further bugfix and annotation transfer for dna/protein (still issues with non-codon...

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