From 702481fe6f87f0a418ddfec7b1d014ec2b8c22b2 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 21 Dec 2007 15:06:06 +0000
Subject: [PATCH] further bugfix and annotation transfer for dna/protein
 (still issues with non-codon translation mapping
 generation)

---
 src/jalview/analysis/Dna.java |  100 ++++++++++++++++++++++++++++++++++++-----
 1 file changed, 90 insertions(+), 10 deletions(-)

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 7bac46e..c6bcfda 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -350,16 +350,22 @@ public class Dna
           String seqstring, int[] viscontigs, AlignedCodonFrame codons,
           char gapCharacter, DBRefEntry product)
   {
+    Vector skip=new Vector();
+    int skipint[]=null;
     ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
     // intervals
     int vc, scontigs[] = new int[viscontigs.length];
     int npos = 0;
     for (vc = 0; vc < viscontigs.length; vc += 2)
     {
+      if (vc==0) {
       vismapping.addShift(npos, viscontigs[vc]);
-      scontigs[vc] = npos;
-      npos += viscontigs[vc + 1];
-      scontigs[vc + 1] = npos;
+      } else {
+        // hidden region
+        vismapping.addShift(npos, viscontigs[vc]-viscontigs[vc-1]+1);
+      }
+      scontigs[vc] = viscontigs[vc];
+      scontigs[vc + 1] = viscontigs[vc+1];
     }
 
     StringBuffer protein = new StringBuffer();
@@ -381,9 +387,40 @@ public class Dna
         String aa = ResidueProperties.codonTranslate(new String(codon));
         rf = 0;
         if (aa == null)
-          aa = String.valueOf(gapCharacter);
-        else
         {
+          aa = String.valueOf(gapCharacter);
+          if (skipint==null)
+          {
+            skipint = new int[] { cdp[0],cdp[2] };
+          }
+          skipint[1] = cdp[2];
+        } else {
+          if (skipint!=null)
+          {
+            // edit scontigs
+            skipint[0] = vismapping.shift(skipint[0]);
+            skipint[1] = vismapping.shift(skipint[1]);
+            for (vc=0; vc<scontigs.length; vc+=2)
+            {
+              if (scontigs[vc+1]<skipint[0])
+              {
+                continue;
+              }
+              if (scontigs[vc]<=skipint[0])
+              {
+               if (skipint[0]==scontigs[vc])
+               {
+                 
+               } else {
+                 int[] t = new int[scontigs.length+2];
+                 System.arraycopy(scontigs, 0, t, 0, vc-1);
+                 // scontigs[vc]; //
+               }
+              }
+            }
+            skip.addElement(skipint);
+            skipint=null;
+          }
           if (aa.equals("STOP"))
           {
             aa = "X";
@@ -428,7 +465,9 @@ public class Dna
         }
         aspos++;
         if (aspos >= codons.aaWidth)
+        {
           codons.aaWidth = aspos + 1;
+        }
       }
     }
     if (resSize > 0)
@@ -472,14 +511,12 @@ public class Dna
       if (scontigs != null)
       {
         npos = 0;
-        // Find sequence position for scontigs positions on the nucleotide
-        // sequence string we were passed.
-        for (vc = 0; vc < viscontigs.length; vc += 2)
+        // map scontigs to actual sequence positions on selection
+        for (vc = 0; vc < scontigs.length; vc += 2)
         {
           scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
-          npos += viscontigs[vc];
           scontigs[vc + 1] = selection
-                  .findPosition(npos + scontigs[vc + 1]); // exclusive
+                  .findPosition(scontigs[vc + 1]); // exclusive
           if (scontigs[vc + 1] == selection.getEnd())
             break;
         }
@@ -490,8 +527,51 @@ public class Dna
           System.arraycopy(scontigs, 0, t, 0, vc + 2);
           scontigs = t;
         }
+        /*
+         * delete intervals in scontigs which are not translated.
+         * 1. map skip into sequence position intervals
+         * 2. truncate existing ranges and add new ranges to exclude untranslated regions.
+        if (skip.size()>0)
+        {
+          Vector narange = new Vector();
+          for (vc=0; vc<scontigs.length; vc++)
+          {
+            narange.addElement(new int[] {scontigs[vc]});
+          }
+          int sint=0,iv[];
+          vc = 0;
+          while (sint<skip.size())
+          {
+            skipint = (int[]) skip.elementAt(sint);
+            do {
+              iv = (int[]) narange.elementAt(vc);
+              if (iv[0]>=skipint[0] && iv[0]<=skipint[1])
+              {
+                if (iv[0]==skipint[0])
+                {
+                  // delete beginning of range
+                } else {
+                  // truncate range and create new one if necessary
+                  iv = (int[]) narange.elementAt(vc+1);
+                  if (iv[0]<=skipint[1])
+                  {
+                    // truncate range
+                    iv[0] = skipint[1];
+                  } else {
+                    
+                  }
+                }
+              } else
+                if (iv[0]<skipint[0])
+                {
+                  iv = (int[]) narange.elementAt(vc+1);
+                }
+            } while (iv[0])
+          }
+        }*/
         MapList map = new MapList(scontigs, new int[]
                                                     { 1, resSize }, 3, 1);
+        
         // update newseq as if it was generated as mapping from product
         
         if (product != null)
-- 
1.7.10.2