Removing unused imports

sbliven · sbliven · commit e6b0dccb9715 · 2016-03-09T18:48:26.000+01:00
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/SimpleProfilePairTest.java
@@ -38,7 +38,6 @@
 import java.util.Arrays;
 import org.biojava.nbio.alignment.NeedlemanWunsch;
 import org.biojava.nbio.alignment.SimpleGapPenalty;
-import org.biojava.nbio.core.alignment.SimpleProfilePair;
 import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
 
 import static org.junit.Assert.assertEquals;
diff --git a/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java b/biojava-core/src/main/java/demo/DemoSixFrameTranslation.java
@@ -20,7 +20,6 @@
  */
 package demo;
 
-import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
diff --git a/biojava-core/src/main/java/demo/ParseFastaFileDemo.java b/biojava-core/src/main/java/demo/ParseFastaFileDemo.java
@@ -22,8 +22,6 @@
 
 
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
 import java.io.InputStream;
 import java.util.LinkedHashMap;
 import java.util.logging.Level;
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/TestAmbiguityCompoundSet.java b/biojava-core/src/test/java/org/biojava/nbio/core/TestAmbiguityCompoundSet.java
@@ -28,7 +28,6 @@
 import org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet;
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
 import org.biojava.nbio.core.sequence.io.RNASequenceCreator;
-import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.CompoundSet;
 import org.biojava.nbio.core.sequence.template.Sequence;
 import org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator;
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java
@@ -36,7 +36,6 @@
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
-import java.util.Scanner;
 
 /**
  * Class that loads data from the model files into {@link Model} objects
diff --git a/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriter.java b/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriter.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.sequencing.io.fastq;
 
-import java.io.IOException;
-
 /**
  * Writer for {@link FastqVariant#FASTQ_ILLUMINA} formatted sequences.
  *
diff --git a/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/SangerFastqWriter.java b/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/SangerFastqWriter.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.sequencing.io.fastq;
 
-import java.io.IOException;
-
 /**
  * Writer for {@link FastqVariant#FASTQ_SANGER} formatted sequences.
  *
diff --git a/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/SolexaFastqWriter.java b/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/SolexaFastqWriter.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.sequencing.io.fastq;
 
-import java.io.IOException;
-
 /**
  * Writer for {@link FastqVariant#FASTQ_SOLEXA} formatted sequences.
  *
diff --git a/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/ConvertTest.java b/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/ConvertTest.java
@@ -22,8 +22,6 @@
 
 import java.io.File;
 import java.io.FileWriter;
-import java.io.IOException;
-
 import java.util.List;
 import java.util.Map;
 
diff --git a/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriterTest.java b/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriterTest.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.sequencing.io.fastq;
 
-import java.io.IOException;
-
 /**
  * Unit test for IlluminaFastqWriter.
  */
diff --git a/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/SangerFastqWriterTest.java b/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/SangerFastqWriterTest.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.sequencing.io.fastq;
 
-import java.io.IOException;
-
 /**
  * Unit test for SangerFastqWriter.
  */
diff --git a/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/SolexaFastqWriterTest.java b/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/SolexaFastqWriterTest.java
@@ -20,8 +20,6 @@
  */
 package org.biojava.nbio.sequencing.io.fastq;
 
-import java.io.IOException;
-
 /**
  * Unit test for SolexaFastqWriter.
  */
diff --git a/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java b/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java
@@ -22,7 +22,6 @@
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
diff --git a/biojava-structure-gui/src/main/java/demo/DemoSW3DAligner.java b/biojava-structure-gui/src/main/java/demo/DemoSW3DAligner.java
@@ -27,7 +27,6 @@
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.StructureAlignment;
 import org.biojava.nbio.structure.align.StructureAlignmentFactory;
-import org.biojava.nbio.structure.align.ce.CeParameters;
 import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
@@ -39,10 +39,8 @@
 import javax.swing.JProgressBar;
 import javax.swing.JTabbedPane;
 
-import org.biojava.nbio.structure.PassthroughIdentifier;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIdentifier;
 import org.biojava.nbio.structure.align.StructureAlignment;
 import org.biojava.nbio.structure.align.StructureAlignmentFactory;
 import org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor;
diff --git a/biojava-ws/src/main/java/demo/HmmerDemo.java b/biojava-ws/src/main/java/demo/HmmerDemo.java
@@ -26,7 +26,6 @@
 import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
 import org.biojava.nbio.ws.hmmer.HmmerDomain;
 import org.biojava.nbio.ws.hmmer.HmmerResult;
-import org.biojava.nbio.ws.hmmer.HmmerScan;
 import org.biojava.nbio.ws.hmmer.RemoteHmmerScan;
 
 import java.util.SortedSet;

Original file line number	Diff line number	Diff line change
`@@ -20,8 +20,6 @@`
`20`	`20`	`*/`
`21`	`21`	`package org.biojava.nbio.sequencing.io.fastq;`
`22`	`22`
`23`		`-import java.io.IOException;`
`24`		`-`
`25`	`23`	`/**`
`26`	`24`	`* Writer for {@link FastqVariant#FASTQ_ILLUMINA} formatted sequences.`
`27`	`25`	`*`