X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fstructure%2FStructureMapping.java;h=78634e06d0dee01b9b95f8e570a2bb2831ca2f9e;hb=c3de0b9d18ff5f445536fd5fc818768e28676367;hp=b119e734a235987f03c56be2e8c2ed59f268a0dd;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index b119e73..78634e0 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,24 +1,29 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+
+import java.util.HashMap;
public class StructureMapping
{
@@ -32,11 +37,19 @@ public class StructureMapping
String pdbchain;
- // Mapping index 0 is resNum, index 1 is atomNo
- int[][] mapping;
+ 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 mapping;
public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
- String chain, int[][] mapping, String mappingDetails)
+ String chain, HashMap mapping,
+ String mappingDetails)
{
sequence = seq;
this.pdbfile = pdbfile;
@@ -61,39 +74,99 @@ public class StructureMapping
return pdbid;
}
+ /**
+ *
+ * @param seqpos
+ * @return 0 or corresponding atom number for the sequence position
+ */
public int getAtomNum(int seqpos)
{
- if (mapping.length > seqpos)
+ int[] resNumAtomMap = mapping.get(seqpos);
+ if (resNumAtomMap != null)
{
- return mapping[seqpos][1];
+ return resNumAtomMap[PDB_ATOM_NUM_INDEX];
}
else
{
- return 0;
+ return UNASSIGNED_VALUE;
}
}
+ /**
+ *
+ * @param seqpos
+ * @return 0 or the corresponding residue number for the sequence position
+ */
public int getPDBResNum(int seqpos)
{
- if (mapping.length > seqpos)
+ int[] resNumAtomMap = mapping.get(seqpos);
+ if (resNumAtomMap != null)
{
- return mapping[seqpos][0];
+ return resNumAtomMap[PDB_RES_NUM_INDEX];
}
else
{
- return 0;
+ return UNASSIGNED_VALUE;
}
}
+ /**
+ *
+ * @param pdbResNum
+ * @return -1 or the corresponding sequence position for a pdb residue number
+ */
public int getSeqPos(int pdbResNum)
{
- for (int i = 0; i < mapping.length; i++)
+ for (Integer seqPos : mapping.keySet())
{
- if (mapping[i][0] == pdbResNum)
+ if (pdbResNum == getPDBResNum(seqPos))
{
- return i;
+ return seqPos;
}
}
- return -1;
+ 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 getMapping()
+ {
+ return mapping;
}
}