--- /dev/null
+/*
+ * 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.ext.rbvi.chimera;
+
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Format;
+
+import java.awt.Color;
+import java.util.ArrayList;
+
+/**
+ * Routines for generating Chimera commands for Jalview/Chimera binding
+ *
+ * @author JimP
+ *
+ */
+public class ChimeraCommands
+{
+
+ /**
+ * utility to construct the commands to colour chains by the given alignment
+ * for passing to Chimera
+ *
+ * @returns Object[] { Object[] { <model being coloured>,
+ *
+ */
+ public static StructureMappingcommandSet[] getColourBySequenceCommand(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment)
+ {
+
+ ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ float cols[] = new float[4];
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ StringBuffer command = new StringBuffer();
+ StructureMappingcommandSet smc;
+ ArrayList<String> str = new ArrayList<String>();
+
+ if (mapping == null || mapping.length < 1)
+ continue;
+
+ int startPos = -1, lastPos = -1, startModel = -1, lastModel = -1;
+ String startChain = "", lastChain = "";
+ Color lastCol = null;
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
+ {
+ for (int sp, m = 0; m < mapping.length; m++)
+ {
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+ {
+ SequenceI asp = alignment.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
+ {
+ // no mapping to gaps in sequence
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+
+ if (pos < 1 || pos == lastPos)
+ continue;
+
+ Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+
+ if (fr != null)
+ col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+ if (lastCol != col || lastPos + 1 != pos
+ || pdbfnum != lastModel
+ || !mapping[m].getChain().equals(lastChain))
+ {
+ if (lastCol != null)
+ {
+
+ lastCol.getRGBComponents(cols);
+ String newSelcom = "color " + cols[0] + "," + cols[1]
+ + "," + cols[2] + " #" + startModel + ":"
+ + startPos + "-" + lastPos + "." + lastChain;
+ if (str.size() > 0
+ && (str.get(str.size() - 1).length() + newSelcom
+ .length()) < 4096)
+ {
+ str.set(str.size() - 1, str.get(str.size() - 1) + ";"
+ + newSelcom);
+ }
+ else
+ {
+ str.add(newSelcom);
+ }
+ }
+ lastCol = null;
+ startPos = pos;
+ startModel = pdbfnum;
+ startChain = mapping[m].getChain();
+ }
+ lastCol = col;
+ lastPos = pos;
+ lastModel = pdbfnum;
+ lastChain = mapping[m].getChain();
+ }
+ // final colour range
+ if (lastCol != null)
+ {
+
+ lastCol.getRGBComponents(cols);
+ String newSelcom = "color " + cols[0] + "," + cols[1] + ","
+ + cols[2] + " #" + startModel + ":" + startPos + "-"
+ + lastPos + "." + lastChain;
+ if (str.size() > 0
+ && (str.get(str.size() - 1).length() + newSelcom
+ .length()) < 4096)
+ {
+ str.set(str.size() - 1, str.get(str.size() - 1) + ";"
+ + newSelcom);
+ }
+ else
+ {
+ str.add(newSelcom);
+ }
+ }
+ break;
+ }
+ }
+ }
+ // Finally, add the command set ready to be returned.
+ cset.add(new StructureMappingcommandSet(ChimeraCommands.class,
+ files[pdbfnum], str.toArray(new String[str.size()])));
+ }
+ return cset.toArray(new StructureMappingcommandSet[cset.size()]);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff