/* I've noticed some misprints in BioJavaX Documentation and in the source code. */

Seeker · andreasprlic · commit c7d3dfe5e6c9 · 2016-03-18T23:27:41.000-07:00
diff --git a/wiki/User_talk:Seeker.md b/wiki/User_talk:Seeker.md
@@ -59,6 +59,9 @@ the following text fragment:
  ...
 `
 
+I used the followng code to get values of notes **/function**, **/note**
+and **/translation** of the FEATURE Field:
+
 <java>
 
 RichSequenceIterator seqs = RichSequence.IOTools.readGenbankDNA(br, ns);
@@ -69,6 +72,8 @@ Iterator fsit = seq.getFeatureSet().iterator(); RichFeature rf =
 
 Set noteSet = rf.getNoteSet(); Iterator nit = noteSet.iterator();
 
+String function = "", note = "";
+
 while (nit.hasNext()) {
 
 ` if (fType.equals("CDS")) {`
@@ -81,7 +86,26 @@ while (nit.hasNext()) {
 
 `     note = sn.getValue();`  
 `     System.out.println("Note:\n" + note);`  
+`   } else if (snTermName.equals("translation")) {`
+
+`     translation = sn.getValue();`  
+`     System.out.println("Translation:\n" + translation);`  
 `   }`  
 ` }`
 
 } </java>
+
+The output was as follows:
+
+<code>
+
+`Function:`  
+`4-diphosphocytidyl-2-C-methyl-D-erythritol`  
+`kinase`  
+`Note:`  
+`catalyzes the phosphorylation of`  
+`4-diphosphocytidyl-2-C-methyl-D-erythritol in the`  
+`nonmevalonate pathway of isoprenoid biosynthesis`  
+`Translation:   MRILEKAPAKINLSLDVTRKRPDGYHEVEMIMTTIDLADRIELTELAEDEVRVSSHNRFVPDDQRNLAYQAAKLIKDRYNVKKGVSIMITKVIPVAAGLAGGSSDAAATLRGLNRLWNLNLSAETLAELGAEIGSDVSFCVYGGTALATGRGEKIKHISTPPHCWVILAKPTIGVSTAEVYRALKLDGIEHPDVQGMIEAIEEKSFQKMCSRLGNVLESVTLDMHPEVAMIKNQMKRFGADAVLMSGSGPTVFGLVQYESKVQRIYNGLRGFCDQVYAVRMIGEQNALD`
+
+\<\\code\>
diff --git a/wiki/User_talk:Seeker.mediawiki b/wiki/User_talk:Seeker.mediawiki
@@ -43,6 +43,8 @@ Iwas working with sequence file in GenBank format. This file contained the follo
  ...
 </code>
 
+I used the followng code to get values of notes '''/function''', '''/note''' and '''/translation''' of the FEATURE Field:
+
 <java>
 
 RichSequenceIterator seqs = RichSequence.IOTools.readGenbankDNA(br, ns);
@@ -54,6 +56,8 @@ RichFeature rf = (RichFeature) fsit.next();
 Set noteSet = rf.getNoteSet();
 Iterator nit = noteSet.iterator();
 
+String function = "", note = "";
+
 while (nit.hasNext()) {
 
   if (fType.equals("CDS")) {
@@ -66,7 +70,24 @@ while (nit.hasNext()) {
 
       note = sn.getValue();
       System.out.println("Note:\n" + note);
+    } else if (snTermName.equals("translation")) {
+
+      translation = sn.getValue();
+      System.out.println("Translation:\n" + translation);
     }
   }
 }
-</java>
+</java>
+
+The output was as follows:
+
+<code>
+ Function:
+ 4-diphosphocytidyl-2-C-methyl-D-erythritol
+ kinase
+ Note:
+ catalyzes the phosphorylation of
+ 4-diphosphocytidyl-2-C-methyl-D-erythritol in the
+ nonmevalonate pathway of isoprenoid biosynthesis
+ Translation:   MRILEKAPAKINLSLDVTRKRPDGYHEVEMIMTTIDLADRIELTELAEDEVRVSSHNRFVPDDQRNLAYQAAKLIKDRYNVKKGVSIMITKVIPVAAGLAGGSSDAAATLRGLNRLWNLNLSAETLAELGAEIGSDVSFCVYGGTALATGRGEKIKHISTPPHCWVILAKPTIGVSTAEVYRALKLDGIEHPDVQGMIEAIEEKSFQKMCSRLGNVLESVTLDMHPEVAMIKNQMKRFGADAVLMSGSGPTVFGLVQYESKVQRIYNGLRGFCDQVYAVRMIGEQNALD
+<\code>
