From 9fbe994502b065ae35fbe10e332300b7b059b0c5 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 23 Aug 2011 11:03:50 +0100
Subject: [PATCH] tidy
---
uk/ac/sanger/artemis/io/GFFDocumentEntry.java | 232 +-----------------
1 file changed, 2 insertions(+), 230 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
index 202b24958..16dd6ffa8 100644
--- a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
@@ -72,7 +72,6 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
super(new GFFEntryInformation(), document, listener);
super.in_constructor = true;
// join the separate exons into one feature (if appropriate)
- //combineFeatures();
combineGeneFeatures();
super.in_constructor = false;
finished_constructor = true;
@@ -236,10 +235,7 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
this_feature = original_features.featureAt(i);
// exons
key = this_feature.getKey().getKeyString();
- //if(!key.equals("exon") && !key.equals("polypeptide") &&
- // !key.endsWith("prime_UTR"))
- // continue;
-
+
final Qualifier parent_qualifier = this_feature.getQualifierByName("Parent");
final Qualifier derives_qualifier = this_feature.getQualifierByName("Derives_from");
if(parent_qualifier == null && derives_qualifier == null)
@@ -314,9 +310,7 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
{
ChadoCanonicalGene gene = (ChadoCanonicalGene)enum_genes.nextElement();
combineChadoExons(gene);
-
-
-
+
// inferring CDS and UTRs
if(DatabaseDocument.CHADO_INFER_CDS)
{
@@ -349,12 +343,6 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
{
gene.addSplicedFeatures(transcript_id, cdsFeature);
forcedAdd(cdsFeature);
-
-
-
- /*Feature protein;
- if((protein = gene.getProteinOfTranscript(transcript_id)) != null)
- cdsFeature.addFeatureListener(protein);*/
}
catch (ReadOnlyException e)
{
@@ -551,82 +539,7 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
}
}
- /**
- * Join the separate exons into one feature (if appropriate).
- **/
- /*private void combineFeatures()
- {
- final FeatureVector original_features = getAllFeatures();
-
- // the key of these hashes will be the group name and the value is a
- // FeatureVector containing the feature that are in that group
- final Hashtable forward_feature_groups = new Hashtable();
- final Hashtable reverse_feature_groups = new Hashtable();
-
- Feature this_feature;
- Hashtable this_strand_feature_groups;
- String group_name = null;
-
- for(int i = 0 ; i < original_features.size() ; ++i)
- {
- this_feature = original_features.featureAt(i);
-
- if(this_feature.getLocation().isComplement())
- this_strand_feature_groups = reverse_feature_groups;
- else
- this_strand_feature_groups = forward_feature_groups;
-
- try
- {
- String key = this_feature.getKey().getKeyString();
- if(key.equals("CDS") || key.equals("polypeptide_domain") ||
- key.equals("polypeptide") || key.equals("exon"))
- {
- if(this_feature.getQualifierByName("Parent") != null)
- {
- StringVector values =
- this_feature.getQualifierByName("Parent").getValues();
- group_name = (String)values.elementAt(0);
-
- if(this_feature.getQualifierByName("ID") != null &&
- !key.equals("exon"))
- {
- values =
- this_feature.getQualifierByName("ID").getValues();
- group_name = group_name+values.elementAt(0);
- }
- }
- else
- continue;
- }
- else
- continue;
-
- final FeatureVector other_features =
- (FeatureVector) this_strand_feature_groups.get(group_name);
-
- if(other_features == null)
- {
- final FeatureVector new_feature_vector = new FeatureVector();
- new_feature_vector.add(this_feature);
- this_strand_feature_groups.put(group_name, new_feature_vector);
- }
- else
- other_features.add(this_feature);
-
- }
- catch(InvalidRelationException e)
- {
- throw new Error("internal error - unexpected exception: " + e);
- }
-
- }
-
- combineFeaturesFromHash(forward_feature_groups);
- combineFeaturesFromHash(reverse_feature_groups);
- }*/
-
/**
* Bulk load match features featureLoc's and create a Hashtable with the
* feature_id's as keys and a list of the corresponding featureLocs as values.
