diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 1909bed71e6696b5166214241cbf2f40b4d436e9..f4fe890ea9306bbb74053a6bc7851bef1a928159 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -69,10 +69,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
StringVector gff_lines = null;
/** store for spliced features containing id and range of each segment */
- private Hashtable id_range_store;
+ private Hashtable<String, Range> id_range_store;
/** store a record of the new and old uniquenames that have been changed */
- private Hashtable newIdMapToOldId;
+ private Hashtable<String, String> newIdMapToOldId;
/** store the Timestamp for the feature */
private Timestamp timelastmodified;
@@ -82,7 +82,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
private boolean visible = true;
/** combined feature_relationship.rank store for exons */
- private Hashtable feature_relationship_rank_store;
+ private Hashtable<String, Integer> feature_relationship_rank_store;
/** first tabbed parameter */
private String gffSeqName;
@@ -231,18 +231,22 @@ public class GFFStreamFeature extends SimpleDocumentFeature
duplicatePrefix = "DUP";
if(id_range_store != null)
{
- final Hashtable new_id_range_store = new Hashtable(id_range_store.size());
- final Enumeration enumIdRangeStore = id_range_store.keys();
+ final Hashtable<String, Range> new_id_range_store = new Hashtable<String, Range>(id_range_store.size());
+ final Enumeration<String> enumIdRangeStore = id_range_store.keys();
while(enumIdRangeStore.hasMoreElements())
{
- final String keyId = (String)enumIdRangeStore.nextElement();
- final Range range = (Range)id_range_store.get(keyId);
+ final String keyId = enumIdRangeStore.nextElement();
+ final Range range = id_range_store.get(keyId);
new_id_range_store.put(duplicatePrefix+keyId, range);
}
id_range_store.clear();
this.id_range_store = (Hashtable) new_id_range_store.clone();
- uniquename = getSegmentID(getLocation().getRanges());
+
+ if(getLocation().getRanges().size() > 1)
+ uniquename = getSegmentID(getLocation().getRanges());
+ else
+ uniquename = duplicatePrefix+ (String)getQualifierByName("ID").getValues().get(0);
}
else
uniquename = duplicatePrefix+ (String)getQualifierByName("ID").getValues().get(0);
@@ -347,24 +351,20 @@ public class GFFStreamFeature extends SimpleDocumentFeature
final String rest_of_line = (String)line_bits.elementAt(8);
// parse the rest of the line as ACeDB format attributes
- final Hashtable attributes = parseAttributes(rest_of_line);
-// final String type = (String)line_bits.elementAt(2);
-
- for(final java.util.Enumeration attribute_enum = attributes.keys();
+ final Hashtable<String, StringVector> attributes = parseAttributes(rest_of_line);
+ for(final Enumeration<String> attribute_enum = attributes.keys();
attribute_enum.hasMoreElements();)
{
- String name = (String)attribute_enum.nextElement();
-
- final StringVector values = (StringVector)attributes.get(name);
+ String name = attribute_enum.nextElement();
+ final StringVector values = attributes.get(name);
if(MatchPanel.isClusterTag(name))
{
- List lazyValues = new Vector();
+ List<ClusterLazyQualifierValue> lazyValues = new Vector<ClusterLazyQualifierValue>();
for(int i=0; i<values.size(); i++)
lazyValues.add(
new ClusterLazyQualifierValue( (String)values.get(i), name,
this ));
-
setQualifier(new QualifierLazyLoading(name, lazyValues));
}
else
@@ -455,23 +455,23 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* Store for spliced regions of segments ID's and ranges.
*
*/
- public void setSegmentRangeStore(Hashtable id_range_store)
+ public void setSegmentRangeStore(Hashtable<String, Range> id_range_store)
{
this.id_range_store = id_range_store;
}
- public Hashtable getSegmentRangeStore()
+ public Hashtable<String, Range> getSegmentRangeStore()
{
if(id_range_store == null)
{
- id_range_store = new Hashtable();
+ id_range_store = new Hashtable<String, Range>();
id_range_store.put((String)this.getQualifierByName("ID").getValues().get(0),
this.getLocation().getTotalRange());
}
return id_range_store;
}
- public Hashtable getNewIdMapToOldId()
+ public Hashtable<String, String> getNewIdMapToOldId()
{
return newIdMapToOldId;
}
@@ -480,7 +480,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* Used when changing spliced feature uniquenames
* @param newIdMapToOldId
*/
- public void setNewIdMapToOldId(Hashtable newIdMapToOldId)
+ public void setNewIdMapToOldId(Hashtable<String, String> newIdMapToOldId)
{
this.newIdMapToOldId = newIdMapToOldId;
}
@@ -490,7 +490,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* @param feature_relationship_rank_store
*/
public void setFeature_relationship_rank_store(
- Hashtable feature_relationship_rank_store)
+ Hashtable<String, Integer> feature_relationship_rank_store)
{
this.feature_relationship_rank_store = feature_relationship_rank_store;
}
@@ -499,7 +499,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* Store for ID's and CHADO feature_relationship.rank
* @return
*/
- public Hashtable getFeature_relationship_rank_store()
+ public Hashtable<String, Integer> getFeature_relationship_rank_store()
{
return feature_relationship_rank_store;
}
@@ -514,13 +514,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
if(id_range_store != null)
{
- Enumeration enum_ranges = id_range_store.keys();
+ Enumeration<String> enum_ranges = id_range_store.keys();
//Iterator it = id_range_store.values().iterator();
while(enum_ranges.hasMoreElements())
//while(it.hasNext())
{
- String key = (String)enum_ranges.nextElement();
- Range range = (Range)id_range_store.get(key);
+ String key = enum_ranges.nextElement();
+ Range range = id_range_store.get(key);
if(range.getStart() == r.getStart() &&
range.getEnd() == r.getEnd())
return key;
@@ -963,9 +963,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if (chadoGene != null)
{
if(getUserData() == null)
- {
- uk.ac.sanger.artemis.Feature f = new uk.ac.sanger.artemis.Feature(this);
- }
+ new uk.ac.sanger.artemis.Feature(this);
// the above line constructs the appropriate userData within this current GFFStreamFeature object,
// which is required by the following GeneUtils.deriveResidues()
String residues = GeneUtils.deriveResidues(this);
@@ -1072,9 +1070,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* If the attribute has no value then the Hashtable value will be a zero
* length vector.
**/
- private Hashtable parseAttributes(final String att_val_list)
+ private Hashtable<String, StringVector> parseAttributes(final String att_val_list)
{
- Hashtable attributes = new Hashtable();
+ Hashtable<String, StringVector> attributes = new Hashtable<String, StringVector>();
// StringTokenizer tokeniser = new StringTokenizer(att_val_list, ";", false);
// while(tokeniser.hasMoreTokens())
@@ -1136,7 +1134,8 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(quote_index < 0)
{
// no closing quote - panic
- final Hashtable panic_attributes = new Hashtable();
+ final Hashtable<String, StringVector> panic_attributes =
+ new Hashtable<String, StringVector>();
final StringVector notes = new StringVector();
notes.add(att_val_list);
panic_attributes.put("note", notes);