/*
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 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
package org.mskcc.cbio.oncokb.model;

import java.util.List;

/**
 *
 * @author jiaojiao
 */
public class PortalAlteration {
    
    private String cancertype;
    private Integer numberOfSamples;
    private Gene gene;
    private String proteinChange;
    private Integer startPosition;
    private Integer endPosition;
    private List<String> variants; 
    
    public Integer getStartPosition() {
        return startPosition;
    }

    public void setStartPosition(Integer startPosition) {
        this.startPosition = startPosition;
    }

    public Integer getEndPosition() {
        return endPosition;
    }

    public void setEndPosition(Integer endPosition) {
        this.endPosition = endPosition;
    }
    

    public String getCancertype() {
        return cancertype;
    }

    public void setCancertype(String cancertype) {
        this.cancertype = cancertype;
    }

    public Integer getNumberOfSamples() {
        return numberOfSamples;
    }

    public void setNumberOfSamples(Integer numberOfSamples) {
        this.numberOfSamples = numberOfSamples;
    }
    public Gene getGene() {
        return gene;
    }

    public void setGene(Gene gene) {
        this.gene = gene;
    }
    public String getProteinChange() {
        return proteinChange;
    }

    public void setProteinChange(String proteinChange) {
        this.proteinChange = proteinChange;
    }

    public List<String> getVariants() {
        return variants;
    }

    public void setVariants(List<String> variants) {
        this.variants = variants;
    }
    
    
    
}

@@ -303,24 +303,50 @@
 ation %7B%0A    
+private String cancerType;
 %0A    private
@@ -355,28 +355,29 @@
 tring cancer
-type
+Study
 ;%0A    privat
@@ -549,251 +549,106 @@
 ist%3C
-String%3E variants; %0A    %0A    public Integer getStartPosition() %7B%0A        return startPosi
+Alteration%3E oncoKBAltera
 tion
+s
 ;%0A    
-%7D%0A%0A    public void setStartPosition(Integer startPosition) %7B%0A        this.startPosition = startPosition;%0A    %7D%0A%0A    public Integer getEndPosition
+private String alterationType;%0A%0A    public String getCancerType
 () %7B
@@ -663,27 +663,26 @@
  return 
-endPosition
+cancerType
 ;%0A    %7D%0A
@@ -705,93 +705,83 @@
  set
-EndPosition(Integer endPosition) %7B%0A        this.endPosition = endPosition
+CancerType(String cancerType) %7B%0A        this.cancerType = cancerType
 ;%0A    %7D
-%0A    
 %0A%0A  
@@ -805,20 +805,21 @@
 etCancer
-type
+Study
 () %7B%0A   
@@ -832,28 +832,29 @@
 eturn cancer
-type
+Study
 ;%0A    %7D%0A%0A   
@@ -875,20 +875,21 @@
 etCancer
-type
+Study
 (String 
@@ -894,20 +894,21 @@
 g cancer
-type
+Study
 ) %7B%0A    
@@ -922,20 +922,21 @@
 s.cancer
-type
+Study
  = cance
@@ -940,12 +940,13 @@
 ncer
-type
+Study
 ;%0A  
@@ -1139,32 +1139,33 @@
 fSamples;%0A    %7D%0A
+%0A
     public Gene 
@@ -1269,24 +1269,25 @@
 gene;%0A    %7D%0A
+%0A
     public S
@@ -1473,154 +1473,766 @@
 lic 
-List%3CString%3E getVariants() %7B%0A        return variants;%0A    %7D%0A%0A    public void setVariants(List%3CString%3E variants) %7B%0A        this.variants = variants
+Integer getStartPosition() %7B%0A        return startPosition;%0A    %7D%0A%0A    public void setStartPosition(Integer startPosition) %7B%0A        this.startPosition = startPosition;%0A    %7D%0A%0A    public Integer getEndPosition() %7B%0A        return endPosition;%0A    %7D%0A%0A    public void setEndPosition(Integer endPosition) %7B%0A        this.endPosition = endPosition;%0A    %7D%0A%0A    public List%3CAlteration%3E getOncoKBAlterations() %7B%0A        return oncoKBAlterations;%0A    %7D%0A%0A    public void setOncoKBAlterations(List%3CAlteration%3E oncoKBAlterations) %7B%0A        this.oncoKBAlterations = oncoKBAlterations;%0A    %7D%0A%0A    public String getAlterationType() %7B%0A        return alterationType;%0A    %7D%0A%0A    public void setAlterationType(String alterationType) %7B%0A        this.alterationType = alterationType
 ;%0A  

add new fields