2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.ext.jmol;
20 import jalview.api.FeatureRenderer;
21 import jalview.api.SequenceRenderer;
22 import jalview.datamodel.AlignmentI;
23 import jalview.datamodel.SequenceI;
24 import jalview.structure.StructureMapping;
25 import jalview.structure.StructureMappingcommandSet;
26 import jalview.structure.StructureSelectionManager;
28 import java.awt.Color;
29 import java.util.ArrayList;
32 * Routines for generating Jmol commands for Jalview/Jmol binding another
38 public class JmolCommands
42 * Jmol utility which constructs the commands to colour chains by the given
45 * @returns Object[] { Object[] { <model being coloured>,
48 public static StructureMappingcommandSet[] getColourBySequenceCommand(
49 StructureSelectionManager ssm, String[] files,
50 SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
54 ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
56 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
58 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
59 StringBuffer command = new StringBuffer();
60 StructureMappingcommandSet smc;
61 ArrayList<String> str = new ArrayList<String>();
63 if (mapping == null || mapping.length < 1)
67 for (int s = 0; s < sequence[pdbfnum].length; s++)
69 for (int sp, m = 0; m < mapping.length; m++)
71 if (mapping[m].getSequence() == sequence[pdbfnum][s]
72 && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
74 SequenceI asp = alignment.getSequenceAt(sp);
75 for (int r = 0; r < asp.getLength(); r++)
77 // no mapping to gaps in sequence
78 if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
82 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
84 if (pos < 1 || pos == lastPos)
89 Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
92 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
93 String newSelcom = (mapping[m].getChain() != " " ? ":"
94 + mapping[m].getChain() : "")
103 + col.getBlue() + "]";
104 if (command.length() > newSelcom.length()
105 && command.substring(
106 command.length() - newSelcom.length())
109 command = JmolCommands.condenseCommand(command, pos);
112 // TODO: deal with case when buffer is too large for Jmol to parse
113 // - execute command and flush
116 if (command.length() > 51200)
119 str.add(command.toString());
120 command.setLength(0);
122 command.append("select " + pos);
123 command.append(newSelcom);
131 str.add(command.toString());
132 command.setLength(0);
134 // Finally, add the command set ready to be returned.
135 cset.add(new StructureMappingcommandSet(JmolCommands.class,
136 files[pdbfnum], str.toArray(new String[str.size()])));
139 return cset.toArray(new StructureMappingcommandSet[cset.size()]);
142 public static StringBuffer condenseCommand(StringBuffer command, int pos)
145 // work back to last 'select'
146 int p = command.length(), q = p;
155 } while ((q = command.indexOf("select", p)) == -1 && p > 0);
157 StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
159 command = command.delete(0, q + 7);
163 if (command.indexOf("-") > -1)
165 start = command.substring(0, command.indexOf("-"));
169 start = command.substring(0, command.indexOf(":"));
172 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));