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 import jalview.structures.models.AAStructureBindingModel;
  35
  36 import java.awt.Color;
  37 import java.util.ArrayList;
  38 import java.util.List;
  39
  40 /**
  41  * Routines for generating Jmol commands for Jalview/Jmol binding another
  42  * cruisecontrol test.
  43  *
  44  * @author JimP
  45  *
  46  */
  47 public class JmolCommands
  48 {
  49
  50   /**
  51    * Jmol utility which constructs the commands to colour chains by the given
  52    * alignment
  53    *
  54    * @returns Object[] { Object[] { <model being coloured>,
  55    *
  56    */
  57   public static StructureMappingcommandSet[] getColourBySequenceCommand(
  58           StructureSelectionManager ssm, String[] files,
  59           AAStructureBindingModel binding, AlignmentViewPanel viewPanel)
  60   {
  61     SequenceRenderer sr = binding.getSequenceRenderer(viewPanel);
  62     SequenceI[][] sequence = binding.getSequence();
  63     return getColourBySequenceCommand(ssm, files, sequence, sr, viewPanel);
  64   }
  65
  66   public static StructureMappingcommandSet[] getColourBySequenceCommand(
  67           StructureSelectionManager ssm, String[] files,
  68           SequenceI[][] sequence, SequenceRenderer sr,
  69           AlignmentViewPanel viewPanel)
  70   {
  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<>();
  77
  78     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
  79     {
  80       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  81       StringBuffer command = new StringBuffer();
  82       StructureMappingcommandSet smc;
  83       ArrayList<String> str = new ArrayList<>();
  84
  85       if (mapping == null || mapping.length < 1)
  86       {
  87         continue;
  88       }
  89
  90       for (int s = 0; s < sequence[pdbfnum].length; s++)
  91       {
  92         for (int sp, m = 0; m < mapping.length; m++)
  93         {
  94           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  95                   && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
  96           {
  97             int lastPos = StructureMapping.UNASSIGNED_VALUE;
  98             SequenceI asp = al.getSequenceAt(sp);
  99             for (int r = 0; r < asp.getLength(); r++)
 100             {
 101               // no mapping to gaps in sequence
 102               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
 103               {
 104                 continue;
 105               }
 106               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 107
 108               if (pos == lastPos)
 109               {
 110                 continue;
 111               }
 112               if (pos == StructureMapping.UNASSIGNED_VALUE)
 113               {
 114                 // terminate current colour op
 115                 if (command.length() > 0
 116                         && command.charAt(command.length() - 1) != ';')
 117                 {
 118                   command.append(";");
 119                 }
 120                 // reset lastPos
 121                 lastPos = StructureMapping.UNASSIGNED_VALUE;
 122                 continue;
 123               }
 124
 125               lastPos = pos;
 126
 127               Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
 128                       finder);
 129
 130               /*
 131                * shade hidden regions darker
 132                */
 133               if (!cs.isVisible(r))
 134               {
 135                 col = Color.GRAY;
 136               }
 137
 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())
 145                       .equals(newSelcom))
 146               {
 147                 command = JmolCommands.condenseCommand(command, pos);
 148                 continue;
 149               }
 150               // TODO: deal with case when buffer is too large for Jmol to parse
 151               // - execute command and flush
 152
 153               if (command.length() > 0
 154                       && command.charAt(command.length() - 1) != ';')
 155               {
 156                 command.append(";");
 157               }
 158
 159               if (command.length() > 51200)
 160               {
 161                 // add another chunk
 162                 str.add(command.toString());
 163                 command.setLength(0);
 164               }
 165               command.append("select " + pos);
 166               command.append(newSelcom);
 167             }
 168             // break;
 169           }
 170         }
 171       }
 172       {
 173         // add final chunk
 174         str.add(command.toString());
 175         command.setLength(0);
 176       }
 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()])));
 180
 181     }
 182     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
 183   }
 184
 185   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 186   {
 187
 188     // work back to last 'select'
 189     int p = command.length(), q = p;
 190     do
 191     {
 192       p -= 6;
 193       if (p < 1)
 194       {
 195         p = 0;
 196       }
 197       ;
 198     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 199
 200     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 201
 202     command = command.delete(0, q + 7);
 203
 204     String start;
 205
 206     if (command.indexOf("-") > -1)
 207     {
 208       start = command.substring(0, command.indexOf("-"));
 209     }
 210     else
 211     {
 212       start = command.substring(0, command.indexOf(":"));
 213     }
 214
 215     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 216
 217     return sb;
 218   }
 219
 220 }