[Debian-med-packaging] [SCM] igv branch, master, updated. upstream/1.4.2-7-gc0b6c3d

[Shaun Jackman]

The following commit has been merged in the master branch:
commit c0b6c3dfb12f6c09a4443db65353062d1b87b220
Author: Shaun Jackman <sjackman at gmail.com>
Date:   Wed Jun 23 23:33:08 2010 -0700

    * debian/bin/igv: Use java -classpath rather than java -jar. The
    latter doesn't seem to work for some unexplained reason.
    * debian/igv.1: Remove the mention of java -jar.
    * debian/copyright: Add sections for the jar files in lib.
    * build.xml: Extract the JAR files in lib.

diff --git a/debian/bin/igv b/debian/bin/igv
index 13e4b2a..c8373bf 100755
--- a/debian/bin/igv
+++ b/debian/bin/igv
@@ -1,3 +1,5 @@
 #!/bin/sh
 set -eu
-exec java -jar /usr/share/java/igv.jar "$@"
+p=/usr/share/java
+exec java -classpath "$p/igv.jar:$p/commons-math.jar:$p/concurrent.jar:$p/jargs.jar:$p/jhdf5.jar:$p/net.sourceforge.jlibeps.jar:$p/junit4.jar:$p/log4j-1.2.jar:$p/sam.jar:$p/swing-layout.jar" \
+	org.broad.igv.ui.IGVMainFrame "$@"
diff --git a/debian/copyright b/debian/copyright
index 4eb1172..6796e57 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -7,19 +7,31 @@ Copyright: 2009 The Broad Institute, Inc. and the Massachusetts Institute of Tec
 License: LGPL-2.1
  See `/usr/share/common-licenses/LGPL-2.1'.
 
+Files: src/org/j3d/io/EndianConverter.java
+Copyright: 2001, 2002 Dipl. Ing. P. Szawlowski
+License: LGPL-2.1
+ See `/usr/share/common-licenses/LGPL-2.1'.
+
 Files: src/org/broad/igv/tdf/LEDataInputStream.java
+ lib/ledatastream.jar
 Copyright 1998-2009 Roedy Green, Canadian Mind Products
 License: other
  This software may be copied and used freely for any purpose but
  military. For explanatory text see
  `http://mindprod.com/contact/nonmil.html'.
 
-Files: src/org/j3d/io/EndianConverter.java
-Copyright: 2001, 2002 Dipl. Ing. P. Szawlowski
-License: LGPL-2.1
- See `/usr/share/common-licenses/LGPL-2.1'.
+Files: lib/colt.jar
+Copyright: 1999 CERN - European Organization for Nuclear Research
+License: ISC
+ 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.
 
-Files: src/toolbarButtonGraphics/*
+Files: lib/jlfgr-1_0.jar
 Copyright: 2000 by Sun Microsystems, Inc.
 License: other
  Sun grants you ("Licensee") a non-exclusive,
@@ -62,6 +74,619 @@ License: other
  this Disclaimer to be otherwise enforceable in
  such jurisdiction.
 
+Files: lib/AbsoluteLayout.jar
+Copyright: 1997 - 2009 Sun Microsystems, Inc.
+License: CDDL or GPL-2 with classpath exception
+ See `/usr/share/common-licenses/GPL-2'.
+ .
+ "CLASSPATH" EXCEPTION TO THE GPL VERSION 2
+ .
+ Certain source files distributed by Sun Microsystems, Inc. are
+ subject to the following clarification and special exception to the
+ GPL Version 2, but only where Sun has expressly included in the
+ particular source file's header the words:
+ .
+ "Sun designates this particular file as subject to the "Classpath"
+ exception as provided by Sun in the License file that accompanied
+ this code."
+ .
+ Linking this library statically or dynamically with other modules is
+ making a combined work based on this library. Thus, the terms and
+ conditions of the GNU General Public License Version 2 cover the
+ whole combination.
+ .
+ As a special exception, the copyright holders of this library give
+ you permission to link this library with independent modules to
+ produce an executable, regardless of the license terms of these
+ independent modules, and to copy and distribute the resulting
+ executable under terms of your choice, provided that you also meet,
+ for each linked independent module, the terms and conditions of the
+ license of that module. An independent module is a module which is
+ not derived from or based on this library. If you modify this
+ library, you may extend this exception to your version of the
+ library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
+ .
+ COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0
+ .
+ 1. Definitions.
+ 1.1. “Contributor” means each individual or entity that creates or
+ contributes to the creation of Modifications.
+ 1.2. “Contributor Version” means the combination of the Original
+ Software, prior Modifications used by a Contributor (if any), and the
+ Modifications made by that particular Contributor.
+ 1.3. “Covered Software” means (a) the Original Software, or (b)
+ Modifications, or (c) the combination of files containing Original
+ Software with files containing Modifications, in each case including
+ portions thereof.
+ 1.4. “Executable” means the Covered Software in any form other than
+ Source Code.
+ 1.5. “Initial Developer” means the individual or entity that first
+ makes Original Software available under this License.
+ 1.6. “Larger Work” means a work which combines Covered Software or
+ portions thereof with code not governed by the terms of this License.
+ 1.7. “License” means this document.
+ 1.8. “Licensable” means having the right to grant, to the maximum
+ extent possible, whether at the time of the initial grant or
+ subsequently acquired, any and all of the rights conveyed herein.
+ 1.9 “Modifications” means the Source Code and Executable form of any
+ of the following:
+ A. Any file that results from an addition to, deletion from or
+ modification of the contents of a file containing Original Software
+ or previous Modifications;
+ B. Any new file that contains any part of the Original Software or
+ previous Modification; or
+ C. Any new file that is contributed or otherwise made available under
+ the terms of this License.
+ 1.10. “Original Software” means the Source Code and Executable form
+ of computer software code that is originally released under this
+ License.
+ 1.11. “Patent Claims” means any patent claim(s), now owned or
+ hereafter acquired, including without limitation, method, process,
+ and apparatus claims, in any patent Licensable by grantor.
+ 1.12. “Source Code” means (a) the common form of computer software
+ code in which modifications are made and (b) associated documentation
+ included in or with such code.
+ 1.13. “You” (or “Your”) means an individual or a legal entity
+ exercising rights under, and complying with all of the terms of, this
+ License. For legal entities, “You” includes any entity which
+ controls, is controlled by, or is under common control with You. For
+ purposes of this definition, “control” means (a) the power, direct or
+ indirect, to cause the direction or management of such entity,
+ whether by contract or otherwise, or (b) ownership of more than fifty
+ percent (50%) of the outstanding shares or beneficial ownership of
+ such entity.
+ 2. License Grants.
+ 2.1. The Initial Developer Grant.
+ Conditioned upon Your compliance with Section 3.1 below and subject
+ to third party intellectual property claims, the Initial Developer
+ hereby grants You a world-wide, royalty-free, non-exclusive license:
+ (a) under intellectual property rights (other than patent or
+ trademark) Licensable by Initial Developer, to use, reproduce,
+ modify, display, perform, sublicense and distribute the Original
+ Software (or portions thereof), with or without Modifications, and/or
+ as part of a Larger Work; and
+ (b) under Patent Claims infringed by the making, using or selling of
+ Original Software, to make, have made, use, practice, sell, and offer
+ for sale, and/or otherwise dispose of the Original Software (or
+ portions thereof).
+ (c) The licenses granted in Sections 2.1(a) and (b) are effective on
+ the date Initial Developer first distributes or otherwise makes the
+ Original Software available to a third party under the terms of this
+ License.
+ (d) Notwithstanding Section 2.1(b) above, no patent license is
+ granted: (1) for code that You delete from the Original Software, or
+ (2) for infringements caused by: (i) the modification of the Original
+ Software, or (ii) the combination of the Original Software with other
+ software or devices.
+ 2.2. Contributor Grant.
+ Conditioned upon Your compliance with Section 3.1 below and subject
+ to third party intellectual property claims, each Contributor hereby
+ grants You a world-wide, royalty-free, non-exclusive license:
+ (a) under intellectual property rights (other than patent or
+ trademark) Licensable by Contributor to use, reproduce, modify,
+ display, perform, sublicense and distribute the Modifications created
+ by such Contributor (or portions thereof), either on an unmodified
+ basis, with other Modifications, as Covered Software and/or as part
+ of a Larger Work; and
+ (b) under Patent Claims infringed by the making, using, or selling of
+ Modifications made by that Contributor either alone and/or in
+ combination with its Contributor Version (or portions of such
+ combination), to make, use, sell, offer for sale, have made, and/or
+ otherwise dispose of: (1) Modifications made by that Contributor (or
+ portions thereof); and (2) the combination of Modifications made by
+ that Contributor with its Contributor Version (or portions of such
+ combination).
