src/jalview/ext/jmol/JmolCommands.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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  */
  18 package jalview.ext.jmol;
  19
  20 import jalview.api.FeatureRenderer;
  21 import jalview.api.SequenceRenderer;
  22 import jalview.datamodel.AlignmentI;
  23 import jalview.datamodel.SequenceI;
  24 import jalview.structure.StructureMapping;
  25 import jalview.structure.StructureMappingcommandSet;
  26 import jalview.structure.StructureSelectionManager;
  27
  28 import java.awt.Color;
  29 import java.util.ArrayList;
  30
  31 /**
  32  * Routines for generating Jmol commands for Jalview/Jmol binding another
  33  * cruisecontrol test.
  34  *
  35  * @author JimP
  36  *
  37  */
  38 public class JmolCommands
  39 {
  40
  41   /**
  42    * Jmol utility which constructs the commands to colour chains by the given
  43    * alignment
  44    *
  45    * @returns Object[] { Object[] { <model being coloured>,
  46    *
  47    */
  48   public static StructureMappingcommandSet[] getColourBySequenceCommand(
  49           StructureSelectionManager ssm, String[] files,
  50           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
  51           AlignmentI alignment)
  52   {
  53
  54     ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
  55
  56     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
  57     {
  58       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  59       StringBuffer command = new StringBuffer();
  60       StructureMappingcommandSet smc;
  61       ArrayList<String> str = new ArrayList<String>();
  62
  63       if (mapping == null || mapping.length < 1)
  64         continue;
  65
  66       int lastPos = -1;
  67       for (int s = 0; s < sequence[pdbfnum].length; s++)
  68       {
  69         for (int sp, m = 0; m < mapping.length; m++)
  70         {
  71           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  72                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
  73           {
  74             SequenceI asp = alignment.getSequenceAt(sp);
  75             for (int r = 0; r < asp.getLength(); r++)
  76             {
  77               // no mapping to gaps in sequence
  78               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  79               {
  80                 continue;
  81               }
  82               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  83
  84               if (pos < 1 || pos == lastPos)
  85                 continue;
  86
  87               lastPos = pos;
  88
  89               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  90
  91               if (fr != null)
  92                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
  93               String newSelcom = (mapping[m].getChain() != " " ? ":"
  94                       + mapping[m].getChain() : "")
  95                       + "/"
  96                       + (pdbfnum + 1)
  97                       + ".1"
  98                       + ";color["
  99                       + col.getRed()
 100                       + ","
 101                       + col.getGreen()
 102                       + ","
 103                       + col.getBlue() + "]";
 104               if (command.length() > newSelcom.length()
 105                       && command.substring(
 106                               command.length() - newSelcom.length())
 107                               .equals(newSelcom))
 108               {
 109                 command = JmolCommands.condenseCommand(command, pos);
 110                 continue;
 111               }
 112               // TODO: deal with case when buffer is too large for Jmol to parse
 113               // - execute command and flush
 114
 115               command.append(";");
 116               if (command.length() > 51200)
 117               {
 118                 // add another chunk
 119                 str.add(command.toString());
 120                 command.setLength(0);
 121               }
 122               command.append("select " + pos);
 123               command.append(newSelcom);
 124             }
 125             break;
 126           }
 127         }
 128       }
 129       {
 130         // add final chunk
 131         str.add(command.toString());
 132         command.setLength(0);
 133       }
 134       // Finally, add the command set ready to be returned.
 135       cset.add(new StructureMappingcommandSet(JmolCommands.class,
 136               files[pdbfnum], str.toArray(new String[str.size()])));
 137
 138     }
 139     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
 140   }
 141
 142   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 143   {
 144
 145     // work back to last 'select'
 146     int p = command.length(), q = p;
 147     do
 148     {
 149       p -= 6;
 150       if (p < 1)
 151       {
 152         p = 0;
 153       }
 154       ;
 155     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 156
 157     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 158
 159     command = command.delete(0, q + 7);
 160
 161     String start;
 162
 163     if (command.indexOf("-") > -1)
 164     {
 165       start = command.substring(0, command.indexOf("-"));
 166     }
 167     else
 168     {
 169       start = command.substring(0, command.indexOf(":"));
 170     }
 171
 172     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 173
 174     return sb;
 175   }
 176
 177 }