JAL-1967 JAL-1479 refactored sequence<->structure mapping implementation

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 1541a6a..e9053ed 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -588,9 +588,7 @@ public class StructureSelectionManager
             .getMappingFromS1(false);
     maxChain.transferRESNUMFeatures(seq, null);
 
-    // allocate enough slots to store the mapping from positions in
-    // sequence[s] to the associated chain
-    int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2];
+    HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
     int resNum = -10000;
     int index = 0;
 
@@ -604,8 +602,8 @@ public class StructureSelectionManager
         {
           // TODO (JAL-1836) address root cause: negative residue no in PDB
           // file
-          mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
-          mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+          mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
+              tmp.atomIndex });
         }
       }