*/
package jalview.analysis;
+import java.util.Locale;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.NoSuchElementException;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import jalview.bin.Cache;
import jalview.commands.RemoveGapColCommand;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.util.MapList;
import jalview.util.MappingUtils;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.NoSuchElementException;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
/**
* grab bag of useful alignment manipulation operations Expect these to be
* refactored elsewhere at some point.
// TODO use Character.toLowerCase to avoid creating String objects?
char[] upstream = new String(ds
.getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
- .toLowerCase().toCharArray();
+ .toLowerCase(Locale.ROOT).toCharArray();
char[] downstream = new String(
- ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase()
+ ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase(Locale.ROOT)
.toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
if (cdnaLength != mappedLength && cdnaLength > 2)
{
String lastCodon = String.valueOf(cdnaSeqChars,
- cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase();
+ cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(Locale.ROOT);
for (String stop : ResidueProperties.STOP_CODONS)
{
if (lastCodon.equals(stop))
*/
int startOffset = 0;
if (cdnaLength != mappedLength && cdnaLength > 2
- && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase()
+ && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase(Locale.ROOT)
.equals(ResidueProperties.START))
{
startOffset += CODON_LENGTH;
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
*/
SequenceI newSeq = null;
- final MapList maplist = mapping.getMap();
- if (maplist.isContiguous() && maplist.isFromForwardStrand())
- {
- /*
- * just a subsequence, keep same dataset sequence
- */
- int start = maplist.getFromLowest();
- int end = maplist.getFromHighest();
- newSeq = seq.getSubSequence(start - 1, end);
- newSeq.setName(seqId);
- }
- else
- {
- /*
- * construct by splicing mapped from ranges
- */
- char[] seqChars = seq.getSequence();
- List<int[]> fromRanges = maplist.getFromRanges();
- int cdsWidth = MappingUtils.getLength(fromRanges);
- char[] newSeqChars = new char[cdsWidth];
+ /*
+ * construct CDS sequence by splicing mapped from ranges
+ */
+ char[] seqChars = seq.getSequence();
+ List<int[]> fromRanges = mapping.getMap().getFromRanges();
+ int cdsWidth = MappingUtils.getLength(fromRanges);
+ char[] newSeqChars = new char[cdsWidth];
- int newPos = 0;
- for (int[] range : fromRanges)
+ int newPos = 0;
+ for (int[] range : fromRanges)
+ {
+ if (range[0] <= range[1])
{
- if (range[0] <= range[1])
- {
- // forward strand mapping - just copy the range
- int length = range[1] - range[0] + 1;
- System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
- length);
- newPos += length;
- }
- else
+ // forward strand mapping - just copy the range
+ int length = range[1] - range[0] + 1;
+ System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
+ length);
+ newPos += length;
+ }
+ else
+ {
+ // reverse strand mapping - copy and complement one by one
+ for (int i = range[0]; i >= range[1]; i--)
{
- // reverse strand mapping - copy and complement one by one
- for (int i = range[0]; i >= range[1]; i--)
- {
- newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
- }
+ newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
}
}
}
else
{
- System.err.println(
- "JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
- + mtch.toString());
+ Cache.log.error(
+ "JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:" + mtch.toString());
}
}
}
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
+ // leave as zero
}
/*
* phase > 0 on first codon means 5' incomplete - skip to the start
SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
if (xrefs != null)
{
- for (SequenceI xref : xrefs)
+ // BH 2019.01.25 recoded to remove 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)
{
git://source.jalview.org / jalview.git / blobdiff