X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureMapping.java;h=78634e06d0dee01b9b95f8e570a2bb2831ca2f9e;hb=51e084651cb62b4d7597b2b448c8529d3ab60cca;hp=06e6bc3507f528ac69d7430b6552bd81f773a78d;hpb=6905363d02254a557f93f66a2b69d85aa0b23696;p=jalview.git
diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 06e6bc3..78634e0 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,100 +1,172 @@
-/*
- * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.structure;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+
+import java.util.HashMap;
+
+public class StructureMapping
+{
+ String mappingDetails;
+
+ SequenceI sequence;
+
+ String pdbfile;
+
+ String pdbid;
+
+ 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 mapping;
+
+ public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
+ String chain, HashMap 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;
+ }
+
+ /**
+ *
+ * @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 0 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;
+ }
+ }
+
+ /**
+ *
+ * @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 getMapping()
+ {
+ return mapping;
+ }
+}