Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 39d713d..d2b8412 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -38,7 +38,6 @@ import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenSequences;
@@ -46,7 +45,6 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
 import jalview.json.binding.v1.AlignmentAnnotationPojo;
 import jalview.json.binding.v1.AlignmentPojo;
 import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
@@ -518,15 +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]));
       }
@@ -549,9 +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();
@@ -592,14 +584,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return jalviewColor;
   }
 
-  public AlignViewportI getViewport(AlignmentI al)
-  {
-    AlignViewportI viewport = new AlignViewport(al, getColumnSelection());
-    viewport.setGlobalColourScheme(getColourScheme());
-    viewport.setShowSequenceFeatures(isShowSeqFeatures());
-    return viewport;
-  }
-
   public String getGlobalColorScheme()
   {
     return globalColorScheme;