+ (c) The licenses granted in Sections 2.2(a) and 2.2(b) are effective
+ on the date Contributor first distributes or otherwise makes the
+ Modifications available to a third party.
+ (d) Notwithstanding Section 2.2(b) above, no patent license is
+ granted: (1) for any code that Contributor has deleted from the
+ Contributor Version; (2) for infringements caused by: (i) third party
+ modifications of Contributor Version, or (ii) the combination of
+ Modifications made by that Contributor with other software (except as
+ part of the Contributor Version) or other devices; or (3) under
+ Patent Claims infringed by Covered Software in the absence of
+ Modifications made by that Contributor.
+ 3. Distribution Obligations.
+ 3.1. Availability of Source Code.
+ Any Covered Software that You distribute or otherwise make available
+ in Executable form must also be made available in Source Code form
+ and that Source Code form must be distributed only under the terms of
+ this License. You must include a copy of this License with every copy
+ of the Source Code form of the Covered Software You distribute or
+ otherwise make available. You must inform recipients of any such
+ Covered Software in Executable form as to how they can obtain such
+ Covered Software in Source Code form in a reasonable manner on or
+ through a medium customarily used for software exchange.
+ 3.2. Modifications.
+ The Modifications that You create or to which You contribute are
+ governed by the terms of this License. You represent that You believe
+ Your Modifications are Your original creation(s) and/or You have
+ sufficient rights to grant the rights conveyed by this License.
+ 3.3. Required Notices.
+ You must include a notice in each of Your Modifications that
+ identifies You as the Contributor of the Modification. You may not
+ remove or alter any copyright, patent or trademark notices contained
+ within the Covered Software, or any notices of licensing or any
+ descriptive text giving attribution to any Contributor or the Initial
+ Developer.
+ 3.4. Application of Additional Terms.
+ You may not offer or impose any terms on any Covered Software in
+ Source Code form that alters or restricts the applicable version of
+ this License or the recipients’ rights hereunder. You may choose to
+ offer, and to charge a fee for, warranty, support, indemnity or
+ liability obligations to one or more recipients of Covered Software.
+ However, you may do so only on Your own behalf, and not on behalf of
+ the Initial Developer or any Contributor. You must make it absolutely
+ clear that any such warranty, support, indemnity or liability
+ obligation is offered by You alone, and You hereby agree to indemnify
+ the Initial Developer and every Contributor for any liability
+ incurred by the Initial Developer or such Contributor as a result of
+ warranty, support, indemnity or liability terms You offer.
+ 3.5. Distribution of Executable Versions.
+ You may distribute the Executable form of the Covered Software under
+ the terms of this License or under the terms of a license of Your
+ choice, which may contain terms different from this License, provided
+ that You are in compliance with the terms of this License and that
+ the license for the Executable form does not attempt to limit or
+ alter the recipient’s rights in the Source Code form from the rights
+ set forth in this License. If You distribute the Covered Software in
+ Executable form under a different license, You must make it
+ absolutely clear that any terms which differ from this License are
+ offered by You alone, not by the Initial Developer or Contributor.
+ You hereby agree to indemnify the Initial Developer and every
+ Contributor for any liability incurred by the Initial Developer or
+ such Contributor as a result of any such terms You offer.
+ 3.6. Larger Works.
+ You may create a Larger Work by combining Covered Software with other
+ code not governed by the terms of this License and distribute the
+ Larger Work as a single product. In such a case, You must make sure
+ the requirements of this License are fulfilled for the Covered
+ Software.
+ 4. Versions of the License.
+ 4.1. New Versions.
+ Sun Microsystems, Inc. is the initial license steward and may publish
+ revised and/or new versions of this License from time to time. Each
+ version will be given a distinguishing version number. Except as
+ provided in Section 4.3, no one other than the license steward has
+ the right to modify this License.
