From d7563d2df09ba5146008951448b941a69bf74744 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 13 Jul 2007 15:01:48 +0000
Subject: [PATCH] mapping bug fixes
---
src/jalview/datamodel/AlignedCodonFrame.java | 86 +++++++++++++++++++-------
src/jalview/datamodel/Alignment.java | 6 +-
2 files changed, 66 insertions(+), 26 deletions(-)
diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index c89c170..f4e2d97 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -1,5 +1,8 @@
package jalview.datamodel;
+import java.util.Enumeration;
+import java.util.Vector;
+
import jalview.util.MapList;
/**
@@ -24,6 +27,11 @@ public class AlignedCodonFrame
*/
public AlignedCodonFrame(int aWidth)
{
+ if (aWidth<=0)
+ {
+ codons=null;
+ return;
+ }
codons = new int[aWidth][];
for (int res = 0; res < aWidth; res++)
codons[res] = null;
@@ -57,6 +65,11 @@ public class AlignedCodonFrame
return aaWidth;
}
/**
+ * TODO: not an ideal solution - we reference the aligned amino acid sequences in order to make insertions on them
+ * Better would be dnaAlignment and aaAlignment reference....
+ */
+ Vector a_aaSeqs=new Vector();
+ /**
* increase aaWidth by one and insert a new aligned codon position space at aspos.
* @param aspos
*/
@@ -64,10 +77,15 @@ public class AlignedCodonFrame
{
// this aa appears before the aligned codons at aspos - so shift them in each pair of mapped sequences
aaWidth++;
- for (int sq=0;aaSeqs!=null && sq<aaSeqs.length; sq++) {
- aaSeqs[sq].insertCharAt(aspos, gapCharacter);
+ if (a_aaSeqs!=null)
+ {
+ // we actually have to modify the aligned sequences here, so use the a_aaSeqs vector
+ Enumeration sq = a_aaSeqs.elements();
+ while (sq.hasMoreElements())
+ {
+ ((SequenceI) sq.nextElement()).insertCharAt(aspos, gapCharacter);
+ }
}
-
checkCodonFrameWidth(aspos);
if (aspos<aaWidth)
{
@@ -86,14 +104,17 @@ public class AlignedCodonFrame
*/
SequenceI[] dnaSeqs=null;
/**
- * tied array of protein sequence Objects
+ * tied array of Mappings to protein sequence Objects and
+ SequenceI[] aaSeqs=null;
+ * MapLists where eac maps from the corresponding dnaSeqs element to corresponding aaSeqs element
*/
- SequenceI[] aaSeqs=null;
+ Mapping[] dnaToProt=null;
/**
- * tied array of MapLists where eac maps from the corresponding dnaSeqs element to corresponding aaSeqs element
+ * add a mapping between the dataset sequences for the associated dna and protein sequence objects
+ * @param dnaseq
+ * @param aaseq
+ * @param map
*/
- MapList[] dnaToProt=null;
-
public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)
{
int nlen=1;
@@ -102,21 +123,20 @@ public class AlignedCodonFrame
nlen = dnaSeqs.length+1;
}
SequenceI[] ndna = new SequenceI[nlen];
- SequenceI[] naa = new SequenceI[nlen];
- MapList[] ndtp = new MapList[nlen];
+ Mapping[] ndtp = new Mapping[nlen];
if (dnaSeqs!=null)
{
System.arraycopy(dnaSeqs,0,ndna, 0, dnaSeqs.length);
- System.arraycopy(aaSeqs,0,naa, 0, dnaSeqs.length);
System.arraycopy(dnaToProt,0,ndtp, 0, dnaSeqs.length);
}
dnaSeqs = ndna;
- aaSeqs = naa;
dnaToProt = ndtp;
nlen--;
dnaSeqs[nlen] = (dnaseq.getDatasetSequence()==null) ? dnaseq : dnaseq.getDatasetSequence();
