JAL-2629 remove annotation when exporting for hmmbuild

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 6117baf..8f826f5 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,6 +20,10 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -28,10 +32,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 /**
  * DOCUMENT ME!
  * 
@@ -701,7 +701,7 @@ public class AlignmentAnnotation
     this.calcId = annotation.calcId;
     if (annotation.properties != null)
     {
-      properties = new HashMap<String, String>();
+      properties = new HashMap<>();
       for (Map.Entry<String, String> val : annotation.properties.entrySet())
       {
         properties.put(val.getKey(), val.getValue());
@@ -737,7 +737,7 @@ public class AlignmentAnnotation
       if (annotation.sequenceMapping != null)
       {
         Integer p = null;
-        sequenceMapping = new HashMap<Integer, Annotation>();
+        sequenceMapping = new HashMap<>();
         Iterator<Integer> pos = annotation.sequenceMapping.keySet()
                 .iterator();
         while (pos.hasNext())
@@ -817,7 +817,7 @@ public class AlignmentAnnotation
       int epos = sequenceRef.findPosition(endRes);
       if (sequenceMapping != null)
       {
-        Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+        Map<Integer, Annotation> newmapping = new HashMap<>();
         Iterator<Integer> e = sequenceMapping.keySet().iterator();
         while (e.hasNext())
         {
@@ -944,7 +944,7 @@ public class AlignmentAnnotation
     {
       return;
     }
-    sequenceMapping = new HashMap<Integer, Annotation>();
+    sequenceMapping = new HashMap<>();
 
     int seqPos;
 
@@ -1150,14 +1150,14 @@ public class AlignmentAnnotation
    * @param colSel
    */
   public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
-          ColumnSelection colSel)
+          HiddenColumns hidden)
   {
     this(alignmentAnnotation);
     if (annotations == null)
     {
       return;
     }
-    colSel.makeVisibleAnnotation(this);
+    hidden.makeVisibleAnnotation(this);
   }
 
   public void setPadGaps(boolean padgaps, char gapchar)
@@ -1223,7 +1223,7 @@ public class AlignmentAnnotation
   /**
    * properties associated with the calcId
    */
-  protected Map<String, String> properties = new HashMap<String, String>();
+  protected Map<String, String> properties = new HashMap<>();
 
   /**
    * base colour for line graphs. If null, will be set automatically by
@@ -1267,7 +1267,7 @@ public class AlignmentAnnotation
             .getTo() == sq.getDatasetSequence()) : false;
 
     // TODO build a better annotation element map and get rid of annotations[]
-    Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+    Map<Integer, Annotation> mapForsq = new HashMap<>();
     if (sequenceMapping != null)
     {
       if (sp2sq != null)
@@ -1320,7 +1320,7 @@ public class AlignmentAnnotation
     if (mapping != null)
     {
       Map<Integer, Annotation> old = sequenceMapping;
-      Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
+      Map<Integer, Annotation> remap = new HashMap<>();
       int index = -1;
       for (int mp[] : mapping.values())
       {
@@ -1378,7 +1378,7 @@ public class AlignmentAnnotation
   {
     if (properties == null)
     {
-      properties = new HashMap<String, String>();
+      properties = new HashMap<>();
     }
     properties.put(property, value);
   }
@@ -1494,4 +1494,14 @@ public class AlignmentAnnotation
   {
     return counter++;
   }
+
+  /**
+   * 
+   * @return true for rows that have a range of values in their annotation set
+   */
+  public boolean isQuantitative()
+  {
+    return graphMin < graphMax;
+  }
+
 }