Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 0d6e02f..36fe35a 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -32,7 +32,7 @@ import jalview.bin.BuildDetails;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -51,6 +51,7 @@ import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.ResidueColourScheme;
 import jalview.util.ColorUtils;
+import jalview.util.Format;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
 import java.awt.Color;
@@ -84,9 +85,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private FeatureRenderer fr;
 
-  private List<int[]> hiddenColumns;
-
-  private ColumnSelection columnSelection;
+  private HiddenColumns hiddenColumns;
 
   private List<String> hiddenSeqRefs;
 
@@ -230,8 +229,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
       if (exportSettings.isExportFeatures())
       {
-        jsonAlignmentPojo
-                .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
+        jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
       }
 
       if (exportSettings.isExportGroups() && seqGroups != null
@@ -281,17 +279,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     // hidden column business
     if (getViewport().hasHiddenColumns())
     {
-      List<int[]> hiddenCols = getViewport().getColumnSelection()
-              .getHiddenColumns();
-      StringBuilder hiddenColsBuilder = new StringBuilder();
-      for (int[] range : hiddenCols)
-      {
-        hiddenColsBuilder.append(";").append(range[0]).append("-")
-                .append(range[1]);
-      }
-
-      hiddenColsBuilder.deleteCharAt(0);
-      hiddenSections[0] = hiddenColsBuilder.toString();
+      hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
+              .regionsToString(";", "-");
     }
 
     // hidden rows/seqs business
@@ -320,11 +309,11 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return hiddenSections;
   }
 
-  public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
-          SequenceI[] sqs, FeatureRenderer fr)
+  protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+          SequenceI[] sqs)
   {
     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
-    List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
+    List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
     if (sqs == null)
     {
       return sequenceFeaturesPojo;
@@ -332,41 +321,38 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
     FeatureColourFinder finder = new FeatureColourFinder(fr);
 
+    String[] visibleFeatureTypes = displayedFeatures == null ? null
+            : displayedFeatures.getVisibleFeatures().toArray(
+                    new String[displayedFeatures.getVisibleFeatureCount()]);
+
     for (SequenceI seq : sqs)
     {
-      SequenceI dataSetSequence = seq.getDatasetSequence();
-      SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
-              : seq.getDatasetSequence().getSequenceFeatures();
-
-      seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
-              : seqFeatures;
-      if (seqFeatures == null)
-      {
-        continue;
-      }
-
+      /*
+       * get all features currently visible (and any non-positional features)
+       */
+      List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
+              visibleFeatureTypes);
       for (SequenceFeature sf : seqFeatures)
       {
-        if (displayedFeatures != null
-                && displayedFeatures.isVisible(sf.getType()))
-        {
-          SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
-                  String.valueOf(seq.hashCode()));
-
-          String featureColour = (fr == null) ? null : jalview.util.Format
-                  .getHexString(finder.findFeatureColour(Color.white, seq,
-                          seq.findIndex(sf.getBegin())));
-          jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
-          jsonFeature.setXend(seq.findIndex(sf.getEnd()));
-          jsonFeature.setType(sf.getType());
-          jsonFeature.setDescription(sf.getDescription());
-          jsonFeature.setLinks(sf.links);
-          jsonFeature.setOtherDetails(sf.otherDetails);
-          jsonFeature.setScore(sf.getScore());
-          jsonFeature.setFillColor(featureColour);
-          jsonFeature.setFeatureGroup(sf.getFeatureGroup());
-          sequenceFeaturesPojo.add(jsonFeature);
-        }
+        SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
+                String.valueOf(seq.hashCode()));
+
+        String featureColour = (fr == null) ? null : Format
+                .getHexString(finder.findFeatureColour(Color.white, seq,
+                        seq.findIndex(sf.getBegin())));
+        int xStart = sf.getBegin() == 0 ? 0
+                : seq.findIndex(sf.getBegin()) - 1;
+        int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
+        jsonFeature.setXstart(xStart);
+        jsonFeature.setXend(xEnd);
+        jsonFeature.setType(sf.getType());
+        jsonFeature.setDescription(sf.getDescription());
+        jsonFeature.setLinks(sf.links);
+        jsonFeature.setOtherDetails(sf.otherDetails);
+        jsonFeature.setScore(sf.getScore());
+        jsonFeature.setFillColor(featureColour);
+        jsonFeature.setFeatureGroup(sf.getFeatureGroup());
+        sequenceFeaturesPojo.add(jsonFeature);
       }
     }
     return sequenceFeaturesPojo;
@@ -375,7 +361,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
           Vector<AlignmentAnnotation> annotations)
   {
-    List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
+    List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
     if (annotations == null)
     {
       return jsonAnnotations;
@@ -472,8 +458,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         parseHiddenCols(jvSettingsJsonObj);
       }
 
-      hiddenSequences = new ArrayList<SequenceI>();
-      seqMap = new Hashtable<String, Sequence>();
+      hiddenSequences = new ArrayList<>();
+      seqMap = new Hashtable<>();
       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
               .hasNext();)
       {
@@ -516,7 +502,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 
-        ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+        ArrayList<SequenceI> grpSeqs = new ArrayList<>();
         if (sequenceRefs.size() > 0)
         {
           Iterator<String> seqHashIter = sequenceRefs.iterator();
@@ -650,7 +636,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
   {
-    hiddenSeqRefs = new ArrayList<String>();
+    hiddenSeqRefs = new ArrayList<>();
     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
     {
@@ -667,12 +653,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
     if (hiddenCols != null && !hiddenCols.isEmpty())
     {
-      columnSelection = new ColumnSelection();
+      hiddenColumns = new HiddenColumns();
       String[] rangeStrings = hiddenCols.split(";");
       for (String rangeString : rangeStrings)
       {
         String[] range = rangeString.split("-");
-        columnSelection.hideColumns(Integer.valueOf(range[0]),
+        hiddenColumns.hideColumns(Integer.valueOf(range[0]),
                 Integer.valueOf(range[1]));
       }
     }
@@ -697,8 +683,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         Float score = Float.valueOf(jsonFeature.get("score").toString());
 
         Sequence seq = seqMap.get(seqRef);
-        int featureBegin = seq.findPosition(begin.intValue());
-        int featureEnd = seq.findPosition(end.intValue()) - 1;
+
+        /*
+         * begin/end of 0 is for a non-positional feature
+         */
+        int featureBegin = begin.intValue() == 0 ? 0 : seq
+                .findPosition(begin.intValue());
+        int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
+                .intValue()) - 1;
 
         SequenceFeature sequenceFeature = new SequenceFeature(type,
                 description, featureBegin, featureEnd, score, featureGrp);
@@ -791,20 +783,15 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return annotations;
   }
 
-  public List<int[]> getHiddenColumns()
-  {
-    return hiddenColumns;
-  }
-
   @Override
-  public ColumnSelection getColumnSelection()
+  public HiddenColumns getHiddenColumns()
   {
-    return columnSelection;
+    return hiddenColumns;
   }
 
-  public void setColumnSelection(ColumnSelection columnSelection)
+  public void setHiddenColumns(HiddenColumns hidden)
   {
-    this.columnSelection = columnSelection;
+    this.hiddenColumns = hidden;
   }
 
   @Override