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JAL-2591 simplifying hidden columns usage
[jalview.git]
/
src
/
jalview
/
io
/
JSONFile.java
diff --git
a/src/jalview/io/JSONFile.java
b/src/jalview/io/JSONFile.java
index
816346a
..
a48ee33
100644
(file)
--- a/
src/jalview/io/JSONFile.java
+++ b/
src/jalview/io/JSONFile.java
@@
-279,11
+279,8
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
// hidden column business
if (getViewport().hasHiddenColumns())
{
// hidden column business
if (getViewport().hasHiddenColumns())
{
- List<int[]> hiddenCols = getViewport().getAlignment()
- .getHiddenColumns()
- .getHiddenRegions();
StringBuilder hiddenColsBuilder = new StringBuilder();
StringBuilder hiddenColsBuilder = new StringBuilder();
- for (int[] range : hiddenCols)
+ for (int[] range : getViewport().getAlignment().getHiddenColumns())
{
hiddenColsBuilder.append(";").append(range[0]).append("-")
.append(range[1]);
{
hiddenColsBuilder.append(";").append(range[0]).append("-")
.append(range[1]);
@@
-323,7
+320,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
SequenceI[] sqs, FeatureRenderer fr)
{
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
SequenceI[] sqs, FeatureRenderer fr)
{
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
- List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
+ List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
if (sqs == null)
{
return sequenceFeaturesPojo;
if (sqs == null)
{
return sequenceFeaturesPojo;
@@
-374,7
+371,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
Vector<AlignmentAnnotation> annotations)
{
public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
Vector<AlignmentAnnotation> annotations)
{
- List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
+ List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
if (annotations == null)
{
return jsonAnnotations;
if (annotations == null)
{
return jsonAnnotations;
@@
-471,8
+468,8
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
parseHiddenCols(jvSettingsJsonObj);
}
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();)
{
for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
.hasNext();)
{
@@
-515,7
+512,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
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();
if (sequenceRefs.size() > 0)
{
Iterator<String> seqHashIter = sequenceRefs.iterator();
@@
-649,7
+646,7
@@
public class JSONFile extends AlignFile implements ComplexAlignFile
public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
{
public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
{
- hiddenSeqRefs = new ArrayList<String>();
+ hiddenSeqRefs = new ArrayList<>();
String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
{
String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
{