From 1152ad2009cfc7bf521b6bcb556f6031bbe5b86a Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Mon, 15 Jun 2015 11:39:23 +0100 Subject: [PATCH] JAL-1641 clean up --- src/jalview/api/ComplexAlignFile.java | 3 +-- src/jalview/io/JSONFile.java | 6 ------ 2 files changed, 1 insertion(+), 8 deletions(-) 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(); 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(); -- 1.7.10.2