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Commit f494f192 authored by tcarver's avatar tcarver
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tidy

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uk/ac/sanger/artemis/io/GFFStreamFeature.java
+ 33
− 103
View file @ f494f192
...@@ -60,13 +60,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -60,13 +60,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
private static org.apache.log4j.Logger logger4j = private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(GFFStreamFeature.class); 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 */ /** store for spliced features containing id and range of each segment */
private Hashtable<String, Range> id_range_store; private Hashtable<String, Range> id_range_store;
...@@ -138,17 +131,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -138,17 +131,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
setKey(key); setKey(key);
setLocation(location); setLocation(location);
setQualifiers(qualifiers); 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) if(getQualifierByName("ID") == null)
{ {
String idStr = null; String idStr = null;
...@@ -314,48 +297,41 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -314,48 +297,41 @@ public class GFFStreamFeature extends SimpleDocumentFeature
"(got " + line_bits.size () + "(got " + line_bits.size () +
" fields) from: " + line); " fields) from: " + line);
final String start_base_string = ((String)line_bits.elementAt(3)).trim(); final String start_base_str = line_bits.elementAt(3).trim();
final String end_base_string = ((String)line_bits.elementAt(4)).trim(); final String end_base_str = line_bits.elementAt(4).trim();
final int start_base; final int start_base;
final int end_base; final int end_base;
try try
{ {
start_base = Integer.parseInt(start_base_string); start_base = Integer.parseInt(start_base_str);
end_base = Integer.parseInt(end_base_string); end_base = Integer.parseInt(end_base_str);
} }
catch(NumberFormatException e) catch(NumberFormatException e)
{ {
throw new ReadFormatException("Could not understand the start or end base " + throw new ReadFormatException("Could not understand the start or end base " +
"of a GFF feature: " + start_base_string + "of a GFF feature: " + start_base_str +
" " + end_base_string); " " + end_base_str);
} }
// start of qualifier parsing and setting // start of qualifier parsing and setting
try try
{ {
final boolean complement_flag; final boolean complement_flag;
if(line_bits.elementAt(6).equals("+"))
if(((String)line_bits.elementAt(6)).equals("+"))
complement_flag = false; complement_flag = false;
else if(((String)line_bits.elementAt(6)).equals("-")) else if(line_bits.elementAt(6).equals("-"))
complement_flag = true; complement_flag = true;
else else
{ {
// must be unstranded // must be unstranded
complement_flag = false; 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) if(line_bits.size() == 9)
{ {
final String rest_of_line = (String)line_bits.elementAt(8); final String rest_of_line = line_bits.elementAt(8);
// parse the rest of the line as ACeDB format attributes
final Hashtable<String, StringVector> attributes = parseAttributes(rest_of_line); final Hashtable<String, StringVector> attributes = parseAttributes(rest_of_line);
for(final Enumeration<String> attribute_enum = attributes.keys(); for(final Enumeration<String> attribute_enum = attributes.keys();
attribute_enum.hasMoreElements();) attribute_enum.hasMoreElements();)
...@@ -382,32 +358,20 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -382,32 +358,20 @@ public class GFFStreamFeature extends SimpleDocumentFeature
} }
} }
/*if( !((String)line_bits.elementAt(0)).equals("null") ) if( !line_bits.elementAt(0).equals("null") )
{ setGffSeqName( decode(line_bits.elementAt(0)) );
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)) );
final Key key = new Key((String)line_bits.elementAt(2)); setKey(new Key(line_bits.elementAt(2)));
setKey(key); setGffSource(line_bits.elementAt(1));
/*final Qualifier source_qualifier =
new Qualifier("gff_source", (String)line_bits.elementAt(1));
setQualifier(source_qualifier);*/
this.setGffSource((String)line_bits.elementAt(1));
if( !((String)line_bits.elementAt(5)).equals(".") ) if( !line_bits.elementAt(5).equals(".") )
{ {
final Qualifier score_qualifier = final Qualifier score_qualifier =
new Qualifier("score", (String)line_bits.elementAt(5)); new Qualifier("score", line_bits.elementAt(5));
setQualifier(score_qualifier); setQualifier(score_qualifier);
} }
String frame = (String)line_bits.elementAt(7); String frame = line_bits.elementAt(7);
if(frame.equals ("0")) if(frame.equals ("0"))
frame = "1"; frame = "1";
