src/jalview/ext/jmol/JmolCommands.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   3  * Copyright (C) 2014 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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.ext.jmol;
  20
  21 import jalview.api.FeatureRenderer;
  22 import jalview.api.SequenceRenderer;
  23 import jalview.datamodel.AlignmentI;
  24 import jalview.datamodel.SequenceI;
  25 import jalview.structure.StructureMapping;
  26 import jalview.structure.StructureMappingcommandSet;
  27 import jalview.structure.StructureSelectionManager;
  28
  29 import java.awt.Color;
  30 import java.util.ArrayList;
  31
  32 /**
  33  * Routines for generating Jmol commands for Jalview/Jmol binding another
  34  * cruisecontrol test.
  35  *
  36  * @author JimP
  37  *
  38  */
  39 public class JmolCommands
  40 {
  41
  42   /**
  43    * Jmol utility which constructs the commands to colour chains by the given
  44    * alignment
  45    *
  46    * @returns Object[] { Object[] { <model being coloured>,
  47    *
  48    */
  49   public static StructureMappingcommandSet[] getColourBySequenceCommand(
  50           StructureSelectionManager ssm, String[] files,
  51           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
  52           AlignmentI alignment)
  53   {
  54
  55     ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
  56
  57     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
  58     {
  59       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  60       StringBuffer command = new StringBuffer();
  61       StructureMappingcommandSet smc;
  62       ArrayList<String> str = new ArrayList<String>();
  63
  64       if (mapping == null || mapping.length < 1)
  65         continue;
  66
  67       int lastPos = -1;
  68       for (int s = 0; s < sequence[pdbfnum].length; s++)
  69       {
  70         for (int sp, m = 0; m < mapping.length; m++)
  71         {
  72           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  73                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
  74           {
  75             SequenceI asp = alignment.getSequenceAt(sp);
  76             for (int r = 0; r < asp.getLength(); r++)
  77             {
  78               // no mapping to gaps in sequence
  79               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  80               {
  81                 continue;
  82               }
  83               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  84
  85               if (pos < 1 || pos == lastPos)
  86                 continue;
  87
  88               lastPos = pos;
  89
  90               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  91
  92               if (fr != null)
  93                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
  94               String newSelcom = (mapping[m].getChain() != " " ? ":"
  95                       + mapping[m].getChain() : "")
  96                       + "/"
  97                       + (pdbfnum + 1)
  98                       + ".1"
  99                       + ";color["
 100                       + col.getRed()
 101                       + ","
 102                       + col.getGreen()
 103                       + ","
 104                       + col.getBlue() + "]";
 105               if (command.length() > newSelcom.length()
 106                       && command.substring(
 107                               command.length() - newSelcom.length())
 108                               .equals(newSelcom))
 109               {
 110                 command = JmolCommands.condenseCommand(command, pos);
 111                 continue;
 112               }
 113               // TODO: deal with case when buffer is too large for Jmol to parse
 114               // - execute command and flush
 115
 116               command.append(";");
 117               if (command.length() > 51200)
 118               {
 119                 // add another chunk
 120                 str.add(command.toString());
 121                 command.setLength(0);
 122               }
 123               command.append("select " + pos);
 124               command.append(newSelcom);
 125             }
 126             break;
 127           }
 128         }
 129       }
 130       {
 131         // add final chunk
 132         str.add(command.toString());
 133         command.setLength(0);
 134       }
 135       // Finally, add the command set ready to be returned.
 136       cset.add(new StructureMappingcommandSet(JmolCommands.class,
 137               files[pdbfnum], str.toArray(new String[str.size()])));
 138
 139     }
 140     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
 141   }
 142
 143   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 144   {
 145
 146     // work back to last 'select'
 147     int p = command.length(), q = p;
 148     do
 149     {
 150       p -= 6;
 151       if (p < 1)
 152       {
 153         p = 0;
 154       }
 155       ;
 156     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 157
 158     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 159
 160     command = command.delete(0, q + 7);
 161
 162     String start;
 163
 164     if (command.indexOf("-") > -1)
 165     {
 166       start = command.substring(0, command.indexOf("-"));
 167     }
 168     else
 169     {
 170       start = command.substring(0, command.indexOf(":"));
 171     }
 172
 173     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 174
 175     return sb;
 176   }
 177
 178 }