/**
* bior_pipeline
*
* <p>@author Gregory Dougherty</p>
* Copyright Mayo Clinic, 2011
*
*/
package edu.mayo.bior.pipeline.Treat;
/**
* Class to get non-Allele Frequency variant information from the TreatPipeline to the Table Browser
* <p>@author Gregory Dougherty</p>
*
*/
public class VariantInfo
{
private String chromosome;
private String ref;
private String alt;
private int startPos;
private int endPos;
private int entrezGeneID;
private int firstBuild;
private String dbSNPsID;
private String suspectRegion;
private String clinicalSig;
private String alleleOrigin;
private boolean diseaseVariant;
private String geneSymbol;
private String ensemblGeneID;
private int mutationID;
private String cosmicCDS;
private String cosmicAA;
private boolean strand;
private String omimDisease;
private boolean blacklisted;
private boolean conserved;
private boolean enhancer;
private boolean tfbs;
private boolean tss;
private boolean unique;
private boolean repeat;
private boolean regulatory;
private String landmark;
private String type;
private int minBP;
private int maxBP;
private boolean miRStrand;
private String acc;
private String miRBId;
/**
* Constructor for VariantInfo
*
* @param chromosome Chromosome of the variant this frequency is for
* @param startPos Where in the chromosome the variant starts
* @param endPos Where in the chromosome the variant ends, if it is an indel. -1 if it is an SNV
* @param ref The reference base(s)
* @param alt The alternate base(s)
* @param entrezGeneID The EntrezGeneID, or -1 if none
* @param firstBuild First time it appeared in dbSNPs, -1 if not in
* @param dbSNPsID dbSNPs ID if it has one, or null if it doesn't
* @param suspectRegion String giving one of 6 possible regions
* @param clinicalSig String giving one of 9 possible clinical significance values
* @param alleleOrigin String giving one of 4 (to be 7) possible allelic origin values
* @param diseaseVariant True if variant is know to cause a disease, else false
* @param geneSymbol HGNC Approved Gene Symbol of the gene the Variant is in, null if not in one
* @param ensemblGeneID EnsemblGeneID if it has one, or null if it doesn't
* @param mutationID Cosmic mutation ID, or -1
* @param cosmicCDS Cosmic: nucleotide sequence change
* @param cosmicAA Cosmic: Peptide sequence change
* @param strand Cosmic: NCBI provided + (true) or - (false) strand
* @param omimDisease OMIM disease if it has one, or null if it doesn't
* @param blacklisted True if blacklist score is above the cutoff, false otherwise
* @param conserved True if conserved score is above the cutoff, false otherwise
* @param enhancer True if enhancer score is above the cutoff, false otherwise
* @param tfbs True if tfbs score is above the cutoff, false otherwise
* @param tss True if tss score is above the cutoff, false otherwise
* @param unique True if unique score is above the cutoff, false otherwise
* @param repeat True if repeat score is above the cutoff, false otherwise
* @param regulatory True if regulatory score is above the cutoff, false otherwise
* @param landmark miRBase Landmark, a Chromosome specifier
* @param type miRBase type, generally "miRNA"
* @param minBP Location on the Chromosome where the miRBase item starts
* @param maxBP Location on the Chromosome where the miRBase item ends
* @param miRStrand Which strand of the Chromosome where the miRBase item ends
* @param acc The accession for the entry in miRBase
* @param id The identifier for the entry in miRBase
*/
public VariantInfo (String chromosome, int startPos, int endPos, String ref, String alt, int entrezGeneID,
int firstBuild, String dbSNPsID, String suspectRegion, String clinicalSig,
String alleleOrigin, boolean diseaseVariant, String geneSymbol, String ensemblGeneID,
int mutationID, String cosmicCDS, String cosmicAA, boolean strand, String omimDisease,
boolean blacklisted, boolean conserved, boolean enhancer, boolean tfbs,
boolean tss, boolean unique, boolean repeat, boolean regulatory, String landmark,
String type, int minBP, int maxBP, boolean miRStrand, String acc, String id)
{
this.chromosome = chromosome;
this.startPos = startPos;
this.endPos = endPos;
this.ref = ref;
this.alt = alt;
this.entrezGeneID = entrezGeneID;
this.firstBuild = firstBuild;
this.geneSymbol = geneSymbol;
this.dbSNPsID = dbSNPsID;
