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Cleanup of unnecessary casts #257

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d412ada
Merge pull request #1 from biojava/master
pibizza Feb 28, 2015
a05dfc9
Code cleanup. Removed lots of unnecessary casts.
Feb 28, 2015
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19 changes: 12 additions & 7 deletions biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java
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Expand Up @@ -20,19 +20,24 @@
*/
package org.biojava.nbio.aaproperties.xml;

import org.biojava.nbio.aaproperties.PeptideProperties;
import org.biojava.nbio.aaproperties.xml.*;
import org.junit.Test;
import static org.junit.Assert.assertEquals;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import java.io.*;
import java.util.ArrayList;
import java.util.List;

import static org.junit.Assert.assertEquals;
import org.biojava.nbio.aaproperties.PeptideProperties;
import org.junit.Test;

public class AminoAcidTest {

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12 changes: 7 additions & 5 deletions biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
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Expand Up @@ -24,6 +24,8 @@
*/
package org.biojava.nbio.core.sequence.io;

import java.util.LinkedHashMap;

import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
Expand All @@ -32,14 +34,14 @@
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.io.util.ClasspathResource;
import org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader;
import org.junit.*;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.File;
import java.io.FileInputStream;
import java.util.LinkedHashMap;

/**
*
* @author Scooter Willis <willishf at gmail dot com>
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4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.java
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Expand Up @@ -180,7 +180,7 @@ public void setPDBName(String s) {
* @return and identical copy of this Group object
*/
@Override
public Object clone() {
public AminoAcidImpl clone() {

AminoAcidImpl n = new AminoAcidImpl();
n.setPDBFlag(has3D());
Expand All @@ -193,7 +193,7 @@ public Object clone() {

// copy the atoms
for (Atom atom1 : atoms) {
Atom atom = (Atom) atom1.clone();
Atom atom = atom1.clone();
n.addAtom(atom);
atom.setGroup(n);
}
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
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Expand Up @@ -187,7 +187,7 @@ public interface Atom extends Cloneable, PDBRecord {
* Return an identical copy of this object .
* @return an identical copy of this object
*/
public Object clone();
public Atom clone();

/**
* Set the back-reference to its parent Group.
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java
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Expand Up @@ -189,7 +189,7 @@ public String toString() {
* @return and identical copy of this object
*/
@Override
public Object clone() {
public Atom clone() {
AtomImpl n = new AtomImpl();
n.setOccupancy(getOccupancy());
n.setTempFactor(getTempFactor());
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4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
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Expand Up @@ -574,7 +574,7 @@ public static final void plus(Structure s, Matrix matrix){
} catch (Exception e){
logger.error("Exception: ", e);
}
oldAtom = (Atom)atom.clone();
oldAtom = atom.clone();

double x = atom.getX();
double y = atom.getY() ;
Expand All @@ -596,7 +596,7 @@ public static final void plus(Structure s, Matrix matrix){
} catch (Exception e){
logger.error("Exception: ", e);
}
rotOldAtom = (Atom) atom.clone();
rotOldAtom = atom.clone();
}

}
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
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Expand Up @@ -51,7 +51,7 @@ public interface Chain {
/** returns an identical copy of this Chain.
* @return an identical copy of this Chain
*/
public Object clone();
public Chain clone();

/** add a group to the list of ATOM record group of this chain.
* To add SEQRES records a more complex alignment between ATOM and SEQRES residues
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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
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Expand Up @@ -128,7 +128,7 @@ public Structure getParent() {
* @return an identical copy of this Chain
*/
@Override
public Object clone() {
public ChainImpl clone() {
// go through all groups and add to new Chain.
ChainImpl n = new ChainImpl();
// copy chain data:
Expand All @@ -143,7 +143,7 @@ public Object clone() {
n.setInternalChainID(internalChainID);

for (Group group : groups) {
Group g = (Group) group.clone();
Group g = group.clone();
n.addGroup(g);
g.setChain(n);
}
Expand All @@ -155,7 +155,7 @@ public Object clone() {

List<Group> tmpSeqRes = new ArrayList<Group>();
for (Group seqResGroup : seqResGroups) {
Group g = (Group) seqResGroup.clone();
Group g = seqResGroup.clone();
g.setChain(n);
tmpSeqRes.add(g);
}
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
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Expand Up @@ -221,7 +221,7 @@ public interface Group {
/** returns and identical copy of this Group object .
* @return and identical copy of this Group object
*/
public Object clone();
public Group clone();

/**
* Sets the back-reference to its parent Chain.
Expand Down
4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
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Expand Up @@ -329,7 +329,7 @@ public Iterator<Atom> iterator() {
* @return and identical copy of this Group object
*/
@Override
public Object clone() {
public HetatomImpl clone() {

HetatomImpl n = new HetatomImpl();
n.setPDBFlag(has3D());
Expand All @@ -339,7 +339,7 @@ public Object clone() {

// copy the atoms
for (Atom atom1 : atoms) {
Atom atom = (Atom) atom1.clone();
Atom atom = atom1.clone();
n.addAtom(atom);
atom.setGroup(n);
}
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4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java
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Expand Up @@ -95,7 +95,7 @@ public Atom getP() {
}

@Override
public Object clone(){
public NucleotideImpl clone(){
NucleotideImpl n = new NucleotideImpl();

n.setPDBFlag(has3D());
Expand All @@ -105,7 +105,7 @@ public Object clone(){

// copy the atoms
for (Atom atom1 : atoms) {
Atom atom = (Atom) atom1.clone();
Atom atom = atom1.clone();
n.addAtom(atom);
atom.setGroup(n);
}
Expand Down
2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
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Expand Up @@ -152,7 +152,7 @@ public Structure clone() {

for (int j=0;j<size(i);j++){

Chain cloned_chain = (Chain) getChain(i,j).clone();
Chain cloned_chain = getChain(i,j).clone();

// setting the parent: can only be done from the parent
cloned_chain.setParent(n);
Expand Down
8 changes: 4 additions & 4 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
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Expand Up @@ -486,7 +486,7 @@ public static final Atom[] cloneCAArray(Atom[] ca) throws StructureException{
model.add(newChain);
}

Group parentN = (Group)parentG.clone();
Group parentN = parentG.clone();

newCA[apos] = parentN.getAtom(CA_ATOM_NAME);
newChain.addGroup(parentN);
Expand Down Expand Up @@ -522,7 +522,7 @@ public static Group[] cloneGroups(Atom[] ca) {
model.add(newChain);
}

Group ng = (Group)parentG.clone();
Group ng = parentG.clone();
newGroup[apos] = ng;
newChain.addGroup(ng);
}
Expand All @@ -546,7 +546,7 @@ public static Atom[] duplicateCA2(Atom[] ca2) throws StructureException{
Chain c = null;
String prevChainId = "";
for (Atom a : ca2){
Group g = (Group) a.getGroup().clone(); // works because each group has only a CA atom
Group g = a.getGroup().clone(); // works because each group has only a CA atom

if (c == null ) {
c = new ChainImpl();
Expand All @@ -570,7 +570,7 @@ public static Atom[] duplicateCA2(Atom[] ca2) throws StructureException{
c = null;
prevChainId = "";
for (Atom a : ca2){
Group g = (Group)a.getGroup().clone();
Group g = a.getGroup().clone();

if (c == null ) {
c = new ChainImpl();
Expand Down
6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
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Expand Up @@ -289,8 +289,8 @@ private static Atom[] getAtoms(Atom[] ca, int[] positions, int length, boolean c
int p = positions[i];
Atom a;
if ( clone ){
a = (Atom)ca[p].clone();
a.setGroup((Group)ca[p].getGroup().clone());
a = ca[p].clone();
a.setGroup(ca[p].getGroup().clone());
}
else {
a = ca[p];
Expand Down Expand Up @@ -322,7 +322,7 @@ private static void cloneAtomRange(Atom[] p1, Atom[] p2, int r1, int r2)
for(int i = r1; i < r2; i ++) {

Group g = p2[i].getGroup();
Group newG = (Group)g.clone();
Group newG = g.clone();

p1[i] = newG.getAtom(StructureTools.CA_ATOM_NAME);
Chain parentC = g.getChain();
Expand Down
2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java
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Expand Up @@ -478,7 +478,7 @@ public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
Matrix rotmat = svd.getRotation();
f.setRot(rotmat);

Atom aunitv = (Atom)unitvector.clone();
Atom aunitv = unitvector.clone();
Calc.rotate(aunitv,rotmat);
f.setUnitv(aunitv);

Expand Down
4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
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Expand Up @@ -1842,7 +1842,7 @@ private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) th

for(int l=0; l<nse2; l++) {
Atom a = caA[l];
Group g = (Group)a.getGroup().clone();
Group g = a.getGroup().clone();
//Group g = (Group)a.getParent();

Calc.rotate( g, m);
Expand Down Expand Up @@ -1933,7 +1933,7 @@ private Atom[] getAtoms(Atom[] ca, int length, boolean clone) throws StructureE

