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.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.api.FeatureRenderer;
26 import jalview.api.SequenceRenderer;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.SequenceI;
30 import jalview.renderer.seqfeatures.FeatureColourFinder;
31 import jalview.structure.StructureMapping;
32 import jalview.structure.StructureMappingcommandSet;
33 import jalview.structure.StructureSelectionManager;
34 import jalview.structures.models.AAStructureBindingModel;
36 import java.awt.Color;
37 import java.util.ArrayList;
38 import java.util.List;
41 * Routines for generating Jmol commands for Jalview/Jmol binding another
47 public class JmolCommands
51 * Jmol utility which constructs the commands to colour chains by the given
54 * @returns Object[] { Object[] { <model being coloured>,
57 public static StructureMappingcommandSet[] getColourBySequenceCommand(
58 StructureSelectionManager ssm, String[] files,
59 AAStructureBindingModel binding, AlignmentViewPanel viewPanel)
61 SequenceRenderer sr = binding.getSequenceRenderer(viewPanel);
62 SequenceI[][] sequence = binding.getSequence();
63 return getColourBySequenceCommand(ssm, files, sequence, sr, viewPanel);
66 public static StructureMappingcommandSet[] getColourBySequenceCommand(
67 StructureSelectionManager ssm, String[] files,
68 SequenceI[][] sequence, SequenceRenderer sr,
69 AlignmentViewPanel viewPanel)
71 FeatureRenderer fr = viewPanel.getFeatureRenderer();
72 FeatureColourFinder finder = new FeatureColourFinder(fr);
73 AlignViewportI viewport = viewPanel.getAlignViewport();
74 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
75 AlignmentI al = viewport.getAlignment();
76 List<StructureMappingcommandSet> cset = new ArrayList<>();
78 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
80 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
81 StringBuffer command = new StringBuffer();
82 StructureMappingcommandSet smc;
83 ArrayList<String> str = new ArrayList<>();
85 if (mapping == null || mapping.length < 1)
90 for (int s = 0; s < sequence[pdbfnum].length; s++)
92 for (int sp, m = 0; m < mapping.length; m++)
94 if (mapping[m].getSequence() == sequence[pdbfnum][s]
95 && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
97 int lastPos = StructureMapping.UNASSIGNED_VALUE;
98 SequenceI asp = al.getSequenceAt(sp);
99 for (int r = 0; r < asp.getLength(); r++)
101 // no mapping to gaps in sequence
102 if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
106 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
112 if (pos == StructureMapping.UNASSIGNED_VALUE)
114 // terminate current colour op
115 if (command.length() > 0
116 && command.charAt(command.length() - 1) != ';')
121 lastPos = StructureMapping.UNASSIGNED_VALUE;
127 Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
131 * shade hidden regions darker
133 if (!cs.isVisible(r))
138 String newSelcom = (mapping[m].getChain() != " "
139 ? ":" + mapping[m].getChain()
140 : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
141 + col.getRed() + "," + col.getGreen() + ","
142 + col.getBlue() + "]";
143 if (command.length() > newSelcom.length() && command
144 .substring(command.length() - newSelcom.length())
147 command = JmolCommands.condenseCommand(command, pos);
150 // TODO: deal with case when buffer is too large for Jmol to parse
151 // - execute command and flush
153 if (command.length() > 0
154 && command.charAt(command.length() - 1) != ';')
159 if (command.length() > 51200)
162 str.add(command.toString());
163 command.setLength(0);
165 command.append("select " + pos);
166 command.append(newSelcom);
174 str.add(command.toString());
175 command.setLength(0);
177 // Finally, add the command set ready to be returned.
178 cset.add(new StructureMappingcommandSet(JmolCommands.class,
179 files[pdbfnum], str.toArray(new String[str.size()])));
182 return cset.toArray(new StructureMappingcommandSet[cset.size()]);
185 public static StringBuffer condenseCommand(StringBuffer command, int pos)
188 // work back to last 'select'
189 int p = command.length(), q = p;
198 } while ((q = command.indexOf("select", p)) == -1 && p > 0);
200 StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
202 command = command.delete(0, q + 7);
206 if (command.indexOf("-") > -1)
208 start = command.substring(0, command.indexOf("-"));
212 start = command.substring(0, command.indexOf(":"));
215 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));