ensure successive matches to a regex have distinct annotation name (indice suffix...

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 3e046c2..159d96a 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -11,8 +11,8 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.DBRefEntry;\r
 import jalview.datamodel.Sequence;\r
 import jalview.datamodel.SequenceI;\r
-import jalview.ws.ASequenceFetcher;\r
 import jalview.ws.SequenceFetcher;\r
+import jalview.ws.seqfetcher.ASequenceFetcher;\r
 \r
 /**\r
  * Functions for cross-referencing sequence databases. user must first specify\r
@@ -158,7 +158,8 @@ public class CrossRef
       {\r
         if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))\r
         {\r
-          // retrieve CDS dataset sequences\r
+          System.err.println("TODO: unimplemented sequence retrieval for coding region sequence.");\r
+          // TODO: retrieve CDS dataset sequences\r
           // need global dataset sequence retriever/resolver to reuse refs\r
           // and construct Mapping entry.\r
           // insert gaps in CDS according to peptide gaps.\r
@@ -444,6 +445,7 @@ public class CrossRef
           boolean direct, boolean dna)\r
   {\r
     boolean found = false;\r
+    SequenceI[] typer=new SequenceI[1];\r
     if (dataset == null)\r
       return false;\r
     if (dataset.getSequences() == null)\r
@@ -464,6 +466,17 @@ public class CrossRef
         }\r
         if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())\r
         {\r
+          // check if this is the correct sequence type\r
+          {\r
+            typer[0] = nxt;\r
+            boolean isDna = jalview.util.Comparison.isNucleotide(typer);\r
+            if ((direct && isDna == dna) || (!direct && isDna!=dna))\r
+            {\r
+              // skip this sequence because it is same molecule type\r
+              continue;\r
+            }\r
+          }\r
+\r
           // look for direct or indirect references in common\r
           DBRefEntry[] poss = null, cands = null;\r
           if (direct)\r