11-27 03:47:24 UTC (rev 1177)
@@ -1,36 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?pde version="3.5"?>
-
-<product name="CIShell" uid="cishell.product.id" id="cishell.product" application="cishell.application" version="1.0.0" useFeatures="true" includeLaunchers="true">
-
- <configIni use="default">
- </configIni>
-
- <launcherArgs>
- </launcherArgs>
-
- <plugins>
- </plugins>
-
- <features>
- <feature id="org.cishell.feature" version="0.0.0"/>
- <feature id="org.cishell.reference.gui.feature" version="0.0.0"/>
- <feature id="org.eclipse.rcp" version="0.0.0"/>
- <feature id="org.eclipse.equinox.p2.user.ui" version="0.0.0"/>
- </features>
-
- <configurations>
- <plugin id="org.eclipse.core.runtime" autoStart="true" startLevel="4" />
- <plugin id="org.eclipse.equinox.common" autoStart="true" startLevel="2" />
- <plugin id="org.eclipse.equinox.ds" autoStart="true" startLevel="2" />
- <plugin id="org.eclipse.equinox.p2.reconciler.dropins" autoStart="true" startLevel="4" />
- <plugin id="org.eclipse.equinox.simpleconfigurator" autoStart="true" startLevel="1" />
-
- <!-- Disable update manager. It seems as if this could be achieved by the first line, but in
- fact the second line sets reconcile to false (see org.eclipse.equinox.p2.publisher.eclipse.ConfigCUsAction#publishBundleCUs) -->
- <property name="org.eclipse.update.reconcile" value="false" />
- <plugin id="org.eclipse.update.configurator" autoStart="true" startLevel="4"/>
-
- </configurations>
-
-</product>
Added: branches/tycho/deployment/org.cishell.reference.application/extra-files/configuration/config.ini.bak
===================================================================
--- branches/tycho/deployment/org.cishell.reference.application/extra-files/configuration/config.ini.bak (rev 0)
+++ branches/tycho/deployment/org.cishell.reference.application/extra-files/configuration/config.ini.bak 2010-11-27 03:47:24 UTC (rev 1177)
@@ -0,0 +1,6 @@
+#Product Runtime Configuration File
+
+osgi.splashPath=platform:/base/plugins/org.cishell.reference.gui.brand.cishell
+eclipse.product=org.cishell.reference.gui.brand.cishell.cishell
+osgi.bundles=org.eclipse.equinox.common@2:start,org.eclipse.update.configurator@3:start,org.eclipse.core.runtime@start,org.eclipse.equinox.ds@3:start,org.eclipse.equinox.log@3:start,org.eclipse.equinox.metatype@3:start,org.eclipse.equinox.cm@3:start,org.eclipse.equinox.event@3:start,org.cishell.service.autostart@4:start
+osgi.bundles.defaultStartLevel=4
\ No newline at end of file
Added: branches/tycho/deployment/org.cishell.reference.application/extra-files/configuration/default_menu.xml
===================================================================
--- branches/tycho/deployment/org.cishell.reference.application/extra-files/configuration/default_menu.xml (rev 0)
+++ branches/tycho/deployment/org.cishell.reference.application/extra-files/configuration/default_menu.xml 2010-11-27 03:47:24 UTC (rev 1177)
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- <?xml version="1.0" encoding="ISO-8859-1" ?> -->
+<menu_layout>
+ <top_menu name="File">
+ <menu name="Load..." pid= "org.cishell.reference.gui.persistence.load.FileLoadAlgorithm "/>
+ <menu type="break"/>
+ <menu name="Save..." pid= "org.cishell.reference.gui.persistence.save.Save"/>
+ <menu type="break"/>
+ <menu name="View..." pid= "org.cishell.reference.gui.persistence.view.FileView"/>
+ <menu name="View With..." pid= "org.cishell.reference.gui.persistence.viewwith.FileViewWith"/>
+ <menu type="break"/>
+ <menu type="break"/>
+ <menu name="Exit" type="preserved"/>
+ </top_menu>
+
+ <top_menu name="Tools">
+ <menu name="Scheduler" pid=""/>
+ </top_menu>
+
+ <top_menu name="Help">
+ <menu name="Update" pid=""/>
+ <menu name="Manage Configuration" pid=""/>
+ </top_menu>
+</menu_layout>
Added: branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-apache-commons-collections.txt
===================================================================
--- branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-apache-commons-collections.txt (rev 0)
+++ branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-apache-commons-collections.txt 2010-11-27 03:47:24 UTC (rev 1177)
@@ -0,0 +1,202 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
+ the copyright owner that is granting the License.
