mapping bug fixes

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index c89c170..f4e2d97 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -1,5 +1,8 @@
 package jalview.datamodel;\r
 \r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+\r
 import jalview.util.MapList;\r
 \r
 /**\r
@@ -24,6 +27,11 @@ public class AlignedCodonFrame
    */\r
   public AlignedCodonFrame(int aWidth)\r
   {\r
+    if (aWidth<=0)\r
+   {\r
+      codons=null;\r
+      return;\r
+   }\r
     codons = new int[aWidth][];\r
     for (int res = 0; res < aWidth; res++)\r
       codons[res] = null;\r
@@ -57,6 +65,11 @@ public class AlignedCodonFrame
     return aaWidth;\r
   }\r
   /**\r
+   * TODO: not an ideal solution - we reference the aligned amino acid sequences in order to make insertions on them\r
+   * Better would be dnaAlignment and aaAlignment reference....\r
+   */\r
+  Vector a_aaSeqs=new Vector();\r
+  /**\r
    * increase aaWidth by one and insert a new aligned codon position space at aspos.\r
    * @param aspos\r
    */\r
@@ -64,10 +77,15 @@ public class AlignedCodonFrame
   {            \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
+    if (a_aaSeqs!=null)\r
+    {\r
+      // we actually have to modify the aligned sequences here, so use the a_aaSeqs vector\r
+      Enumeration sq = a_aaSeqs.elements();\r
+      while (sq.hasMoreElements())\r
+      {\r
+        ((SequenceI) sq.nextElement()).insertCharAt(aspos, gapCharacter);\r
+      }\r
     }\r
-\r
     checkCodonFrameWidth(aspos);\r
     if (aspos<aaWidth)\r
     {\r
@@ -86,14 +104,17 @@ public class AlignedCodonFrame
    */\r
   SequenceI[] dnaSeqs=null;\r
   /**\r
-   * tied array of protein sequence Objects\r
+   * tied array of Mappings to protein sequence Objects and \r
+     SequenceI[] aaSeqs=null;\r
+   * MapLists where eac maps from the corresponding dnaSeqs element to corresponding aaSeqs element  \r
    */\r
-  SequenceI[] aaSeqs=null;\r
+  Mapping[] dnaToProt=null;\r
   /**\r
-   * tied array of MapLists where eac maps from the corresponding dnaSeqs element to corresponding aaSeqs element  \r
+   * add a mapping between the dataset sequences for the associated dna and protein sequence objects\r
+   * @param dnaseq\r
+   * @param aaseq\r
+   * @param map\r
    */\r
-  MapList[] dnaToProt=null;\r
-  \r
   public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)\r
   { \r
     int nlen=1;\r
@@ -102,21 +123,20 @@ public class AlignedCodonFrame
       nlen = dnaSeqs.length+1;\r
     }\r
     SequenceI[] ndna = new SequenceI[nlen];\r
-    SequenceI[] naa = new SequenceI[nlen];\r
-    MapList[] ndtp = new MapList[nlen];\r
+    Mapping[] ndtp = new Mapping[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
+    Mapping mp = new Mapping(map);\r
+    mp.to = (aaseq.getDatasetSequence()==null) ? aaseq : aaseq.getDatasetSequence();\r
+    a_aaSeqs.addElement(aaseq);\r
+    dnaToProt[nlen] = mp;\r
   }\r
 \r
 \r
@@ -126,10 +146,28 @@ public class AlignedCodonFrame
   }\r
   public SequenceI[] getAaSeqs()\r
   {\r
-    return aaSeqs;\r
+    if (dnaToProt==null)\r
+      return null;\r
+    SequenceI[] sqs = new SequenceI[dnaToProt.length];\r
+    for (int sz=0; sz<dnaToProt.length; sz++)\r
+    {\r
+      sqs[sz]  = dnaToProt[sz].to;\r
+    }\r
+    return sqs;\r
   }\r
   public MapList[] getdnaToProt()\r
   {\r
+    if (dnaToProt==null)\r
+      return null;\r
+    MapList[] sqs = new MapList[dnaToProt.length];\r
+    for (int sz=0; sz<dnaToProt.length; sz++)\r
+    {\r
+      sqs[sz]  = dnaToProt[sz].map;\r
+    }\r
+    return sqs;\r
+  }\r
+  public Mapping[] getProtMappings()\r
+  {\r
     return dnaToProt;\r
   }\r
   /**\r
@@ -147,7 +185,7 @@ public class AlignedCodonFrame
     for (int ds=0;ds<dnaSeqs.length; ds++)\r
     {\r
       if (dnaSeqs[ds]==dnaSeqRef || dnaSeqs[ds]==dnads)\r
-        return aaSeqs[ds];\r
+        return dnaToProt[ds].to;\r
     }\r
     return null;\r
   }\r
@@ -158,14 +196,14 @@ public class AlignedCodonFrame
    */\r
   public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)\r
   {\r
-    if (aaSeqs==null)\r
+    if (dnaToProt==null)\r
     {\r
       return null;\r
     }\r
     SequenceI aads = aaSeqRef.getDatasetSequence();\r
-    for (int as=0;as<aaSeqs.length; as++)\r
+    for (int as=0;as<dnaToProt.length; as++)\r
     {\r
-      if (aaSeqs[as]==aaSeqRef || aaSeqs[as]==aads)\r
+      if (dnaToProt[as].to==aaSeqRef || dnaToProt[as].to==aads)\r
         return dnaSeqs[as];\r
     }\r
     return null;\r
@@ -189,25 +227,25 @@ public class AlignedCodonFrame
   {\r
     int[] codon;\r
     SequenceI ds = seq.getDatasetSequence();\r
-    for (int mi = 0; mi<aaSeqs.length; mi++)\r
+    for (int mi = 0; mi<dnaToProt.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
+        codon = dnaToProt[mi].map.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
+              results.addResult(dnaToProt[mi].to, codon[i], codon[i+1]);\r
             }\r
         }\r
       } else\r
-        if (aaSeqs[mi]==seq || aaSeqs[mi]==ds)\r
+        if (dnaToProt[mi].to==seq || dnaToProt[mi].to==ds)\r
         {\r
           // DEBUG System.err.println("aa pos "+index);\r
           {\r
-            codon = dnaToProt[mi].locateInFrom(index, index);\r
+            codon = dnaToProt[mi].map.locateInFrom(index, index);\r
             if (codon!=null)\r
             {\r
             for (int i=0; i<codon.length; i+=2)\r

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b3a5266..c474142 100755 (executable)
--- 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;