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Commit eb1177c2 authored by tcarver's avatar tcarver
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fix for naming duplicate features

parent e1705276
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uk/ac/sanger/artemis/io/GFFStreamFeature.java
+ 32
− 33
View file @ eb1177c2
......@@ -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();
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);
......
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