X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=e9053ed0d65b3c615fc490d813892d5aa012b8e4;hb=4ff572f7cf17f5ca9c23f82bbe41005af8af55cc;hp=1541a6a83df8c599f0f270c44cc375bbe850b09f;hpb=8449c7161636af09d658905fe3affbc84fd10150;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 1541a6a..e9053ed 100644
--- 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 });
         }
       }