AlignedCodonFrame holds mapping information between individual cDNA regions on dna...

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
new file mode 100644 (file)
index 0000000..c89c170
--- /dev/null
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -0,0 +1,222 @@
+package jalview.datamodel;\r
+\r
+import jalview.util.MapList;\r
+\r
+/**\r
+ * Stores mapping between the columns of a protein alignment and a DNA alignment\r
+ * and a list of individual codon to amino acid mappings between sequences.\r
+ */\r
+\r
+public class AlignedCodonFrame\r
+{\r
+  /**\r
+   * array of nucleotide positions for aligned codons at column of aligned proteins.\r
+   */\r
+  public int[][] codons = null;\r
+  /**\r
+   * width of protein sequence alignement\r
+   * implicit assertion that codons.length >= aaWidth\r
+   */\r
+  public int aaWidth=0;\r
+  /**\r
+   * initialise codon frame with a nominal alignment width\r
+   * @param aWidth\r
+   */\r
+  public AlignedCodonFrame(int aWidth)\r
+  {\r
+    codons = new int[aWidth][];\r
+    for (int res = 0; res < aWidth; res++)\r
+      codons[res] = null;\r
+  }\r
+\r
+  /**\r
+   * ensure that codons array is at least as wide as aslen residues\r
+   * @param aslen\r
+   * @return (possibly newly expanded) codon array\r
+   */\r
+  public int[][] checkCodonFrameWidth(int aslen)\r
+  {\r
+    if (codons.length <= aslen + 1)\r
+    {\r
+      // probably never have to do this ?\r
+      int[][] c = new int[codons.length + 10][];\r
+      for (int i = 0; i < codons.length; i++)\r
+      {\r
+        c[i] = codons[i];\r
+        codons[i] = null;\r
+      }\r
+      codons = c;\r
+    }\r
+    return codons;\r
+  }\r
+  /**\r
+   * @return width of aligned translated amino acid residues \r
+   */\r
+  public int getaaWidth()\r
+  {\r
+    return aaWidth;\r
+  }\r
+  /**\r
+   * increase aaWidth by one and insert a new aligned codon position space at aspos.\r
+   * @param aspos\r
+   */\r
+  public void insertAAGap(int aspos, char gapCharacter)\r
+  {            \r
+    // this aa appears before the aligned codons at aspos - so shift them in each pair of mapped sequences\r
+    aaWidth++;\r
+    for (int sq=0;aaSeqs!=null && sq<aaSeqs.length; sq++) {\r
+      aaSeqs[sq].insertCharAt(aspos, gapCharacter);\r
+    }\r
+\r
+    checkCodonFrameWidth(aspos);\r
+    if (aspos<aaWidth)\r
+    {\r
+      aaWidth++;\r
+      System.arraycopy(codons, aspos, codons, aspos+1, aaWidth-aspos);\r
+      codons[aspos]=null; // clear so new codon position can be marked.\r
+    }\r
+  }\r
+\r
+  public void setAaWidth(int aapos)\r
+  {\r
+    aaWidth = aapos;\r
+  }\r
+  /**\r
+   * tied array of na Sequence objects.\r
+   */\r
+  SequenceI[] dnaSeqs=null;\r
+  /**\r
+   * tied array of protein sequence Objects\r
+   */\r
+  SequenceI[] aaSeqs=null;\r
+  /**\r
+   * tied array of MapLists where eac maps from the corresponding dnaSeqs element to corresponding aaSeqs element  \r
+   */\r
+  MapList[] dnaToProt=null;\r
+  \r
+  public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)\r
+  { \r
+    int nlen=1;\r
+    if (dnaSeqs!=null)\r
+    {\r
+      nlen = dnaSeqs.length+1;\r
+    }\r
+    SequenceI[] ndna = new SequenceI[nlen];\r
+    SequenceI[] naa = new SequenceI[nlen];\r
+    MapList[] ndtp = new MapList[nlen];\r
+    if (dnaSeqs!=null)\r
+    {\r
+      System.arraycopy(dnaSeqs,0,ndna, 0, dnaSeqs.length);\r
+      System.arraycopy(aaSeqs,0,naa, 0, dnaSeqs.length);\r
+      System.arraycopy(dnaToProt,0,ndtp, 0, dnaSeqs.length);\r
