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JAL-1759 merge from develop
[jalview.git]
/
src
/
jalview
/
datamodel
/
xdb
/
embl
/
EmblEntry.java
diff --git
a/src/jalview/datamodel/xdb/embl/EmblEntry.java
b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index
3f890ba
..
9c9447e
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblEntry.java
@@
-20,11
+20,6
@@
*/
package jalview.datamodel.xdb.embl;
*/
package jalview.datamodel.xdb.embl;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
@@
-33,6
+28,10
@@
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import java.util.Hashtable;
+import java.util.Map.Entry;
+import java.util.Vector;
+
/**
* Data model for one entry returned from an EMBL query, as marshalled by a
* Castor binding file
/**
* Data model for one entry returned from an EMBL query, as marshalled by a
* Castor binding file
@@
-397,7
+396,7
@@
public class EmblEntry
boolean noPeptide, String sourceDb)
{ // TODO: ensure emblEntry.getSequences behaves correctly for returning all
// cases of noNa and noPeptide
boolean noPeptide, String sourceDb)
{ // TODO: ensure emblEntry.getSequences behaves correctly for returning all
// cases of noNa and noPeptide
- Vector seqs = new Vector();
+ Vector<SequenceI> seqs = new Vector<SequenceI>();
Sequence dna = null;
if (!noNa)
{
Sequence dna = null;
if (!noNa)
{
@@
-415,26
+414,23
@@
public class EmblEntry
// TODO: transform EMBL Database refs to canonical form
if (dbRefs != null)
{
// TODO: transform EMBL Database refs to canonical form
if (dbRefs != null)
{
- for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
- .addDBRef((DBRefEntry) i.next()))
+ for (DBRefEntry dbref : dbRefs)
{
{
- ;
+ dna.addDBRef(dbref);
}
}
}
try
{
}
}
}
try
{
- for (Iterator i = features.iterator(); i.hasNext();)
+ for (EmblFeature feature: features)
{
{
- EmblFeature feature = (EmblFeature) i.next();
if (!noNa)
{
if (!noNa)
{
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ if (feature.dbRefs != null)
{
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
+ for (DBRefEntry dbref : feature.dbRefs)
{
{
- ;
+ dna.addDBRef(dbref);
}
}
}
}
}
}
@@
-445,14
+441,14
@@
public class EmblEntry
else
{
// General feature type.
else
{
// General feature type.
+ // TODO this is just duplicated code ??
if (!noNa)
{
if (!noNa)
{
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ if (feature.dbRefs != null)
{
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
+ for (DBRefEntry dbref : feature.dbRefs)
{
{
- ;
+ dna.addDBRef(dbref);
}
}
}
}
}
}
@@
-474,7
+470,7
@@
public class EmblEntry
SequenceI[] sqs = new SequenceI[seqs.size()];
for (int i = 0, j = seqs.size(); i < j; i++)
{
SequenceI[] sqs = new SequenceI[seqs.size()];
for (int i = 0, j = seqs.size(); i < j; i++)
{
- sqs[i] = (SequenceI) seqs.elementAt(i);
+ sqs[i] = seqs.elementAt(i);
seqs.set(i, null);
}
return sqs;
seqs.set(i, null);
}
return sqs;
@@
-496,19
+492,16
@@
public class EmblEntry
* flag for generation of Peptide sequence objects
*/
private void parseCodingFeature(EmblFeature feature, String sourceDb,
* flag for generation of Peptide sequence objects
*/
private void parseCodingFeature(EmblFeature feature, String sourceDb,
- Vector seqs, Sequence dna, boolean noPeptide)
+ Vector<SequenceI> seqs, Sequence dna, boolean noPeptide)
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
// extract coding region(s)
jalview.datamodel.Mapping map = null;
int[] exon = null;
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
// extract coding region(s)
jalview.datamodel.Mapping map = null;
int[] exon = null;
- if (feature.locations != null && feature.locations.size() > 0)
+ if (feature.locations != null)
{
{
- for (Enumeration locs = feature.locations.elements(); locs
- .hasMoreElements();)
+ for (EmblFeatureLocations loc : feature.locations)
{
{
- EmblFeatureLocations loc = (EmblFeatureLocations) locs
- .nextElement();
int[] se = loc.getElementRanges(accession);
if (exon == null)
{
int[] se = loc.getElementRanges(accession);
if (exon == null)
{
@@
-526,19
+519,17
@@
public class EmblEntry
String prseq = null;
String prname = new String();
String prid = null;
String prseq = null;
String prname = new String();
String prid = null;
- Hashtable vals = new Hashtable();
+ Hashtable<String, String> vals = new Hashtable<String, String>();
int prstart = 1;
// get qualifiers
int prstart = 1;
// get qualifiers
- if (feature.getQualifiers() != null
- && feature.getQualifiers().size() > 0)