+ 4.2. Effect of New Versions.
+ You may always continue to use, distribute or otherwise make the
+ Covered Software available under the terms of the version of the
+ License under which You originally received the Covered Software. If
+ the Initial Developer includes a notice in the Original Software
+ prohibiting it from being distributed or otherwise made available
+ under any subsequent version of the License, You must distribute and
+ make the Covered Software available under the terms of the version of
+ the License under which You originally received the Covered Software.
+ Otherwise, You may also choose to use, distribute or otherwise make
+ the Covered Software available under the terms of any subsequent
+ version of the License published by the license steward.
+ 4.3. Modified Versions.
+ When You are an Initial Developer and You want to create a new
+ license for Your Original Software, You may create and use a modified
+ version of this License if You: (a) rename the license and remove any
+ references to the name of the license steward (except to note that
+ the license differs from this License); and (b) otherwise make it
+ clear that the license contains terms which differ from this License.
+ 5. DISCLAIMER OF WARRANTY.
+ COVERED SOFTWARE IS PROVIDED UNDER THIS LICENSE ON AN “AS IS” BASIS,
+ WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
+ WITHOUT LIMITATION, WARRANTIES THAT THE COVERED SOFTWARE IS FREE OF
+ DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR
+ NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF
+ THE COVERED SOFTWARE IS WITH YOU. SHOULD ANY COVERED SOFTWARE PROVE
+ DEFECTIVE IN ANY RESPECT, YOU (NOT THE INITIAL DEVELOPER OR ANY OTHER
+ CONTRIBUTOR) ASSUME THE COST OF ANY NECESSARY SERVICING, REPAIR OR
+ CORRECTION. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART
+ OF THIS LICENSE. NO USE OF ANY COVERED SOFTWARE IS AUTHORIZED
+ HEREUNDER EXCEPT UNDER THIS DISCLAIMER.
+ 6. TERMINATION.
+ 6.1. This License and the rights granted hereunder will terminate
+ automatically if You fail to comply with terms herein and fail to
+ cure such breach within 30 days of becoming aware of the breach.
+ Provisions which, by their nature, must remain in effect beyond the
+ termination of this License shall survive.
+ 6.2. If You assert a patent infringement claim (excluding declaratory
+ judgment actions) against Initial Developer or a Contributor (the
+ Initial Developer or Contributor against whom You assert such claim
+ is referred to as “Participant”) alleging that the Participant
+ Software (meaning the Contributor Version where the Participant is a
+ Contributor or the Original Software where the Participant is the
+ Initial Developer) directly or indirectly infringes any patent, then
+ any and all rights granted directly or indirectly to You by such
+ Participant, the Initial Developer (if the Initial Developer is not
+ the Participant) and all Contributors under Sections 2.1 and/or 2.2
+ of this License shall, upon 60 days notice from Participant terminate
+ prospectively and automatically at the expiration of such 60 day
+ notice period, unless if within such 60 day period You withdraw Your
+ claim with respect to the Participant Software against such
+ Participant either unilaterally or pursuant to a written agreement
+ with Participant.
+ 6.3. In the event of termination under Sections 6.1 or 6.2 above, all
+ end user licenses that have been validly granted by You or any
+ distributor hereunder prior to termination (excluding licenses
+ granted to You by any distributor) shall survive termination.
+ 7. LIMITATION OF LIABILITY.
+ UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, WHETHER TORT
+ (INCLUDING NEGLIGENCE), CONTRACT, OR OTHERWISE, SHALL YOU, THE
+ INITIAL DEVELOPER, ANY OTHER CONTRIBUTOR, OR ANY DISTRIBUTOR OF
+ COVERED SOFTWARE, OR ANY SUPPLIER OF ANY OF SUCH PARTIES, BE LIABLE
+ TO ANY PERSON FOR ANY INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL
+ DAMAGES OF ANY CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR
+ LOST PROFITS, LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR
+ MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN
+ IF SUCH PARTY SHALL HAVE BEEN INFORMED OF THE POSSIBILITY OF SUCH
+ DAMAGES. THIS LIMITATION OF LIABILITY SHALL NOT APPLY TO LIABILITY
+ FOR DEATH OR PERSONAL INJURY RESULTING FROM SUCH PARTY’S NEGLIGENCE
+ TO THE EXTENT APPLICABLE LAW PROHIBITS SUCH LIMITATION. SOME
+ JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF INCIDENTAL
+ OR CONSEQUENTIAL DAMAGES, SO THIS EXCLUSION AND LIMITATION MAY NOT
+ APPLY TO YOU.
