JAL-1260 v2 patch from David Roldán-Martínez

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

diff --git a/src/jalview/io/xdb/genbank/GenBankSequence.java b/src/jalview/io/xdb/genbank/GenBankSequence.java
new file mode 100644 (file)
index 0000000..279601c
--- /dev/null
+++ b/src/jalview/io/xdb/genbank/GenBankSequence.java
@@ -0,0 +1,57 @@
+package jalview.io.xdb.genbank;
+
+import java.util.Vector;
+/**
+ * A line like the following:
+ *   1 aatgaaggtt catttttcat tctcacaaac taatgaaacc ctgcttatct taaaccaacc
+ * will be mapped as:
+ *     id: 1
+ *  sequences: {"aatgaaggtt", "catttttcat", "tctcacaaac", "taatgaaacc", "ctgcttatct", "taaaccaacc"}
+ *  Each sequence has 8 nucleotides long
+ * @author darolmar
+ *
+ */
+public class GenBankSequence {
+       //Initial position
+       private int id;
+       //Sequences in that line
+       private Vector<String> sequences;
+
+       public GenBankSequence() {
+               super();
+               sequences = new Vector<String>();
+       }
+
+       public int getId() {
+               return id;
+       }
+
+       public void setId(int id) {
+               this.id = id;
+       }
+
+       public Vector<String> getSequences() {
+               return sequences;
+       }
+
+       public void setSequences(Vector<String> sequences) {
+               this.sequences = sequences;
+       }
+       
+       public String getSequencesAsString(){
+               StringBuffer sb = new StringBuffer();
+               for (String seq:sequences)                      
+                       sb.append(seq).append(" ");                             
+               return sb.toString();           
+       }
+       
+       public String toString(){
+               StringBuffer sb = new StringBuffer()
+                       .append("        ").append(this.id);
+               for (String seq:sequences)                      
+                       sb.append(" ").append(seq);
+               sb.append("\n");                                
+               return sb.toString();
+       }
+       
+}