debian/0000755000000000000000000000000012216112561007163 5ustar debian/control0000644000000000000000000000252512213564365010604 0ustar Source: treeview Section: contrib/science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Thorsten Alteholz Build-Depends: debhelper (>= 9), ant, default-jdk, libnanoxml2-java, libcommons-configuration-java, libcommons-lang-java, libxerces2-java, docbook-xsl, docbook-to-man, xsltproc, fop, libservlet3.0-java Standards-Version: 3.9.4 Homepage: http://jtreeview.sourceforge.net Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/treeview/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/treeview/trunk/ Package: treeview Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre, libnanoxml2-java, libcommons-configuration-java, libcommons-lang-java Recommends: cluster3 Suggests: mapletree, smile Description: Java re-implementation of Michael Eisen's TreeView TreeView creates a matrix-like display of expression data, known as Eisen clustering. The original implementation was a Windows program named TreeView by Michael Eisen. This TreeView package, sometimes also referred to as jTreeView, was rewritten in Java under a free license. . Java TreeView is an extensible viewer for microarray data in PCL or CDT format. debian/treeview.install0000644000000000000000000000025412136235040012405 0ustar debian/scripts/treeview usr/bin TreeView.jar usr/share/treeview plugins/* usr/share/treeview/plugins static/images usr/share/treeview static/coordinates usr/share/treeview debian/copyright0000644000000000000000000001100412136457521011123 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: treeview Source: http://treeview.sourceforge.net/ Files: * Copyright: 2001-2003 Alok Saldanha License: GPL-2 Files: src/LinkedView.java Copyright: 2001-2003 Alok Saldanha 2013 Alex Segal, Lawrence Berkeley Lab License: GPL-2 Files: src/edu/* Copyright: 2001-2003 Alok Saldanha 2013 Alex Segal, Lawrence Berkeley Lab License: GPL-2 Files: edu/stanford/genetics/treeview/NatField.java Copyright: 1997 Rob Arthan, Lemma 1 Ltd. 2001-2003 Alok Saldanha 2013 Alex Segal, Lawrence Berkeley Lab License: GPL-2 Files: com/gurge/amd/Quantize.java Copyright: 2000 Adam Doppelt, E. I. du Pont de Nemours and Company License: ImageMagick Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files ("ImageMagick"), to deal in ImageMagick without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of ImageMagick, and to permit persons to whom the ImageMagick is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of ImageMagick. . The software is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall E. I. du Pont de Nemours and Company be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with ImageMagick or the use or other dealings in ImageMagick. . Except as contained in this notice, the name of the E. I. du Pont de Nemours and Company shall not be used in advertising or otherwise to promote the sale, use or other dealings in ImageMagick without prior written authorization from the E. I. du Pont de Nemours and Company. Files: edu/stanford/genetics/treeview/QSortAlgorithm.java Copyright: 1994-1995 James Gosling, Sun Microsystems, Inc. License: SUN Permission to use, copy, modify, and distribute this software and its documentation for NON-COMMERCIAL or COMMERCIAL purposes and without fee is hereby granted. Please refer to the file http://java.sun.com/copy_trademarks.html for further important copyright and trademark information and to http://java.sun.com/licensing.html for further important licensing information for the Java (tm) Technology. . SUN MAKES NO REPRESENTATIONS OR WARRANTIES ABOUT THE SUITABILITY OF THE SOFTWARE, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. SUN SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THIS SOFTWARE OR ITS DERIVATIVES. . THIS SOFTWARE IS NOT DESIGNED OR INTENDED FOR USE OR RESALE AS ON-LINE CONTROL EQUIPMENT IN HAZARDOUS