this.ensemblGeneID = ensemblGeneID;
this.mutationID = mutationID;
this.cosmicCDS = cosmicCDS;
this.cosmicAA = cosmicAA;
this.strand = strand;
this.omimDisease = omimDisease;
this.blacklisted = blacklisted;
this.conserved = conserved;
this.enhancer = enhancer;
this.tfbs = tfbs;
this.tss = tss;
this.unique = unique;
this.repeat = repeat;
this.regulatory = regulatory;
this.landmark = landmark;
this.type = type;
this.minBP = minBP;
this.maxBP = maxBP;
this.miRStrand = miRStrand;
this.acc = acc;
this.miRBId = id;
}
/**
* @return the chromosome
*/
public final String getChromosome ()
{
return chromosome;
}
/**
* @return the ref
*/
public final String getRef ()
{
return ref;
}
/**
* @return the alt
*/
public final String getAlt ()
{
return alt;
}
/**
* @return the startPos
*/
public final int getStartPos ()
{
return startPos;
}
/**
* @return the endPos
*/
public final int getEndPos ()
{
return endPos;
}
/**
* @return the entrezGeneID
*/
public final int getEntrezGeneID ()
{
return entrezGeneID;
}
/**
* @return the firstBuild
*/
public final int getFirstBuild ()
{
return firstBuild;
}
/**
* @return the dbSNPsID
*/
public final String getDbSNPsID ()
{
return dbSNPsID;
}
/**
* @return the suspectRegion
*/
public final String getSuspectRegion ()
{
return suspectRegion;
}
/**
* @return the clinicalSig
*/
public final String getClinicalSig ()
{
return clinicalSig;
}
/**
* @return the alleleOrigin
*/
public final String getAlleleOrigin ()
{
return alleleOrigin;
}
/**
* @return the diseaseVariant
*/
public final boolean isDiseaseVariant ()
{
return diseaseVariant;
}
/**
* @return the geneSymbol
*/
public final String getGeneSymbol ()
{
return geneSymbol;
}
/**
* @return the ensemblGeneID
*/
public final String getEnsemblGeneID ()
{
return ensemblGeneID;
}
/**
* @return the mutationID
*/
public final int getMutationID ()
{
return mutationID;
}
/**
* @return the cosmicCDS
*/
public final String getCosmicCDS ()
{
return cosmicCDS;
}
/**
* @return the cosmicAA
*/
public final String getCosmicAA ()
{
return cosmicAA;
}
/**
* @return the strand
*/
public final boolean isStrand ()
{
return strand;
}
/**
* @return the omimDisease
*/
public final String getOMIMDisease ()
{
return omimDisease;
}
/**
* @return the blacklisted
*/
public final boolean isBlacklisted ()
{
return blacklisted;
}
/**
* @return the conserved
*/
public final boolean isConserved ()
{
return conserved;
}
/**
* @return the enhancer
*/
public final boolean isEnhancer ()
{
return enhancer;
}
/**
* @return the tfbs
*/
public final boolean isTfbs ()
{
return tfbs;
}
/**
* @return the tss
*/
public final boolean isTss ()
{
return tss;
}
/**
* @return the unique
*/
public final boolean isUnique ()
{
return unique;
}
/**
* @return the repeat
*/
public final boolean isRepeat ()
{
return repeat;
}
/**
* @return the regulatory
*/
public final boolean isRegulatory ()
{
return regulatory;
}
/**
* @return the omimDisease
*/
public final String getOmimDisease ()
{
return omimDisease;
}
/**
* @return the landmark
*/
public final String getLandmark ()
{
return landmark;
}
/**
* @return the type
*/
public final String getType ()
{
return type;
}
/**
* @return the minBP
*/
public final int getMinBP ()
{
return minBP;
}
/**
* @return the maxBP
*/
public final int getMaxBP ()
{
return maxBP;
}
/**
* @return the miRStrand
*/
public final boolean isMiRStrand ()
{
return miRStrand;
}
/**
* @return the acc
*/
public final String getAcc ()
{
return acc;
}
/**
* @return the id
*/
public final String getId ()
{
return miRBId;
}
/* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode ()
{
final int prime = 31;
int result = 1;
result = prime * result + (blacklisted ? 1231 : 1237);
result = prime * result + ((chromosome == null) ? 0 : chromosome.hashCode ());
result = prime * result + ((ref == null) ? 0 : ref.hashCode ());
result = prime * result + ((alt == null) ? 0 : alt.hashCode ());
result = prime * result + (conserved ? 1231 : 1237);
result = prime * result + ((dbSNPsID == null) ? 0 : dbSNPsID.hashCode ());
result = prime * result + ((suspectRegion == null) ? 0 : suspectRegion.hashCode ());
result = prime * result + ((clinicalSig == null) ? 0 : clinicalSig.hashCode ());
result = prime * result + ((alleleOrigin == null) ? 0 : alleleOrigin.hashCode ());
result = prime * result + (diseaseVariant ? 1231 : 1237);
