From 349ef01fe53c28dc78bec2d321f9c833a4b6e023 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sun, 17 Jun 2007 12:59:15 +0000
Subject: [PATCH] AlignedCodonFrame holds mapping information between
individual cDNA regions on dna and translated peptide
sequences
---
src/jalview/datamodel/AlignedCodonFrame.java | 222 ++++++++++++++++++++++++++
src/jalview/datamodel/Alignment.java | 81 ++++++++++
src/jalview/datamodel/AlignmentI.java | 28 ++++
3 files changed, 331 insertions(+)
create mode 100644 src/jalview/datamodel/AlignedCodonFrame.java
diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
new file mode 100644
index 0000000..c89c170
--- /dev/null
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -0,0 +1,222 @@
+package jalview.datamodel;
+
+import jalview.util.MapList;
+
+/**
+ * Stores mapping between the columns of a protein alignment and a DNA alignment
+ * and a list of individual codon to amino acid mappings between sequences.
+ */
+
+public class AlignedCodonFrame
+{
+ /**
+ * array of nucleotide positions for aligned codons at column of aligned proteins.
+ */
+ public int[][] codons = null;
+ /**
+ * width of protein sequence alignement
+ * implicit assertion that codons.length >= aaWidth
+ */
+ public int aaWidth=0;
+ /**
+ * initialise codon frame with a nominal alignment width
+ * @param aWidth
+ */
+ public AlignedCodonFrame(int aWidth)
+ {
+ codons = new int[aWidth][];
+ for (int res = 0; res < aWidth; res++)
+ codons[res] = null;
+ }
+
+ /**
+ * ensure that codons array is at least as wide as aslen residues
+ * @param aslen
+ * @return (possibly newly expanded) codon array
+ */
+ public int[][] checkCodonFrameWidth(int aslen)
+ {
+ if (codons.length <= aslen + 1)
+ {
+ // probably never have to do this ?
+ int[][] c = new int[codons.length + 10][];
+ for (int i = 0; i < codons.length; i++)
+ {
+ c[i] = codons[i];
+ codons[i] = null;
+ }
+ codons = c;
+ }
+ return codons;
+ }
+ /**
+ * @return width of aligned translated amino acid residues
+ */
+ public int getaaWidth()
+ {
+ return aaWidth;
+ }
+ /**
+ * increase aaWidth by one and insert a new aligned codon position space at aspos.
+ * @param aspos
+ */
+ public void insertAAGap(int aspos, char gapCharacter)
+ {
+ // 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);
+ }
+
+ checkCodonFrameWidth(aspos);
+ if (aspos<aaWidth)
+ {
+ aaWidth++;
+ System.arraycopy(codons, aspos, codons, aspos+1, aaWidth-aspos);
+ codons[aspos]=null; // clear so new codon position can be marked.
+ }
+ }
+
+ public void setAaWidth(int aapos)
+ {
+ aaWidth = aapos;
+ }
+ /**
+ * tied array of na Sequence objects.
+ */
+ SequenceI[] dnaSeqs=null;
+ /**
+ * tied array of protein sequence Objects
+ */
+ SequenceI[] aaSeqs=null;
+ /**
+ * tied array of MapLists where eac maps from the corresponding dnaSeqs element to corresponding aaSeqs element
+ */
+ MapList[] dnaToProt=null;
+
+ public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)
+ {
+ int nlen=1;
+ if (dnaSeqs!=null)
+ {
+ nlen = dnaSeqs.length+1;
+ }
+ SequenceI[] ndna = new SequenceI[nlen];
+ SequenceI[] naa = new SequenceI[nlen];
+ MapList[] ndtp = new MapList[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;
+ }
+
+
+ public SequenceI[] getdnaSeqs()
+ {
+ return dnaSeqs;
+ }
+ public SequenceI[] getAaSeqs()
+ {
+ return aaSeqs;
+ }
+ public MapList[] getdnaToProt()
+ {
+ return dnaToProt;
+ }
+ /**
+ *
+ * @param sequenceRef
+ * @return null or corresponding aaSeq entry for dnaSeq entry
+ */
+ public SequenceI getAaForDnaSeq(SequenceI dnaSeqRef)
+ {
+ if (dnaSeqs==null)
+ {
+ return null;
+ }
+ SequenceI dnads = dnaSeqRef.getDatasetSequence();
+ for (int ds=0;ds<dnaSeqs.length; ds++)
+ {
+ if (dnaSeqs[ds]==dnaSeqRef || dnaSeqs[ds]==dnads)
+ return aaSeqs[ds];
+ }
+ return null;
+ }
+ /**
+ *
+ * @param sequenceRef
+ * @return null or corresponding aaSeq entry for dnaSeq entry
+ */
+ public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
+ {
+ if (aaSeqs==null)
+ {
+ return null;
+ }
+ SequenceI aads = aaSeqRef.getDatasetSequence();
+ for (int as=0;as<aaSeqs.length; as++)
+ {
+ if (aaSeqs[as]==aaSeqRef || aaSeqs[as]==aads)
+ return dnaSeqs[as];
+ }
+ return null;
+ }
+ /**
+ * test to see if codon frame involves seq in any way
