JAL-1260 source formatting according to utils/eclipse/JalviewCodeStyle.xml

[jalview.git] / src / jalview / io / DnaUtils.java

diff --git a/src/jalview/io/DnaUtils.java b/src/jalview/io/DnaUtils.java
index acd0bb9..5d5a603 100644 (file)
--- a/src/jalview/io/DnaUtils.java
+++ b/src/jalview/io/DnaUtils.java
@@ -7,55 +7,78 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Vector;
 
-public class DnaUtils {
-
-       /**
-        * @param gbf CDS feature data
-        * @param sequences ORIGIN data
-        * @return Nucleotid String (sequence) of CDS
-        */
-       public static String getSequence(GenBankFeature gbf, Vector<GenBankSequence> sequences){
-               if (!gbf.getType().equals(GenBankFeature.CDS)){
-                       //If the feature is not a CDS, no sequence is returned
-                       return null;
-               }else{
-                       String range = gbf.getQualifier("range");
-                       if (range.startsWith("join")){
-                               //TODO
-                               //It's a composed sequence
-                       }else{
-                               //It's a simple range
-                               String[] positions = range.split("..");
-                               int initRange = Integer.parseInt(positions[0]);
-                               int endRange = Integer.parseInt(positions[1]);
-                               String sourceSequence = getNucleotidesFromSequenceVector(sequences);
-                               return sourceSequence.substring(initRange, endRange);
-                       }
-               }
-               return null;
-               
-       }
-       private static boolean isSequenceInRange(int initRange, int endRange, GenBankSequence gbs){             
-               return ((initRange>=gbs.getId()) && (endRange>=gbs.getId()));
-       }
-       private static String getNucleotidesInRangeFromSequence(int initRange, int endRange, GenBankSequence gbs){
-               return "";
-       }
-       public static String getNucleotidesFromSequenceVector(Vector<GenBankSequence> v){
-               StringBuffer sb = new StringBuffer();
-               for (GenBankSequence gbs:v){
-                       Vector<String> seqs = gbs.getSequences();
-                       for (String s:seqs)
-                               sb.append(s);
-               }
-               return sb.toString();
-       }
-       /**
-        * @param args
-        */
-       public static void main(String[] args) {
-               // TODO Auto-generated method stub
-
-       }
+public class DnaUtils
+{
+
+  /**
+   * @param gbf
+   *          CDS feature data
+   * @param sequences
+   *          ORIGIN data
+   * @return Nucleotid String (sequence) of CDS
+   */
+  public static String getSequence(GenBankFeature gbf,
+          Vector<GenBankSequence> sequences)
+  {
+    if (!gbf.getType().equals(GenBankFeature.CDS))
+    {
+      // If the feature is not a CDS, no sequence is returned
+      return null;
+    }
+    else
+    {
+      String range = gbf.getQualifier("range");
+      if (range.startsWith("join"))
+      {
+        // TODO
+        // It's a composed sequence
+      }
+      else
+      {
+        // It's a simple range
+        String[] positions = range.split("..");
+        int initRange = Integer.parseInt(positions[0]);
+        int endRange = Integer.parseInt(positions[1]);
+        String sourceSequence = getNucleotidesFromSequenceVector(sequences);
+        return sourceSequence.substring(initRange, endRange);
+      }
+    }
+    return null;
+
+  }
+
+  private static boolean isSequenceInRange(int initRange, int endRange,
+          GenBankSequence gbs)
+  {
+    return ((initRange >= gbs.getId()) && (endRange >= gbs.getId()));
+  }
+
+  private static String getNucleotidesInRangeFromSequence(int initRange,
+          int endRange, GenBankSequence gbs)
+  {
+    return "";
+  }
+
+  public static String getNucleotidesFromSequenceVector(
+          Vector<GenBankSequence> v)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (GenBankSequence gbs : v)
+    {
+      Vector<String> seqs = gbs.getSequences();
+      for (String s : seqs)
+        sb.append(s);
+    }
+    return sb.toString();
+  }
+
+  /**
+   * @param args
+   */
+  public static void main(String[] args)
+  {
+    // TODO Auto-generated method stub
+
+  }
 
 }