...@@ -452,7 +416,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -452,7 +416,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
throw new Error("internal error - unexpected exception: " + e); 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 ...@@ -520,9 +484,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(id_range_store != null) if(id_range_store != null)
{ {
Enumeration<String> 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(enum_ranges.hasMoreElements())
//while(it.hasNext())
{ {
String key = enum_ranges.nextElement(); String key = enum_ranges.nextElement();
Range range = id_range_store.get(key); Range range = id_range_store.get(key);
...@@ -547,7 +509,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -547,7 +509,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* @param rv * @param rv
* @return * @return
*/ */
public String getSegmentID(RangeVector rv) public String getSegmentID(final RangeVector rv)
{ {
String id = ""; String id = "";
if(id_range_store != null) if(id_range_store != null)
...@@ -628,11 +590,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -628,11 +590,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
} }
/** /**
* For gff-version 3: * 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 "+") * Remove URL escaping rule (e.g. space="%20" or "+")
*/ */
public static String decode(String s) public static String decode(String s)
...@@ -648,15 +608,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -648,15 +608,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature
while( (ind = s.indexOf(enc)) > -1) while( (ind = s.indexOf(enc)) > -1)
s = s.substring(0,ind) + dec + s.substring(ind+enc.length()); s = s.substring(0,ind) + dec + s.substring(ind+enc.length());
} }
return s; return s;
} }
/** /**
* For gff-version 3: * 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 "+") * Add URL escaping rule (e.g. space="%20" or "+")
*/ */
public static String encode(String s) public static String encode(String s)
...@@ -672,11 +630,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -672,11 +630,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
while( (ind = s.indexOf(dec)) > -1 ) while( (ind = s.indexOf(dec)) > -1 )
s = s.substring(0,ind) + enc + s.substring(ind+1); s = s.substring(0,ind) + enc + s.substring(ind+1);
} }
return s; return s;
} }
/** /**
* Return the reference of a new copy of this Feature. * Return the reference of a new copy of this Feature.
**/ **/
...@@ -843,7 +800,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -843,7 +800,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
frame + "\t" + frame + "\t" +
attribute_string + "\n"); attribute_string + "\n");
} }
} }
/** /**
...@@ -899,7 +855,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -899,7 +855,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
"Target", "Gap", "Note", "Target", "Gap", "Note",
"Dbxref", "Ontology_term" }; "Dbxref", "Ontology_term" };
int count = 0; int count = 0;
Qualifier this_qualifier;
final int names_length = names.length; final int names_length = names.length;
if(myId != null) if(myId != null)
...@@ -911,13 +866,11 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -911,13 +866,11 @@ public class GFFStreamFeature extends SimpleDocumentFeature
for(int i=1; i<names_length; i++) 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) if(this_qualifier == null)
continue; continue;
// GSV :: see new getQualifierString signature
// this qualifier is one of the reserved qualifiers
final String this_qualifier_str = getQualifierString(this_qualifier, true); final String this_qualifier_str = getQualifierString(this_qualifier, true);
if(this_qualifier_str == null) if(this_qualifier_str == null)
continue; continue;
...@@ -929,11 +882,8 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -929,11 +882,8 @@ public class GFFStreamFeature extends SimpleDocumentFeature
} }
boolean lname; boolean lname;
final int qualifiers_size = qualifiers.size(); for(Qualifier this_qualifier: qualifiers)
for(int i = 0; i < qualifiers_size; i++)
{ {
this_qualifier = (Qualifier)qualifiers.elementAt(i);
lname = false; lname = false;
for(int j=0; j<names_length; j++) for(int j=0; j<names_length; j++)
if(this_qualifier.getName().equals(names[j])) if(this_qualifier.getName().equals(names[j]))
...@@ -946,9 +896,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -946,9 +896,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
(this_qualifier.getName().equals("history") && System.getProperty("nohistory") != null) ) (this_qualifier.getName().equals("history") && System.getProperty("nohistory") != null) )
continue; continue;
// GSV :: see new getQualifierString signature final String this_qualifier_str = getQualifierString(this_qualifier, false);
// this qualifier is NOT one of the reserved qualifiers
