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