src/jalview/ext/rbvi/chimera/ChimeraCommands.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   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
  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.rbvi.chimera;
  22
  23 import jalview.api.FeatureRenderer;
  24 import jalview.api.SequenceRenderer;
  25 import jalview.api.structures.JalviewStructureDisplayI;
  26 import jalview.datamodel.AlignmentI;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.structure.StructureMapping;
  29 import jalview.structure.StructureMappingcommandSet;
  30 import jalview.structure.StructureSelectionManager;
  31 import jalview.util.Format;
  32
  33 import java.awt.Color;
  34 import java.util.ArrayList;
  35
  36 /**
  37  * Routines for generating Chimera commands for Jalview/Chimera binding
  38  *
  39  * @author JimP
  40  *
  41  */
  42 public class ChimeraCommands
  43 {
  44
  45   /**
  46    * utility to construct the commands to colour chains by the given alignment
  47    * for passing to Chimera
  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       float cols[] = new float[4];
  63       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  64       StringBuffer command = new StringBuffer();
  65       StructureMappingcommandSet smc;
  66       ArrayList<String> str = new ArrayList<String>();
  67
  68       if (mapping == null || mapping.length < 1)
  69         continue;
  70
  71       int startPos = -1, lastPos = -1, startModel = -1, lastModel = -1;
  72       String startChain = "", lastChain = "";
  73       Color lastCol = null;
  74       for (int s = 0; s < sequence[pdbfnum].length; s++)
  75       {
  76         for (int sp, m = 0; m < mapping.length; m++)
  77         {
  78           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  79                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
  80           {
  81             SequenceI asp = alignment.getSequenceAt(sp);
  82             for (int r = 0; r < asp.getLength(); r++)
  83             {
  84               // no mapping to gaps in sequence
  85               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  86               {
  87                 continue;
  88               }
  89               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  90
  91               if (pos < 1 || pos == lastPos)
  92                 continue;
  93
  94               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  95
  96               if (fr != null)
  97                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
  98               if (lastCol != col || lastPos + 1 != pos
  99                       || pdbfnum != lastModel
 100                       || !mapping[m].getChain().equals(lastChain))
 101               {
 102                 if (lastCol != null)
 103                 {
 104
 105                   lastCol.getRGBComponents(cols);
 106                   String newSelcom = "color " + cols[0] + "," + cols[1]
 107                           + "," + cols[2] + " #" + startModel + ":"
 108                           + startPos + "-" + lastPos + "." + lastChain;
 109                   if (str.size() > 0
 110                           && (str.get(str.size() - 1).length() + newSelcom
 111                                   .length()) < 4096)
 112                   {
 113                     str.set(str.size() - 1, str.get(str.size() - 1) + ";"
 114                             + newSelcom);
 115                   }
 116                   else
 117                   {
 118                     str.add(newSelcom);
 119                   }
 120                 }
 121                 lastCol = null;
 122                 startPos = pos;
 123                 startModel = pdbfnum;
 124                 startChain = mapping[m].getChain();
 125               }
 126               lastCol = col;
 127               lastPos = pos;
 128               lastModel = pdbfnum;
 129               lastChain = mapping[m].getChain();
 130             }
 131             // final colour range
 132             if (lastCol != null)
 133             {
 134
 135               lastCol.getRGBComponents(cols);
 136               String newSelcom = "color " + cols[0] + "," + cols[1] + ","
 137                       + cols[2] + " #" + startModel + ":" + startPos + "-"
 138                       + lastPos + "." + lastChain;
 139               if (str.size() > 0
 140                       && (str.get(str.size() - 1).length() + newSelcom
 141                               .length()) < 4096)
 142               {
 143                 str.set(str.size() - 1, str.get(str.size() - 1) + ";"
 144                         + newSelcom);
 145               }
 146               else
 147               {
 148                 str.add(newSelcom);
 149               }
 150             }
 151             break;
 152           }
 153         }
 154       }
 155       // Finally, add the command set ready to be returned.
 156       cset.add(new StructureMappingcommandSet(ChimeraCommands.class,
 157               files[pdbfnum], str.toArray(new String[str.size()])));
 158     }
 159     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
 160   }
 161
 162 }