+
+ "Legal Entity" shall mean the union of the acting entity and all
+ other entities that control, are controlled by, or are under common
+ control with that entity. For the purposes of this definition,
+ "control" means (i) the power, direct or indirect, to cause the
+ direction or management of such entity, whether by contract or
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ outstanding shares, or (iii) beneficial ownership of such entity.
+
+ "You" (or "Your") shall mean an individual or Legal Entity
+ exercising permissions granted by this License.
+
+ "Source" form shall mean the preferred form for making modifications,
+ including but not limited to software source code, documentation
+ source, and configuration files.
+
+ "Object" form shall mean any form resulting from mechanical
+ transformation or translation of a Source form, including but
+ not limited to compiled object code, generated documentation,
+ and conversions to other media types.
+
+ "Work" shall mean the work of authorship, whether in Source or
+ Object form, made available under the License, as indicated by a
+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
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Added: branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-cishell.txt
===================================================================
--- branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-cishell.txt (rev 0)
+++ branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-cishell.txt 2010-11-27 03:47:24 UTC (rev 1177)
@@ -0,0 +1,20 @@
+CIShell: Cyberinfrastructure Shell
+Copyright 2005 Indiana University
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+implied. See the License for the specific language governing
+permissions and limitations under the License.
+
+Project Contacts:
+Bruce Herr (bh...@bh...)
+Weixia Huang (hu...@in...)
+Shashikant Penumarthy (sp...@in...)
+Dr. Katy Borner (ka...@in...)
Added: branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-colt.txt
===================================================================
--- branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-colt.txt (rev 0)
+++ branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-colt.txt 2010-11-27 03:47:24 UTC (rev 1177)
@@ -0,0 +1,10 @@
+ Packages cern.colt* , cern.jet*, cern.clhep
+
+Copyright (c) 1999 CERN - European Organization for Nuclear Research.
+
+Permission to use, copy, modify, distribute and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. CERN makes no representations about the suitability of this software for any purpose. It is provided "as is" without expressed or implied warranty.
+
+ Packages hep.aida.*
+
+Written by Pavel Binko, Dino Ferrero Merlino, Wolfgang Hoschek, Tony Johnson, Andreas Pfeiffer, and others. Check the FreeHEP home page for more info. Permission to use and/or redistribute this work is granted under the terms of the LGPL License, with the exception that any usage related to military applications is expressly forbidden. The software and documentation made available under the terms of this license are provided with no warranty.
+
Added: branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-jung.txt
===================================================================
--- branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-jung.txt (rev 0)
+++ branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-jung.txt 2010-11-27 03:47:24 UTC (rev 1177)
@@ -0,0 +1 @@
+BSD License
Added: branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-knopflerfish.txt
===================================================================
--- branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-knopflerfish.txt (rev 0)
+++ branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-knopflerfish.txt 2010-11-27 03:47:24 UTC (rev 1177)
@@ -0,0 +1,35 @@
+/*
+ * Copyright (c) 2003-2006, KNOPFLERFISH project
+ * All rights reserved.
+ *
+ * http://www.knopflerfish.org/license.html
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions and the following
+ * disclaimer in the documentation and/or other materials
+ * provided with the distribution.