result = prime * result + endPos;
result = prime * result + (enhancer ? 1231 : 1237);
result = prime * result + ((ensemblGeneID == null) ? 0 : ensemblGeneID.hashCode ());
result = prime * result + entrezGeneID;
result = prime * result + firstBuild;
result = prime * result + ((geneSymbol == null) ? 0 : geneSymbol.hashCode ());
result = prime * result + ((omimDisease == null) ? 0 : omimDisease.hashCode ());
result = prime * result + (regulatory ? 1231 : 1237);
result = prime * result + (repeat ? 1231 : 1237);
result = prime * result + startPos;
result = prime * result + (tfbs ? 1231 : 1237);
result = prime * result + (tss ? 1231 : 1237);
result = prime * result + (unique ? 1231 : 1237);
result = prime * result + mutationID; // Ignore rest of Cosmic, they all key on mutationID
result = prime * result + ((miRBId == null) ? 0 : miRBId.hashCode ());
return result;
}
/* (non-Javadoc)
* @see java.lang.Object#equals(java.lang.Object)
*/
@Override
public boolean equals (Object obj)
{
if (this == obj)
return true;
if (obj == null)
return false;
if (!(obj instanceof VariantInfo))
return false;
VariantInfo other = (VariantInfo) obj;
if (blacklisted != other.blacklisted)
return false;
if (diseaseVariant != other.diseaseVariant)
return false;
if (conserved != other.conserved)
return false;
if (endPos != other.endPos)
return false;
if (enhancer != other.enhancer)
return false;
if (entrezGeneID != other.entrezGeneID)
return false;
if (firstBuild != other.firstBuild)
return false;
if (regulatory != other.regulatory)
return false;
if (repeat != other.repeat)
return false;
if (startPos != other.startPos)
return false;
if (tfbs != other.tfbs)
return false;
if (tss != other.tss)
return false;
if (unique != other.unique)
return false;
if (mutationID != other.mutationID) // Ignore rest of Cosmic, they all key on mutationID
return false;
if (miRBId == null) // Ignore rest of miRBase, they all key on id
{
if (other.miRBId != null)
return false;
}
else if (!miRBId.equals (other.miRBId))
return false;
if (chromosome == null)
{
if (other.chromosome != null)
return false;
}
else if (!chromosome.equals (other.chromosome))
return false;
if (ref == null)
{
if (other.ref != null)
return false;
}
else if (!ref.equals (other.ref))
return false;
if (alt == null)
{
if (other.alt != null)
return false;
}
else if (!alt.equals (other.alt))
return false;
if (dbSNPsID == null)
{
if (other.dbSNPsID != null)
return false;
}
else if (!dbSNPsID.equals (other.dbSNPsID))
return false;
if (ensemblGeneID == null)
{
if (other.ensemblGeneID != null)
return false;
}
else if (!ensemblGeneID.equals (other.ensemblGeneID))
return false;
if (geneSymbol == null)
{
if (other.geneSymbol != null)
return false;
}
else if (!geneSymbol.equals (other.geneSymbol))
return false;
if (omimDisease == null)
{
if (other.omimDisease != null)
return false;
}
else if (!omimDisease.equals (other.omimDisease))
return false;
if (suspectRegion == null)
{
if (other.suspectRegion != null)
return false;
}
else if (!suspectRegion.equals (other.suspectRegion))
return false;
if (clinicalSig == null)
{
if (other.clinicalSig != null)
return false;
}
else if (!clinicalSig.equals (other.clinicalSig))
return false;
if (alleleOrigin == null)
{
if (other.alleleOrigin != null)
return false;
}
else if (!alleleOrigin.equals (other.alleleOrigin))
return false;
return true;
}
/**
* Return a tab delimited string with the columns in the order of {@link #toTabString ()}
*
* @return Tab delimited string, no tab at beginning or end
*/
public static String tabHeader ()
{
StringBuilder builder = new StringBuilder ();
builder.append ("chromosome\tref\talt\tstartPos\tendPos\tentrezGeneID\tdbSNPsID\tfirstBuild\t");
builder.append ("alleleOrigin\tclinicalSig\tsuspectRegion\tdiseaseVariant\t");
builder.append ("geneSymbol\tensemblGeneID\tmutationID\tcosmicCDS\tcosmicAA\tstrand\tOMIMDisease\t");
builder.append ("blacklisted\tconserved\tenhancer\ttfbs\ttss\tunique\trepeat\tregulatory\t");
builder.append ("landmark\ttype\tmnBP\tmaxBP\tstrand\tacc\tID");
return builder.toString ();
}
/**
* Return a tab delimited string with the columns in the order of {@link #tabHeader ()}
*
* @return Tab delimited string, no tab at beginning or end
*/
public String toTabString ()
{
StringBuilder builder = new StringBuilder ();
