diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 162d45f94ae416b43f1538d0d6b5973bd7fae3dc..c0d3657852d1e439c65fd827f36bda3ef35347ef 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -60,13 +60,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(GFFStreamFeature.class);
-
- /**
- * This is the line of GFF input that was read to get this
- * GFFStreamFeature. A GFFStreamFeature that was created from multiple GFF
- * lines will have a gff_lines variable that contains multiple line.
- **/
- StringVector gff_lines = null;
/** store for spliced features containing id and range of each segment */
private Hashtable<String, Range> id_range_store;
@@ -138,17 +131,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
setKey(key);
setLocation(location);
setQualifiers(qualifiers);
-
- /*
- if(getQualifierByName("score") == null)
- setQualifier(new Qualifier("score", "."));
-
- if(getQualifierByName("gff_source") == null)
- setQualifier(new Qualifier("gff_source", "artemis"));
-
- if(getQualifierByName("gff_seqname") == null)
- setQualifier(new Qualifier("gff_seqname", "."));
- */
+
if(getQualifierByName("ID") == null)
{
String idStr = null;
@@ -314,48 +297,41 @@ public class GFFStreamFeature extends SimpleDocumentFeature
"(got " + line_bits.size () +
" fields) from: " + line);
- final String start_base_string = ((String)line_bits.elementAt(3)).trim();
- final String end_base_string = ((String)line_bits.elementAt(4)).trim();
+ final String start_base_str = line_bits.elementAt(3).trim();
+ final String end_base_str = line_bits.elementAt(4).trim();
final int start_base;
final int end_base;
try
{
- start_base = Integer.parseInt(start_base_string);
- end_base = Integer.parseInt(end_base_string);
+ start_base = Integer.parseInt(start_base_str);
+ end_base = Integer.parseInt(end_base_str);
}
catch(NumberFormatException e)
{
throw new ReadFormatException("Could not understand the start or end base " +
- "of a GFF feature: " + start_base_string +
- " " + end_base_string);
+ "of a GFF feature: " + start_base_str +
+ " " + end_base_str);
}
// start of qualifier parsing and setting
try
{
final boolean complement_flag;
-
- if(((String)line_bits.elementAt(6)).equals("+"))
+ if(line_bits.elementAt(6).equals("+"))
complement_flag = false;
- else if(((String)line_bits.elementAt(6)).equals("-"))
+ else if(line_bits.elementAt(6).equals("-"))
complement_flag = true;
else
{
// must be unstranded
complement_flag = false;
-
- // best we can do
- //final String note_string = "this feature is unstranded";
- //setQualifier(new Qualifier("note", note_string));
}
if(line_bits.size() == 9)
{
- final String rest_of_line = (String)line_bits.elementAt(8);
-
- // parse the rest of the line as ACeDB format attributes
+ final String rest_of_line = line_bits.elementAt(8);
final Hashtable<String, StringVector> attributes = parseAttributes(rest_of_line);
for(final Enumeration<String> attribute_enum = attributes.keys();
attribute_enum.hasMoreElements();)
@@ -382,32 +358,20 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
}
- /*if( !((String)line_bits.elementAt(0)).equals("null") )
- {
- final Qualifier gff_seqname =
- new Qualifier("gff_seqname", decode((String)line_bits.elementAt(0)));
-
- setQualifier(gff_seqname);
- }*/
- if( !((String)line_bits.elementAt(0)).equals("null") )
- setGffSeqName( decode((String)line_bits.elementAt(0)) );
+ if( !line_bits.elementAt(0).equals("null") )
+ setGffSeqName( decode(line_bits.elementAt(0)) );
- final Key key = new Key((String)line_bits.elementAt(2));
- setKey(key);
-
- /*final Qualifier source_qualifier =
- new Qualifier("gff_source", (String)line_bits.elementAt(1));
- setQualifier(source_qualifier);*/
- this.setGffSource((String)line_bits.elementAt(1));
+ setKey(new Key(line_bits.elementAt(2)));
+ setGffSource(line_bits.elementAt(1));
- if( !((String)line_bits.elementAt(5)).equals(".") )
+ if( !line_bits.elementAt(5).equals(".") )
{
final Qualifier score_qualifier =
- new Qualifier("score", (String)line_bits.elementAt(5));
+ new Qualifier("score", line_bits.elementAt(5));
setQualifier(score_qualifier);
}
- String frame = (String)line_bits.elementAt(7);
+ String frame = line_bits.elementAt(7);
if(frame.equals ("0"))
frame = "1";
@@ -452,7 +416,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
throw new Error("internal error - unexpected exception: " + e);
}
- this.gff_lines = new StringVector(line);
+ //this.gff_lines = new StringVector(line);
}
/**
@@ -520,9 +484,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(id_range_store != null)
{
Enumeration<String> enum_ranges = id_range_store.keys();
- //Iterator it = id_range_store.values().iterator();
while(enum_ranges.hasMoreElements())
- //while(it.hasNext())
{
String key = enum_ranges.nextElement();
Range range = id_range_store.get(key);
@@ -547,7 +509,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* @param rv
* @return
*/
- public String getSegmentID(RangeVector rv)
+ public String getSegmentID(final RangeVector rv)
{
String id = "";
if(id_range_store != null)
@@ -628,11 +590,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
-
/**
* For gff-version 3:
- * http://song.sourceforge.net/gff3-jan04.shtml
- *
+ * http://www.sequenceontology.org/gff3.shtml
* Remove URL escaping rule (e.g. space="%20" or "+")
*/
public static String decode(String s)
@@ -648,15 +608,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature
while( (ind = s.indexOf(enc)) > -1)
s = s.substring(0,ind) + dec + s.substring(ind+enc.length());
}
-
return s;
}
/**
* For gff-version 3:
- * http://song.sourceforge.net/gff3-jan04.shtml
- *
+ * http://www.sequenceontology.org/gff3.shtml
* Add URL escaping rule (e.g. space="%20" or "+")
*/
public static String encode(String s)
@@ -672,11 +630,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
while( (ind = s.indexOf(dec)) > -1 )
s = s.substring(0,ind) + enc + s.substring(ind+1);
}
-
return s;
}
-
+
/**
* Return the reference of a new copy of this Feature.