+ 8. U.S. GOVERNMENT END USERS.
+ The Covered Software is a “commercial item,” as that term is defined
+ in 48 C.F.R. 2.101 (Oct. 1995), consisting of “commercial computer
+ software” (as that term is defined at 48 C.F.R. §252.227-7014(a)(1))
+ and “commercial computer software documentation” as such terms are
+ used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R.
+ 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all
+ U.S. Government End Users acquire Covered Software with only those
+ rights set forth herein. This U.S. Government Rights clause is in
+ lieu of, and supersedes, any other FAR, DFAR, or other clause or
+ provision that addresses Government rights in computer software under
+ this License.
+ 9. MISCELLANEOUS.
+ This License represents the complete agreement concerning subject
+ matter hereof. If any provision of this License is held to be
+ unenforceable, such provision shall be reformed only to the extent
+ necessary to make it enforceable. This License shall be governed by
+ the law of the jurisdiction specified in a notice contained within
+ the Original Software (except to the extent applicable law, if any,
+ provides otherwise), excluding such jurisdiction’s conflict-of-law
+ provisions. Any litigation relating to this License shall be subject
+ to the jurisdiction of the courts located in the jurisdiction and
+ venue specified in a notice contained within the Original Software,
+ with the losing party responsible for costs, including, without
+ limitation, court costs and reasonable attorneys’ fees and expenses.
+ The application of the United Nations Convention on Contracts for the
+ International Sale of Goods is expressly excluded. Any law or
+ regulation which provides that the language of a contract shall be
+ construed against the drafter shall not apply to this License. You
+ agree that You alone are responsible for compliance with the United
+ States export administration regulations (and the export control laws
+ and regulation of any other countries) when You use, distribute or
+ otherwise make available any Covered Software.
+ 10. RESPONSIBILITY FOR CLAIMS.
+ As between Initial Developer and the Contributors, each party is
+ responsible for claims and damages arising, directly or indirectly,
+ out of its utilization of rights under this License and You agree to
+ work with Initial Developer and Contributors to distribute such
+ responsibility on an equitable basis. Nothing herein is intended or
+ shall be deemed to constitute any admission of liability.
+ NOTICE PURSUANT TO SECTION 9 OF THE COMMON DEVELOPMENT AND
+ DISTRIBUTION LICENSE (CDDL)
+ The code released under the CDDL shall be governed by the laws of the
+ State of California (excluding conflict-of-law provisions). Any
+ litigation relating to this License shall be subject to the
+ jurisdiction of the Federal Courts of the Northern District of
+ California and the state courts of the State of California, with
+ venue lying in Santa Clara County, California.
+
+Files: lib/jide*
+Copyright: 2002-2010 JIDE Software, Inc
+License: other
+ SOFTWARE LICENSE AGREEMENT FOR JIDE SOFTWARE, INC.'S PRODUCTS
+ .
+ IMPORTANT - READ CAREFULLY: This JIDE Software, Inc. ("JIDE")
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+ (an individual developer of software applications) and JIDE for the
+ JIDE software product accompanying this SLA, which includes computer
+ software and may include associated source code, media, printed
+ materials, and "on-line" or electronic documentation ("SOFTWARE
+ PRODUCT"). By installing, copying, or otherwise using the SOFTWARE
+ PRODUCT, you agree to be bound by the terms of this SLA. If you do
+ not agree to the terms of this SLA, do not install, use, distribute
+ in any manner, or replicate in any manner, any part, file or portion
+ of the SOFTWARE PRODUCT.
+ .
+ The SOFTWARE PRODUCT is protected by copyright laws and international
+ copyright treaties, as well as other intellectual property laws and
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+ RIGOROUS ENFORCEMENT OF INTELLECTUAL PROPERTY RIGHTS. If the licensed
+ right of use for this SOFTWARE PRODUCT is purchased by you with any
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+ part, as the basis for creating a product that provides the same, or
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+ SUPPORT FOR SOURCE CODE.
