X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=a2b047212b5ea4991cac7adfa145d22b415b08dc;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=c3408bdedd9d396f06d6ec1a203c06887ad7b53a;hpb=e2c3b3602486cee3f85dd8dfc7856a5ce6701669;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index c3408bd..a2b0472 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -20,6 +20,12 @@
  */
 package jalview.analysis;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.Iterator;
+import java.util.List;
+
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
@@ -28,7 +34,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.Mapping;
@@ -41,11 +46,6 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.ShiftList;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.List;
-
 public class Dna
 {
   private static final String STOP_ASTERIX = "*";
@@ -60,7 +60,7 @@ public class Dna
 
   private final String[] seqstring;
 
-  private final List<int[]> contigs;
+  private final Iterator<int[]> contigs;
 
   private final char gapChar;
 
@@ -70,6 +70,10 @@ public class Dna
 
   private final AlignmentI dataset;
 
+  private ShiftList vismapping;
+
+  private int[] startcontigs;
+
   /*
    * Working variables for the translation.
    * 
@@ -91,7 +95,7 @@ public class Dna
    * @param viewport
    * @param visibleContigs
    */
-  public Dna(AlignViewportI viewport, List<int[]> visibleContigs)
+  public Dna(AlignViewportI viewport, Iterator<int[]> visibleContigs)
   {
     this.selection = Arrays.asList(viewport.getSequenceSelection());
     this.seqstring = viewport.getViewAsString(true);
@@ -100,6 +104,45 @@ public class Dna
     this.annotations = viewport.getAlignment().getAlignmentAnnotation();
     this.dnaWidth = viewport.getAlignment().getWidth();
     this.dataset = viewport.getAlignment().getDataset();
+    initContigs();
+  }
+
+  /**
+   * Initialise contigs used as starting point for translateCodingRegion
+   */
+  private void initContigs()
+  {
+    vismapping = new ShiftList(); // map from viscontigs to seqstring
+    // intervals
+
+    int npos = 0;
+    int[] lastregion = null;
+    ArrayList<Integer> tempcontigs = new ArrayList<>();
+    while (contigs.hasNext())
+    {
+      int[] region = contigs.next();
+      if (lastregion == null)
+      {
+        vismapping.addShift(npos, region[0]);
+      }
+      else
+      {
+        // hidden region
+        vismapping.addShift(npos, region[0] - lastregion[1] + 1);
+      }
+      lastregion = region;
+      tempcontigs.add(region[0]);
+      tempcontigs.add(region[1]);
+    }
+
+    startcontigs = new int[tempcontigs.size()];
+    int i = 0;
+    for (Integer val : tempcontigs)
+    {
+      startcontigs[i] = val;
+      i++;
+    }
+    tempcontigs = null;
   }
 
   /**
@@ -119,7 +162,8 @@ public class Dna
    * @param ac2
    * @return
    */
-  public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
+  public static final int compareCodonPos(AlignedCodon ac1,
+          AlignedCodon ac2)
   {
     return comparator.compare(ac1, ac2);
     // return jalview_2_8_2compare(ac1, ac2);
@@ -150,10 +194,11 @@ public class Dna
   }
 
   /**
+   * Translates cDNA using the specified code table
    * 
    * @return
    */
-  public AlignmentI translateCdna()
+  public AlignmentI translateCdna(GeneticCodeI codeTable)
   {
     AlignedCodonFrame acf = new AlignedCodonFrame();
 
@@ -165,7 +210,7 @@ public class Dna
     for (s = 0; s < sSize; s++)
     {
       SequenceI newseq = translateCodingRegion(selection.get(s),
-              seqstring[s], acf, pepseqs);
+              seqstring[s], acf, pepseqs, codeTable);
 
