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.FeatureRenderer;
  25 import jalview.api.SequenceRenderer;
  26 import jalview.datamodel.AlignmentI;
  27 import jalview.datamodel.ColumnSelection;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.structure.StructureMapping;
  30 import jalview.structure.StructureMappingcommandSet;
  31 import jalview.structure.StructureSelectionManager;
  32
  33 import java.awt.Color;
  34 import java.util.ArrayList;
  35 import java.util.List;
  36
  37 /**
  38  * Routines for generating Jmol commands for Jalview/Jmol binding another
  39  * cruisecontrol test.
  40  *
  41  * @author JimP
  42  *
  43  */
  44 public class JmolCommands
  45 {
  46
  47   /**
  48    * Jmol utility which constructs the commands to colour chains by the given
  49    * alignment
  50    *
  51    * @returns Object[] { Object[] { <model being coloured>,
  52    *
  53    */
  54   public static StructureMappingcommandSet[] getColourBySequenceCommand(
  55           StructureSelectionManager ssm, String[] files,
  56           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
  57           AlignViewportI viewport)
  58   {
  59     ColumnSelection cs = viewport.getColumnSelection();
  60     AlignmentI al = viewport.getAlignment();
  61     List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
  62
  63     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
  64     {
  65       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  66       StringBuffer command = new StringBuffer();
  67       StructureMappingcommandSet smc;
  68       ArrayList<String> str = new ArrayList<String>();
  69
  70       if (mapping == null || mapping.length < 1)
  71       {
  72         continue;
  73       }
  74
  75       int lastPos = -1;
  76       for (int s = 0; s < sequence[pdbfnum].length; s++)
  77       {
  78         for (int sp, m = 0; m < mapping.length; m++)
  79         {
  80           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  81                   && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
  82           {
  83             SequenceI asp = al.getSequenceAt(sp);
  84             for (int r = 0; r < asp.getLength(); r++)
  85             {
  86               // no mapping to gaps in sequence
  87               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  88               {
  89                 continue;
  90               }
  91               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  92
  93               if (pos < 1 || pos == lastPos)
  94               {
  95                 continue;
  96               }
  97
  98               lastPos = pos;
  99
 100               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 101
 102               if (fr != null)
 103               {
 104                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
 105               }
 106
 107               /*
 108                * shade hidden regions darker
 109                */
 110               if (!cs.isVisible(r))
 111               {
 112                 // col = ColorUtils.darkerThan(col);
 113                 col = Color.GRAY;
 114               }
 115
 116               String newSelcom = (mapping[m].getChain() != " " ? ":"
 117                       + mapping[m].getChain() : "")
 118                       + "/"
 119                       + (pdbfnum + 1)
 120                       + ".1"
 121                       + ";color["
 122                       + col.getRed()
 123                       + ","
 124                       + col.getGreen()
 125                       + ","
 126                       + col.getBlue() + "]";
 127               if (command.length() > newSelcom.length()
 128                       && command.substring(
 129                               command.length() - newSelcom.length())
 130                               .equals(newSelcom))
 131               {
 132                 command = JmolCommands.condenseCommand(command, pos);
 133                 continue;
 134               }
 135               // TODO: deal with case when buffer is too large for Jmol to parse
 136               // - execute command and flush
 137
 138               command.append(";");
 139               if (command.length() > 51200)
 140               {
 141                 // add another chunk
 142                 str.add(command.toString());
 143                 command.setLength(0);
 144               }
 145               command.append("select " + pos);
 146               command.append(newSelcom);
 147             }
 148             // break;
 149           }
 150         }
 151       }
 152       {
 153         // add final chunk
 154         str.add(command.toString());
 155         command.setLength(0);
 156       }
 157       // Finally, add the command set ready to be returned.
 158       cset.add(new StructureMappingcommandSet(JmolCommands.class,
 159               files[pdbfnum], str.toArray(new String[str.size()])));
 160
 161     }
 162     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
 163   }
 164
 165   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 166   {
 167
 168     // work back to last 'select'
 169     int p = command.length(), q = p;
 170     do
 171     {
 172       p -= 6;
 173       if (p < 1)
 174       {
 175         p = 0;
 176       }
 177       ;
 178     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 179
 180     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 181
 182     command = command.delete(0, q + 7);
 183
 184     String start;
 185
 186     if (command.indexOf("-") > -1)
 187     {
 188       start = command.substring(0, command.indexOf("-"));
 189     }
 190     else
 191     {
 192       start = command.substring(0, command.indexOf(":"));
 193     }
 194
 195     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 196
 197     return sb;
 198   }
 199
 200 }