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+ DESCRIPTION OF OTHER RIGHTS AND LIMITATIONS.
+ .
+ Not for Resale Software. If the SOFTWARE PRODUCT is labeled and
+ provided as "Not for Resale" or "NFR", then, notwithstanding other
+ sections of this SLA, you may not resell, distribute, or otherwise
+ transfer for value or benefit in any manner, the SOFTWARE PRODUCT or
+ any derivative work using the SOFTWARE PRODUCT. You may not transfer,
+ rent, lease, lend, copy, modify, translate, sublicense, time-share or
+ electronically transmit the SOFTWARE PRODUCT, media or documentation.
+ This also applies to any and all intermediate files, source code, and
+ compiled executables.
+ .
+ Limitations on Reverse Engineering, Decompilation, and Disassembly.
+ You may not reverse engineer, decompile, create derivative works,
+ modify, translate, or disassemble the SOFTWARE PRODUCT, and only to
+ the extent that such activity is expressly permitted by applicable
+ law notwithstanding this limitation. You agree to take all
+ reasonable, legal and appropriate measures to prohibit the illegal
+ dissemination of the SOFTWARE PRODUCT or any of its constituent parts
+ and redistributables to the fullest extent of all applicable local,
+ US Codes and International Laws and Treaties regarding
+ anti-circumvention, including but not limited to, the Geneva and
+ Berne World Intellectual Property Organization (WIPO) Diplomatic
+ Conferences.
+ .
+ Rental. You may not rent, lease, or lend the SOFTWARE PRODUCT.
+ .
+ Separation of Components, Their Constituent Parts and
+ Redistributables. The SOFTWARE PRODUCT is licensed as a single
+ product. The SOFTWARE PRODUCT and its constituent parts and any
+ provided redistributables may not be reverse engineered, decompiled,
+ disassembled, nor placed for distribution, sale, or resale as
+ individual creations by you or any individual not expressly given
+ such permission by JIDE. The provision of source code, if included
+ with the SOFTWARE PRODUCT, does not constitute transfer of any legal
+ rights to such code, and resale or distribution of all or any portion
+ of all source code and intellectual property will be prosecuted to
+ the fullest extent of all applicable local, federal and international
+ laws. All JIDE libraries, source code, redistributables and other
+ files remain JIDE's exclusive property. You may not distribute any
+ files, except those that JIDE has expressly designated as
+ Redistributable.
+ .
+ The SOFTWARE PRODUCT may include certain files ("Redistributables")
+ intended for distribution by you to the users of programs you create.
+ Redistributables include jar file (or class files if you intend to
+ package all JIDE classes into your own jar). Developer Guide of
+ SOFTWARE PRODUCT (if any) or any other documents (such as javadoc)
+ which are intended to teach you how to use the SOFTWARE PRODUCT, and
+ sample code are not considered as redistributables. Subject to all of
+ the terms and conditions in this SLA, you may reproduce and
+ distribute exact copies of the Redistributables, provided that such
+ copies are made from the original copy of the SOFTWARE PRODUCT or the
+ copy transferred to a hard disk. Copies of Redistributables may only
+ be distributed with and for the sole purpose of executing application
+ programs permitted under this SLA that you have created using the
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+ Support Services. JIDE may provide you with support services related
+ to the SOFTWARE PRODUCT ("Support Services"). Use of Support Services
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+ manual, in on-line documentation and/or other JIDE provided
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+ of the SOFTWARE PRODUCT (including any portions thereof) be used for
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+ portions thereof) for developing programs created with the SOFTWARE
+ PRODUCT. In particular, you may not share copies of the
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+ the license to another developer within the team. After the transfer,
+ you are no longer allowed to use SOFTWARE PRODUCT.
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+ Termination. Without prejudice to any other rights or remedies, JIDE
+ will terminate this SLA upon your failure to comply with all the
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+ copies of the SOFTWARE PRODUCT and all of its component parts
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+ of such technology with the next generally available release from any
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+ .
+ Time Limitation: There is no time limitation on using the SOFTWARE
+ PRODUCT as long as you don't violate this license agreement.
