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made the constructors protected. Protected also mean package-protected, so other methods in the utils class can call these constructors (mainly the parser), as well as any inheriting classes. Also fixed some Intellij suggested clean-ups and documentation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1071 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-22 16:01:59 +00:00
parent 9e25229014
commit 4a92a999a0
1 changed files with 12 additions and 17 deletions
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29
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -45,11 +45,11 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
this.stop = stop == -1 ? start : stop; this.stop = stop == -1 ? start : stop;
}*/ }*/
GenomeLoc(final SAMRecord read) { protected GenomeLoc(final SAMRecord read) {
this(read.getHeader().getSequence(read.getReferenceIndex()).getSequenceName(), read.getReferenceIndex(), read.getAlignmentStart(), read.getAlignmentEnd()); this(read.getHeader().getSequence(read.getReferenceIndex()).getSequenceName(), read.getReferenceIndex(), read.getAlignmentStart(), read.getAlignmentEnd());
} }
GenomeLoc( final String contig, final int contigIndex, final long start, final long stop ) { protected GenomeLoc( final String contig, final int contigIndex, final long start, final long stop ) {
this.contigName = contig; this.contigName = contig;
this.contigIndex = contigIndex; this.contigIndex = contigIndex;
this.start = start; this.start = start;
@ -60,16 +60,17 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
this(contig, pos, pos ); this(contig, pos, pos );
} }
*/ */
GenomeLoc( final GenomeLoc toCopy ) { protected GenomeLoc( final GenomeLoc toCopy ) {
this( toCopy.getContig(), toCopy.contigIndex, toCopy.getStart(), toCopy.getStop() ); this( toCopy.getContig(), toCopy.contigIndex, toCopy.getStart(), toCopy.getStop() );
} }
/** /**
* Returns true iff we have a specified series of locations to process AND we are past the last * Returns true if we have a specified series of locations to process AND we are past the last
* location in the list. It means that, in a serial processing of the genome, that we are done. * location in the list. It means that, in a serial processing of the genome, that we are done.
* *
* @param curr Current genome Location * @param curr Current genome Location
* @param locs a list of genomic locations
* @return true if we are past the last location to process * @return true if we are past the last location to process
*/ */
public static boolean pastFinalLocation(GenomeLoc curr, List<GenomeLoc> locs) { public static boolean pastFinalLocation(GenomeLoc curr, List<GenomeLoc> locs) {
@ -80,7 +81,8 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
* A key function that returns true if the proposed GenomeLoc curr is within the list of * A key function that returns true if the proposed GenomeLoc curr is within the list of
* locations we are processing in this TraversalEngine * locations we are processing in this TraversalEngine
* *
* @param curr * @param curr the current location
* @param locs a list of genomic locations
* @return true if we should process GenomeLoc curr, otherwise false * @return true if we should process GenomeLoc curr, otherwise false
*/ */
public static boolean inLocations(GenomeLoc curr, ArrayList<GenomeLoc> locs) { public static boolean inLocations(GenomeLoc curr, ArrayList<GenomeLoc> locs) {
@ -158,17 +160,11 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
public final boolean isSingleBP() { return stop == start; } public final boolean isSingleBP() { return stop == start; }
public final boolean disjointP(GenomeLoc that) { public final boolean disjointP(GenomeLoc that) {
if ( this.contigIndex != that.contigIndex ) return true; // different chromosomes return this.contigIndex != that.contigIndex || this.start > that.stop || that.start > this.stop;
if ( this.start > that.stop ) return true; // this guy is past that
if ( that.start > this.stop ) return true; // that guy is past our start
return false;
} }
public final boolean discontinuousP(GenomeLoc that) { public final boolean discontinuousP(GenomeLoc that) {
if ( this.contigIndex != that.contigIndex ) return true; // different chromosomes return this.contigIndex != that.contigIndex || (this.start - 1) > that.stop || (that.start - 1) > this.stop;
if ( (this.start - 1) > that.stop ) return true; // this guy is past that
if ( (that.start - 1) > this.stop ) return true; // that guy is past our start
return false;
} }
public final boolean overlapsP(GenomeLoc that) { public final boolean overlapsP(GenomeLoc that) {
@ -190,8 +186,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
} }
public final boolean containsP(GenomeLoc that) { public final boolean containsP(GenomeLoc that) {
if ( ! onSameContig(that) ) return false; return onSameContig(that) && getStart() <= that.getStart() && getStop() >= that.getStop();
return getStart() <= that.getStart() && getStop() >= that.getStop();
} }
public final boolean onSameContig(GenomeLoc that) { public final boolean onSameContig(GenomeLoc that) {
@ -272,8 +267,8 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
/** /**
* conpare this genomeLoc's contig to another genome loc * conpare this genomeLoc's contig to another genome loc
* @param that * @param that the genome loc to compare contigs with
* @return * @return 0 if equal, -1 if that.contig is greater, 1 if this.contig is greater
*/ */
public final int compareContigs( GenomeLoc that ) { public final int compareContigs( GenomeLoc that ) {
if (this.contigIndex == that.contigIndex) if (this.contigIndex == that.contigIndex)