Skip to content

Commit ac22449

Browse files
andreasprlicandreasprlic
committed
Ran Optimize Imports across the whole project.
1 parent c0b168f commit ac22449

File tree

668 files changed

+3078
-5188
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

668 files changed

+3078
-5188
lines changed

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/CommandPrompt.java‎

Lines changed: 9 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,15 @@
2020
*/
2121
package org.biojava3.aaproperties;
2222

23+
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
24+
import org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet;
25+
import org.biojava3.core.exceptions.CompoundNotFoundException;
26+
import org.biojava3.core.sequence.ProteinSequence;
27+
import org.biojava3.core.sequence.compound.AminoAcidCompound;
28+
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
29+
import org.biojava3.core.sequence.io.*;
30+
import org.biojava3.core.sequence.template.CompoundSet;
31+
2332
import java.io.File;
2433
import java.io.FileInputStream;
2534
import java.io.IOException;
@@ -30,19 +39,6 @@
3039
import java.util.Map;
3140
import java.util.Map.Entry;
3241

33-
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
34-
import org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet;
35-
import org.biojava3.core.exceptions.CompoundNotFoundException;
36-
import org.biojava3.core.sequence.ProteinSequence;
37-
import org.biojava3.core.sequence.compound.AminoAcidCompound;
38-
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
39-
import org.biojava3.core.sequence.io.FastaReader;
40-
import org.biojava3.core.sequence.io.GenbankReader;
41-
import org.biojava3.core.sequence.io.GenericFastaHeaderParser;
42-
import org.biojava3.core.sequence.io.GenericGenbankHeaderParser;
43-
import org.biojava3.core.sequence.io.ProteinSequenceCreator;
44-
import org.biojava3.core.sequence.template.CompoundSet;
45-
4642
public class CommandPrompt {
4743

4844
/**

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/Constraints.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -20,13 +20,13 @@
2020
*/
2121
package org.biojava3.aaproperties;
2222

23-
import java.util.HashMap;
24-
import java.util.Map;
25-
2623
import org.biojava3.aaproperties.PeptideProperties.SingleLetterAACode;
2724
import org.biojava3.core.sequence.compound.AminoAcidCompound;
2825
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
2926

27+
import java.util.HashMap;
28+
import java.util.Map;
29+
3030
/**
3131
* This class is used to support the implementation of properties stated in IPeptideProperties.
3232
* It initializes several values that would be needed for the computation of properties such as

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/IPeptideProperties.java‎

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -22,16 +22,15 @@
2222
*/
2323
package org.biojava3.aaproperties;
2424

25-
import java.io.File;
26-
import java.io.FileNotFoundException;
27-
import java.util.Map;
28-
29-
import javax.xml.bind.JAXBException;
30-
3125
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
3226
import org.biojava3.core.sequence.ProteinSequence;
3327
import org.biojava3.core.sequence.compound.AminoAcidCompound;
3428

29+
import javax.xml.bind.JAXBException;
30+
import java.io.File;
31+
import java.io.FileNotFoundException;
32+
import java.util.Map;
33+
3534

3635
/**
3736
* An interface to generate some basic physico-chemical properties of protein sequences.<br/>

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/PeptideProperties.java‎

Lines changed: 8 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -20,15 +20,6 @@
2020
*/
2121
package org.biojava3.aaproperties;
2222

23-
import java.io.File;
24-
import java.io.FileNotFoundException;
25-
import java.util.HashMap;
26-
import java.util.HashSet;
27-
import java.util.Map;
28-
import java.util.Set;
29-
30-
import javax.xml.bind.JAXBException;
31-
3223
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
3324
import org.biojava3.core.exceptions.CompoundNotFoundException;
3425
import org.biojava3.core.sequence.ProteinSequence;
@@ -37,6 +28,14 @@
3728
import org.slf4j.Logger;
3829
import org.slf4j.LoggerFactory;
3930

31+
import javax.xml.bind.JAXBException;
32+
import java.io.File;
33+
import java.io.FileNotFoundException;
34+
import java.util.HashMap;
35+
import java.util.HashSet;
36+
import java.util.Map;
37+
import java.util.Set;
38+
4039
/**
4140
* This is an adaptor class which enable the ease of generating protein properties.
4241
* At least one adaptor method is written for each available properties provided in IPeptideProperties.

