X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=1ce22f2265c8f8632ff84d3a5f56636519b2b8b1;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=cbe871d207fd0655a7f7d57f5f0e49d984c0bae3;hpb=f51988e32f73bc830fdb2800b97f12cad8d9594e;p=jalview.git
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index cbe871d..1ce22f2 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
@@ -14,6 +14,7 @@
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
@@ -125,7 +126,7 @@ public class Dna
{
SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
viscontigs, codons, gapCharacter,
- (product != null) ? product[s] : null); // possibly anonymous
+ (product != null) ? product[s] : null, false); // possibly anonymous
// product
if (newseq != null)
{
@@ -420,13 +421,36 @@ public class Dna
* @param codons
* Definition of global ORF alignment reference frame
* @param gapCharacter
- * @param newSeq
* @return sequence ready to be added to alignment.
+ * @deprecated Use {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)} instead
*/
public static SequenceI translateCodingRegion(SequenceI selection,
String seqstring, int[] viscontigs, AlignedCodonFrame codons,
char gapCharacter, DBRefEntry product)
{
+ return translateCodingRegion(selection, seqstring, viscontigs, codons,
+ gapCharacter, product, false);
+ }
+
+ /**
+ * Translate a na sequence
+ *
+ * @param selection
+ * sequence displayed under viscontigs visible columns
+ * @param seqstring
+ * ORF read in some global alignment reference frame
+ * @param viscontigs
+ * mapping from global reference frame to visible seqstring ORF read
+ * @param codons
+ * Definition of global ORF alignment reference frame
+ * @param gapCharacter
+ * @param starForStop when true stop codons will translate as '*', otherwise as 'X'
+ * @return sequence ready to be added to alignment.
+ */
+ public static SequenceI translateCodingRegion(SequenceI selection,
+ String seqstring, int[] viscontigs, AlignedCodonFrame codons,
+ char gapCharacter, DBRefEntry product, final boolean starForStop)
+ {
java.util.List skip = new ArrayList();
int skipint[] = null;
ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
@@ -483,23 +507,75 @@ public class Dna
// edit scontigs
skipint[0] = vismapping.shift(skipint[0]);
skipint[1] = vismapping.shift(skipint[1]);
- for (vc = 0; vc < scontigs.length; vc += 2)
+ for (vc = 0; vc < scontigs.length; )
{
if (scontigs[vc + 1] < skipint[0])
{
+ // before skipint starts
+ vc += 2;
continue;
}
+ if (scontigs[vc]>skipint[1])
+ {
+ // finished editing so
+ break;
+ }
+ // Edit the contig list to include the skipped region which did not translate
+ int[] t;
+ // from : s1 e1 s2 e2 s3 e3
+ // to s: s1 e1 s2 k0 k1 e2 s3 e3
+ // list increases by one unless one boundary (s2==k0 or e2==k1) matches, and decreases by one if skipint intersects whole visible contig
if (scontigs[vc] <= skipint[0])
{
if (skipint[0] == scontigs[vc])
{
-
+ // skipint at start of contig
+ // shift the start of this contig
+ if (scontigs[vc + 1] > skipint[1])
+ {
+ scontigs[vc] = skipint[1];
+ vc+=2;
+ }
+ else
+ {
+ if (scontigs[vc+1]==skipint[1])
+ {
+ // remove the contig
+ t = new int[scontigs.length - 2];
+ if (vc > 0)
+ {
+ System.arraycopy(scontigs, 0, t, 0, vc - 1);
+ }
+ if (vc + 2 < t.length)
+ {
+ System.arraycopy(scontigs, vc + 2, t, vc, t.length
+ - vc + 2);
+ }
+ scontigs=t;
+ } else {
+ // truncate contig to before the skipint region
+ scontigs[vc+1] = skipint[0]-1;
+ vc+=2;
+ }
+ }
}
else
{
- int[] t = new int[scontigs.length + 2];
- System.arraycopy(scontigs, 0, t, 0, vc - 1);
- // scontigs[vc]; //
+ // scontig starts before start of skipint
+ if (scontigs[vc+1]