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+ UPGRADES. If the SOFTWARE PRODUCT is labeled as an upgrade, you must
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+ (including but not limited to any images, demos, source code,
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+ music, text, and "applets" incorporated into the SOFTWARE PRODUCT),
+ the accompanying printed materials, and any copies of the SOFTWARE
+ PRODUCT are owned by JIDE or its subsidiaries. The SOFTWARE PRODUCT
+ is protected by copyright laws and international treaty provisions.
+ Therefore, you must treat the SOFTWARE PRODUCT like any other
+ copyrighted material except that you may install the SOFTWARE PRODUCT
+ for use by you, a single developer. You may not copy any printed
+ materials accompanying the SOFTWARE PRODUCT.
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+ GENERAL PROVISIONS. This SLA may only be modified in writing signed
+ by you and an authorized officer of JIDE. If any provision of this
+ SLA is found void or unenforceable, the remainder will remain valid
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+ this SLA is governed by the laws of the State of CA.
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+ you, agree and ascend to the adherence to all applicable
+ international treaties regarding copyright and intellectual property
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+ law(s) to the benefit and protection of JIDE ownership of, and
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+ damages thereto will also apply.
+ .
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+ to contact JIDE for any reason, please contact us via our support web
+ pages at http://www.jidesoft.com/.
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+ PRODUCT. THE PRODUCT AND ANY RELATED DOCUMENTATION IS PROVIDED "AS
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+ LIMITATION OF LIABILITY. TO THE MAXIMUM EXTENT PERMITTED BY
+ APPLICABLE LAW, IN NO EVENT SHALL JIDE OR ITS SUPPLIERS BE LIABLE FOR
+ ANY SPECIAL, INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES
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+ BUSINESS PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS
+ INFORMATION, ANY OTHER PECUNIARY LOSS, ATTORNEY FEES AND COURT COSTS)
+ ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE PRODUCT OR
+ THE PROVISION OF OR FAILURE TO PROVIDE SUPPORT SERVICES, EVEN IF JIDE
+ HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
 Files: debian/*
 Copyright: 2010 Shaun Jackman <sjackman at debian.org>
 License: ISC
diff --git a/debian/igv.1 b/debian/igv.1
index 376a494..b86b038 100644
--- a/debian/igv.1
+++ b/debian/igv.1
@@ -3,10 +3,6 @@
 igv \- Integrative Genomics Viewer
 .SH SYNOPSIS
 .B igv
-.br
-or
-.br
-\fBjava\fR -jar /usr/share/java/igv.jar
 .SH DESCRIPTION
 The Integrative Genomics Viewer (IGV) is a high-performance
 visualization tool for interactive exploration of large, integrated
diff --git a/debian/patches/debian-changes-1.4.2-1 b/debian/patches/debian-changes-1.4.2-1
index 3c7081d..9e52818 100644
--- a/debian/patches/debian-changes-1.4.2-1
+++ b/debian/patches/debian-changes-1.4.2-1
@@ -1,28 +1,3 @@
-Description: Upstream changes introduced in version 1.4.2-1
- This patch has been created by dpkg-source during the package build.
- Here's the last changelog entry, hopefully it gives details on why
- those changes were made:
- .
- igv (1.4.2-1) UNRELEASED; urgency=low
- .
-   * Initial release. Closes: #585457.
- .
- The person named in the Author field signed this changelog entry.
