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.varna;
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.StructureSelectionManager;
26 import jalview.util.Comparison;
28 import java.awt.Color;
29 import java.util.ArrayList;
32 * Routines for generating Jmol commands for Jalview/Jmol binding another
38 public class VarnaCommands
42 * Jmol utility which constructs the commands to colour chains by the given
46 public static String[] getColourBySequenceCommand(
47 StructureSelectionManager ssm, String[] files,
48 SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
51 ArrayList<String> str = new ArrayList<String>();
52 StringBuffer command = new StringBuffer();
54 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
56 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
58 if (mapping == null || mapping.length < 1)
62 for (int s = 0; s < sequence[pdbfnum].length; s++)
64 for (int sp, m = 0; m < mapping.length; m++)
66 if (mapping[m].getSequence() == sequence[pdbfnum][s]
67 && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
69 SequenceI asp = alignment.getSequenceAt(sp);
70 for (int r = 0; r < asp.getLength(); r++)
72 // no mapping to gaps in sequence
73 if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
77 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
79 if (pos < 1 || pos == lastPos)
84 Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
87 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
88 String newSelcom = (mapping[m].getChain() != " " ? ":"
89 + mapping[m].getChain() : "")
98 + col.getBlue() + "]";
99 if (command.length() > newSelcom.length()
100 && command.substring(
101 command.length() - newSelcom.length())
104 command = VarnaCommands.condenseCommand(command, pos);
107 // TODO: deal with case when buffer is too large for Jmol to parse
108 // - execute command and flush
111 if (command.length() > 51200)
114 str.add(command.toString());
115 command.setLength(0);
117 command.append("select " + pos);
118 command.append(newSelcom);
127 str.add(command.toString());
128 command.setLength(0);
130 return str.toArray(new String[str.size()]);
133 public static StringBuffer condenseCommand(StringBuffer command, int pos)
136 // work back to last 'select'
137 int p = command.length(), q = p;
146 } while ((q = command.indexOf("select", p)) == -1 && p > 0);
148 StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
150 command = command.delete(0, q + 7);
154 if (command.indexOf("-") > -1)
156 start = command.substring(0, command.indexOf("-"));
160 start = command.substring(0, command.indexOf(":"));
163 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));