JAL-3563 adds Jalview.setSynchronous()

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

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 40789ed..4b99911 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;
@@ -29,6 +30,12 @@ import java.util.List;
 
 public class StructureMapping
 {
+  public static final int UNASSIGNED_VALUE = Integer.MIN_VALUE;
+
+  private static final int PDB_RES_NUM_INDEX = 0;
+
+  private static final int PDB_ATOM_NUM_INDEX = 1;
+
   String mappingDetails;
 
   SequenceI sequence;
@@ -39,16 +46,12 @@ public class StructureMapping
 
   String pdbchain;
 
-  public static final int UNASSIGNED_VALUE = -1;
-
-  private static final int PDB_RES_NUM_INDEX = 0;
-
-  private static final int PDB_ATOM_NUM_INDEX = 1;
-
   // Mapping key is residue index while value is an array containing PDB resNum,
   // and atomNo
   HashMap<Integer, int[]> mapping;
 
+  jalview.datamodel.Mapping seqToPdbMapping = null;
+
   /**
    * Constructor
    * 
@@ -73,6 +76,14 @@ 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 +120,8 @@ 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)
   {
@@ -134,7 +146,7 @@ public class StructureMapping
    */
   public List<int[]> getPDBResNumRanges(int fromSeqPos, int toSeqPos)
   {
-    List<int[]> result = new ArrayList<int[]>();
+    List<int[]> result = new ArrayList<>();
     int startRes = -1;
     int endRes = -1;
 
@@ -247,4 +259,117 @@ public class StructureMapping
   {
     return mapping;
   }
+
+  public Mapping getSeqToPdbMapping()
+  {
+    return seqToPdbMapping;
+  }
+
+  /**
+   * A hash function that satisfies the contract that if two mappings are
+   * equal(), they have the same hashCode
+   */
+  @Override
+  public int hashCode()
+  {
+    final int prime = 31;
+    int result = 1;
+    result = prime * result
+            + ((mappingDetails == null) ? 0 : mappingDetails.hashCode());
+    result = prime * result
+            + ((pdbchain == null) ? 0 : pdbchain.hashCode());
+    result = prime * result + ((pdbfile == null) ? 0 : pdbfile.hashCode());
+    result = prime * result + ((pdbid == null) ? 0 : pdbid.hashCode());
+    result = prime * result
+            + ((seqToPdbMapping == null) ? 0 : seqToPdbMapping.hashCode());
+    result = prime * result
+            + ((sequence == null) ? 0 : sequence.hashCode());
+    return result;
+  }
+
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (this == obj)
+    {
+      return true;
+    }
+    if (obj == null)
+    {
+      return false;
+    }
+    if (getClass() != obj.getClass())
+    {
+      return false;
+    }
+    StructureMapping other = (StructureMapping) obj;
+    if (mappingDetails == null)
+    {
+      if (other.mappingDetails != null)
+      {
+        return false;
+      }
+    }
+    else if (!mappingDetails.equals(other.mappingDetails))
+    {
+      return false;
+    }
+    if (pdbchain == null)
+    {
+      if (other.pdbchain != null)
+      {
+        return false;
+      }
+    }
+    else if (!pdbchain.equals(other.pdbchain))
+    {
+      return false;
+    }
+    if (pdbfile == null)
+    {
+      if (other.pdbfile != null)
+      {
+        return false;
+      }
+    }
+    else if (!pdbfile.equals(other.pdbfile))
+    {
+      return false;
+    }
+    if (pdbid == null)
+    {
+      if (other.pdbid != null)
+      {
+        return false;
+      }
+    }
+    else if (!pdbid.equals(other.pdbid))
+    {
+      return false;
+    }
+    if (seqToPdbMapping == null)
+    {
+      if (other.seqToPdbMapping != null)
+      {
+        return false;
+      }
+    }
+    else if (!seqToPdbMapping.equals(other.seqToPdbMapping))
+    {
+      return false;
+    }
+    if (sequence != other.sequence)
+    {
+      return false;
+    }
+
+    return true;
+  }
+
+  @Override
+  public String toString()
+  {
+    return "[StructureMapping " + pdbfile + "\n" + mappingDetails + "]";
+  }
+
 }