String this_qualifier_str = getQualifierString(this_qualifier, false);
if(this_qualifier_str == null) if(this_qualifier_str == null)
continue; continue;
...@@ -987,9 +935,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -987,9 +935,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* @param q the qualifier to represent as a <code>String</code> * @param q the qualifier to represent as a <code>String</code>
* @param reserved indicate if this is one of the reserved tags or not * @param reserved indicate if this is one of the reserved tags or not
* @return the <code>String</code> representation * @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 ) private String getQualifierString(Qualifier q, boolean reserved )
{ {
...@@ -1004,7 +949,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -1004,7 +949,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
/* /*
* GSV : * GSV :
*
* The Bio::FeatureIO perl module falls over if there are Uppercased * The Bio::FeatureIO perl module falls over if there are Uppercased
* attribute names for tags which aren't part of the standard reserved * attribute names for tags which aren't part of the standard reserved
* set. So we lowercase these, since in the specification it says : * set. So we lowercase these, since in the specification it says :
...@@ -1012,7 +956,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -1012,7 +956,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* "All attributes that begin with an uppercase letter are reserved for * "All attributes that begin with an uppercase letter are reserved for
* later use. Attributes that begin with a lowercase letter can be used * later use. Attributes that begin with a lowercase letter can be used
* freely by applications." * freely by applications."
*
* see http://www.sequenceontology.org/gff3.shtml * see http://www.sequenceontology.org/gff3.shtml
*/ */
String nameToBuffer = encode(name); String nameToBuffer = encode(name);
...@@ -1073,7 +1016,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -1073,7 +1016,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* Adapted from code by Matthew Pocock for the BioJava project. * Adapted from code by Matthew Pocock for the BioJava project.
* *
* Modified for gff-version 3. * Modified for gff-version 3.
*
* @return Return a Hashtable. Each key is an attribute name and each value * @return Return a Hashtable. Each key is an attribute name and each value
* of the Hashtable is a StringVector containing the attribute values. * of the Hashtable is a StringVector containing the attribute values.
* If the attribute has no value then the Hashtable value will be a zero * If the attribute has no value then the Hashtable value will be a zero
...@@ -1081,12 +1023,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -1081,12 +1023,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
**/ **/
private Hashtable<String, StringVector> parseAttributes(final String att_val_list) private Hashtable<String, StringVector> parseAttributes(final String att_val_list)
{ {
Hashtable<String, StringVector> attributes = new Hashtable<String, StringVector>(); final Hashtable<String, StringVector> attr = new Hashtable<String, StringVector>();
// StringTokenizer tokeniser = new StringTokenizer(att_val_list, ";", false);
// while(tokeniser.hasMoreTokens())
// {
// final String this_token = tokeniser.nextToken().trim();
int ind_start = 0; int ind_start = 0;
int ind_end; int ind_end;
...@@ -1098,17 +1035,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -1098,17 +1035,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
final String this_token = decode(att_val_list.substring(ind_start, ind_end).trim()); final String this_token = decode(att_val_list.substring(ind_start, ind_end).trim());
ind_start = ind_end+1; 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(" "); int index_of_first_space = this_token.indexOf(" ");
String att_name; final String att_name;
StringVector att_values = new StringVector(); StringVector att_values = new StringVector();
if( this_token.indexOf("=") > -1 && if( this_token.indexOf("=") > -1 &&
...@@ -1207,14 +1137,14 @@ public class GFFStreamFeature extends SimpleDocumentFeature ...@@ -1207,14 +1137,14 @@ public class GFFStreamFeature extends SimpleDocumentFeature
att_values.set(0,(String)att_values.get(0)); att_values.set(0,(String)att_values.get(0));
} }
} }
if(attributes.get(att_name) != null) if(attr.get(att_name) != null)
((StringVector)attributes.get(att_name)).add(att_values); attr.get(att_name).add(att_values);
else else
attributes.put(att_name, att_values); attr.put(att_name, att_values);
} }
return attributes; return attr;
} }
/** /**
......
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