/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
-import java.util.Map;
public class Dna
{
* @param ac2
* @return
*/
- private static int jalview_2_8_2compare(AlignedCodon ac1, AlignedCodon ac2)
+ private static int jalview_2_8_2compare(AlignedCodon ac1,
+ AlignedCodon ac2)
{
if (ac1 == null || ac2 == null || (ac1.equals(ac2)))
{
int s;
int sSize = selection.size();
- List<SequenceI> pepseqs = new ArrayList<SequenceI>();
+ List<SequenceI> pepseqs = new ArrayList<>();
for (s = 0; s < sSize; s++)
{
SequenceI newseq = translateCodingRegion(selection.get(s),
if (dnarefs != null)
{
// intersect with pep
- List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> mappedrefs = new ArrayList<>();
DBRefEntry[] refs = dna.getDBRefs();
for (int d = 0; d < refs.length; d++)
{
String seqstring, AlignedCodonFrame acf,
List<SequenceI> proteinSeqs)
{
- List<int[]> skip = new ArrayList<int[]>();
+ List<int[]> skip = new ArrayList<>();
int skipint[] = null;
ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
// intervals
/*
* Filled up a reading frame...
*/
- AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+ AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
+ cdp[2]);
String aa = ResidueProperties.codonTranslate(new String(codon));
rf = 0;
final String gapString = String.valueOf(gapChar);
aa = gapString;
if (skipint == null)
{
- skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /*
- * cdp[0],
- * cdp[2]
- */};
+ skipint = new int[] { alignedCodon.pos1,
+ alignedCodon.pos3 /*
+ * cdp[0],
+ * cdp[2]
+ */ };
}
skipint[1] = alignedCodon.pos3; // cdp[2];
}
}
if (vc + 2 < t.length)
{
- System.arraycopy(scontigs, vc + 2, t, vc, t.length
- - vc + 2);
+ System.arraycopy(scontigs, vc + 2, t, vc,
+ t.length - vc + 2);
}
scontigs = t;
}
skip.add(skipint);
skipint = null;
}
- if (aa.equals("STOP"))
+ if (aa.equals(ResidueProperties.STOP))
{
aa = STOP_ASTERIX;
}
}
else if (!alignedCodons[aspos].equals(alignedCodon))
{
- throw new IllegalStateException("Tried to coalign "
- + alignedCodons[aspos].toString() + " with "
- + alignedCodon.toString());
+ throw new IllegalStateException(
+ "Tried to coalign " + alignedCodons[aspos].toString()
+ + " with " + alignedCodon.toString());
}
if (aspos >= aaWidth)
{
*/
MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
- transferCodedFeatures(selection, newseq, map, null, null);
+ transferCodedFeatures(selection, newseq, map);
/*
* Construct a dataset sequence for our new peptide.
/**
* Given a peptide newly translated from a dna sequence, copy over and set any
- * features on the peptide from the DNA. If featureTypes is null, all features
- * on the dna sequence are searched (rather than just the displayed ones), and
- * similarly for featureGroups.
+ * features on the peptide from the DNA.
*
* @param dna
* @param pep
* @param map
- * @param featureTypes
- * hash whose keys are the displayed feature type strings
- * @param featureGroups
- * hash where keys are feature groups and values are Boolean objects
- * indicating if they are displayed.
*/
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
- MapList map, Map<String, Object> featureTypes,
- Map<String, Boolean> featureGroups)
+ MapList map)
{
- SequenceFeature[] sfs = dna.getSequenceFeatures();
- Boolean fgstate;
DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
DBRefSource.DNACODINGDBS);
if (dnarefs != null)
}
}
}
- if (sfs != null)
+ for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
{
- for (SequenceFeature sf : sfs)
- {
- fgstate = (featureGroups == null) ? null : featureGroups
- .get(sf.featureGroup);
- if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
- && (fgstate == null || fgstate.booleanValue()))
+ if (FeatureProperties.isCodingFeature(null, sf.getType()))
{
- if (FeatureProperties.isCodingFeature(null, sf.getType()))
+ // if (map.intersectsFrom(sf[f].begin, sf[f].end))
{
- // if (map.intersectsFrom(sf[f].begin, sf[f].end))
- {
- }
}
}
- }
}
}
public AlignmentI reverseCdna(boolean complement)
{
int sSize = selection.size();
- List<SequenceI> reversed = new ArrayList<SequenceI>();
+ List<SequenceI> reversed = new ArrayList<>();
for (int s = 0; s < sSize; s++)
{
SequenceI newseq = reverseSequence(selection.get(s).getName(),
}
/**
+ * Answers the reverse complement of the input string
+ *
+ * @see #getComplement(char)
+ * @param s
+ * @return
+ */
+ public static String reverseComplement(String s)
+ {
+ StringBuilder sb = new StringBuilder(s.length());
+ for (int i = s.length() - 1; i >= 0; i--)
+ {
+ sb.append(Dna.getComplement(s.charAt(i)));
+ }
+ return sb.toString();
+ }
+
+ /**
* Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
* are treated as on http://reverse-complement.com/. Anything else is left
* unchanged.