X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FDna.java;h=2e56e6759ed750e5736fab19abb9985af0b7c6bf;hb=f73031db2e38bfe6e3f1cd42f91b0f9b0130071a;hp=52859242b27e472635a801ce98936d0a447f9b92;hpb=e661be216bf4c257c6d6c6eb1bb98dd8fc39a0ae;p=jalview.git
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 5285924..2e56e67 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,19 +1,22 @@
/*
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* 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 .
+ * 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 +128,8 @@ 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 +424,39 @@ 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
@@ -483,7 +513,7 @@ public class Dna
// edit scontigs
skipint[0] = vismapping.shift(skipint[0]);
skipint[1] = vismapping.shift(skipint[1]);
- for (vc = 0; vc < scontigs.length; )
+ for (vc = 0; vc < scontigs.length;)
{
if (scontigs[vc + 1] < skipint[0])
{
@@ -491,16 +521,19 @@ public class Dna
vc += 2;
continue;
}
- if (scontigs[vc]>skipint[1])
+ if (scontigs[vc] > skipint[1])
{
// finished editing so
break;
}
- // Edit the contig list to include the skipped region which did not translate
+ // 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
+ // 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])
@@ -510,11 +543,11 @@ public class Dna
if (scontigs[vc + 1] > skipint[1])
{
scontigs[vc] = skipint[1];
- vc+=2;
+ vc += 2;
}
else
{
- if (scontigs[vc+1]==skipint[1])
+ if (scontigs[vc + 1] == skipint[1])
{
// remove the contig
t = new int[scontigs.length - 2];
@@ -525,32 +558,38 @@ public class Dna
if (vc + 2 < t.length)
{
System.arraycopy(scontigs, vc + 2, t, vc, t.length
- - vc + 2);
+ - vc + 2);
}
- scontigs=t;
- } else {
+ scontigs = t;
+ }
+ else
+ {
// truncate contig to before the skipint region
- scontigs[vc+1] = skipint[0]-1;
- vc+=2;
+ scontigs[vc + 1] = skipint[0] - 1;
+ vc += 2;
}
}
}
else
{
// scontig starts before start of skipint
- if (scontigs[vc+1]