builder.append (chromosome);
builder.append ("\t");
builder.append (ref);
builder.append ("\t");
builder.append (alt);
builder.append ("\t");
builder.append (startPos);
builder.append ("\t");
builder.append (endPos);
builder.append ("\t");
builder.append (entrezGeneID);
builder.append ("\t");
builder.append (dbSNPsID);
builder.append ("\t");
builder.append (firstBuild);
builder.append ("\t");
builder.append (alleleOrigin);
builder.append ("\t");
builder.append (clinicalSig);
builder.append ("\t");
builder.append (suspectRegion);
builder.append ("\t");
builder.append (diseaseVariant);
builder.append ("\t");
builder.append (geneSymbol);
builder.append ("\t");
builder.append (ensemblGeneID);
builder.append ("\t");
if (mutationID > 0)
{
builder.append (mutationID);
builder.append ("\t");
builder.append (cosmicCDS);
builder.append ("\t");
builder.append (cosmicAA);
if (strand)
builder.append ("\t+\t");
else
builder.append ("\t-\t");
}
else
builder.append ("-1\t\t\t\t");
builder.append (omimDisease);
builder.append ("\t");
builder.append (blacklisted);
builder.append ("\t");
builder.append (conserved);
builder.append ("\t");
builder.append (enhancer);
builder.append ("\t");
builder.append (tfbs);
builder.append ("\t");
builder.append (tss);
builder.append ("\t");
builder.append (unique);
builder.append ("\t");
builder.append (repeat);
builder.append ("\t");
builder.append (regulatory);
if (miRBId != null)
{
builder.append ("\t");
builder.append (landmark);
builder.append ("\t");
builder.append (type);
builder.append ("\t");
builder.append (minBP);
builder.append ("\t");
builder.append (maxBP);
if (miRStrand)
builder.append ("\t+\t");
else
builder.append ("\t-\t");
builder.append (acc);
builder.append ("\t");
builder.append (miRBId);
}
else
builder.append ("\t\t\t\t\t\t\t");
return builder.toString ();
}
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
@Override
public String toString ()
{
StringBuilder builder = new StringBuilder ();
builder.append ("VariantInfo [chromosome = ");
builder.append (chromosome);
builder.append (", (");
builder.append (ref);
builder.append (" -> ");
builder.append (alt);
builder.append ("), [");
builder.append (startPos);
if (endPos >= 0)
{
builder.append (", ");
builder.append (endPos);
}
builder.append ("], entrezGeneID = ");
builder.append (entrezGeneID);
builder.append (", dbSNPsID = ");
builder.append (dbSNPsID);
builder.append (", firstBuild = ");
builder.append (firstBuild);
builder.append (", alleleOrigin = ");
builder.append (alleleOrigin);
builder.append (", clinicalSig = ");
builder.append (clinicalSig);
builder.append (", suspectRegion = ");
builder.append (suspectRegion);
builder.append (", diseaseVariant = ");
builder.append (diseaseVariant);
builder.append (", geneSymbol = ");
builder.append (geneSymbol);
builder.append (", ensemblGeneID = ");
builder.append (ensemblGeneID);
builder.append (", mutationID = ");
if (mutationID > 0)
{
builder.append (mutationID);
builder.append (", cosmicCDS = ");
builder.append (cosmicCDS);
builder.append (", cosmicAA = ");
builder.append (cosmicAA);
builder.append (", strand = ");
if (strand)
builder.append ("+");
else
builder.append ("-");
}
else
builder.append ("-1");
builder.append (", omimDisease = ");
builder.append (omimDisease);
builder.append (", blacklisted = ");
builder.append (blacklisted);
builder.append (", conserved = ");
builder.append (conserved);
builder.append (", enhancer = ");
builder.append (enhancer);
builder.append (", tfbs = ");
builder.append (tfbs);
builder.append (", tss = ");
builder.append (tss);
builder.append (", unique = ");
builder.append (unique);
builder.append (", repeat = ");
builder.append (repeat);
builder.append (", regulatory = ");
builder.append (regulatory);
builder.append ("]");
if (miRBId != null)
{
builder.append (", landmark = ");
builder.append (landmark);
builder.append (", type = ");
builder.append (type);
builder.append (", minBP = ");
builder.append (minBP);
builder.append (", maxBP = ");
builder.append (maxBP);
if (miRStrand)
builder.append (", miRStrand = '+'");
else
builder.append (", miRStrand = '-'");
builder.append (", acc = ");
builder.append (acc);
builder.append (", miRBId = ");
builder.append (miRBId);
}
else
builder.append (", miRBId = Nothing");
return builder.toString ();
}
}