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,
  52           AlignmentI alignment)
  53   {
  54     ArrayList<String> str = new ArrayList<String>();
  55     StringBuffer command = new StringBuffer();
  56
  57     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
  58     {
  59       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  60
  61       if (mapping == null || mapping.length < 1)
  62       {
  63         continue;
  64       }
  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               {
  86                 continue;
  87               }
  88
  89               lastPos = pos;
  90
  91               Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
  92                       finder);
  93
  94               String newSelcom = (mapping[m].getChain() != " " ? ":"
  95                       + mapping[m].getChain() : "")
  96                       + "/"
  97                       + (pdbfnum + 1)
  98                       + ".1"
  99                       + ";color["
 100                       + col.getRed()
 101                       + ","
 102                       + col.getGreen()
 103                       + ","
 104                       + col.getBlue() + "]";
 105               if (command.length() > newSelcom.length()
 106                       && command.substring(
 107                               command.length() - newSelcom.length())
 108                               .equals(newSelcom))
 109               {
 110                 command = VarnaCommands.condenseCommand(command, pos);
 111                 continue;
 112               }
 113               // TODO: deal with case when buffer is too large for Jmol to parse
 114               // - execute command and flush
 115
 116               command.append(";");
 117               if (command.length() > 51200)
 118               {
 119                 // add another chunk
 120                 str.add(command.toString());
 121                 command.setLength(0);
 122               }
 123               command.append("select " + pos);
 124               command.append(newSelcom);
 125             }
 126             break;
 127           }
 128         }
 129       }
 130     }
 131     {
 132       // add final chunk
 133       str.add(command.toString());
 134       command.setLength(0);
 135     }
 136     return str.toArray(new String[str.size()]);
 137   }
 138
 139   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 140   {
 141
 142     // work back to last 'select'
 143     int p = command.length(), q = p;
 144     do
 145     {
 146       p -= 6;
 147       if (p < 1)
 148       {
 149         p = 0;
 150       }
 151       ;
 152     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 153
 154     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 155
 156     command = command.delete(0, q + 7);
 157
 158     String start;
 159
 160     if (command.indexOf("-") > -1)
 161     {
 162       start = command.substring(0, command.indexOf("-"));
 163     }
 164     else
 165     {
 166       start = command.substring(0, command.indexOf(":"));
 167     }
 168
 169     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 170
 171     return sb;
 172   }
 173
 174 }