ENVIRONMENTS REQUIRING FAIL-SAFE PERFORMANCE, SUCH AS IN THE OPERATION OF NUCLEAR FACILITIES, AIRCRAFT NAVIGATION OR COMMUNICATION SYSTEMS, AIR TRAFFIC CONTROL, DIRECT LIFE SUPPORT MACHINES, OR WEAPONS SYSTEMS, IN WHICH THE FAILURE OF THE SOFTWARE COULD LEAD DIRECTLY TO DEATH, PERSONAL INJURY, OR SEVERE PHYSICAL OR ENVIRONMENTAL DAMAGE ("HIGH RISK ACTIVITIES"). SUN SPECIFICALLY DISCLAIMS ANY EXPRESS OR IMPLIED WARRANTY OF FITNESS FOR HIGH RISK ACTIVITIES. Files: debian/* Copyright: 2004 Steffen Moeller 2013 Thorsten Alteholz License: GPL-2 License: GPL-2 This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 dated June, 1991. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. debian/changelog0000644000000000000000000000302412215774352011047 0ustar treeview (1.1.6.4+dfsg-1) unstable; urgency=low * New upstream release. -- Thorsten Alteholz Tue, 17 Sep 2013 18:00:00 +0200 treeview (1.1.6.3+dfsg-1) unstable; urgency=low * New upstream release. * debian/rules: tidy up a bit * debian/control: change VCS*-lines according to lintian -- Thorsten Alteholz Fri, 28 Jun 2013 18:00:00 +0200 treeview (1.1.6.2+dfsg-1) unstable; urgency=low * Initial release (Closes: #243771) [ Thorsten Alteholz ] * debian/watch: watch file added * debian/rules: target get-orig-source added * debian/control: debhelper 9 * debian/control: standards version 3.9.4 (no other changes) * debian/control: vcs fields added * debian/control: team maintenance * new upstream release: 1.1.6.2 [ Steffen Moeller ] * New upstream release. [ Andreas Tille ] * debian/source/format: 3.0 (quilt) * Added myself to Uploaders -- Thorsten Alteholz Fri, 26 Apr 2013 18:00:00 +0200 treeview (1.0.5-0.3) UNRELEASED; urgency=low * lintian clean -- Steffen Moeller Wed, 14 Apr 2004 23:02:54 +0200 treeview (1.0.5-0.2) UNRELEASED; urgency=low * Added little man page. * Moved to contrib because of dependency to non-free Java. * Added build-dependency. -- Steffen Moeller Wed, 8 Apr 2004 12:02:54 +0200 treeview (1.0.5-0.1) UNRELEASED; urgency=low * Initial Release. -- Steffen Moeller Wed, 7 Apr 2004 22:02:54 +0200 debian/compat0000644000000000000000000000000212134310143010354 0ustar 9 debian/scripts/0000755000000000000000000000000012216112561010652 5ustar debian/scripts/treeview0000644000000000000000000000054312134343260012432 0ustar #!/bin/sh if [ -z $JAVA_HOME ]; then java=java else java=$JAVA_HOME/bin/java fi if [ -x /usr/share/treeview ]; then if [ -r /usr/share/treeview/TreeView.jar ]; then cd /usr/share/treeview && $java -jar TreeView.jar else echo "Could not find /usr/share/treeview/TreeView.jar" fi else echo "Could not find /usr/share/treeview directory." fi debian/treeview.sgml0000644000000000000000000000676612125621050011715 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> FIRSTNAME"> SURNAME"> April 7, 2004"> 1"> moeller@pzr.uni-rostock.de"> TREEVIEW"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2003 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; Presentation of Eisen-clustering &dhpackage; DESCRIPTION TreeView is the Java-based Linux variant of the well-known Windows program of Michael Eisen for the display of clusterings of DNA microarray expression data. This manual page was written for the &debian; distribution because the original program does not have a manual page. Instead, it has documentation in the &gnu; Info format; see below. SEE ALSO cluster3 (1), mapletree (1) http://jtreeview.sourceforge.net AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/watch0000644000000000000000000000017712134560462010227 0ustar version=3 opts=uversionmangle=s/r/\./g,dversionmangle=s/\+dfsg// \ http://sf.net/jtreeview/TreeView-([\d\.]+.