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Finish fixing header names and documentation links

Conflicts:

	components/common/src/loci/common/services/OMENotesService.java
	components/formats-bsd/src/loci/formats/ResourceNamer.java
	docs/sphinx/developers/xsd-fu.txt
	license/loci-legacy/license.txt
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melissalinkert committed Feb 12, 2014
1 parent 1cf7420 commit 0cc8746471f9461ce60c700f559c0a8b53c397b7
Showing 354 changed files with 392 additions and 498 deletions.
@@ -192,7 +192,7 @@ FindBugs Ant task
JGoodies Forms
JAR file: forms-1.3.0.jar
URL: http://www.jgoodies.com/freeware/forms/index.html
Notes: used for layout by SciFIO, Data Browser and OME Notes
Notes: used for layout by Data Browser and OME Notes
License: BSD
ImageJ
@@ -297,7 +297,7 @@ Apache XML-RPC
<target name="dist" description="OME hook: build and publish Bio-Formats dist">
<ant target="tools"/>
<ant target="tools-ome"/>
<ant target="jar-scifio-tests"/>
<ant target="jar-formats-bsd-tests"/>
<ant antfile="ome.xml" inheritRefs="false" inheritAll="false"/>
</target>

@@ -1,7 +1,7 @@
<!--
checkstyle.xml
Checkstyle configuration file for use with SciFIO.
Checkstyle configuration file.
Run "ant style" to check for source code style deviations.
-->

@@ -1,6 +1,6 @@
/*
* #%L
* OME SCIFIO package for reading and converting scientific file formats.
* OME Bio-Formats command line tools.
* %%
* Copyright (C) 2005 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* OME SCIFIO package for reading and converting scientific file formats.
* OME Bio-Formats command line tools.
* %%
* Copyright (C) 2005 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* OME SCIFIO package for reading and converting scientific file formats.
* OME Bio-Formats command line tools.
* %%
* Copyright (C) 2005 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -11,11 +11,12 @@
<dependencySet>
<excludes>
<!-- exclude things included in loci_tools.jar -->
<exclude>ome:bio-formats</exclude>
<exclude>ome:loci_plugins</exclude>
<exclude>ome:ome-xml</exclude>
<exclude>ome:common</exclude>
<exclude>ome:scifio</exclude>
<exclude>ome:formats-api</exclude>
<exclude>ome:formats-bsd</exclude>
<exclude>ome:formats-gpl</exclude>
<exclude>ome:lwf-stubs</exclude>
<exclude>gov.nih.imagej:imagej</exclude>
<exclude>com.esotericsoftware.kryo:kryo</exclude>
@@ -31,20 +31,4 @@ component.runtime-cp = ${component.classpath}:\
${lib.dir}/logback-core-${logback.version}.jar:\
${lib.dir}/slf4j-api-${slf4j.version}.jar

# Used by TestNG suite that tests the absence of class from poi-loci.jar
component.cp.no-poi = ${artifact.dir}/scifio.jar:\
${lib.dir}/forms-1.3.0.jar:\
${lib.dir}/logback-classic-${logback.version}.jar:\
${lib.dir}/logback-core-${logback.version}.jar:\
${lib.dir}/slf4j-api-${slf4j.version}.jar:\
${lib.dir}/testng-6.8.jar

# Used by TestNG suite that tests the absence of class from netcdf-4.0.jar
component.cp.no-netcdf = ${artifact.dir}/scifio.jar:\
${lib.dir}/forms-1.3.0.jar:\
${lib.dir}/logback-classic-${logback.version}.jar:\
${lib.dir}/logback-core-${logback.version}.jar:\
${lib.dir}/slf4j-api-${slf4j.version}.jar:\
${lib.dir}/testng-6.8.jar

testng.xml.template = ${test.dir}/loci/common/utests/testng-template.xml
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Common package for I/O and related utilities
* %%
* Copyright (C) 2005 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Common package for I/O and related utilities
* %%
* Copyright (C) 2005 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison

This file was deleted.

@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Common package for I/O and related utilities
* %%
* Copyright (C) 2005 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Common package for I/O and related utilities
* %%
* Copyright (C) 2005 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Common package for I/O and related utilities
* %%
* Copyright (C) 2005 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
###
# #%L
# Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
# Common package for I/O and related utilities
# %%
# Copyright (C) 2005 - 2013 Open Microscopy Environment:
# - Board of Regents of the University of Wisconsin-Madison
@@ -38,8 +38,6 @@
# NOTE: All service classes must be fully qualified
#

# OME notes service (implementation in legacy ome-notes component)
loci.common.services.OMENotesService=loci.ome.notes.services.OMENotesServiceImpl
# OME-XML service (interface and implementation in bio-formats component)
loci.formats.services.OMEXMLService=loci.formats.services.OMEXMLServiceImpl
# POI service (interface and implementation in bio-formats component)
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
@@ -1,6 +1,6 @@
/*
* #%L
* Legacy layer preserving compatibility between legacy Bio-Formats and SCIFIO.
* Tests for the common I/O package.
* %%
* Copyright (C) 2008 - 2013 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison

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