X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=675a44a625a3ab4b104402f821062c85b5e87e47;hb=dab5cea53c80d566d12455951077db33e2490631;hp=e74d4b5964688260315bdb5ce02361b5e3c7934f;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index e74d4b5..675a44a 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,27 +1,25 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Vector;
-
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
@@ -37,6 +35,10 @@ import jalview.schemes.ResidueProperties;
import jalview.util.MapList;
import jalview.util.ShiftList;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
+
public class Dna
{
/**
@@ -50,9 +52,13 @@ public class Dna
{
if (cdp2 == null
|| (cdp1[0] == cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2]))
+ {
return 0;
+ }
if (cdp1[0] < cdp2[0] || cdp1[1] < cdp2[1] || cdp1[2] < cdp2[2])
+ {
return -1; // one base in cdp1 precedes the corresponding base in the
+ }
// other codon
return 1; // one base in cdp1 appears after the corresponding base in the
// other codon.
@@ -126,7 +132,8 @@ public class Dna
{
SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
viscontigs, codons, gapCharacter,
- (product != null) ? product[s] : null, false); // possibly anonymous
+ (product != null) ? product[s] : null, false); // possibly
+ // anonymous
// product
if (newseq != null)
{
@@ -143,7 +150,9 @@ public class Dna
}
}
if (codons.aaWidth == 0)
+ {
return null;
+ }
SequenceI[] newseqs = new SequenceI[pepseqs.size()];
pepseqs.copyInto(newseqs);
AlignmentI al = new Alignment(newseqs);
@@ -261,7 +270,9 @@ public class Dna
// generate seqstring for this sequence based on mapping
if (sqstr.length() > alwidth)
+ {
alwidth = sqstr.length();
+ }
cdnasqs.addElement(sqstr.toString());
cdnasqi.addElement(dna);
cdnaprod.addElement(intersect);
@@ -309,6 +320,13 @@ public class Dna
continue;
}
+ // skip hidden sequence annotations
+ final SequenceI seqRef = annotations[i].sequenceRef;
+ if (seqRef != null && !annotations[i].visible)
+ {
+ continue;
+ }
+
aSize = codons.getaaWidth(); // aa alignment width.
jalview.datamodel.Annotation[] anots = (annotations[i].annotations == null) ? null
: new jalview.datamodel.Annotation[aSize];
@@ -317,7 +335,7 @@ public class Dna
for (a = 0; a < aSize; a++)
{
// process through codon map.
- if (codons.codons[a] != null
+ if (a < codons.codons.length && codons.codons[a] != null
&& codons.codons[a][0] == (codons.codons[a][2] - 2))
{
anots[a] = getCodonAnnotation(codons.codons[a],
@@ -340,10 +358,10 @@ public class Dna
{
aa.setScore(annotations[i].getScore());
}
- if (annotations[i].sequenceRef != null)
+ if (seqRef != null)
{
SequenceI aaSeq = codons
- .getAaForDnaSeq(annotations[i].sequenceRef);
+ .getAaForDnaSeq(seqRef);
if (aaSeq != null)
{
// aa.compactAnnotationArray(); // throw away alignment annotation
@@ -404,7 +422,7 @@ public class Dna
}
if (contrib > 1)
{
- annot.value /= (float) contrib;
+ annot.value /= contrib;
}
return annot;
}
@@ -422,8 +440,11 @@ public class Dna
* Definition of global ORF alignment reference frame
* @param gapCharacter
* @return sequence ready to be added to alignment.
- * @deprecated Use {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)} instead
+ * @deprecated Use
+ * {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)}
+ * instead
*/
+ @Deprecated
public static SequenceI translateCodingRegion(SequenceI selection,
String seqstring, int[] viscontigs, AlignedCodonFrame codons,
char gapCharacter, DBRefEntry product)
@@ -444,7 +465,8 @@ public class Dna
* @param codons
* Definition of global ORF alignment reference frame
* @param gapCharacter
- * @param starForStop when true stop codons will translate as '*', otherwise as 'X'
+ * @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,
@@ -507,7 +529,7 @@ 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])
{
@@ -515,16 +537,19 @@ 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])
@@ -534,11 +559,11 @@ 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];
@@ -549,32 +574,38 @@ 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]