src/jalview/ext/jmol/JmolCommands.java

   1 /*******************************************************************************
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 /**
  19  *
  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         continue;
  69
  70       int lastPos = -1;
  71       for (int s = 0; s < sequence[pdbfnum].length; s++)
  72       {
  73         for (int sp, m = 0; m < mapping.length; m++)
  74         {
  75           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  76                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
  77           {
  78             SequenceI asp = alignment.getSequenceAt(sp);
  79             for (int r = 0; r < asp.getLength(); r++)
  80             {
  81               // no mapping to gaps in sequence
  82               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  83               {
  84                 continue;
  85               }
  86               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  87
  88               if (pos < 1 || pos == lastPos)
  89                 continue;
  90
  91               lastPos = pos;
  92
  93               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  94
  95               if (fr != null)
  96                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
  97               String newSelcom = (mapping[m].getChain() != " " ? ":"
  98                       + mapping[m].getChain() : "")
  99                       + "/"
 100                       + (pdbfnum + 1)
 101                       + ".1"
 102                       + ";color["
 103                       + col.getRed()
 104                       + ","
 105                       + col.getGreen()
 106                       + ","
 107                       + col.getBlue() + "]";
 108               if (command.length() > newSelcom.length()
 109                       && command.substring(
 110                               command.length() - newSelcom.length())
 111                               .equals(newSelcom))
 112               {
 113                 command = JmolCommands.condenseCommand(command, pos);
 114                 continue;
 115               }
 116               // TODO: deal with case when buffer is too large for Jmol to parse
 117               // - execute command and flush
 118
 119               command.append(";");
 120               if (command.length() > 51200)
 121               {
 122                 // add another chunk
 123                 str.add(command.toString());
 124                 command.setLength(0);
 125               }
 126               command.append("select " + pos);
 127               command.append(newSelcom);
 128             }
 129             break;
 130           }
 131         }
 132       }
 133       {
 134         // add final chunk
 135         str.add(command.toString());
 136         command.setLength(0);
 137       }
 138       // Finally, add the command set ready to be returned.
 139       cset.add(new StructureMappingcommandSet(JmolCommands.class,
 140               files[pdbfnum], str.toArray(new String[str.size()])));
 141
 142     }
 143     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
 144   }
 145
 146   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 147   {
 148
 149     // work back to last 'select'
 150     int p = command.length(), q = p;
 151     do
 152     {
 153       p -= 6;
 154       if (p < 1)
 155       {
 156         p = 0;
 157       }
 158       ;
 159     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 160
 161     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 162
 163     command = command.delete(0, q + 7);
 164
 165     String start;
 166
 167     if (command.indexOf("-") > -1)
 168     {
 169       start = command.substring(0, command.indexOf("-"));
 170     }
 171     else
 172     {
 173       start = command.substring(0, command.indexOf(":"));
 174     }
 175
 176     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 177
 178     return sb;
 179   }
 180
 181 }