2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.jmol;
23 import jalview.api.FeatureRenderer;
24 import jalview.api.SequenceRenderer;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.SequenceI;
27 import jalview.structure.StructureMapping;
28 import jalview.structure.StructureMappingcommandSet;
29 import jalview.structure.StructureSelectionManager;
30 import jalview.util.Comparison;
32 import java.awt.Color;
33 import java.util.ArrayList;
36 * Routines for generating Jmol commands for Jalview/Jmol binding another
42 public class JmolCommands
46 * Jmol utility which constructs the commands to colour chains by the given
49 * @returns Object[] { Object[] { <model being coloured>,
52 public static StructureMappingcommandSet[] getColourBySequenceCommand(
53 StructureSelectionManager ssm, String[] files,
54 SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
58 ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
60 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
62 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
63 StringBuffer command = new StringBuffer();
64 StructureMappingcommandSet smc;
65 ArrayList<String> str = new ArrayList<String>();
67 if (mapping == null || mapping.length < 1)
73 for (int s = 0; s < sequence[pdbfnum].length; s++)
75 for (int sp, m = 0; m < mapping.length; m++)
77 if (mapping[m].getSequence() == sequence[pdbfnum][s]
78 && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
80 SequenceI asp = alignment.getSequenceAt(sp);
81 for (int r = 0; r < asp.getLength(); r++)
83 // no mapping to gaps in sequence
84 if (Comparison.isGap(asp.getCharAt(r)))
88 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
90 if (pos < 1 || pos == lastPos)
97 Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
101 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
103 String newSelcom = (mapping[m].getChain() != " " ? ":"
104 + mapping[m].getChain() : "")
113 + col.getBlue() + "]";
114 if (command.length() > newSelcom.length()
115 && command.substring(
116 command.length() - newSelcom.length())
119 command = JmolCommands.condenseCommand(command, pos);
122 // TODO: deal with case when buffer is too large for Jmol to parse
123 // - execute command and flush
126 if (command.length() > 51200)
129 str.add(command.toString());
130 command.setLength(0);
132 command.append("select " + pos);
133 command.append(newSelcom);
141 str.add(command.toString());
142 command.setLength(0);
144 // Finally, add the command set ready to be returned.
145 cset.add(new StructureMappingcommandSet(JmolCommands.class,
146 files[pdbfnum], str.toArray(new String[str.size()])));
149 return cset.toArray(new StructureMappingcommandSet[cset.size()]);
152 public static StringBuffer condenseCommand(StringBuffer command, int pos)
155 // work back to last 'select'
156 int p = command.length(), q = p;
165 } while ((q = command.indexOf("select", p)) == -1 && p > 0);
167 StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
169 command = command.delete(0, q + 7);
173 if (command.indexOf("-") > -1)
175 start = command.substring(0, command.indexOf("-"));
179 start = command.substring(0, command.indexOf(":"));
182 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));