+    }\r
+    dnaSeqs = ndna;\r
+    aaSeqs = naa;\r
+    dnaToProt = ndtp;\r
+    nlen--;\r
+    dnaSeqs[nlen] = (dnaseq.getDatasetSequence()==null) ? dnaseq : dnaseq.getDatasetSequence();\r
+    aaSeqs[nlen] = (aaseq.getDatasetSequence()==null) ? aaseq : aaseq.getDatasetSequence();\r
+    dnaToProt[nlen] = map;\r
+  }\r
+\r
+\r
+  public SequenceI[] getdnaSeqs()\r
+  {\r
+    return dnaSeqs;\r
+  }\r
+  public SequenceI[] getAaSeqs()\r
+  {\r
+    return aaSeqs;\r
+  }\r
+  public MapList[] getdnaToProt()\r
+  {\r
+    return dnaToProt;\r
+  }\r
+  /**\r
+   * \r
+   * @param sequenceRef\r
+   * @return null or corresponding aaSeq entry for dnaSeq entry\r
+   */\r
+  public SequenceI getAaForDnaSeq(SequenceI dnaSeqRef)\r
+  {\r
+    if (dnaSeqs==null)\r
+    {\r
+      return null;\r
+    }\r
+    SequenceI dnads = dnaSeqRef.getDatasetSequence();\r
+    for (int ds=0;ds<dnaSeqs.length; ds++)\r
+    {\r
+      if (dnaSeqs[ds]==dnaSeqRef || dnaSeqs[ds]==dnads)\r
+        return aaSeqs[ds];\r
+    }\r
+    return null;\r
+  }\r
+  /**\r
+   * \r
+   * @param sequenceRef\r
+   * @return null or corresponding aaSeq entry for dnaSeq entry\r
+   */\r
+  public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)\r
+  {\r
+    if (aaSeqs==null)\r
+    {\r
+      return null;\r
+    }\r
+    SequenceI aads = aaSeqRef.getDatasetSequence();\r
+    for (int as=0;as<aaSeqs.length; as++)\r
+    {\r
+      if (aaSeqs[as]==aaSeqRef || aaSeqs[as]==aads)\r
+        return dnaSeqs[as];\r
+    }\r
+    return null;\r
+  }\r
+  /**\r
+   * test to see if codon frame involves seq in any way\r
+   * @param seq a nucleotide or protein sequence\r
+   * @return true if a mapping exists to or from this sequence to any translated sequence\r
+   */\r
+  public boolean involvesSequence(SequenceI seq)\r
+  {\r
+    return getAaForDnaSeq(seq)!=null || getDnaForAaSeq(seq)!=null;\r
+  }\r
+  /**\r
+   * Add search results for regions in other sequences that translate or are translated from a particular position in seq \r
+   * @param seq\r
+   * @param index position in seq\r
+   * @param results where highlighted regions go\r
+   */\r
+  public void markMappedRegion(SequenceI seq, int index, SearchResults results)\r
+  {\r
+    int[] codon;\r
+    SequenceI ds = seq.getDatasetSequence();\r
+    for (int mi = 0; mi<aaSeqs.length; mi++)\r
+    {\r
+      if (dnaSeqs[mi]==seq || dnaSeqs[mi]==ds)\r
+      {\r
+        // DEBUG System.err.println("dna pos "+index);\r
+        codon = dnaToProt[mi].locateInTo(index,index);\r
+        if (codon!=null)\r
+        {\r
+          for (int i=0; i<codon.length; i+=2)\r
+            {\r
+              results.addResult(aaSeqs[mi], codon[i], codon[i+1]);\r
+            }\r
+        }\r
+      } else\r
+        if (aaSeqs[mi]==seq || aaSeqs[mi]==ds)\r
+        {\r
+          // DEBUG System.err.println("aa pos "+index);\r
+          {\r
+            codon = dnaToProt[mi].locateInFrom(index, index);\r
+            if (codon!=null)\r
+            {\r
+            for (int i=0; i<codon.length; i+=2)\r
+              {\r
+                results.addResult(dnaSeqs[mi], codon[i], codon[i+1]);\r
+              }\r
+          }\r
+        }\r
+        }\r
+    }\r
+  }\r
+}\r

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 677f436..b3a5266 100755 (executable)
--- 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 (executable)
--- 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);
+  
 }