-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.structure;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class StructureMapping\r
-{\r
- String mappingDetails;\r
- SequenceI sequence;\r
- String pdbfile;\r
- String pdbid;\r
- String pdbchain;\r
-\r
- //Mapping index 0 is resNum, index 1 is atomNo\r
- int[][] mapping;\r
-\r
- public StructureMapping(SequenceI seq,\r
- String pdbfile,\r
- String pdbid,\r
- String chain,\r
- int[][] mapping,\r
- String mappingDetails)\r
- {\r
- sequence = seq;\r
- this.pdbfile = pdbfile;\r
- this.pdbid = pdbid;\r
- this.pdbchain = chain;\r
- this.mapping = mapping;\r
- this.mappingDetails = mappingDetails;\r
- }\r
-\r
- public SequenceI getSequence()\r
- {\r
- return sequence;\r
- }\r
-\r
- public String getChain()\r
- {\r
- return pdbchain;\r
- }\r
-\r
- public String getPdbId()\r
- {\r
- return pdbid;\r
- }\r
-\r
- public int getAtomNum(int seqpos)\r
- {\r
- if (mapping.length > seqpos)\r
- {\r
- return mapping[seqpos][1];\r
- }\r
- else\r
- {\r
- return 0;\r
- }\r
- }\r
-\r
- public int getPDBResNum(int seqpos)\r
- {\r
- if (mapping.length > seqpos)\r
- {\r
- return mapping[seqpos][0];\r
- }\r
- else\r
- {\r
- return 0;\r
- }\r
- }\r
-\r
- public int getSeqPos(int pdbResNum)\r
- {\r
- for (int i = 0; i < mapping.length; i++)\r
- {\r
- if (mapping[i][0] == pdbResNum)\r
- {\r
- return i;\r
- }\r
- }\r
- return -1;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.SequenceI;
+
+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;
+ }
+
+ /**
+ *
+ * @param seqpos
+ * @return 0 or corresponding atom number for the sequence position
+ */
+ public int getAtomNum(int seqpos)
+ {
+ if (mapping.length > seqpos)
+ {
+ return mapping[seqpos][1];
+ }
+ else
+ {
+ return 0;
+ }
+ }
+
+ /**
+ *
+ * @param seqpos
+ * @return 0 or the corresponding residue number for the sequence position
+ */
+ public int getPDBResNum(int seqpos)
+ {
+ if (mapping.length > seqpos)
+ {
+ return mapping[seqpos][0];
+ }
+ else
+ {
+ return 0;
+ }
+ }
+
+ /**
+ *
+ * @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++)
+ {
+ if (mapping[i][0] == pdbResNum)
+ {
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ /**
+ * 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff