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Merged
josemduarte merged 2 commits into from
Mar 14, 2018
Merged

Removed v4 deprecations #749

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9dbf83c
Removing deprecations from v4
josemduarte Mar 12, 2018
5975b17
Removing class deprecations from v4
josemduarte Mar 12, 2018
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12 changes: 0 additions & 12 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
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Expand Up @@ -107,18 +107,6 @@ public StockholmConsensusAnnotation getConsAnnotation() {
return consAnnotation;
}

/**
* Actually this function should be called appendToSequence
*
* @param seqName
* @param seqText
* @deprecated Use {@link #appendToSequence(String,String)} instead
*/
@Deprecated
public void addSequence(String seqName, String seqText) {
appendToSequence(seqName, seqText);
}

/**
* @param seqName
* @param seqText
Expand Down
6 changes: 0 additions & 6 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/NucleotideCompound.java
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Expand Up @@ -104,12 +104,6 @@ public Set<NucleotideCompound> getConstituents() {
return constituents;
}

/**@deprecated replaced with {@link #getConstituents()} due to typographical error */
@Deprecated
public Set<NucleotideCompound> getConsituents() {
return getConstituents();
}

public boolean isAmbiguous() {
return !constituents.isEmpty();
}
Expand Down
78 changes: 0 additions & 78 deletions .../src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java
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Expand Up @@ -67,84 +67,6 @@ public class RNAToAminoAcidTranslator extends
// first residue in the resulting ProteinSequence
private final boolean waitForStartCodon;

/**
* @deprecated Retained for backwards compatability, setting
* {@link #stopAtStopCodons} to <code>false</code>
*/
@Deprecated
public RNAToAminoAcidTranslator(
SequenceCreatorInterface<AminoAcidCompound> creator,
CompoundSet<NucleotideCompound> nucleotides,
CompoundSet<Codon> codons,
CompoundSet<AminoAcidCompound> aminoAcids, Table table,
boolean trimStops, boolean initMetOnly, boolean translateNCodons) {

super(creator, nucleotides, aminoAcids);
this.trimStops = trimStops;
this.initMetOnly = initMetOnly;
this.translateNCodons = translateNCodons;

quickLookup = new HashMap<Table.CaseInsensitiveTriplet, Codon>(codons
.getAllCompounds().size());
aminoAcidToCodon = new HashMap<AminoAcidCompound, List<Codon>>();

List<Codon> codonList = table.getCodons(nucleotides, aminoAcids);
for (Codon codon : codonList) {
quickLookup.put(codon.getTriplet(), codon);
codonArray[codon.getTriplet().intValue()] = codon;

List<Codon> codonL = aminoAcidToCodon.get(codon.getAminoAcid());
if (codonL == null) {
codonL = new ArrayList<Codon>();
aminoAcidToCodon.put(codon.getAminoAcid(), codonL);
}
codonL.add(codon);

}
unknownAminoAcidCompound = aminoAcids.getCompoundForString("X");
methionineAminoAcidCompound = aminoAcids.getCompoundForString("M");
// Set to false for backwards compatability
stopAtStopCodons = false;
waitForStartCodon = false;
}

@Deprecated
public RNAToAminoAcidTranslator(
SequenceCreatorInterface<AminoAcidCompound> creator,
CompoundSet<NucleotideCompound> nucleotides,
CompoundSet<Codon> codons,
CompoundSet<AminoAcidCompound> aminoAcids, Table table,
boolean trimStops, boolean initMetOnly, boolean translateNCodons,
boolean stopAtStopCodons) {

super(creator, nucleotides, aminoAcids);
this.trimStops = trimStops;
this.initMetOnly = initMetOnly;
this.translateNCodons = translateNCodons;

quickLookup = new HashMap<Table.CaseInsensitiveTriplet, Codon>(codons
.getAllCompounds().size());
aminoAcidToCodon = new HashMap<AminoAcidCompound, List<Codon>>();

List<Codon> codonList = table.getCodons(nucleotides, aminoAcids);
for (Codon codon : codonList) {
quickLookup.put(codon.getTriplet(), codon);
codonArray[codon.getTriplet().intValue()] = codon;

List<Codon> codonL = aminoAcidToCodon.get(codon.getAminoAcid());
if (codonL == null) {
codonL = new ArrayList<Codon>();
aminoAcidToCodon.put(codon.getAminoAcid(), codonL);
}
codonL.add(codon);

}
unknownAminoAcidCompound = aminoAcids.getCompoundForString("X");
methionineAminoAcidCompound = aminoAcids.getCompoundForString("M");
this.stopAtStopCodons = stopAtStopCodons;
// Set for backwards compatibility
waitForStartCodon = false;
}

public RNAToAminoAcidTranslator(
SequenceCreatorInterface<AminoAcidCompound> creator,
Expand Down
22 changes: 0 additions & 22 deletions biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
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Expand Up @@ -313,28 +313,6 @@ public String toString() {
return s;
}

/**
* @deprecated
*/
@Deprecated
public static void main(String[] args)
throws Exception {
//Feature f= new Feature();
//intentionally perverse
//f.group= "gene_id transcript; transcript \"gene_id fantom2\"; ";
// f.addAttribute( "author", "julian" );
// f.addAttribute( "curator", "nick" );
// f.addAttribute( "author", "hanno" );
//Log.log( f.group );
//f.addAttribute( "perverse", "foo;goo" );
//assert f.getAttribute( "perverse").equals( "foo;goo" );
// assert f.getAttribute( "gene_id" ).equals( "transcript" );
// assert f.getAttribute( "author" ).equals( "julian hanno" );
// assert f.getAttribute( "curator" ).equals( "nick" );
// assert f.getAttribute( "transcript").equals( "gene_id fantom2" );
//Log.log( "passed test." );
}

@Override
public HashMap<String, String> getAttributes() {

Expand Down
10 changes: 0 additions & 10 deletions biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
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Expand Up @@ -497,16 +497,6 @@ public FeatureList sortByStart() {
return new FeatureList(Arrays.asList(array));
}

/**
* @deprecated
*
*/
// FIXME features may have a null location() !!
@Deprecated
static public void main(String[] args) {
}


/**
* Add a list of attributes that will be used as indexes for queries
* @param indexes the List containing the attribute_id
Expand Down
116 changes: 1 addition & 115 deletions biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
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Expand Up @@ -20,10 +20,6 @@
*/
package org.biojava.nbio.genome.parsers.gff;

import org.biojava.nbio.genome.App;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;


/**
* A location on a sequence.
Expand Down Expand Up @@ -72,16 +68,10 @@
*/
public class Location implements Iterable<Location>
{
private static final Logger logger = LoggerFactory.getLogger(App.class);


private int mStart;
private int mEnd;

// /**
// */
// private Location()
// {
// }

/**
* Construct new location from coordinates.
Expand Down Expand Up @@ -895,108 +885,4 @@ private boolean isHealthy()
return ( mStart <= mEnd ) && (( mStart <= 0 && mEnd <= 0 ) || (mStart >= 0 && mEnd >= 0));
}

//shorthand for testing
static private Location L( int s, int e )
{
return new Location( s, e );
}

@SuppressWarnings("unused")
static private Location R( int s, int e )
{
return new Location( -e, -s );
}


/**
* @deprecated
*/
@Deprecated
@SuppressWarnings("unused")
public static void main(String[] args )
throws Exception
{
Location p3_7= new Location( 3, 7 );
Location p16_19= new Location( 16, 19 );
Location p15_19= new Location( 15, 19 );
Location p15_16= new Location( 15, 16 );
Location p10_17= new Location( 10, 17 );
Location p10_12= new Location( 10, 12 );
Location p14_17= new Location( 14, 17 );
Location p14_14= new Location( 14, 14 );

Location r13_17= new Location( 13, 17 );
Location r21_25= new Location( 21, 25 );

Location r4_7= new Location( 4, 7 );
Location r2_5= new Location( 2, 5 );
Location r0_3= new Location( 0, 3 );
Location r5_8= new Location( 5, 8 );

//distance
assert L(14,14).distance( L(3,7) ) == 7;
assert L(3,7).distance( L(14,14) ) == 7;
assert L(1,4).distance( L(7, 10) ) == 3;

//union
assert p10_12.union( p14_17 ).equals( p10_17 );
assert p14_17.union( p10_12 ).equals( p10_17 );
assert p15_19.union( p15_16).equals( p15_19 );

//intersection
assert r13_17.union( r21_25 ).intersection( r21_25 ).equals( new Location( 21, 25 ));


//isBefore
assert r2_5.isBefore( r5_8 );
assert !r2_5.isBefore( r4_7 );

//isAfter
assert r5_8.isAfter( r2_5 );
assert !r5_8.isAfter( r4_7 );

//contains
assert p15_19.contains( p16_19 );

//overlaps
assert r2_5.overlaps( r4_7 );
assert r2_5.overlaps( r0_3 );
assert !r5_8.overlaps( r2_5 );
assert !r2_5.overlaps( r5_8 );


//prefix
assert L(2,20).prefix(1).equals( L(2,3));
assert L(2,20).prefix(-1).equals( L(2,19));
assert L(2,20).prefix( L(10,12)).equals( L(2,10));

//suffix
assert L(2,20).suffix(1).equals( L(3,20));
assert L(2,20).suffix(-1).equals( L(19,20));
assert L(2,20).suffix( L(10,12)).equals( L(12,20));


//upstream
//downstream

//startsBefore
//startsAfter
//endsBefore
//endsAfter

//equals

//percentoverlap


//plus
//minus
//isNegative
//oppposite

//fromBio, etc.

logger.info("JavaGene.Location Passed.");
}

}
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