**/
@@ -843,7 +800,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
frame + "\t" +
attribute_string + "\n");
}
-
}
/**
@@ -899,7 +855,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
"Target", "Gap", "Note",
"Dbxref", "Ontology_term" };
int count = 0;
- Qualifier this_qualifier;
final int names_length = names.length;
if(myId != null)
@@ -911,13 +866,11 @@ public class GFFStreamFeature extends SimpleDocumentFeature
for(int i=1; i<names_length; i++)
{
- this_qualifier = (Qualifier)qualifiers.getQualifierByName(names[i]);
+ Qualifier this_qualifier = qualifiers.getQualifierByName(names[i]);
if(this_qualifier == null)
continue;
-
- // GSV :: see new getQualifierString signature
- // this qualifier is one of the reserved qualifiers
+
final String this_qualifier_str = getQualifierString(this_qualifier, true);
if(this_qualifier_str == null)
continue;
@@ -929,11 +882,8 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
boolean lname;
- final int qualifiers_size = qualifiers.size();
- for(int i = 0; i < qualifiers_size; i++)
+ for(Qualifier this_qualifier: qualifiers)
{
- this_qualifier = (Qualifier)qualifiers.elementAt(i);
-
lname = false;
for(int j=0; j<names_length; j++)
if(this_qualifier.getName().equals(names[j]))
@@ -946,9 +896,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
(this_qualifier.getName().equals("history") && System.getProperty("nohistory") != null) )
continue;
- // GSV :: see new getQualifierString signature
- // this qualifier is NOT one of the reserved qualifiers
- String this_qualifier_str = getQualifierString(this_qualifier, false);
+ final String this_qualifier_str = getQualifierString(this_qualifier, false);
if(this_qualifier_str == null)
continue;
@@ -987,9 +935,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* @param q the qualifier to represent as a <code>String</code>
* @param reserved indicate if this is one of the reserved tags or not
* @return the <code>String</code> representation
- *
- * GSV: modified the signature to force the caller to declare if this
- * qualifier is one of the reserved ones.
*/
private String getQualifierString(Qualifier q, boolean reserved )
{
@@ -1004,7 +949,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
/*
* GSV :
- *
* The Bio::FeatureIO perl module falls over if there are Uppercased
* attribute names for tags which aren't part of the standard reserved
* set. So we lowercase these, since in the specification it says :
@@ -1012,7 +956,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* "All attributes that begin with an uppercase letter are reserved for
* later use. Attributes that begin with a lowercase letter can be used
* freely by applications."
- *
* see http://www.sequenceontology.org/gff3.shtml
*/
String nameToBuffer = encode(name);
@@ -1073,7 +1016,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* Adapted from code by Matthew Pocock for the BioJava project.
*
* Modified for gff-version 3.
- *
* @return Return a Hashtable. Each key is an attribute name and each value
* of the Hashtable is a StringVector containing the attribute values.
* If the attribute has no value then the Hashtable value will be a zero
@@ -1081,12 +1023,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
**/
private Hashtable<String, StringVector> parseAttributes(final String att_val_list)
{
- Hashtable<String, StringVector> attributes = new Hashtable<String, StringVector>();
-
-// StringTokenizer tokeniser = new StringTokenizer(att_val_list, ";", false);
-// while(tokeniser.hasMoreTokens())
-// {
-// final String this_token = tokeniser.nextToken().trim();
+ final Hashtable<String, StringVector> attr = new Hashtable<String, StringVector>();
int ind_start = 0;
int ind_end;
@@ -1098,17 +1035,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
final String this_token = decode(att_val_list.substring(ind_start, ind_end).trim());
ind_start = ind_end+1;
-
- /*if(this_token.startsWith("feature_relationship_rank="))
- {
- setFeature_relationship_rank(
- Integer.parseInt(this_token.substring(26)) );
- continue;
- }*/
int index_of_first_space = this_token.indexOf(" ");
- String att_name;
+ final String att_name;
StringVector att_values = new StringVector();
if( this_token.indexOf("=") > -1 &&
@@ -1207,14 +1137,14 @@ public class GFFStreamFeature extends SimpleDocumentFeature
att_values.set(0,(String)att_values.get(0));
}
}
-
- if(attributes.get(att_name) != null)
- ((StringVector)attributes.get(att_name)).add(att_values);
+
+ if(attr.get(att_name) != null)
+ attr.get(att_name).add(att_values);
else
- attributes.put(att_name, att_values);
+ attr.put(att_name, att_values);
}
- return attributes;
+ return attr;
}
/**