*/
public class AlignmentUtils
{
-
private static final int CODON_LENGTH = 3;
private static final String SEQUENCE_VARIANT = "sequence_variant:";
- private static final String ID = "ID";
+ /*
+ * the 'id' attribute is provided for variant features fetched from
+ * Ensembl using its REST service with JSON format
+ */
+ public static final String VARIANT_ID = "id";
/**
* A data model to hold the 'normal' base value at a position, and an optional
return false;
}
String name = seq2.getName();
- final DBRefEntry[] xrefs = seq1.getDBRefs();
+ final List<DBRefEntry> xrefs = seq1.getDBRefs();
if (xrefs != null)
{
- for (DBRefEntry xref : xrefs)
+ for (int ix = 0, nx = xrefs.size(); ix < nx; ix++)
{
+ DBRefEntry xref = xrefs.get(ix);
String xrefName = xref.getSource() + "|" + xref.getAccessionId();
// case-insensitive test, consistent with DBRefEntry.equalRef()
if (xrefName.equalsIgnoreCase(name))
// need to
// synthesize an xref.
- for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs())
+ List<DBRefEntry> primrefs = dnaDss.getPrimaryDBRefs();
+ for (int ip = 0, np = primrefs.size(); ip < np; ip++)
{
+ DBRefEntry primRef = primrefs.get(ip);
/*
* create a cross-reference from CDS to the source sequence's
* primary reference and vice versa
dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq
.getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
-
// problem here is that the cross-reference is synthesized -
// cdsSeq.getName() may be like 'CDS|dnaaccession' or
// 'CDS|emblcdsacc'
.getInverse()));
proteinProduct.addDBRef(proteinToCdsRef);
}
-
/*
* transfer any features on dna that overlap the CDS
*/
List<DBRefEntry> direct = new ArrayList<>();
HashSet<String> directSources = new HashSet<>();
- if (contig.getDBRefs() != null)
+ List<DBRefEntry> refs = contig.getDBRefs();
+ if (refs != null)
{
- for (DBRefEntry dbr : contig.getDBRefs())
+ for (int ib = 0, nb = refs.size(); ib < nb; ib++)
{
- if (dbr.hasMap() && dbr.getMap().getMap().isTripletMap())
+ DBRefEntry dbr = refs.get(ib);
+ MapList map;
+ if (dbr.hasMap() && (map = dbr.getMap().getMap()).isTripletMap())
{
- MapList map = dbr.getMap().getMap();
// check if map is the CDS mapping
if (mapping.getMap().equals(map))
{
}
}
}
- DBRefEntry[] onSource = DBRefUtils.selectRefs(
+ List<DBRefEntry> onSource = DBRefUtils.selectRefs(
proteinProduct.getDBRefs(),
directSources.toArray(new String[0]));
List<DBRefEntry> propagated = new ArrayList<>();
// and generate appropriate mappings
- for (DBRefEntry cdsref : direct)
+ for (int ic = 0, nc = direct.size(); ic < nc; ic++)
{
+ DBRefEntry cdsref = direct.get(ic);
+ Mapping m = cdsref.getMap();
// clone maplist and mapping
MapList cdsposmap = new MapList(
Arrays.asList(new int[][]
{ new int[] { cdsSeq.getStart(), cdsSeq.getEnd() } }),
- cdsref.getMap().getMap().getToRanges(), 3, 1);
- Mapping cdsmap = new Mapping(cdsref.getMap().getTo(),
- cdsref.getMap().getMap());
+ m.getMap().getToRanges(), 3, 1);
+ Mapping cdsmap = new Mapping(m.getTo(),m.getMap());
// create dbref
DBRefEntry newref = new DBRefEntry(cdsref.getSource(),
int phase = 0;
try
{
- phase = Integer.parseInt(sf.getPhase());
+ String s = sf.getPhase();
+ if (s != null)
+ {
+ phase = Integer.parseInt(s);
+ }
} catch (NumberFormatException e)
{
- // ignore
+ // SwingJS -- need to avoid these.