*)-src\.tar\.gz debian/upstream0000644000000000000000000000062612136457522010764 0ustar Reference: Author: Alok J. Saldanha Title: Java Treeview -- extensible visualization of microarray data Journal: Bioinformatics Year: 2004 Volume: 20 Number: 17 Pages: 3246-3248 DOI: 10.1093/bioinformatics/bth349 PMID: 21653522 URL: http://bioinformatics.oxfordjournals.org/content/20/17/3246.abstract eprint: http://bioinformatics.oxfordjournals.org/content/20/17/3246.full.pdf+html debian/get-orig-source0000755000000000000000000000230712213564365012140 0ustar #!/bin/bash # bail out upon error set -e PACKAGE=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` TARDIR=../tarballs VERSION=`uscan --rename --verbose --force-download | grep "Newest version on remote site is .* local version is .*" | head -n 1 | sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"` echo "I: remote version $VERSION" RVERSION=`echo $VERSION|sed "s/\(.*\)\./\1r/"` echo "I: file version $RVERSION" mkdir -p $TARDIR cd $TARDIR UTAR="${PACKAGE}_${VERSION}.orig.tar.gz" echo "I: $UTAR" mv ../${UTAR} . tar -xzf ${UTAR} mv TreeView-${RVERSION}-src ${PACKAGE}_${VERSION}+dfsg.orig # .orig is requested by Developers Reference 3.4.4 6.7.8.2 cd ${PACKAGE}_${VERSION}+dfsg.orig # do some magic here # we do not need windows stuff here rm windows-installer.tar.gz rm lib/nanoxml-2.2.2.jar # these jars are only needed for mac osx rm compile_lib/jarbundler-1.8.1.jar rm compile_lib/xercesImpl.jar rm compile_lib/xml-apis.jar # not needed? rm src/edu/stanford/genetics/treeview/plugin/dendroview/dendroview.jar cd .. rm $UTAR GZIP="--best --no-name" tar czf ${PACKAGE}_${VERSION}+dfsg.orig.tar.gz ${PACKAGE}_${VERSION}+dfsg.orig rm -rf ${PACKAGE}_${VERSION}+dfsg.orig debian/docs0000644000000000000000000000001612125621050010030 0ustar debian/README debian/treeview.doc-base.programmer-guide0000644000000000000000000000073012136175443015672 0ustar Document: treeview-programmer-guide Title: Java TreeView Programmer Guide Author: Alok Saldanha Abstract: The manual presents an overview on the functionalities that GENtle contributes to the cloning process. Section: Science/Biology Format: pdf Files: /usr/share/doc/treeview/html/JTVProgrammerGuide/JTVProgrammerGuide.pdf.gz Format: html Files: /usr/share/doc/treeview/html/JTVProgrammerGuide/*.html Index: /usr/share/doc/treeview/html/JTVProgrammerGuide/index.html debian/menu0000644000000000000000000000016312135205102010044 0ustar ?package(treeview):needs="X11" section="Applications/Science/Biology" title="treeview" command="/usr/bin/treeview" debian/treeview.manpages0000644000000000000000000000001312135202336012524 0ustar treeview.1 debian/patches/0000755000000000000000000000000012216112561010612 5ustar debian/patches/series0000644000000000000000000000002012135215772012027 0ustar classpath.patch debian/patches/classpath.patch0000644000000000000000000000625312216033014013616 0ustar Description: do not use internal lib Author: Thorsten Alteholz Index: treeview_1.1.6.4+dfsg.orig/build.xml =================================================================== --- treeview_1.1.6.4+dfsg.orig.orig/build.xml 2013-09-17 12:56:26.000000000 +0200 +++ treeview_1.1.6.4+dfsg.orig/build.xml 2013-09-17 12:59:03.000000000 +0200 @@ -83,6 +83,9 @@ + + + @@ -211,7 +214,7 @@ excludes="edu/stanford/genetics/treeview/plugin/**"> - + @@ -226,7 +229,7 @@ excludes="*coordinates/*,edu/stanford/genetics/treeview/plugin/**,edu/stanford/genetics/treeview/reg/**"> - + @@ -242,7 +245,7 @@ - + @@ -337,51 +340,11 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + debian/README0000644000000000000000000000374412125621050010050 0ustar ######################################################################## # Treeview README file # # CONTENTS: # # 1) Description of files # 2) Cluster-3.0-OSX Integration # ######################################################################## 1) Description of files: APPLET: TreeView-X.X.X-applet.tar.gz working sample applet distribution - needs documentation! UNIX: TreeView-X.X.X-bin.tar.gz distribution for unix/linux/etc WINDOWS: TreeView-X.X.X-win.zip similar to .tar.gz, but easier to unpack on windows also includes