+ *
+ * - Neither the name of the KNOPFLERFISH project nor the names of its
+ * contributors may be used to endorse or promote products derived
+ * from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ * COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ * OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
Added: branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-prefuse.txt
===================================================================
--- branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-prefuse.txt (rev 0)
+++ branches/tycho/deployment/org.cishell.reference.application/extra-files/licenses/license-prefuse.txt 2010-11-27 03:47:24 UTC (rev 1177)
@@ -0,0 +1,35 @@
+
+ Copyright (c) 2004, 2005 Regents of the University of California.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+ 3. All advertising materials mentioning features or use of this software
+ must display the following acknowledgement:
+
+ This product includes software developed by the Group for User
+ Interface Research at the University of California at Berkeley.
+
+ 4. The name of the University may not be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
Added: branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/isi/barabasi-vespignani-wasserman.isi
===================================================================
--- branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/isi/barabasi-vespignani-wasserman.isi (rev 0)
+++ branches/tycho/deployment/org.cishell.reference.application/extra-files/sampledata/isi/barabasi-vespignani-wasserman.isi 2010-11-27 03:47:24 UTC (rev 1177)
@@ -0,0 +1,19929 @@
+FN ISI Export Format
+VR 1.0
+PT J
+AU Wuchty, S
+ Barabasi, AL
+ Ferdig, MT
+TI Stable evolutionary signal in a Yeast protein interaction network
+SO BMC EVOLUTIONARY BIOLOGY
+LA English
+DT Article
+ID SACCHAROMYCES-CEREVISIAE; FUNCTIONAL MODULES; INTERACTION MAP; CELLULAR
+ NETWORKS; COMPLEX NETWORKS; IDENTIFICATION; ORGANIZATION; ORTHOLOGS;
+ PATTERNS; DATABASE
+AB Background: The recently emerged protein interaction network paradigm
+ can provide novel and important insights into the innerworkings of a
+ cell. Yet, the heavy burden of both false positive and false negative
+ protein-protein interaction data casts doubt on the broader usefulness
+ of these interaction sets. Approaches focusing on one-protein-at-a-time
+ have been powerfully employed to demonstrate the high degree of
+ conservation of proteins participating in numerous interactions; here,
+ we expand his 'node' focused paradigm to investigate the relative
+ persistence of 'link' based evolutionary signals in a protein
+ interaction network of S. cerevisiae and point out the value of this
+ relatively untapped source of information.
+ Results: The trend for highly connected proteins to be preferably
+ conserved in evolution is stable, even in the context of tremendous
+ noise in the underlying protein interactions as well as in the
+ assignment of orthology among five higher eukaryotes. We find that
+ local clustering around interactions correlates with preferred
+ evolutionary conservation of the participating proteins; furthermore
+ the correlation between high local clustering and evolutionary
+ conservation is accompanied by a stable elevated degree of coexpression
+ of the interacting proteins. We use this conserved interaction data,
+ combined with P. falciparum /Yeast orthologs, as proof-of-principle
+ that high-order network topology can be used comparatively to deduce
+ local network structure in non-model organisms.
+ Conclusion: High local clustering is a criterion for the reliability of
+ an interaction and coincides with preferred evolutionary conservation
+ and significant coexpression. These strong and stable correlations
+ indicate that evolutionary units go beyond a single protein to include
+ the interactions among them. In particular, the stability of these
+ signals in the face of extreme noise suggests that empirical protein
+ interaction data can be integrated with orthologous clustering around
+ these protein interactions to reliably infer local network structures
+ in non-model organisms.
+C1 Northwestern Univ, NW Inst Complex, Evanston, IL 60202 USA.
+ Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA.
+ Univ Notre Dame, Dept Biol, Notre Dame, IN 46556 USA.
+RP Wuchty, S, Northwestern Univ, NW Inst Complex, Chambers Hall,600 Foster
+ St, Evanston, IL 60202 USA.
+EM s-w...@no...
+ al...@nd...
+ mf...@nd...
+CR ALBERT R, 2000, NATURE, V406, P378
+ ALBERT R, 2002, REV MOD PHYS, V74, P47
+ BABU MM, 2004, CURR OPIN STRUC BIOL, V14, P283
+ BARABAI A, 2004, NATURE REV GEN, P101
+ BARABASI AL, 1999, SCIENCE, V286, P509
+ BORK P, 2004, CURR OPIN STRUC BIOL, V14, P292
+ BOZDEC...
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