AP11-218

IntersectAustralia · Jun 24, 2013 · 1352845 · 1352845
1 parent 2627f48
commit 1352845
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Showing 8 changed files with 4 additions and 7 deletions.
diff --git a/dist/codon_finder.jar b/dist/codon_finder.jar
diff --git a/dist/nucleotide_to_amino_acid.jar b/dist/nucleotide_to_amino_acid.jar
diff --git a/dist/protein_generator.jar b/dist/protein_generator.jar
diff --git a/dist/results_analyser.jar b/dist/results_analyser.jar
diff --git a/dist/samifier.jar b/dist/samifier.jar
diff --git a/dist/virtual_protein_merger.jar b/dist/virtual_protein_merger.jar
diff --git a/src/au/org/intersect/samifier/Version.java b/src/au/org/intersect/samifier/Version.java
@@ -2,5 +2,5 @@
 
 public interface Version {
 
-    String VERSION = "1.0.5";
+    String VERSION = "1.0.6";
 }
diff --git a/src/au/org/intersect/samifier/generator/VirtualProteinMascotLocationGenerator.java b/src/au/org/intersect/samifier/generator/VirtualProteinMascotLocationGenerator.java
@@ -91,9 +91,7 @@ public List<ProteinLocation> generateLocations()
                     }
                 }
             }
-
-
-
+
             for (int i = 0; i < locations.size(); i++) {
                 locations.get(i).setName("q" + i);
             }
@@ -134,7 +132,6 @@ public List<ProteinLocation> doGenerateLocations()
         for (PeptideSearchResult peptideSearchResult : peptideSearchResults) {
             GeneInfo geneInfo = genome.getGene(peptideSearchResult
                     .getProteinName());
-
             if (geneInfo == null) {
                 System.err.println(peptideSearchResult.getProteinName()
                         + " not found in the genome");
@@ -186,9 +183,9 @@ private int getStartPosition(int startPosition, int stopPosition) {
     private List<ProteinLocation> mergeProteins(List<ProteinLocation> locations) {
         Map<Integer, ProteinLocation> proteinMap = new HashMap<Integer, ProteinLocation>();
         for (ProteinLocation location : locations) {
-            ProteinLocation loc = proteinMap.get(location.getStop());
+            ProteinLocation loc = proteinMap.get(location.getStartIndex());
             if (loc == null) {
-                proteinMap.put(location.getStop(), location);
+                proteinMap.put(location.getStartIndex(), location);
             } else {
                loc.update(location);
             }