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