+ if (feature.getQualifiers() != null)
{
{
- for (Iterator quals = feature.getQualifiers().iterator(); quals
- .hasNext();)
+ for (Qualifier q : feature.getQualifiers())
{
{
- Qualifier q = (Qualifier) quals.next();
- if (q.getName().equals("translation"))
+ String qname = q.getName();
+ if (qname.equals("translation"))
{
{
- StringBuffer prsq = new StringBuffer(q.getValues()[0]);
+ StringBuilder prsq = new StringBuilder(q.getValues()[0]);
int p = prsq.indexOf(" ");
while (p > -1)
{
int p = prsq.indexOf(" ");
while (p > -1)
{
@@
-549,15
+540,15
@@
public class EmblEntry
prsq = null;
}
prsq = null;
}
- else if (q.getName().equals("protein_id"))
+ else if (qname.equals("protein_id"))
{
prid = q.getValues()[0];
}
{
prid = q.getValues()[0];
}
- else if (q.getName().equals("codon_start"))
+ else if (qname.equals("codon_start"))
{
prstart = Integer.parseInt(q.getValues()[0]);
}
{
prstart = Integer.parseInt(q.getValues()[0]);
}
- else if (q.getName().equals("product"))
+ else if (qname.equals("product"))
{
prname = q.getValues()[0];
}
{
prname = q.getValues()[0];
}
@@
-565,7
+556,7
@@
public class EmblEntry
{
// throw anything else into the additional properties hash
String[] s = q.getValues();
{
// throw anything else into the additional properties hash
String[] s = q.getValues();
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
if (s != null)
{
for (int i = 0; i < s.length; i++)
if (s != null)
{
for (int i = 0; i < s.length; i++)
@@
-574,15
+565,15
@@
public class EmblEntry
sb.append("\n");
}
}
sb.append("\n");
}
}
- vals.put(q.getName(), sb.toString());
+ vals.put(qname, sb.toString());
}
}
}
Sequence product = null;
DBRefEntry protEMBLCDS = null;
exon = adjustForPrStart(prstart, exon);
}
}
}
Sequence product = null;
DBRefEntry protEMBLCDS = null;
exon = adjustForPrStart(prstart, exon);
- boolean noProteinDbref=true;
-
+ boolean noProteinDbref = true;
+
if (prseq != null && prname != null && prid != null)
{
// extract proteins.
if (prseq != null && prname != null && prid != null)
{
// extract proteins.
@@
-663,9
+654,9
@@
public class EmblEntry
protEMBLCDS = new DBRefEntry(pcdnaref);
protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
product.addDBRef(protEMBLCDS);
protEMBLCDS = new DBRefEntry(pcdnaref);
protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
product.addDBRef(protEMBLCDS);
-
- }
-
+
+ }
+
}
}
// add cds feature to dna seq - this may include the stop codon
}
}
// add cds feature to dna seq - this may include the stop codon
@@
-676,31
+667,25
@@
public class EmblEntry
sf.setEnd(exon[xint + 1]);
sf.setType(feature.getName());
sf.setFeatureGroup(sourceDb);
sf.setEnd(exon[xint + 1]);
sf.setType(feature.getName());
sf.setFeatureGroup(sourceDb);
- sf.setDescription("Exon " + (1 + xint / 2)
- + " for protein '" + prname + "' EMBLCDS:" + prid);
+ sf.setDescription("Exon " + (1 + xint / 2) + " for protein '"
+ + prname + "' EMBLCDS:" + prid);
sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
sf.setValue(FeatureProperties.EXONPRODUCT, prname);
sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
sf.setValue(FeatureProperties.EXONPRODUCT, prname);
- if (vals != null && vals.size() > 0)
+ if (vals != null)
{
{
- Enumeration kv = vals.keys();
- while (kv.hasMoreElements())
+ for (Entry<String, String> val : vals.entrySet())
{
{
- Object key = kv.nextElement();
- if (key != null)
- {
- sf.setValue(key.toString(), vals.get(key));
- }
+ sf.setValue(val.getKey(), val.getValue());
}
}
dna.addSequenceFeature(sf);
}
}
// add dbRefs to sequence
}
}
dna.addSequenceFeature(sf);
}
}
// add dbRefs to sequence
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ if (feature.dbRefs != null)
{
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
+ for (DBRefEntry ref : feature.dbRefs)
{
{
- DBRefEntry ref = (DBRefEntry) dbr.next();
ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
.getSource()));
// Hard code the kind of protein product accessions that EMBL cite
ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
.getSource()));
// Hard code the kind of protein product accessions that EMBL cite
@@
-755,7
+740,7
@@
public class EmblEntry
.setMap(new Mapping(product, map.getMap().getInverse()));
}
product.addDBRef(protEMBLCDS);
.setMap(new Mapping(product, map.getMap().getInverse()));
}
product.addDBRef(protEMBLCDS);
-
+
// Add converse mapping reference
if (map != null)
{
// Add converse mapping reference
if (map != null)
{