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.SequenceRendererI;
  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, SequenceRendererI 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       StringBuffer command = new StringBuffer();
  72       List<String> str = new ArrayList<>();
  73
  74       if (mapping == null || mapping.length < 1)
  75       {
  76         continue;
  77       }
  78
  79       for (int s = 0; s < sequence[pdbfnum].length; s++)
  80       {
  81         for (int sp, m = 0; m < mapping.length; m++)
  82         {
  83           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  84                   && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
  85           {
  86             int lastPos = StructureMapping.UNASSIGNED_VALUE;
  87             SequenceI asp = al.getSequenceAt(sp);
  88             for (int r = 0; r < asp.getLength(); r++)
  89             {
  90               // no mapping to gaps in sequence
  91               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  92               {
  93                 continue;
  94               }
  95               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  96
  97               if (pos == lastPos)
  98               {
  99                 continue;
 100               }
 101               if (pos == StructureMapping.UNASSIGNED_VALUE)
 102               {
 103                 // terminate current colour op
 104                 if (command.length() > 0
 105                         && command.charAt(command.length() - 1) != ';')
 106                 {
 107                   command.append(";");
 108                 }
 109                 // reset lastPos
 110                 lastPos = StructureMapping.UNASSIGNED_VALUE;
 111                 continue;
 112               }
 113
 114               lastPos = pos;
 115
 116               Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
 117                       finder);
 118
 119               /*
 120                * shade hidden regions darker
 121                */
 122               if (!cs.isVisible(r))
 123               {
 124                 col = Color.GRAY;
 125               }
 126
 127               String newSelcom = (mapping[m].getChain() != " "
 128                       ? ":" + mapping[m].getChain()
 129                       : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
 130                       + col.getRed() + "," + col.getGreen() + ","
 131                       + col.getBlue() + "]";
 132               if (command.length() > newSelcom.length() && command
 133                       .substring(command.length() - newSelcom.length())
 134                       .equals(newSelcom))
 135               {
 136                 command = JmolCommands.condenseCommand(command, pos);
 137                 continue;
 138               }
 139               // TODO: deal with case when buffer is too large for Jmol to parse
 140               // - execute command and flush
 141
 142               if (command.length() > 0
 143                       && command.charAt(command.length() - 1) != ';')
 144               {
 145                 command.append(";");
 146               }
 147
 148               if (command.length() > 51200)
 149               {
 150                 // add another chunk
 151                 str.add(command.toString());
 152                 command.setLength(0);
 153               }
 154               command.append("select " + pos);
 155               command.append(newSelcom);
 156             }
 157             // break;
 158           }
 159         }
 160       }
 161       {
 162         // add final chunk
 163         str.add(command.toString());
 164         command.setLength(0);
 165       }
 166       // Finally, add the command set ready to be returned.
 167       cset.add(new StructureMappingcommandSet(JmolCommands.class,
 168               files[pdbfnum], str.toArray(new String[str.size()])));
 169
 170     }
 171     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
 172   }
 173
 174   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 175   {
 176
 177     // work back to last 'select'
 178     int p = command.length(), q = p;
 179     do
 180     {
 181       p -= 6;
 182       if (p < 1)
 183       {
 184         p = 0;
 185       }
 186       ;
 187     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 188
 189     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 190
 191     command = command.delete(0, q + 7);
 192
 193     String start;
 194
 195     if (command.indexOf("-") > -1)
 196     {
 197       start = command.substring(0, command.indexOf("-"));
 198     }
 199     else
 200     {
 201       start = command.substring(0, command.indexOf(":"));
 202     }
 203
 204     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 205
 206     return sb;
 207   }
 208
 209 }