@@ -710,29 +623,6 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
}
}
-
- // now merge the exons in the ChadoCanonicalGene feature
- /*Enumeration enum_exon_set = new_exon_set.keys();
- int num = 0;
- while(enum_exon_set.hasMoreElements())
- {
- String transcript_id = (String)enum_exon_set.nextElement();
- try
- {
- if(num == 0)
- gene.addSplicedFeatures(transcript_id,
- (Feature)new_exon_set.get(transcript_id), true );
- else
- gene.addSplicedFeatures(transcript_id,
- (Feature)new_exon_set.get(transcript_id));
- num++;
- }
- catch(InvalidRelationException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }*/
}
@@ -885,124 +775,6 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
throw new Error("internal error - unexpected exception: " + e);
}
}
-
- /**
- * Combine the features (which are exons) and delete the orignals from this
- * Entry. The key of this hash will be the group name and the value is a
- * FeatureVector containing the feature that are in that group. Groups
- * that have more than one member will be combined.
- **/
- /*private void combineFeaturesFromHash(final Hashtable feature_groups)
- {
- final Enumeration enumFeat = feature_groups.keys();
- String name;
- FeatureVector feature_group;
-
- while(enumFeat.hasMoreElements())
- {
- name = (String)enumFeat.nextElement();
-
- feature_group = (FeatureVector)feature_groups.get(name);
-
- if(feature_group.size() > 1)
- {
- // combine the features (exons) and delete the orignals
-
- final RangeVector new_range_vector = new RangeVector();
- QualifierVector qualifier_vector = new QualifierVector();
- Hashtable id_range_store = new Hashtable();
- Timestamp lasttimemodified = null;
-
- for (int i = 0 ; i < feature_group.size() ; ++i)
- {
- final GFFStreamFeature this_feature =
- (GFFStreamFeature)feature_group.elementAt(i);
- lasttimemodified = this_feature.getLastModified();
-
- final Location this_feature_location = this_feature.getLocation();
-
- if(this_feature_location.getRanges().size() > 1)
- {
- throw new Error("internal error - new location should have " +
- "exactly one range");
- }
-
- final Range new_range =
- (Range)this_feature_location.getRanges().elementAt(0);
-
- Qualifier id_qualifier = this_feature.getQualifierByName("ID");
- if(id_qualifier != null)
- {
- String id = (String)(id_qualifier.getValues()).elementAt(0);
- id_range_store.put(new_range, id);
- }
-
-
- if(this_feature_location.isComplement())
- new_range_vector.insertElementAt(new_range, 0);
- else
- new_range_vector.add(new_range);
-
- removeInternal(this_feature);
- qualifier_vector.addAll(this_feature.getQualifiers());
- }
-
- final Feature first_old_feature = feature_group.featureAt(0);
-
- final Location new_location = new Location(new_range_vector,
- first_old_feature.getLocation().isComplement());
-
- qualifier_vector = mergeQualifiers(qualifier_vector,
- first_old_feature.getLocation().isComplement());
-
- final GFFStreamFeature new_feature = new GFFStreamFeature(first_old_feature.getKey(),
- new_location, qualifier_vector);
-
- if(lasttimemodified != null)
- new_feature.setLastModified(lasttimemodified);
- new_feature.setSegmentRangeStore(id_range_store);
-
- try
- {
- new_feature.setLocation(new_location);
-
- final Qualifier gene_qualifier =
- new_feature.getQualifierByName("gene");
-
- if(gene_qualifier != null &&
- gene_qualifier.getValues().size() > 0 &&
- ((String)(gene_qualifier.getValues()).elementAt(0)).startsWith("Phat"))
- {
- // special case to handle incorrect output of the Phat gene
- // prediction tool
- new_feature.removeQualifierByName("codon_start");
- }
- else
- {
- final Qualifier old_codon_start_qualifier =
- first_old_feature.getQualifierByName("codon_start");
-
- if(old_codon_start_qualifier != null)
- new_feature.setQualifier(old_codon_start_qualifier);
- }
-
- forcedAdd(new_feature);
- }
- catch(ReadOnlyException e)
- {
- throw new Error("internal error - unexpected exception: " + e);
- }
- catch(OutOfRangeException e)
- {
- throw new Error("internal error - unexpected exception: " + e);
- }
- catch(EntryInformationException e)
- {
- throw new Error("internal error - unexpected exception: " + e);
- }
- }
- }
- }*/
private QualifierVector mergeQualifiers(QualifierVector qualifier_vector,
boolean complement)
--
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