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Commit 9db37303 authored by tjc's avatar tjc
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read in mapping files 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8238 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 7023862e
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uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
+ 122
− 50
View file @ 9db37303
......@@ -20,15 +20,20 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java,v 1.15 2008-07-15 15:40:08 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java,v 1.16 2008-07-16 10:12:44 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.util.*;
import java.io.IOException;
import java.io.InputStream;
import java.util.Enumeration;
import java.util.Properties;
import java.util.Vector;
/**
* This class extends the Entry class with the data for the entry coming from
......@@ -36,7 +41,7 @@ import java.io.IOException;
* entry.
*
* @author Kim Rutherford
* @version $Id: PublicDBDocumentEntry.java,v 1.15 2008-07-15 15:40:08 tjc Exp $
* @version $Id: PublicDBDocumentEntry.java,v 1.16 2008-07-16 10:12:44 tjc Exp $
**/
public class PublicDBDocumentEntry extends SimpleDocumentEntry
......@@ -44,31 +49,14 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
{
// database keys mapping to EMBL keys with any extra
// qualifiers to add in.
final private static Object[][] DATABASE_MAP_KEYS =
{
{"pseudogenic_transcript", "mRNA", new Qualifier("pseudo")},
{"pseudogenic_exon", "CDS", new Qualifier("pseudo")},
{"pseudogene", "gene", new Qualifier("pseudo")},
{DatabaseDocument.EXONMODEL, "CDS", null},
{"polypeptide_motif", "CDS_motif", null},
{"five_prime_UTR", "5'UTR", null},
{"three_prime_UTR", "3'UTR", null},
{"polypeptide_domain", "CDS_domain", null},
{"region", "misc_feature", null},
{"remark", "misc_feature", null},
{"sequence_difference", "misc_feature", null},
{"SECIS_element", "misc_feature", new Qualifier("note", "SECIS_element")}
};
private static Object[][] DATABASE_MAP_KEYS;
// database qualifiers mapping to EMBL qualifiers
final static String[][] DATABASE_QUALIFIERS_TO_MAP =
{
{"comment", "note"},
{"Dbxref", "db_xref"},
{"private", "note"},
{"orthologous_to", "ortholog"},
{"paralogous_to", "paralog"}
};
private static String[][] DATABASE_QUALIFIERS_TO_MAP;
// database qualifiers to ignore when converting to embl
private static Object[] DATABASE_QUALIFIERS_TO_REMOVE;
/**
* Create a new PublicDBDocumentEntry object associated with the given
......@@ -155,6 +143,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
}
}
/**
* Map GFF features to EMBL/Genbank
* @param feature
......@@ -162,27 +151,15 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
*/
private Object mapGffToNativeFeature(final Feature feature)
{
final String[] QUALIFIERS_TO_REMOVE =
{
"timelastmodified",
"ID",
"comment", // convert to note
"feature_id",
"Parent",
"Derives_from",
"feature_relationship_rank",
"isObsolete"
};
if(DATABASE_MAP_KEYS == null)
initDatabaseMappings();
Key key = feature.getKey();
QualifierVector qualifiers = feature.getQualifiers().copy();
if(getEntryInformation().isValidQualifier(QUALIFIERS_TO_REMOVE[0]))
{
/*if(key.getKeyString().startsWith("pseudo"))
key = handlePseudo(key,qualifiers);*/
key = map(key, qualifiers);
if(getEntryInformation().isValidQualifier((String) DATABASE_QUALIFIERS_TO_REMOVE[0]))
{
try
{
if(this instanceof EmblDocumentEntry)
......@@ -205,8 +182,6 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
// flatten gene model - combining qualifiers
key = map(key, qualifiers);
if(key.getKeyString().equals(DatabaseDocument.EXONMODEL))
{
ChadoCanonicalGene chadoGene = ((GFFStreamFeature)feature).getChadoGene();
......@@ -238,10 +213,10 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
}
}
for(int i=0; i<QUALIFIERS_TO_REMOVE.length; i++)
for(int i=0; i<DATABASE_QUALIFIERS_TO_REMOVE.length; i++)
{
if(!getEntryInformation().isValidQualifier(QUALIFIERS_TO_REMOVE[i]))
qualifiers.removeQualifierByName(QUALIFIERS_TO_REMOVE[i]);
if(!getEntryInformation().isValidQualifier((String) DATABASE_QUALIFIERS_TO_REMOVE[i]))
qualifiers.removeQualifierByName((String) DATABASE_QUALIFIERS_TO_REMOVE[i]);
}
if(key.getKeyString().equals("polypeptide"))
......@@ -298,6 +273,8 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
if(!newValues.get(j).equals(""))
tmpNewValues.add(newValues.get(j));
}
if(tmpNewValues.size() == 0)
continue;
newQualifier = new Qualifier("orthologous_to", tmpNewValues);
}
......@@ -320,12 +297,14 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
/**
*
* Maps database (SO) keys to EMBl keys.
