From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Mon, 15 Jun 2015 10:39:23 +0000 (+0100)
Subject: JAL-1641 clean up
X-Git-Tag: Release_2_10_0~609^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=1152ad2009cfc7bf521b6bcb556f6031bbe5b86a

JAL-1641 clean up
---

diff --git a/src/jalview/api/ComplexAlignFile.java b/src/jalview/api/ComplexAlignFile.java
index 92243fb..133a739 100644
--- a/src/jalview/api/ComplexAlignFile.java
+++ b/src/jalview/api/ComplexAlignFile.java
@@ -6,9 +6,8 @@ import jalview.schemes.ColourSchemeI;
 
 /**
  * This interface should be implemented by complex file parser with the ability
- * to store linked data and complex view states in addition to alingment data
+ * to store linked data and complex view states in addition to Alignment data
  * 
- * @author tcnofoegbu
  *
  */
 public interface ComplexAlignFile
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index ff129a4..d2b8412 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -516,15 +516,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   public void parseHiddenCols(JSONObject jvSettingsJson)
   {
-    // hiddenColumns = new ArrayList<int[]>();
     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
     if(hiddenCols != null && !hiddenCols.isEmpty()){
       columnSelection = new ColumnSelection();
       String[] rangeStrings = hiddenCols.split(";");
       for(String rangeString : rangeStrings){
         String[] range = rangeString.split("-");
-        // hiddenColumns.add(new int[]
-        // { Integer.valueOf(range[0]), Integer.valueOf(range[1]) });
         columnSelection.hideColumns(Integer.valueOf(range[0]),
                 Integer.valueOf(range[1]));
       }
@@ -547,9 +544,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         String descripiton = (String) jsonFeature.get("description");
         String seqRef = (String) jsonFeature.get("sequenceRef");
         Float score = Float.valueOf(jsonFeature.get("score").toString());
-        // Hashtable otherDetails = (Hashtable) jsonFeature
-        // .get("otherDetails");
-        // sequenceFeature.otherDetails = otherDetails;
 
         Sequence seq = seqMap.get(seqRef);
         SequenceFeature sequenceFeature = new SequenceFeature();