JAL-2069 spike updated with latest (FeatureTypeSettings)

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 06cdec4..6b797d7 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -30,6 +30,7 @@ import java.awt.Color;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 
@@ -517,10 +518,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       if (s != null && !sequences.contains(s))
       {
-        List<SequenceI> before = sequences;
         sequences.add(s);
-        changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
-                sequences);
+        changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+                sequences.size() - 1, sequences.size());
       }
 
       if (recalc)
@@ -645,8 +645,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     conservation.description = "Conservation for group " + getName()
             + " less than " + consPercGaps + "% gaps";
     // preserve width if already set
-    int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
-            : endRes + 1)
+    int aWidth = (conservation.annotations != null)
+            ? (endRes < conservation.annotations.length
+                    ? conservation.annotations.length
+                    : endRes + 1)
             : endRes + 1;
     conservation.annotations = null;
     conservation.annotations = new Annotation[aWidth]; // should be alignment
@@ -666,8 +668,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     consensus.description = "Percent Identity";
     consensusData = cnsns;
     // preserve width if already set
-    int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
-            : endRes + 1)
+    int aWidth = (consensus.annotations != null)
+            ? (endRes < consensus.annotations.length
+                    ? consensus.annotations.length
+                    : endRes + 1)
             : endRes + 1;
     consensus.annotations = null;
     consensus.annotations = new Annotation[aWidth]; // should be alignment width
@@ -713,10 +717,9 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
-      List<SequenceI> before = sequences;
       sequences.remove(s);
-      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
-              sequences);
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+              sequences.size() + 1, sequences.size());
 
       if (recalc)
       {
@@ -1314,38 +1317,16 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<>();
-    if (calcId == null)
-    {
-      return aa;
-    }
-    for (AlignmentAnnotation a : getAlignmentAnnotation())
-    {
-      if (calcId.equals(a.getCalcId()))
-      {
-        aa.add(a);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotation(
+            Arrays.asList(getAlignmentAnnotation()), calcId);
   }
 
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
-    for (AlignmentAnnotation ann : getAlignmentAnnotation())
-    {
-      if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
-              .equals(calcId)))
-              && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
-              && (label == null || (ann.label != null && ann.label
-                      .equals(label))))
-      {
-        aa.add(ann);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
   }
 
   /**
@@ -1356,17 +1337,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public boolean hasAnnotation(String calcId)
   {
-    if (calcId != null && !"".equals(calcId))
-    {
-      for (AlignmentAnnotation a : getAlignmentAnnotation())
-      {
-        if (a.getCalcId() == calcId)
-        {
-          return true;
-        }
-      }
-    }
-    return false;
+    return AlignmentAnnotation
+            .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
   }
 
   /**
@@ -1376,10 +1348,10 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
-      List<SequenceI> before = sequences;
+      int before = sequences.size();
       sequences.clear();
       changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
-              sequences);
+              sequences.size());
     }
   }
 
@@ -1467,7 +1439,8 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public boolean isNucleotide()
   {
-    if (context != null) {
+    if (context != null)
+    {
       return context.isNucleotide();
     }
     return false;