- aaSeqs[nlen] = (aaseq.getDatasetSequence()==null) ? aaseq : aaseq.getDatasetSequence();
- dnaToProt[nlen] = map;
+ Mapping mp = new Mapping(map);
+ mp.to = (aaseq.getDatasetSequence()==null) ? aaseq : aaseq.getDatasetSequence();
+ a_aaSeqs.addElement(aaseq);
+ dnaToProt[nlen] = mp;
}
@@ -126,10 +146,28 @@ public class AlignedCodonFrame
}
public SequenceI[] getAaSeqs()
{
- return aaSeqs;
+ if (dnaToProt==null)
+ return null;
+ SequenceI[] sqs = new SequenceI[dnaToProt.length];
+ for (int sz=0; sz<dnaToProt.length; sz++)
+ {
+ sqs[sz] = dnaToProt[sz].to;
+ }
+ return sqs;
}
public MapList[] getdnaToProt()
{
+ if (dnaToProt==null)
+ return null;
+ MapList[] sqs = new MapList[dnaToProt.length];
+ for (int sz=0; sz<dnaToProt.length; sz++)
+ {
+ sqs[sz] = dnaToProt[sz].map;
+ }
+ return sqs;
+ }
+ public Mapping[] getProtMappings()
+ {
return dnaToProt;
}
/**
@@ -147,7 +185,7 @@ public class AlignedCodonFrame
for (int ds=0;ds<dnaSeqs.length; ds++)
{
if (dnaSeqs[ds]==dnaSeqRef || dnaSeqs[ds]==dnads)
- return aaSeqs[ds];
+ return dnaToProt[ds].to;
}
return null;
}
@@ -158,14 +196,14 @@ public class AlignedCodonFrame
*/
public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
{
- if (aaSeqs==null)
+ if (dnaToProt==null)
{
return null;
}
SequenceI aads = aaSeqRef.getDatasetSequence();
- for (int as=0;as<aaSeqs.length; as++)
+ for (int as=0;as<dnaToProt.length; as++)
{
- if (aaSeqs[as]==aaSeqRef || aaSeqs[as]==aads)
+ if (dnaToProt[as].to==aaSeqRef || dnaToProt[as].to==aads)
return dnaSeqs[as];
}
return null;
@@ -189,25 +227,25 @@ public class AlignedCodonFrame
{
int[] codon;
SequenceI ds = seq.getDatasetSequence();
- for (int mi = 0; mi<aaSeqs.length; mi++)
+ for (int mi = 0; mi<dnaToProt.length; mi++)
{
if (dnaSeqs[mi]==seq || dnaSeqs[mi]==ds)
{
// DEBUG System.err.println("dna pos "+index);
- codon = dnaToProt[mi].locateInTo(index,index);
+ codon = dnaToProt[mi].map.locateInTo(index,index);
if (codon!=null)
{
for (int i=0; i<codon.length; i+=2)
{
- results.addResult(aaSeqs[mi], codon[i], codon[i+1]);
+ results.addResult(dnaToProt[mi].to, codon[i], codon[i+1]);
}
}
} else
- if (aaSeqs[mi]==seq || aaSeqs[mi]==ds)
+ if (dnaToProt[mi].to==seq || dnaToProt[mi].to==ds)
{
// DEBUG System.err.println("aa pos "+index);
{
- codon = dnaToProt[mi].locateInFrom(index, index);
+ codon = dnaToProt[mi].map.locateInFrom(index, index);
if (codon!=null)
{
for (int i=0; i<codon.length; i+=2)
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b3a5266..c474142 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -108,6 +108,8 @@ public class Alignment
public SequenceI[] getSequencesArray()
{
+ if (sequences==null)
+ return null;
SequenceI[] reply = new SequenceI[sequences.size()];
for (int i = 0; i < sequences.size(); i++)
{
@@ -740,7 +742,7 @@ public class Alignment
}
AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
- t[codonFrameList.length+1] = codons;
+ t[codonFrameList.length] = codons;
codonFrameList = t;
}
@@ -763,7 +765,7 @@ public class Alignment
for (int f=0;f<codonFrameList.length; f++)
{
if (codonFrameList[f].involvesSequence(seq))
- cframes.add(codonFrameList[f]);
+ cframes.addElement(codonFrameList[f]);
}
if (cframes.size()==0)
return null;
--
1.7.10.2