JAL-1260 v2 patch from David Roldán-Martínez

[jalview.git] / src / jalview / io / xdb / genbank / GenBankFeature.java

diff --git a/src/jalview/io/xdb/genbank/GenBankFeature.java b/src/jalview/io/xdb/genbank/GenBankFeature.java
new file mode 100644 (file)
index 0000000..0de2e65
--- /dev/null
+++ b/src/jalview/io/xdb/genbank/GenBankFeature.java
@@ -0,0 +1,68 @@
+package jalview.io.xdb.genbank;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+
+public class GenBankFeature {
+       public static final String MISC_TYPE = "misc_feature";
+       public static final String SOURCE = "source";
+       public static final String CDS = "CDS";
+       public static final String GENE = "gene";
+       public static final String EXON = "exon";
+       public static final String INTRON = "intron";
+       public static final String PRIM_TRANSCRIPT = "prim_transcript";
+       public static final String mRNA = "mRNA";
+       public static final String MOBILE_ELEMENT = "mobile_element";
+       public static final String VARIATION = "variation";
+       
+       private String type;
+       private Hashtable<String,String> qualifiers = new Hashtable<String,String>();
+       private GenBankLocation location = null;
+       
+       public GenBankFeature() {
+               super();
+       }
+
+       public GenBankFeature(String type) {
+               super();
+               this.type = type;
+       }
+       
+       public void addQualifier(String key, String value){
+               this.qualifiers.put(key, value);
+       }
+       public void updateQualifier(String key, String newValue){
+               this.qualifiers.remove(key);
+               this.qualifiers.put(key, newValue);
+       }
+       
+       public String getQualifier(String key){
+               return this.qualifiers.get(key);
+       }
+
+       public String getType() {
+               return type;
+       }
+
+       public void setType(String type) {
+               this.type = type;
+       }
+       public Enumeration<String> getQualifiersNames(){
+               return this.qualifiers.keys();
+       }
+       public int getQualifiersSize(){
+               return this.qualifiers.size();
+       }
+
+       public Hashtable<String, String> getFields() {
+               return qualifiers;
+       }
+
+       public GenBankLocation getLocation() {
+               return location;
+       }
+
+       public void setLocation(GenBankLocation location) {
+               this.location = location;
+       }
+}