+ * @param seq a nucleotide or protein sequence
+ * @return true if a mapping exists to or from this sequence to any translated sequence
+ */
+ public boolean involvesSequence(SequenceI seq)
+ {
+ return getAaForDnaSeq(seq)!=null || getDnaForAaSeq(seq)!=null;
+ }
+ /**
+ * Add search results for regions in other sequences that translate or are translated from a particular position in seq
+ * @param seq
+ * @param index position in seq
+ * @param results where highlighted regions go
+ */
+ public void markMappedRegion(SequenceI seq, int index, SearchResults results)
+ {
+ int[] codon;
+ SequenceI ds = seq.getDatasetSequence();
+ for (int mi = 0; mi<aaSeqs.length; mi++)
+ {
+ if (dnaSeqs[mi]==seq || dnaSeqs[mi]==ds)
+ {
+ // DEBUG System.err.println("dna pos "+index);
+ codon = dnaToProt[mi].locateInTo(index,index);
+ if (codon!=null)
+ {
+ for (int i=0; i<codon.length; i+=2)
+ {
+ results.addResult(aaSeqs[mi], codon[i], codon[i+1]);
+ }
+ }
+ } else
+ if (aaSeqs[mi]==seq || aaSeqs[mi]==ds)
+ {
+ // DEBUG System.err.println("aa pos "+index);
+ {
+ codon = dnaToProt[mi].locateInFrom(index, index);
+ if (codon!=null)
+ {
+ for (int i=0; i<codon.length; i+=2)
+ {
+ results.addResult(dnaSeqs[mi], codon[i], codon[i+1]);
+ }
+ }
+ }
+ }
+ }
+ }
+}
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 677f436..b3a5266 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -725,5 +725,86 @@ public class Alignment
{
return alignmentProperties;
}
+ AlignedCodonFrame[] codonFrameList=null;
+ /* (non-Javadoc)
+ * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ */
+ public void addCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons==null)
+ return;
+ if (codonFrameList==null)
+ {
+ codonFrameList = new AlignedCodonFrame[] { codons };
+ return;
+ }
+ AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
+ System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
+ t[codonFrameList.length+1] = codons;
+ codonFrameList = t;
+ }
+ /* (non-Javadoc)
+ * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
+ */
+ public AlignedCodonFrame getCodonFrame(int index)
+ {
+ return codonFrameList[index];
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ */
+ public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+ {
+ if (seq==null || codonFrameList==null)
+ return null;
+ Vector cframes=new Vector();
+ for (int f=0;f<codonFrameList.length; f++)
+ {
+ if (codonFrameList[f].involvesSequence(seq))
+ cframes.add(codonFrameList[f]);
+ }
+ if (cframes.size()==0)
+ return null;
+ AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
+ cframes.copyInto(cfr);
+ return cfr;
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.datamodel.AlignmentI#getCodonFrames()
+ */
+ public AlignedCodonFrame[] getCodonFrames()
+ {
+ return codonFrameList;
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ */
+ public boolean removeCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons==null || codonFrameList==null)
+ return false;
+ boolean removed=false;
+ int i=0,iSize=codonFrameList.length;
+ while (i<iSize)
+ {
+ if (codonFrameList[i]==codons)
+ {
+ removed=true;
+ if (i+1<iSize)
+ {
+ System.arraycopy(codonFrameList,i+1,codonFrameList, i, iSize-i-1);
+ }
+ iSize--;
+ }
+ else
+ {
+ i++;
+ }
+ }
+ return removed;
+ }
}
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 34a5ff2..82aff33 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -267,4 +267,32 @@ public interface AlignmentI
* @return hashtable of alignment properties (or null if none are defined)
*/
public Hashtable getProperties();
+
+ /**
+ * add a reference to a frame of aligned codons for this alignment
+ * @param codons
+ */
+ public void addCodonFrame(AlignedCodonFrame codons);
+ /**
+ * remove a particular codon frame reference from this alignment
+ * @param codons
+ * @return true if codon frame was removed.
+ */
+ public boolean removeCodonFrame(AlignedCodonFrame codons);
+ /**
+ * get all codon frames associated with this alignment
+ * @return
+ */
+ public AlignedCodonFrame[] getCodonFrames();
+ /**
+ * get a particular codon frame
+ * @param index
+ * @return
+ */
+ public AlignedCodonFrame getCodonFrame(int index);
+ /**
+ * get codon frames involving sequenceI
+ */
+ public AlignedCodonFrame[] getCodonFrame(SequenceI seq);
+
}
--
1.7.10.2