setup.exe, an installer written by Michiel Jan Laurens de Hoon SOURCE: TreeView-X.X.X-src.tar.gz source distribution MAC OS X: TreeView-X.X.X-osx.dmg distribution for mac os x Mac OS 9: Instructions for Mac OS9: Unfortunately, i no longer have access to an OS9 machine, and can no longer easily build a new distro. Here's what you need to do in order to get the latest treeview running: 1) download and expand the TreeView-1.0.1-os9.sit file 2) download and expand the latest TreeView-X.X.X-bin.tar.gz file 3) copy over the TreeView.jar file to the 1.0.1-os9 folder, replacing the original. MANUAL: JTVUserManual-X.X.X.pdf manual in pdf format, if updated since the last one also available on the website, with the html version. ######################################################################## 2) Cluster-3.0-OSX-Integration The following is a brief description of how to get the "Launch Treeview" button of cluster 3.0 (see http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm) to work nicely on Mac OSX. 1) download the TreeView-X.X.X-bin.tar.gz file. This should unpack to make a TreeView-X.X.X-bin folder. Be sure not to get the TreeView-X.X.X-osx.dmg file by mistake. 2) Rename the TreeView-X.X.X-bin folder to TreeView 3) Move the TreeView folder to the Applications folder in the finder Double-clicking "Cluster" in the Applications folder, and then clicking the java treeview button should now work debian/treeview.docs0000644000000000000000000000002612136457522011677 0ustar doc/html appletStatic debian/treeview.doc-base.user-manual0000644000000000000000000000176312136175350014661 0ustar Document: treeview-user-manual Title: Java TreeView User Manual Author: Alok Saldanha Abstract: This user manual has three chapters. Each chapter has a purpose: - To assist the novice with installation - To document all features - To provide troubleshooting assistance New users should glance over the contents to see what the program has to offer, perhaps reading a section if it may be of interest. Familiar users may return if some errors arise, or if there is a feature they remember exists, but don't remember how to use. This manual may be partially out of date. It has not been fully checked since 1.0.7, please email the mailing lists or the project admins on jtreeview.sf.net if you notice a section that appears to be out of date. Section: Science/Biology Format: pdf Files: /usr/share/doc/treeview/html/JTVUserManual/JTVUserManual.pdf.gz Format: html Files: /usr/share/doc/treeview/html/JTVUserManual/*.html Index: /usr/share/doc/treeview/html/JTVUserManual/index.html debian/README.source0000644000000000000000000000066412136457521011361 0ustar treeview for Debian ------------------- The following files have been removed as it seems that they are not needed for a Debian package: # Debian version is used lib/nanoxml-2.2.2.jar # not needed for build src/edu/stanford/genetics/treeview/plugin/dendroview/dendroview.jar # only needed for os X compile_lib/jarbundler-1.8.1.jar compile_lib/xercesImpl.jar compile_lib/xml-apis.jar # only needed for windows windows-installer.tar.gz debian/dirs0000644000000000000000000000006212125621050010042 0ustar usr/bin usr/share/treeview usr/share/doc/treeview debian/rules0000755000000000000000000000103212213564365010251 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # GNU copyright 1997 to 1999 by Joey Hess. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ treeview.1: debian/treeview.sgml docbook-to-man $< > $@ override_dh_auto_build: treeview.1 dh_auto_build ant jar ant plugins (cd doc; export XSL=/usr/share/sgml/docbook/stylesheet/xsl/docbook-xsl; export FOP=/usr/bin; perl ./createAllDoc.pl) override_dh_auto_install: dh_auto_install get-orig-source: ./debian/get-orig-source debian/source/0000755000000000000000000000000012216112561010463 5ustar debian/source/format0000644000000000000000000000001412125621050011666 0ustar 3.0 (quilt)