       if (newseq != null)
       {
@@ -208,29 +253,30 @@ public class Dna
     for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
-      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+      List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
               jalview.datamodel.DBRefSource.DNACODINGDBS);
       if (dnarefs != null)
       {
         // intersect with pep
         List<DBRefEntry> mappedrefs = new ArrayList<>();
-        DBRefEntry[] refs = dna.getDBRefs();
-        for (int d = 0; d < refs.length; d++)
+        List<DBRefEntry> refs = dna.getDBRefs();
+        for (int d = 0, nd = refs.size(); d < nd; d++)
         {
-          if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
-                  && refs[d].getMap().getMap().getFromRatio() == 3
-                  && refs[d].getMap().getMap().getToRatio() == 1)
+          DBRefEntry ref = refs.get(d);
+          if (ref.getMap() != null && ref.getMap().getMap() != null
+                  && ref.getMap().getMap().getFromRatio() == 3
+                  && ref.getMap().getMap().getToRatio() == 1)
           {
-            mappedrefs.add(refs[d]); // add translated protein maps
+            mappedrefs.add(ref); // add translated protein maps
           }
         }
-        dnarefs = mappedrefs.toArray(new DBRefEntry[mappedrefs.size()]);
-        for (int d = 0; d < dnarefs.length; d++)
+        dnarefs = mappedrefs;// .toArray(new DBRefEntry[mappedrefs.size()]);
+        for (int d = 0, nd = dnarefs.size(); d < nd; d++)
         {
-          Mapping mp = dnarefs[d].getMap();
+          Mapping mp = dnarefs.get(d).getMap();
           if (mp != null)
           {
-            for (int vc = 0; vc < viscontigs.length; vc += 2)
+            for (int vc = 0, nv = viscontigs.length; vc < nv; vc += 2)
             {
               int[] mpr = mp.locateMappedRange(viscontigs[vc],
                       viscontigs[vc + 1]);
@@ -385,37 +431,21 @@ public class Dna
    * @param acf
    *          Definition of global ORF alignment reference frame
    * @param proteinSeqs
+   * @param codeTable
    * @return sequence ready to be added to alignment.
    */
   protected SequenceI translateCodingRegion(SequenceI selection,
           String seqstring, AlignedCodonFrame acf,
-          List<SequenceI> proteinSeqs)
+          List<SequenceI> proteinSeqs, GeneticCodeI codeTable)
   {
     List<int[]> skip = new ArrayList<>();
-    int skipint[] = null;
-    ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
-    // intervals
-    int vc = 0;
-    int[] scontigs = new int[contigs.size() * 2];
+    int[] skipint = null;
+
     int npos = 0;
-    int[] lastregion = null;
-    for (int[] region : contigs)
-    {
-      if (lastregion == null)
-      {
-        vismapping.addShift(npos, region[0]);
-      }
-      else
-      {
-        // hidden region
-        vismapping.addShift(npos, region[0] - lastregion[1] + 1);
-      }
-      lastregion = region;
+    int vc = 0;
 
-      scontigs[vc] = region[0];
-      scontigs[vc + 1] = region[1];
-      vc++;
-    }
+    int[] scontigs = new int[startcontigs.length];
+    System.arraycopy(startcontigs, 0, scontigs, 0, startcontigs.length);
 
     // allocate a roughly sized buffer for the protein sequence
     StringBuilder protein = new StringBuilder(seqstring.length() / 2);
@@ -441,7 +471,7 @@ public class Dna
          */
         AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
                 cdp[2]);
-        String aa = ResidueProperties.codonTranslate(new String(codon));
+        String aa = codeTable.translate(new String(codon));
         rf = 0;
         final String gapString = String.valueOf(gapChar);
         if (aa == null)
@@ -548,7 +578,7 @@ public class Dna
             skip.add(skipint);
             skipint = null;
           }
-          if (aa.equals("STOP"))
+          if (aa.equals(ResidueProperties.STOP))
           {
             aa = STOP_ASTERIX;
           }
@@ -769,28 +799,29 @@ public class Dna
   private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
           MapList map)
   {
-    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
-            DBRefSource.DNACODINGDBS);
-    if (dnarefs != null)
-    {
-      // intersect with pep
-      for (int d = 0; d < dnarefs.length; d++)
-      {
-        Mapping mp = dnarefs[d].getMap();
-        if (mp != null)
-        {
-        }
-      }
-    }
+    // BH 2019.01.25 nop?
+    // List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+    // DBRefSource.DNACODINGDBS);
+    // if (dnarefs != null)
+    // {
+    // // intersect with pep
+    // for (int d = 0, nd = dnarefs.size(); d < nd; d++)
+    // {
+    // Mapping mp = dnarefs.get(d).getMap();
+    // if (mp != null)
+    // {
+    // }
+    // }
+    // }
     for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
     {
-        if (FeatureProperties.isCodingFeature(null, sf.getType()))
+      if (FeatureProperties.isCodingFeature(null, sf.getType()))
+      {
+        // if (map.intersectsFrom(sf[f].begin, sf[f].end))
         {
-          // if (map.intersectsFrom(sf[f].begin, sf[f].end))
-          {
 
-          }
         }
+      }
     }
   }
 
@@ -855,6 +886,23 @@ public class Dna
   }
 
   /**
+   * Answers the reverse complement of the input string
+   * 
+   * @see #getComplement(char)
+   * @param s
+   * @return
+   */
+  public static String reverseComplement(String s)
+  {
+    StringBuilder sb = new StringBuilder(s.length());
+    for (int i = s.length() - 1; i >= 0; i--)
+    {
+      sb.append(Dna.getComplement(s.charAt(i)));
+    }
+    return sb.toString();
+  }
+
+  /**
    * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
    * are treated as on http://reverse-complement.com/. Anything else is left
    * unchanged.