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