Merge branch 'bugs/JAL-2780_JAL-2781_pdbnegativenums' into releases/Release_2_10_4_Branch

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

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 40789ed..fcf322d 100644 (file)
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -21,6 +21,7 @@
 package jalview.structure;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
 
 import java.util.ArrayList;
@@ -39,7 +40,7 @@ public class StructureMapping
 
   String pdbchain;
 
-  public static final int UNASSIGNED_VALUE = -1;
+  public static final int UNASSIGNED_VALUE = Integer.MIN_VALUE;
 
   private static final int PDB_RES_NUM_INDEX = 0;
 
@@ -49,6 +50,7 @@ public class StructureMapping
   // and atomNo
   HashMap<Integer, int[]> mapping;
 
+  jalview.datamodel.Mapping seqToPdbMapping = null;
   /**
    * Constructor
    * 
@@ -73,6 +75,14 @@ public class StructureMapping
     this.mappingDetails = mappingDetails;
   }
 
+  public StructureMapping(SequenceI seq, String pdbFile2, String pdbId2,
+          String chain, HashMap<Integer, int[]> mapping2,
+          String mappingOutput, Mapping seqToPdbMapping)
+  {
+    this(seq, pdbFile2, pdbId2, chain, mapping2, mappingOutput);
+    this.seqToPdbMapping = seqToPdbMapping;
+  }
+
   public SequenceI getSequence()
   {
     return sequence;
@@ -109,7 +119,8 @@ public class StructureMapping
   /**
    * 
    * @param seqpos
-   * @return 0 or the corresponding residue number for the sequence position
+   * @return UNASSIGNED_VALUE or the corresponding residue number for the
+   *         sequence position
    */
   public int getPDBResNum(int seqpos)
   {
@@ -247,4 +258,9 @@ public class StructureMapping
   {
     return mapping;
   }
+
+  public Mapping getSeqToPdbMapping()
+  {
+    return seqToPdbMapping;
+  }
 }