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JAL-4386 Added further checks for sequences that have no secondary structure.
[jalview.git]
/
src
/
jalview
/
viewmodel
/
seqfeatures
/
FeaturesDisplayed.java
diff --git
a/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
b/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
index
81a06a3
..
d7da519
100644
(file)
--- a/
src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
+++ b/
src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-23,22
+23,21
@@
package jalview.viewmodel.seqfeatures;
import jalview.api.FeaturesDisplayedI;
import java.util.Collection;
import jalview.api.FeaturesDisplayedI;
import java.util.Collection;
+import java.util.Collections;
import java.util.HashSet;
import java.util.HashSet;
-import java.util.Iterator;
+import java.util.Set;
public class FeaturesDisplayed implements FeaturesDisplayedI
{
public class FeaturesDisplayed implements FeaturesDisplayedI
{
- private HashSet<String> featuresDisplayed = new HashSet<String>();
+ private Set<String> featuresDisplayed = new HashSet<>();
- private HashSet<String> featuresRegistered = new HashSet<String>();
+ private Set<String> featuresRegistered = new HashSet<>();
public FeaturesDisplayed(FeaturesDisplayedI featuresDisplayed2)
{
public FeaturesDisplayed(FeaturesDisplayedI featuresDisplayed2)
{
- Iterator<String> fdisp = featuresDisplayed2.getVisibleFeatures();
- String ftype;
- while (fdisp.hasNext())
+ Set<String> fdisp = featuresDisplayed2.getVisibleFeatures();
+ for (String ftype : fdisp)
{
{
- ftype = fdisp.next();
featuresDisplayed.add(ftype);
featuresRegistered.add(ftype);
}
featuresDisplayed.add(ftype);
featuresRegistered.add(ftype);
}
@@
-46,13
+45,12
@@
public class FeaturesDisplayed implements FeaturesDisplayedI
public FeaturesDisplayed()
{
public FeaturesDisplayed()
{
- // TODO Auto-generated constructor stub
}
@Override
}
@Override
- public Iterator<String> getVisibleFeatures()
+ public Set<String> getVisibleFeatures()
{
{
- return featuresDisplayed.iterator();
+ return Collections.unmodifiableSet(featuresDisplayed);
}
@Override
}
@Override
@@
-62,7
+60,7
@@
public class FeaturesDisplayed implements FeaturesDisplayedI
}
@Override
}
@Override
- public boolean areVisible(Collection featureTypes)
+ public boolean areVisible(Collection<String> featureTypes)
{
return featuresDisplayed.containsAll(featureTypes);
}
{
return featuresDisplayed.containsAll(featureTypes);
}
@@
-75,7
+73,7
@@
public class FeaturesDisplayed implements FeaturesDisplayedI
}
@Override
}
@Override
- public void setAllVisible(Collection makeVisible)
+ public void setAllVisible(Collection<String> makeVisible)
{
featuresDisplayed.addAll(makeVisible);
featuresRegistered.addAll(makeVisible);
{
featuresDisplayed.addAll(makeVisible);
featuresRegistered.addAll(makeVisible);
@@
-95,6
+93,13
@@
public class FeaturesDisplayed implements FeaturesDisplayedI
}
@Override
}
@Override
+ public void setHidden(String featureType)
+ {
+ featuresDisplayed.remove(featureType);
+ featuresRegistered.add(featureType);
+ }
+
+ @Override
public boolean isRegistered(String type)
{
return featuresRegistered.contains(type);
public boolean isRegistered(String type)
{
return featuresRegistered.contains(type);
@@
-107,7
+112,7
@@
public class FeaturesDisplayed implements FeaturesDisplayedI
}
@Override
}
@Override
- public int getRegisterdFeaturesCount()
+ public int getRegisteredFeaturesCount()
{
return featuresRegistered.size();
}
{
return featuresRegistered.size();
}