X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=00793bec35b906eeaacd0b58f7170230c8df70f2;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=a3a0fe11bc9475a54578748026332cb51d3d5094;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index a3a0fe1..00793be 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,22 +1,26 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
+import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Vector;
@@ -124,17 +128,21 @@ 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)
{
pepseqs.addElement(newseq);
SequenceI ds = newseq;
- while (ds.getDatasetSequence() != null)
+ if (dataset != null)
{
- ds = ds.getDatasetSequence();
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ dataset.addSequence(ds);
}
- dataset.addSequence(ds);
}
}
if (codons.aaWidth == 0)
@@ -416,14 +424,40 @@ 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)
{
- Vector skip = new Vector();
+ 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
// intervals
@@ -479,32 +513,93 @@ 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] < skipint[1])
+ {
+ // skipint truncates end of scontig
+ scontigs[vc + 1] = skipint[0] - 1;
+ vc += 2;
+ }
+ else
+ {
+ // divide region to new contigs
+ t = new int[scontigs.length + 2];
+ System.arraycopy(scontigs, 0, t, 0, vc + 1);
+ t[vc + 1] = skipint[0];
+ t[vc + 2] = skipint[1];
+ System.arraycopy(scontigs, vc + 1, t, vc + 3,
+ scontigs.length - (vc + 1));
+ scontigs = t;
+ vc += 4;
+ }
}
}
}
- skip.addElement(skipint);
+ skip.add(skipint);
skipint = null;
}
if (aa.equals("STOP"))
{
- aa = "X";
+ aa = starForStop ? "*" : "X";
}
resSize++;
}
@@ -561,8 +656,16 @@ public class Dna
protein.toString());
if (rf != 0)
{
- jalview.bin.Cache.log
- .debug("trimming contigs for incomplete terminal codon.");
+ if (jalview.bin.Cache.log != null)
+ {
+ jalview.bin.Cache.log
+ .debug("trimming contigs for incomplete terminal codon.");
+ }
+ else
+ {
+ System.err
+ .println("trimming contigs for incomplete terminal codon.");
+ }
// map and trim contigs to ORF region
vc = scontigs.length - 1;
lastnpos = vismapping.shift(lastnpos); // place npos in context of
@@ -675,7 +778,8 @@ public class Dna
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
MapList map, Hashtable featureTypes, Hashtable featureGroups)
{
- SequenceFeature[] sf = dna.getDatasetSequence().getSequenceFeatures();
+ SequenceFeature[] sf = (dna.getDatasetSequence() != null ? dna
+ .getDatasetSequence() : dna).getSequenceFeatures();
Boolean fgstate;
jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
.selectRefs(dna.getDBRef(),