doc: fix javadoc

src/main/java/net/imglib2/realtransform/AbstractRealTransformSequence.java

@@ -11,13 +11,13 @@
  * %%
  * 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.
- * 
+ *
  * 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
@@ -44,8 +44,10 @@
  * Shared properties of {@link RealTransformSequence} and
  * {@link InvertibleRealTransformSequence}, sequences of something that extends
  * {@link RealTransform RealTransforms}. If empty, will behave as the identity transformation.
- * 
+ *
  * @author Stephan Saalfeld
+ *
+ * @param <R> transformation
  */
 public class AbstractRealTransformSequence< R extends RealTransform > implements RealTransform
 {
@@ -104,10 +106,10 @@ public int numTargetDimensions()
 
 	/**
 	 * Returns true if either the sequence is empty, or if
-	 * every transform in the sequence returns true for {@link isIdentity}.  This 
+	 * every transform in the sequence returns true for {@link isIdentity}.  This
 	 * sequence could behave as the identity even if this method returns false,
 	 * for example, if it contains only a transform and its inverse.
-	 * 
+	 *
 	 * @return true if empty or contains only identity transforms.
 	 */
 	@Override
@@ -121,7 +123,7 @@ public boolean isIdentity()
 		{
 			// if any transform in the sequence is not identity, this sequence
 			// is not the identity
-			for ( R t : transforms )
+			for ( final R t : transforms )
 			{
 				if ( !t.isIdentity() )
 					return false;

src/main/java/net/imglib2/realtransform/AffineRealRandomAccessible.java

@@ -11,13 +11,13 @@
  * %%
  * 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.
- * 
+ *
  * 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
@@ -51,6 +51,9 @@
  * any relative move.
  *
  * @author Stephan Saalfeld
+ *
+ * @param <T> data type
+ * @param <R> transformation
  */
 public class AffineRealRandomAccessible< T, R extends AffineGet > extends RealTransformRealRandomAccessible< T, R >
 {

src/main/java/net/imglib2/realtransform/PositionFieldTransform.java

@@ -11,13 +11,13 @@
  * %%
  * 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.
- * 
+ *
  * 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
@@ -82,7 +82,7 @@ public PositionFieldTransform( final RealRandomAccessible< ? extends RealLocaliz
 	/**
 	 *
 	 * @param <T>
-	 *            type of the positions
+	 *            position type
 	 * @param positions
 	 *            interleaved target coordinate, this means that the components
 	 *            of the target coordinates are in the 0th dimension
@@ -95,6 +95,7 @@ public < T extends RealType< T > > PositionFieldTransform( final RandomAccessibl
 	/**
 	 *
 	 * @param <T>
+	 *            position type
 	 * @param positions
 	 *            interleaved target coordinate, this means that the components
 	 *            of the target coordinates are in the 0th dimension
@@ -110,7 +111,7 @@ public < T extends RealType< T > > PositionFieldTransform( final RandomAccessibl
 	/**
 	 *
 	 * @param <T>
-	 *            type of the positions
+	 *            position type
 	 * @param positions
 	 *            interleaved target coordinate, this means that the components
 	 *            of the target coordinates are in the 0th dimension
@@ -127,7 +128,7 @@ public < T extends RealType< T > > PositionFieldTransform( final RandomAccessibl
 	/**
 	 *
 	 * @param <T>
-	 *            type of the positions
+	 *            position type
 	 * @param positions
 	 *            interleaved target coordinate, this means that the components
 	 *            of the target coordinates are in the 0th dimension
@@ -282,11 +283,13 @@ public static RandomAccessibleInterval< DoubleType > createPositionField(
 	 * target dimension. For example,
 	 *
 	 * <pre>
-	 * {@code () -> DoubleType.createVector(transform.numTargetDimensions())}
+	 * {@code
+	 * () -> DoubleType.createVector( transform.numTargetDimensions() )
+	 * }
 	 * </pre>
 	 *
 	 * @param <T>
-	 *            the type of the output
+	 *            output type
 	 * @param transform
 	 *            the transform to be converted
 	 * @param interval
@@ -331,11 +334,13 @@ public static < T extends RealType< T > > RandomAccessibleInterval< T > createPo
 	 * target dimension. For example,
 	 *
 	 * <pre>
-	 * {@code () -> DoubleType.createVector(transform.numTargetDimensions())}
+	 * {@code
+	 * () -> DoubleType.createVector( transform.numTargetDimensions() )
+	 * }
 	 * </pre>
 	 *
 	 * @param <T>
-	 *            the type of the output
+	 *            output type
 	 * @param transform
 	 *            the transform to be converted
 	 * @param interval

src/main/java/net/imglib2/realtransform/RealTransform.java

@@ -169,6 +169,8 @@ public default void apply( final float[] source, final float[] target )
 	 *            target dimension, must be {@code >=}
 	 *            {@link #numTargetDimensions()}
 	 *
+	 * @return the d-th dimension of the transformed target vector
+	 *
 	 * TODO This default implementation creates and calculates the entire
 	 *            target vector and extracts the dimension from that vector.
 	 *            Override for this to be more efficient.
@@ -193,6 +195,8 @@ public default double applyDimension( final double[] source, final int d )
 	 *            target dimension, must be {@code >=}
 	 *            {@link #numTargetDimensions()}
 	 *
+	 * @return the d-th dimension of the transformed target vector
+	 *
 	 * TODO This default implementation creates and calculates the entire
 	 *            target vector and extracts the dimension from that vector.
 	 *            Override for this to be more efficient.
@@ -217,6 +221,8 @@ public default double applyDimension( final long[] source, final int d )
 	 *            target dimension, must be {@code >=}
 	 *            {@link #numTargetDimensions()}
 	 *
+	 * @return the d-th dimension of the transformed target vector
+	 *
 	 * TODO This default implementation creates and calculates the entire
 	 *            target vector and extracts the dimension from that vector.
 	 *            Override for this to be more efficient.

src/main/java/net/imglib2/realtransform/RealTransformRandomAccessible.java

@@ -11,13 +11,13 @@
  * %%
  * 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.
- * 
+ *
  * 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
@@ -52,6 +52,9 @@
  * {@link RandomAccess} after modifying the transformation.
  *
  * @author Stephan Saalfeld
+ *
+ * @param <T> data type
+ * @param <R> transformation
  */
 public class RealTransformRandomAccessible< T, R extends RealTransform > extends RealTransformRealRandomAccessible< T, R > implements RandomAccessible< T >
 {

src/main/java/net/imglib2/realtransform/RealTransformRealRandomAccessible.java

@@ -11,13 +11,13 @@
  * %%
  * 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.
- * 
+ *
  * 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
@@ -50,6 +50,9 @@
  * a new {@link RandomAccess} after modifying the transformation.
  *
  * @author Stephan Saalfeld
+ *
+ * @param <T> data type
+ * @param <R> transformation
  */
 public class RealTransformRealRandomAccessible< T, R extends RealTransform > implements RealRandomAccessible< T >
 {

src/main/java/net/imglib2/realtransform/StackingRealRandomAccessible.java

@@ -11,13 +11,13 @@
  * %%
  * 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.
- * 
+ *
  * 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
@@ -48,6 +48,8 @@
  * f(5) = g(5,2,3) = g(5,1,6) = g(5,18,-20)...
  *
  * @author Stephan Saalfeld
+ *
+ * @param <T> data type
  */
 public class StackingRealRandomAccessible< T > implements RealRandomAccessible< T >
 {