Atom a;
if ( clone ){
Group g = (Group)ca[i].getGroup().clone();
Group g = ca[i].getGroup().clone();
a = g.getAtom(StructureTools.CA_ATOM_NAME);
}
else {
Expand Down
4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
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Expand Up @@ -476,7 +476,7 @@ public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCal
atoms1[pos] = ca1[pair.a];
// Clone residue to allow modification
Atom atom2 = ca2duplicated[pair.b];
Group g = (Group) atom2.getGroup().clone();
Group g = atom2.getGroup().clone();
atoms2[pos] = g.getAtom( atom2.getName() );
pos++;
}
Expand Down Expand Up @@ -516,7 +516,7 @@ public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCal
for(int i=1;i<blocks.size();i++) {
blockRMSDs[i] = -1; //TODO Recalculate for the FATCAT text format
blockRotationMatrices[i] = (Matrix) blockRotationMatrices[0].clone();
blockShifts[i] = (Atom) blockShifts[0].clone();
blockShifts[i] = blockShifts[0].clone();
}

}
Expand Down
4 changes: 2 additions & 2 deletions ...ava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
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Expand Up @@ -1922,7 +1922,7 @@ private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) th

for(int l=0; l<nse2; l++) {
Atom a = caA[l];
Group g = (Group)a.getGroup().clone();
Group g = a.getGroup().clone();
//Group g = (Group)a.getParent();

Calc.rotate( g, m);
Expand Down Expand Up @@ -2018,7 +2018,7 @@ private Atom[] getAtoms(Atom[] ca, int length, boolean clone) throws StructureE

Atom a;
if ( clone ){
Group g = (Group)ca[i].getGroup().clone();
Group g = ca[i].getGroup().clone();
a = g.getAtom(StructureTools.CA_ATOM_NAME);
}
else {
Expand Down
2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
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Expand Up @@ -95,7 +95,7 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureExce

int pos = 0;
for (Atom a : ca2){
Group g = (Group)a.getGroup().clone(); // works because each group has only a CA atom
Group g = a.getGroup().clone(); // works because each group has only a CA atom

ca2clone[pos] = g.getAtom(StructureTools.CA_ATOM_NAME);

Expand Down
2 changes: 1 addition & 1 deletion ...a-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
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Expand Up @@ -232,7 +232,7 @@ private static final Atom[] getFragment(Atom[] caall, int pos, int fragmentLengt

for (int i=0;i< fragmentLength;i++){
if (clone){
tmp[i] = (Atom)caall[i+pos].clone();
tmp[i] = caall[i+pos].clone();
} else {
tmp[i] = caall[i+pos];
}
Expand Down
2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
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Expand Up @@ -670,7 +670,7 @@ private static double getRmsd(int focusResn, int[] focusRes1, int[] focusRes2, A

for ( int i =0 ; i< focusResn;i++){
tmp1[i] = ca1[focusRes1[i]];
tmp2[i] = (Atom)ca2[focusRes2[i]].clone();
tmp2[i] = ca2[focusRes2[i]].clone();
if (tmp1[i].getCoords() == null){
System.err.println("tmp1 got null: " +i + " pos: " + focusRes1[i]);
}
Expand Down
6 changes: 3 additions & 3 deletions ...c/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
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Expand Up @@ -95,15 +95,15 @@ public StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2
for(int i = 0; i < len1; i ++) {
Atom a = c1[i+b1];
//cod1[i] = (Atom)a.clone();
Group parent = (Group)a.getGroup().clone();
Group parent = a.getGroup().clone();
//cod1[i].setParent(parent);
cod1[i] = parent.getAtom(StructureTools.CA_ATOM_NAME);
//cod1[i] = c1[i];
}
for(int i = 0; i < len2; i ++) {
Atom a = c2[i+b2];
//cod2[i]= (Atom)a.clone();
Group parent = (Group)a.getGroup().clone();
Group parent = a.getGroup().clone();
//cod2[i].setParent(parent);
cod2[i] = parent.getAtom(StructureTools.CA_ATOM_NAME);
//cod2[i] = c2[i];
Expand Down Expand Up @@ -247,7 +247,7 @@ private void superimposeBySet ()
r2 = equSet[1][i];

tmp1[i] = cod1[ r1 ];
tmp2[i] = (Atom)cod2[ r2 ].clone(); // have to be cloned!
tmp2[i] = cod2[ r2 ].clone(); // have to be cloned!
//tmp2[i] = cod2[ r2 ];


Expand Down
4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AlignTools.java
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Expand Up @@ -41,7 +41,7 @@ public static Atom[] getFragmentFromIdxList(Atom[] caall, int[] idx){
for (int p = 0 ; p < idx.length;p++){

int pos1 = idx[p];
subset[p] = (Atom) caall[pos1].clone();
subset[p] = caall[pos1].clone();
}
return subset;
}
Expand All @@ -61,7 +61,7 @@ public static Atom[] getFragment(Atom[] caall, int pos, int fragmentLength){
Atom[] tmp = new Atom[fragmentLength];

for (int i=0;i< fragmentLength;i++){
tmp[i] = (Atom)caall[i+pos].clone();
tmp[i] = caall[i+pos].clone();
}
return tmp;

Expand Down
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