-Author: Shaun Jackman <sjackman at debian.org>
-Bug-Debian: http://bugs.debian.org/585457
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
-
 --- igv-1.4.2.orig/build.xml
 +++ igv-1.4.2/build.xml
 @@ -6,7 +6,7 @@
@@ -34,12 +9,20 @@ Last-Update: <YYYY-MM-DD>
  
      <!-- Platform specific input files -->
      <property name="native.dir"        value="${basedir}/native/" />
-@@ -54,27 +54,23 @@
+@@ -49,36 +49,25 @@
+                 <exclude name="**/manifest.mf"/>
+             </fileset>
+         </copy>
++        <unjar dest="${tmp.dir}"> 
++            <fileset dir="lib"/>
++        </unjar>
+ 
+ 
          <!-- Create class path for manifest -->
          <path id="@jars">
-             <pathelement path="${lib.dir}AbsoluteLayout.jar" />
+-            <pathelement path="${lib.dir}AbsoluteLayout.jar" />
 -            <pathelement path="${lib.dir}ATV-3.1.jar" />
-             <pathelement path="${lib.dir}colt.jar" />
+-            <pathelement path="${lib.dir}colt.jar" />
 -            <pathelement path="${lib.dir}commons-math-1.1.jar" />
 +            <pathelement path="${lib.dir}commons-math.jar" />
              <pathelement path="${lib.dir}concurrent.jar" />
@@ -47,36 +30,46 @@ Last-Update: <YYYY-MM-DD>
              <pathelement path="${lib.dir}jhdf5.jar" />
 -            <pathelement path="${lib.dir}jhdf.jar" />
 -            <pathelement path="${lib.dir}jibble.jar" />
-+            <pathelement path="${lib.dir}net.sourceforge.jlibeps.jar" />
-             <pathelement path="${lib.dir}jide-action.jar" />
-             <pathelement path="${lib.dir}jide-common.jar" />
-             <pathelement path="${lib.dir}jide-components.jar" />
-             <pathelement path="${lib.dir}jide-dialogs.jar" />
-             <pathelement path="${lib.dir}jide-dock.jar" />
-             <pathelement path="${lib.dir}jide-grids.jar" />
+-            <pathelement path="${lib.dir}jide-action.jar" />
+-            <pathelement path="${lib.dir}jide-common.jar" />
+-            <pathelement path="${lib.dir}jide-components.jar" />
+-            <pathelement path="${lib.dir}jide-dialogs.jar" />
+-            <pathelement path="${lib.dir}jide-dock.jar" />
+-            <pathelement path="${lib.dir}jide-grids.jar" />
 -            <pathelement path="${lib.dir}junit-4.5.jar" />
 -            <pathelement path="${lib.dir}jlfgr-1_0.jar" />
-+            <pathelement path="${lib.dir}junit4.jar" />
-             <pathelement path="${lib.dir}ledatastream.jar" />
+-            <pathelement path="${lib.dir}ledatastream.jar" />
 -            <pathelement path="${lib.dir}log4j-1.2.15.jar" />
 -            <pathelement path="${lib.dir}maf.jar" />
 -            <pathelement path="${lib.dir}sam-1.08.jar" />
 -            <pathelement path="${lib.dir}swing-layout-1.0.jar" />
++            <pathelement path="${lib.dir}net.sourceforge.jlibeps.jar" />
++            <pathelement path="${lib.dir}junit4.jar" />
 +            <pathelement path="${lib.dir}log4j-1.2.jar" />
 +            <pathelement path="${lib.dir}sam.jar" />
 +            <pathelement path="${lib.dir}swing-layout.jar" />
          </path>
  
          <pathconvert property="class-path" pathsep=" " dirsep="/" refid="@jars">
-@@ -105,7 +101,7 @@
+-            <map from="${lib.dir}" to="lib/"/>
+         </pathconvert>
+ 
+         <tstamp>
+@@ -105,8 +94,13 @@
      </target>
  
      <target name="compile" depends="init">
 -        <javac srcdir="${src.dir}"  debug="on" destdir="${tmp.dir}">
 +        <javac srcdir="${src.dir}" excludes="org/broad/igv/maf/*" debug="on" destdir="${tmp.dir}">
              <classpath refid="@jars" />
++            <classpath>
++                <fileset dir="lib">
++                    <include name="**/*.jar"/>
++                </fileset>
++            </classpath>
          </javac>
      </target>
+ 
 --- igv-1.4.2.orig/src/org/broad/igv/PreferenceManager.java
 +++ igv-1.4.2/src/org/broad/igv/PreferenceManager.java
 @@ -25,7 +25,9 @@ package org.broad.igv;
@@ -101,7 +94,7 @@ Last-Update: <YYYY-MM-DD>
          }
 --- igv-1.4.2.orig/src/org/broad/igv/h5/HDF5LocalWriter.java
 +++ igv-1.4.2/src/org/broad/igv/h5/HDF5LocalWriter.java
-@@ -491,7 +491,7 @@ public class HDF5LocalWriter implements
+@@ -491,7 +491,7 @@ public class HDF5LocalWriter implements 
                  buf =
                          new double[]{((Number) value).doubleValue()};
              } else {

-- 
Integrative Genomics Viewer