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       {
  68         continue;
  69       }
  70
  71       int lastPos = -1;
  72       for (int s = 0; s < sequence[pdbfnum].length; s++)
  73       {
  74         for (int sp, m = 0; m < mapping.length; m++)
  75         {
  76           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  77                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
  78           {
  79             SequenceI asp = alignment.getSequenceAt(sp);
  80             for (int r = 0; r < asp.getLength(); r++)
  81             {
  82               // no mapping to gaps in sequence
  83               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  84               {
  85                 continue;
  86               }
  87               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  88
  89               if (pos < 1 || pos == lastPos)
  90               {
  91                 continue;
  92               }
  93
  94               lastPos = pos;
  95
  96               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  97
  98               if (fr != null)
  99               {
 100                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
 101               }
 102               String newSelcom = (mapping[m].getChain() != " " ? ":"
 103                       + mapping[m].getChain() : "")
 104                       + "/"
 105                       + (pdbfnum + 1)
 106                       + ".1"
 107                       + ";color["
 108                       + col.getRed()
 109                       + ","
 110                       + col.getGreen()
 111                       + ","
 112                       + col.getBlue() + "]";
 113               if (command.length() > newSelcom.length()
 114                       && command.substring(
 115                               command.length() - newSelcom.length())
 116                               .equals(newSelcom))
 117               {
 118                 command = JmolCommands.condenseCommand(command, pos);
 119                 continue;
 120               }
 121               // TODO: deal with case when buffer is too large for Jmol to parse
 122               // - execute command and flush
 123
 124               command.append(";");
 125               if (command.length() > 51200)
 126               {
 127                 // add another chunk
 128                 str.add(command.toString());
 129                 command.setLength(0);
 130               }
 131               command.append("select " + pos);
 132               command.append(newSelcom);
 133             }
 134             // break;
 135           }
 136         }
 137       }
 138       {
 139         // add final chunk
 140         str.add(command.toString());
 141         command.setLength(0);
 142       }
 143       // Finally, add the command set ready to be returned.
 144       cset.add(new StructureMappingcommandSet(JmolCommands.class,
 145               files[pdbfnum], str.toArray(new String[str.size()])));
 146
 147     }
 148     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
 149   }
 150
 151   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 152   {
 153
 154     // work back to last 'select'
 155     int p = command.length(), q = p;
 156     do
 157     {
 158       p -= 6;
 159       if (p < 1)
 160       {
 161         p = 0;
 162       }
 163       ;
 164     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 165
 166     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 167
 168     command = command.delete(0, q + 7);
 169
 170     String start;
 171
 172     if (command.indexOf("-") > -1)
 173     {
 174       start = command.substring(0, command.indexOf("-"));
 175     }
 176     else
 177     {
 178       start = command.substring(0, command.indexOf(":"));
 179     }
 180
 181     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 182
 183     return sb;
 184   }
 185
 186 }