jalviewX
File JmolCommands.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| JmolCommands | 46 | 62 | 26 | 19 |
Contributing tests
This file is covered by 4 tests.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 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. | |
| 11 | * | |
| 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. | |
| 16 | * | |
| 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. | |
| 20 | */ | |
| 21 | package jalview.ext.jmol; | |
| 22 | ||
| 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 | ||
| 35 | import java.awt.Color; | |
| 36 | import java.util.ArrayList; | |
| 37 | import java.util.List; | |
| 38 | ||
| 39 | /** | |
| 40 | * Routines for generating Jmol commands for Jalview/Jmol binding another | |
| 41 | * cruisecontrol test. | |
| 42 | * | |
| 43 | * @author JimP | |
| 44 | * | |
| 45 | */ | |
| 46 | public class JmolCommands | |
| 47 | { | |
| 48 | ||
| 49 | /** | |
| 50 | * Jmol utility which constructs the commands to colour chains by the given | |
| 51 | * alignment | |
| 52 | * | |
| 53 | * @returns Object[] { Object[] { <model being coloured>, | |
| 54 | * | |
| 55 | */ | |
| 56 | 11 |  public static StructureMappingcommandSet[] getColourBySequenceCommand( |
| 57 | StructureSelectionManager ssm, String[] files, | |
| 58 | SequenceI[][] sequence, SequenceRenderer sr, | |
| 59 | AlignmentViewPanel viewPanel) | |
| 60 | { | |
| 61 | 11 | FeatureRenderer fr = viewPanel.getFeatureRenderer(); |
| 62 | 11 | FeatureColourFinder finder = new FeatureColourFinder(fr); |
| 63 | 11 | AlignViewportI viewport = viewPanel.getAlignViewport(); |
| 64 | 11 | HiddenColumns cs = viewport.getAlignment().getHiddenColumns(); |
| 65 | 11 | AlignmentI al = viewport.getAlignment(); |
| 66 | 11 | List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>(); |
| 67 | ||
| 68 | 26 | for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
| 69 | { | |
| 70 | 15 | StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); |
| 71 | 15 | StringBuffer command = new StringBuffer(); |
| 72 | 15 | StructureMappingcommandSet smc; |
| 73 | 15 | ArrayList<String> str = new ArrayList<String>(); |
| 74 | ||
| 75 | 15 | if (mapping == null || mapping.length < 1) |
| 76 | { | |
| 77 | 2 | continue; |
| 78 | } | |
| 79 | ||
| 80 | 26 | for (int s = 0; s < sequence[pdbfnum].length; s++) |
| 81 | { | |
| 82 | 27 | for (int sp, m = 0; m < mapping.length; m++) |
| 83 | { | |
| 84 | ? | if (mapping[m].getSequence() == sequence[pdbfnum][s] |
| 85 | && (sp = al.findIndex(sequence[pdbfnum][s])) > -1) | |
| 86 | { | |
| 87 | 13 | int lastPos = StructureMapping.UNASSIGNED_VALUE; |
| 88 | 13 | SequenceI asp = al.getSequenceAt(sp); |
| 89 | 3291 | for (int r = 0; r < asp.getLength(); r++) |
| 90 | { | |
| 91 | // no mapping to gaps in sequence | |
| 92 | 3278 | if (jalview.util.Comparison.isGap(asp.getCharAt(r))) |
| 93 | { | |
| 94 | 0 | continue; |
| 95 | } | |
| 96 | 3278 | int pos = mapping[m].getPDBResNum(asp.findPosition(r)); |
| 97 | ||
| 98 | 3278 | if (pos == lastPos) |
| 99 | { | |
| 100 | 0 | continue; |
| 101 | } | |
| 102 | 3278 | if (pos == StructureMapping.UNASSIGNED_VALUE) |
| 103 | { | |
| 104 | // terminate current colour op | |
| 105 | 0 | if (command.length() > 0 |
| 106 | && command.charAt(command.length() - 1) != ';') | |