}
/*
* phase > 0 on first codon means 5' incomplete - skip to the start
/*
* variants in first codon base
*/
- for (DnaVariant var : codonVariants[0])
+ for (DnaVariant dnavar : codonVariants[0])
{
- if (var.variant != null)
+ if (dnavar.variant != null)
{
- String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
+ String alleles = (String) dnavar.variant.getValue(Gff3Helper.ALLELES);
if (alleles != null)
{
for (String base : alleles.split(","))
+ base3.toLowerCase();
String canonical = base1.toUpperCase() + base2.toLowerCase()
+ base3.toLowerCase();
- if (addPeptideVariant(peptide, peptidePos, residue, var,
+ if (addPeptideVariant(peptide, peptidePos, residue, dnavar,
codon, canonical))
{
count++;
peptidePos, var.getSource());
StringBuilder attributes = new StringBuilder(32);
- String id = (String) var.variant.getValue(ID);
+ String id = (String) var.variant.getValue(VARIANT_ID);
if (id != null)
{
if (id.startsWith(SEQUENCE_VARIANT))
{
id = id.substring(SEQUENCE_VARIANT.length());
}
- sf.setValue(ID, id);
- attributes.append(ID).append("=").append(id);
+ sf.setValue(VARIANT_ID, id);
+ attributes.append(VARIANT_ID).append("=").append(id);
// TODO handle other species variants JAL-2064
StringBuilder link = new StringBuilder(32);
try
SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
if (xrefs != null)
{
- for (SequenceI xref : xrefs)
+ // BH 2019.01.25 streamlined this triply nested loop to remove all iterators
+
+ for (int ix = 0, nx = xrefs.length; ix < nx; ix++)
{
- DBRefEntry[] dbrefs = xref.getDBRefs();
+ SequenceI xref = xrefs[ix];
+ List<DBRefEntry> dbrefs = xref.getDBRefs();
if (dbrefs != null)
{
- for (DBRefEntry dbref : dbrefs)
+ for (int ir = 0, nir = dbrefs.size(); ir < nir; ir++)
{
- if (dbref.getMap() == null || dbref.getMap().getTo() == null
- || dbref.getMap().getTo().isProtein() != isProtein)
+ DBRefEntry dbref = dbrefs.get(ir);
+ Mapping map = dbref.getMap();
+ SequenceI mto;
+ if (map == null || (mto = map.getTo()) == null
+ || mto.isProtein() != isProtein)
{
continue;
}
- SequenceI mappedTo = dbref.getMap().getTo();
+ SequenceI mappedTo = mto;
SequenceI match = matcher.findIdMatch(mappedTo);
if (match == null)
{
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.JSONUtils;
+import jalview.util.Platform;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
/**
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
+
List<String> queries = new ArrayList<>();
queries.add(query);
- BufferedReader fp = getSequenceReader(queries);
- if (fp == null)
- {
- return null;
- }
-
- SequenceI seq = parseFeaturesJson(fp);
+ SequenceI seq = parseFeaturesJson(queries);
+ if (seq == null)
+ return null;
return new Alignment(new SequenceI[] { seq });
+
}
/**
* @param br
* @return
*/
- private SequenceI parseFeaturesJson(BufferedReader br)
+ @SuppressWarnings("unchecked")
- private SequenceI parseFeaturesJson(List<String> queries)
++ private SequenceI parseFeaturesJson(List<String> queries)
{
-
-
SequenceI seq = new Sequence("Dummy", "");
--
- JSONParser jp = new JSONParser();
try
{
-
- JSONArray responses = (JSONArray) jp.parse(br);
- Iterator rvals = responses.iterator();
- while (rvals.hasNext())
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1, MODE_ITERATOR, null);
+ if (rvals == null)
+ {
+ return null;
++ }
+ while (rvals.hasNext())
+ {
try
{
- JSONObject obj = (JSONObject) rvals.next();
+ Map<String, Object> obj = (Map<String, Object>) rvals.next();
String type = obj.get("feature_type").toString();
int start = Integer.parseInt(obj.get("start").toString());
int end = Integer.parseInt(obj.get("end").toString());
String source = obj.get("source").toString();
String strand = obj.get("strand").toString();
String alleles = JSONUtils
- .arrayToList((JSONArray) obj.get("alleles"));
+ .arrayToStringList((List<Object>) obj.get("alleles"));
String clinSig = JSONUtils
- .arrayToList(
- (JSONArray) obj.get("clinical_significance"));
+ .arrayToStringList(
+ (List<Object>) obj.get("clinical_significance"));
/*
* convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
{
type = SequenceOntologyI.CDS;
}
-
+
String desc = getFirstNotNull(obj, "alleles", "external_name",
JSON_ID);
SequenceFeature sf = new SequenceFeature(type, desc, start, end,
sf.setValue("clinical_significance", clinSig);
seq.addSequenceFeature(sf);
+
} catch (Throwable t)
{
// ignore - keep trying other features
}
} catch (ParseException | IOException e)
{
+ e.printStackTrace();
// ignore
}
return seq;
}
-
- /**
- * Returns the first non-null attribute found (if any) as a string
+ /**
+ * Returns the first non-null attribute found (if any) as a string, formatted
+ * suitably for display as feature description or tooltip. Answers null if
+ * none of the attribute keys is present.
*
* @param obj
* @param keys
* @return
*/
- protected String getFirstNotNull(JSONObject obj, String... keys)
++ @SuppressWarnings("unchecked")
+ protected String getFirstNotNull(Map<String, Object> obj, String... keys)
{
-- String desc = null;
--
for (String key : keys)
{
Object val = obj.get(key);
if (val != null)
{
- String s = val.toString();
- String s = val instanceof JSONArray
- ? JSONUtils.arrayToList((JSONArray) val)
++ String s = val instanceof List<?>
++ ? JSONUtils.arrayToStringList((List<Object>) val)
+ : val.toString();
if (!s.isEmpty())
{
return s;
}
}
}
-- return desc;
++ return null;
}
/**
* @param obj
* @param key
*/
- protected void setFeatureAttribute(SequenceFeature sf, JSONObject obj,
+ protected void setFeatureAttribute(SequenceFeature sf, Map<String, Object> obj,
String key)
{
Object object = obj.get(key);
git://source.jalview.org / jalview.git / commitdiff