src/jalview/ext/jmol/JmolCommands.java

   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   public static StructureMappingcommandSet[] getColourBySequenceCommand(
  57           StructureSelectionManager ssm, String[] files,
  58           SequenceI[][] sequence, SequenceRenderer sr,
  59           AlignmentViewPanel viewPanel)
  60   {
  61     FeatureRenderer fr = viewPanel.getFeatureRenderer();
  62     FeatureColourFinder finder = new FeatureColourFinder(fr);
  63     AlignViewportI viewport = viewPanel.getAlignViewport();
  64     HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
  65     AlignmentI al = viewport.getAlignment();
  66     List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
  67
  68     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
  69     {
  70       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  71       StringBuilder command = new StringBuilder();
  72       StructureMappingcommandSet smc;
  73       ArrayList<String> str = new ArrayList<String>();
  74
  75       if (mapping == null || mapping.length < 1)
  76       {
  77         continue;
  78       }
  79
  80       for (int s = 0; s < sequence[pdbfnum].length; s++)
  81       {
  82         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             int lastPos = StructureMapping.UNASSIGNED_VALUE;
  88             SequenceI asp = al.getSequenceAt(sp);
  89             for (int r = 0; r < asp.getLength(); r++)
  90             {
  91               // no mapping to gaps in sequence
  92               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  93               {
  94                 continue;
  95               }
  96               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  97
  98               if (pos == lastPos)
  99               {
 100                 continue;
 101               }
 102               if (pos == StructureMapping.UNASSIGNED_VALUE)
 103               {
 104                 // terminate current colour op
 105                 if (command.length() > 0
 106                         && command.charAt(command.length() - 1) != ';')
 107                 {
 108                   command.append(";");
 109                 }
 110                 // reset lastPos
 111                 lastPos = StructureMapping.UNASSIGNED_VALUE;
 112                 continue;
 113               }
 114
 115               lastPos = pos;
 116
 117               Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
 118                       finder);
 119
 120               /*
 121                * shade hidden regions darker
 122                */
 123               if (!cs.isVisible(r))
 124               {
 125                 col = Color.GRAY;
 126               }
 127
 128               // todo JAL-3152 handle 'no chain' case without errors
 129               boolean hasChain = true || mapping[m].getChain() != " ";
 130                           String chainSpec = hasChain
 131                       ? ":" + mapping[m].getChain()
 132                       : "";
 133                           String newSelcom = chainSpec + "/" + (pdbfnum + 1) + ".1" + ";color["
 134                       + col.getRed() + "," + col.getGreen() + ","
 135                       + col.getBlue() + "]";
 136               if (command.length() > newSelcom.length() && command
 137                       .substring(command.length() - newSelcom.length())
 138                       .equals(newSelcom))
 139               {
 140                 command = JmolCommands.condenseCommand(command, pos);
 141                 continue;
 142               }
 143               // TODO: deal with case when buffer is too large for Jmol to parse
 144               // - execute command and flush
 145
 146               if (command.length() > 0
 147                       && command.charAt(command.length() - 1) != ';')
 148               {
 149                 command.append(";");
 150               }
 151
 152               if (command.length() > 51200)
 153               {
 154                 // add another chunk
 155                 str.add(command.toString());
 156                 command.setLength(0);
 157               }
 158               command.append("select " + pos);
 159               command.append(newSelcom);
 160             }
 161             // break;
 162           }
 163         }
 164       }
 165       {
 166         // add final chunk
 167         str.add(command.toString());
 168         command.setLength(0);
 169       }
 170       // Finally, add the command set ready to be returned.
 171       cset.add(new StructureMappingcommandSet(JmolCommands.class,
 172               files[pdbfnum], str.toArray(new String[str.size()])));
 173
 174     }
 175     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
 176   }
 177
 178   public static StringBuilder condenseCommand(StringBuilder command, int pos)
 179   {
 180
 181     // work back to last 'select'
 182     int p = command.length(), q = p;
 183     do
 184     {
 185       p -= 6;
 186       if (p < 1)
 187       {
 188         p = 0;
 189       }
 190       ;
 191     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 192
 193     StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
 194
 195     command = command.delete(0, q + 7);
 196
 197     String start;
 198
 199     if (command.indexOf("-") > -1)
 200     {
 201       start = command.substring(0, command.indexOf("-"));
 202     }
 203     else
 204     {
 205       start = command.substring(0, command.indexOf(":"));
 206     }
 207
 208     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 209
 210     return sb;
 211   }
 212
 213 }