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
melissalinkert · Feb 27, 2014 · 0cc8746 · 0cc8746
1 parent 1cf7420
commit 0cc8746
Show file tree

Hide file tree

Showing 354 changed files with 392 additions and 498 deletions.
diff --git a/build.xml b/build.xml
@@ -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>
 

diff --git a/checkstyle.xml b/checkstyle.xml
@@ -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.
 -->
 

diff --git a/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java b/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java
@@ -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

diff --git a/components/bio-formats-tools/src/loci/formats/tools/ImageFaker.java b/components/bio-formats-tools/src/loci/formats/tools/ImageFaker.java
@@ -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

diff --git a/components/bio-formats-tools/src/loci/formats/tools/ImageInfo.java b/components/bio-formats-tools/src/loci/formats/tools/ImageInfo.java
@@ -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

diff --git a/components/bundles/ome-tools/assembly.xml b/components/bundles/ome-tools/assembly.xml
@@ -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>

diff --git a/components/common/build.properties b/components/common/build.properties
@@ -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
diff --git a/components/common/src/loci/common/services/AbstractService.java b/components/common/src/loci/common/services/AbstractService.java
@@ -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

diff --git a/components/common/src/loci/common/services/DependencyException.java b/components/common/src/loci/common/services/DependencyException.java
@@ -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

diff --git a/components/common/src/loci/common/services/OMENotesService.java b/components/common/src/loci/common/services/OMENotesService.java
diff --git a/components/common/src/loci/common/services/Service.java b/components/common/src/loci/common/services/Service.java
@@ -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

diff --git a/components/common/src/loci/common/services/ServiceException.java b/components/common/src/loci/common/services/ServiceException.java
@@ -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

diff --git a/components/common/src/loci/common/services/ServiceFactory.java b/components/common/src/loci/common/services/ServiceFactory.java
@@ -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

diff --git a/components/common/src/loci/common/services/services.properties b/components/common/src/loci/common/services/services.properties
@@ -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)

diff --git a/components/common/test/loci/common/utests/BufferAlignmentReadTest.java b/components/common/test/loci/common/utests/BufferAlignmentReadTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/BufferAlignmentWriteTest.java b/components/common/test/loci/common/utests/BufferAlignmentWriteTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/DataToolsTest.java b/components/common/test/loci/common/utests/DataToolsTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/EncodingTest.java b/components/common/test/loci/common/utests/EncodingTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/EndiannessTest.java b/components/common/test/loci/common/utests/EndiannessTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/LocationTest.java b/components/common/test/loci/common/utests/LocationTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/RandomAccessInputStreamTest.java b/components/common/test/loci/common/utests/RandomAccessInputStreamTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadByteArrayTest.java b/components/common/test/loci/common/utests/ReadByteArrayTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadByteBufferTest.java b/components/common/test/loci/common/utests/ReadByteBufferTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadByteSubArrayTest.java b/components/common/test/loci/common/utests/ReadByteSubArrayTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadByteTest.java b/components/common/test/loci/common/utests/ReadByteTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadCharTest.java b/components/common/test/loci/common/utests/ReadCharTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadDoubleTest.java b/components/common/test/loci/common/utests/ReadDoubleTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadFloatTest.java b/components/common/test/loci/common/utests/ReadFloatTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadIntTest.java b/components/common/test/loci/common/utests/ReadIntTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadLineTest.java b/components/common/test/loci/common/utests/ReadLineTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadLongTest.java b/components/common/test/loci/common/utests/ReadLongTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadOnlyTest.java b/components/common/test/loci/common/utests/ReadOnlyTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadShortTest.java b/components/common/test/loci/common/utests/ReadShortTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadUnsignedByteTest.java b/components/common/test/loci/common/utests/ReadUnsignedByteTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/ReadUnsignedShortTest.java b/components/common/test/loci/common/utests/ReadUnsignedShortTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/SkipBytesTest.java b/components/common/test/loci/common/utests/SkipBytesTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/TypeDetectionTest.java b/components/common/test/loci/common/utests/TypeDetectionTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/URLHandleTest.java b/components/common/test/loci/common/utests/URLHandleTest.java
@@ -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

diff --git a/components/common/test/loci/common/utests/WriteByteArrayTest.java b/components/common/test/loci/common/utests/WriteByteArrayTest.java
@@ -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