| 107 | { | |
| 108 | 0 | command.append(";"); |
| 109 | } | |
| 110 | // reset lastPos | |
| 111 | 0 | lastPos = StructureMapping.UNASSIGNED_VALUE; |
| 112 | 0 | continue; |
| 113 | } | |
| 114 | ||
| 115 | 3278 | lastPos = pos; |
| 116 | ||
| 117 | 3278 | Color col = sr.getResidueColour(sequence[pdbfnum][s], r, |
| 118 | finder); | |
| 119 | ||
| 120 | /* | |
| 121 | * shade hidden regions darker | |
| 122 | */ | |
| 123 | 3278 | if (!cs.isVisible(r)) |
| 124 | { | |
| 125 | 6 | col = Color.GRAY; |
| 126 | } | |
| 127 | ||
| 128 | 3278 | String newSelcom = (mapping[m].getChain() != " " |
| 129 | ? ":" + mapping[m].getChain() | |
| 130 | : "") + "/" + (pdbfnum + 1) + ".1" + ";color[" | |
| 131 | + col.getRed() + "," + col.getGreen() + "," | |
| 132 | + col.getBlue() + "]"; | |
| 133 | 3278 | if (command.length() > newSelcom.length() && command |
| 134 | .substring(command.length() - newSelcom.length()) | |
| 135 | .equals(newSelcom)) | |
| 136 | { | |
| 137 | 3259 | command = JmolCommands.condenseCommand(command, pos); |
| 138 | 3259 | continue; |
| 139 | } | |
| 140 | // TODO: deal with case when buffer is too large for Jmol to parse | |
| 141 | // - execute command and flush | |
| 142 | ||
| 143 | 19 | if (command.length() > 0 |
| 144 | && command.charAt(command.length() - 1) != ';') | |
| 145 | { | |
| 146 | 6 | command.append(";"); |
| 147 | } | |
| 148 | ||
| 149 | 19 | if (command.length() > 51200) |
| 150 | { | |
| 151 | // add another chunk | |
| 152 | 0 | str.add(command.toString()); |
| 153 | 0 | command.setLength(0); |
| 154 | } | |
| 155 | 19 | command.append("select " + pos); |
| 156 | 19 | command.append(newSelcom); |
| 157 | } | |
| 158 | // break; | |
| 159 | } | |
| 160 | } | |
| 161 | } | |
| 162 | { | |
| 163 | // add final chunk | |
| 164 | 13 | str.add(command.toString()); |
| 165 | 13 | command.setLength(0); |
| 166 | } | |
| 167 | // Finally, add the command set ready to be returned. | |
| 168 | 13 | cset.add(new StructureMappingcommandSet(JmolCommands.class, |
| 169 | files[pdbfnum], str.toArray(new String[str.size()]))); | |
| 170 | ||
| 171 | } | |
| 172 | 11 | return cset.toArray(new StructureMappingcommandSet[cset.size()]); |
| 173 | } | |
| 174 | ||
| 175 | 3259 | public static StringBuffer condenseCommand(StringBuffer command, int pos) |
| 176 | { | |
| 177 | ||
| 178 | // work back to last 'select' | |
| 179 | 3259 | int p = command.length(), q = p; |
| 180 | 3259 | do |
| 181 | { | |
| 182 | 22792 | p -= 6; |
| 183 | 22792 | if (p < 1) |
| 184 | { | |
| 185 | 3247 | p = 0; |
| 186 | } | |
| 187 | 22792 | ; |
| 188 | ? | } while ((q = command.indexOf("select", p)) == -1 && p > 0); |
| 189 | ||
| 190 | 3259 | StringBuffer sb = new StringBuffer(command.substring(0, q + 7)); |
| 191 | ||
| 192 | 3259 | command = command.delete(0, q + 7); |
| 193 | ||
| 194 | 3259 | String start; |
| 195 | ||
| 196 | 3259 | if (command.indexOf("-") > -1) |
| 197 | { | |
| 198 | 3244 | start = command.substring(0, command.indexOf("-")); |
| 199 | } | |
| 200 | else | |
| 201 | { | |
| 202 | 15 | start = command.substring(0, command.indexOf(":")); |
| 203 | } | |
| 204 | ||
| 205 | 3259 | sb.append(start + "-" + pos + command.substring(command.indexOf(":"))); |
| 206 | ||
| 207 | 3259 | return sb; |
| 208 | } | |
| 209 | ||
| 210 | } |