X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureMapping.java;h=4174f5b8316eb82d900217207a4567d31ea1712d;hb=9b8a7cae41e5d0e2dfcd806319ca2d301dd133c5;hp=06e6bc3507f528ac69d7430b6552bd81f773a78d;hpb=6905363d02254a557f93f66a2b69d85aa0b23696;p=jalview.git

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 06e6bc3..4174f5b 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,100 +1,368 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.structure;
-
-import jalview.datamodel.*;
-
-public class StructureMapping
-{
-  String mappingDetails;
-  SequenceI sequence;
-  String pdbfile;
-  String pdbid;
-  String pdbchain;
-
-  //Mapping index 0 is resNum, index 1 is atomNo
-  int[][] mapping;
-
-  public StructureMapping(SequenceI seq,
-                          String pdbfile,
-                          String pdbid,
-                          String chain,
-                          int[][] mapping,
-                          String mappingDetails)
-  {
-    sequence = seq;
-    this.pdbfile = pdbfile;
-    this.pdbid = pdbid;
-    this.pdbchain = chain;
-    this.mapping = mapping;
-    this.mappingDetails = mappingDetails;
-  }
-
-  public SequenceI getSequence()
-  {
-    return sequence;
-  }
-
-  public String getChain()
-  {
-    return pdbchain;
-  }
-
-  public String getPdbId()
-  {
-    return pdbid;
-  }
-
-  public int getAtomNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][1];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getPDBResNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][0];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getSeqPos(int pdbResNum)
-  {
-    for (int i = 0; i < mapping.length; i++)
-    {
-      if (mapping[i][0] == pdbResNum)
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.structure;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+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;
+
+  String pdbfile;
+
+  String pdbid;
+
+  String pdbchain;
+
+  // 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
+   * 
+   * @param seq
+   * @param pdbfile
+   * @param pdbid
+   * @param chain
+   * @param mapping
+   *          a map from sequence to two values, { resNo, atomNo } in the
+   *          structure
+   * @param mappingDetails
+   */
+  public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
+          String chain, HashMap<Integer, int[]> mapping,
+          String mappingDetails)
+  {
+    sequence = seq;
+    this.pdbfile = pdbfile;
+    this.pdbid = pdbid;
+    this.pdbchain = chain;
+    this.mapping = mapping;
+    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;
+  }
+
+  public String getChain()
+  {
+    return pdbchain;
+  }
+
+  public String getPdbId()
+  {
+    return pdbid;
+  }
+
+  /**
+   * 
+   * @param seqpos
+   * @return 0 or corresponding atom number for the sequence position
+   */
+  public int getAtomNum(int seqpos)
+  {
+    int[] resNumAtomMap = mapping.get(seqpos);
+    if (resNumAtomMap != null)
+    {
+      return resNumAtomMap[PDB_ATOM_NUM_INDEX];
+    }
+    else
+    {
+      return UNASSIGNED_VALUE;
+    }
+  }
+
+  /**
+   * 
+   * @param seqpos
+   * @return UNASSIGNED_VALUE or the corresponding residue number for the
+   *         sequence position
+   */
+  public int getPDBResNum(int seqpos)
+  {
+    int[] resNumAtomMap = mapping.get(seqpos);
+    if (resNumAtomMap != null)
+    {
+      return resNumAtomMap[PDB_RES_NUM_INDEX];
+    }
+    else
+    {
+      return UNASSIGNED_VALUE;
+    }
+  }
+
+  /**
+   * Returns a (possibly empty) list of [start, end] residue positions in the
+   * mapped structure, corresponding to the given range of sequence positions
+   * 
+   * @param fromSeqPos
+   * @param toSeqPos
+   * @return
+   */
+  public List<int[]> getPDBResNumRanges(int fromSeqPos, int toSeqPos)
+  {
+    List<int[]> result = new ArrayList<>();
+    int startRes = -1;
+    int endRes = -1;
+
+    for (int i = fromSeqPos; i <= toSeqPos; i++)
+    {
+      int resNo = getPDBResNum(i);
+      if (resNo == UNASSIGNED_VALUE)
+      {
+        continue; // no mapping from this sequence position
+      }
+      if (startRes == -1)
+      {
+        startRes = resNo;
+        endRes = resNo;
+      }
+      if (resNo >= startRes && resNo <= endRes)
+      {
+        // within the current range - no change
+        continue;
+      }
+      if (resNo == startRes - 1)
+      {
+        // extend beginning of current range
+        startRes--;
+        continue;
+      }
+      if (resNo == endRes + 1)
+      {
+        // extend end of current range
+        endRes++;
+        continue;
+      }
+
+      /*
+       * resNo is not within or contiguous with last range,
+       * so write out the last range
+       */
+      result.add(new int[] { startRes, endRes });
+      startRes = resNo;
+      endRes = resNo;
+    }
+
+    /*
+     * and add the last range
+     */
+    if (startRes != -1)
+    {
+      result.add(new int[] { startRes, endRes });
+    }
+
+    return result;
+  }
+
+  /**
+   * 
+   * @param pdbResNum
+   * @return -1 or the corresponding sequence position for a pdb residue number
+   */
+  public int getSeqPos(int pdbResNum)
+  {
+    for (Integer seqPos : mapping.keySet())
+    {
+      if (pdbResNum == getPDBResNum(seqPos))
+      {
+        return seqPos;
+      }
+    }
+    return UNASSIGNED_VALUE;
+  }
+
+  /**
+   * transfer a copy of an alignment annotation row in the PDB chain coordinate
+   * system onto the mapped sequence
+   * 
+   * @param ana
+   * @return the copy that was remapped to the mapped sequence
+   * @note this method will create a copy and add it to the dataset sequence for
+   *       the mapped sequence as well as the mapped sequence (if it is not a
+   *       dataset sequence).
+   */
+  public AlignmentAnnotation transfer(AlignmentAnnotation ana)
+  {
+    AlignmentAnnotation ala_copy = new AlignmentAnnotation(ana);
+    SequenceI ds = sequence;
+    while (ds.getDatasetSequence() != null)
+    {
+      ds = ds.getDatasetSequence();
+    }
+    // need to relocate annotation from pdb coordinates to local sequence
+    // -1,-1 doesn't look at pdbresnum but fails to remap sequence positions...
+
+    ala_copy.remap(ds, mapping, -1, -1, 0);
+    ds.addAlignmentAnnotation(ala_copy);
+    if (ds != sequence)
+    {
+      // mapping wasn't to an original dataset sequence, so we make a copy on
+      // the mapped sequence too
+      ala_copy = new AlignmentAnnotation(ala_copy);
+      sequence.addAlignmentAnnotation(ala_copy);
+    }
+    return ala_copy;
+  }
+
+  public String getMappingDetailsOutput()
+  {
+    return mappingDetails;
+  }
+
+  public HashMap<Integer, int[]> getMapping()
+  {
+    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;
+  }
+}