* @param key
* @return
*/
protected static Key mapKeys(final Key key)
{
if(DATABASE_MAP_KEYS == null)
initDatabaseMappings();
for(int i=0; i<DATABASE_MAP_KEYS.length; i++)
{
if(key.getKeyString().equals(DATABASE_MAP_KEYS[i][0]))
......@@ -343,6 +322,8 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
*/
private Key map(final Key key, final QualifierVector qualifiers)
{
if(DATABASE_MAP_KEYS == null)
initDatabaseMappings();
for(int i=0; i<DATABASE_MAP_KEYS.length; i++)
{
if(key.getKeyString().equals(DATABASE_MAP_KEYS[i][0]))
......@@ -356,7 +337,12 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
{
try
{
int nvalues = newQualifier.getValues().size();
final int nvalues;
if(newQualifier.getValues() == null)
nvalues = 0;
else
nvalues = newQualifier.getValues().size();
final int type;
if(nvalues == 0)
type = QualifierInfo.NO_VALUE;
......@@ -413,4 +399,90 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
else
return new GenbankStreamSequence (sequence);
}
/**
* Read key and qualifier mappings for CHADO to EMBL
**/
private static void initDatabaseMappings()
{
final InputStream keyStream =
Options.class.getResourceAsStream("/etc/key_mapping");
final InputStream qualifierStream =
Options.class.getResourceAsStream("/etc/qualifier_mapping");
final Properties keyMapProperties = new Properties();
final Properties qualifierMapProperties = new Properties();
try
{
keyMapProperties.load(keyStream);
qualifierMapProperties.load(qualifierStream);
}
catch(IOException e)
{
e.printStackTrace();
}
// parse the keyMapProperties
DATABASE_MAP_KEYS = new Object[keyMapProperties.size()][3];
final Enumeration keysenum = keyMapProperties.propertyNames();
int n = 0;
while(keysenum.hasMoreElements())
{
String current_map_name = (String) keysenum.nextElement();
final StringVector property_values =
Options.getPropertyValues(keyMapProperties, current_map_name);
DATABASE_MAP_KEYS[n][0] = current_map_name;
DATABASE_MAP_KEYS[n][1] = property_values.get(0);
if(property_values.size() == 2)
{
String qualifierString[] = ((String)property_values.get(1)).split("=");
final uk.ac.sanger.artemis.io.Qualifier qualifier;
if(qualifierString.length == 2)
qualifier = new uk.ac.sanger.artemis.io.Qualifier(qualifierString[0], qualifierString[1]);
else
qualifier = new uk.ac.sanger.artemis.io.Qualifier(qualifierString[0]);
DATABASE_MAP_KEYS[n][2] = qualifier;
}
else
DATABASE_MAP_KEYS[n][2] = null;
n++;
}
// parse the qualifier mappings
Enumeration qualifiersenum = qualifierMapProperties.propertyNames();
n = 0;
Vector qualifiersToRemove = new Vector();
while(qualifiersenum.hasMoreElements())
{
String current_map_name = (String) qualifiersenum.nextElement();
final StringVector property_values =
Options.getPropertyValues(qualifierMapProperties, current_map_name);
if(property_values == null || property_values.size() == 0)
qualifiersToRemove.add(current_map_name);
else
n++;
}
DATABASE_QUALIFIERS_TO_MAP = new String[n][2];
DATABASE_QUALIFIERS_TO_REMOVE = qualifiersToRemove.toArray();
qualifiersenum = qualifierMapProperties.propertyNames();
n = 0;
while(qualifiersenum.hasMoreElements())
{
String current_map_name = (String) qualifiersenum.nextElement();
final StringVector property_values =
Options.getPropertyValues(qualifierMapProperties, current_map_name);
if(property_values != null && property_values.size() > 0)
{
DATABASE_QUALIFIERS_TO_MAP[n][0] = current_map_name;
DATABASE_QUALIFIERS_TO_MAP[n][1] = (String) property_values.get(0);
n++;
}
}
}
}
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