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/PeptidePropertiesImpl.java‎

Lines changed: 9 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -20,16 +20,6 @@
2020
*/
2121
package org.biojava3.aaproperties;
2222

23-
import java.io.File;
24-
import java.io.FileInputStream;
25-
import java.io.FileNotFoundException;
26-
import java.util.HashMap;
27-
import java.util.Map;
28-
29-
import javax.xml.bind.JAXBContext;
30-
import javax.xml.bind.JAXBException;
31-
import javax.xml.bind.Unmarshaller;
32-
3323
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
3424
import org.biojava3.aaproperties.xml.ElementTable;
3525
import org.biojava3.aaproperties.xml.MyValidationEventHandler;
@@ -39,6 +29,15 @@
3929
import org.slf4j.Logger;
4030
import org.slf4j.LoggerFactory;
4131

32+
import javax.xml.bind.JAXBContext;
33+
import javax.xml.bind.JAXBException;
34+
import javax.xml.bind.Unmarshaller;
35+
import java.io.File;
36+
import java.io.FileInputStream;
37+
import java.io.FileNotFoundException;
38+
import java.util.HashMap;
39+
import java.util.Map;
40+
4241
/**
4342
* This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.
4443
*

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/Utils.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -20,12 +20,12 @@
2020
*/
2121
package org.biojava3.aaproperties;
2222

23-
import java.util.HashSet;
24-
import java.util.Set;
25-
2623
import org.slf4j.Logger;
2724
import org.slf4j.LoggerFactory;
2825

26+
import java.util.HashSet;
27+
import java.util.Set;
28+
2929
/**
3030
* This is a utility class that contains utility methods which will facilitates the coding of other methods
3131
*

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/IProfeatProperties.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,10 +20,10 @@
2020
*/
2121
package org.biojava3.aaproperties.profeat;
2222

23-
import java.util.Map;
24-
2523
import org.biojava3.core.sequence.ProteinSequence;
2624

25+
import java.util.Map;
26+
2727
public interface IProfeatProperties {
2828
/**
2929
* Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf<br/>

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/ProfeatProperties.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,14 +20,14 @@
2020
*/
2121
package org.biojava3.aaproperties.profeat;
2222

23-
import java.util.Map;
24-
2523
import org.biojava3.aaproperties.profeat.IProfeatProperties.ATTRIBUTE;
2624
import org.biojava3.aaproperties.profeat.IProfeatProperties.DISTRIBUTION;
2725
import org.biojava3.aaproperties.profeat.IProfeatProperties.GROUPING;
2826
import org.biojava3.aaproperties.profeat.IProfeatProperties.TRANSITION;
2927
import org.biojava3.core.sequence.ProteinSequence;
3028

29+
import java.util.Map;
30+
3131
/**
3232
* This is an adaptor class which enable the ease of generating profeat properties.
3333
* At least one adaptor method is written for each available properties provided in IProfeatProperties.

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/profeat/ProfeatPropertiesImpl.java‎

Lines changed: 3 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -20,19 +20,12 @@
2020
*/
2121
package org.biojava3.aaproperties.profeat;
2222

23+
import org.biojava3.aaproperties.profeat.convertor.*;
24+
import org.biojava3.core.sequence.ProteinSequence;
25+
2326
import java.util.HashMap;
2427
import java.util.Map;
2528

26-
import org.biojava3.aaproperties.profeat.convertor.Convert2Charge;
27-
import org.biojava3.aaproperties.profeat.convertor.Convert2Hydrophobicity;
28-
import org.biojava3.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume;
29-
import org.biojava3.aaproperties.profeat.convertor.Convert2Polarity;
30-
import org.biojava3.aaproperties.profeat.convertor.Convert2Polarizability;
31-
import org.biojava3.aaproperties.profeat.convertor.Convert2SecondaryStructure;
32-
import org.biojava3.aaproperties.profeat.convertor.Convert2SolventAccessibility;
33-
import org.biojava3.aaproperties.profeat.convertor.Convertor;
34-
import org.biojava3.core.sequence.ProteinSequence;
35-
3629
public class ProfeatPropertiesImpl implements IProfeatProperties{
3730

3831
@Override

‎biojava-aa-prop/src/main/java/org/biojava3/aaproperties/xml/AminoAcidComposition.java‎

Lines changed: 1 addition & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -20,14 +20,9 @@
2020
*/
2121
package org.biojava3.aaproperties.xml;
2222

23+
import javax.xml.bind.annotation.*;
2324
import java.util.List;
2425

25-
import javax.xml.bind.annotation.XmlAccessorType;
26-
import javax.xml.bind.annotation.XmlAttribute;
27-
import javax.xml.bind.annotation.XmlElement;
28-
import javax.xml.bind.annotation.XmlRootElement;
29-
import javax.xml.bind.annotation.XmlAccessType;
30-
3126
@XmlRootElement(name = "compoundcomposition", namespace ="http://biojava.org")
3227
@XmlAccessorType(XmlAccessType.NONE)
3328
public class AminoAcidComposition {

0 commit comments

Comments
 (0)