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.ColorI;
  24 import jalview.api.FeatureRenderer;
  25 import jalview.api.SequenceRenderer;
  26 import jalview.datamodel.AlignmentI;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.structure.StructureMapping;
  29 import jalview.structure.StructureSelectionManager;
  30
  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, FeatureRenderer fr,
  51           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               ColorI col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  91
  92               if (fr != null)
  93               {
  94                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
  95               }
  96               String newSelcom = (mapping[m].getChain() != " " ? ":"
  97                       + mapping[m].getChain() : "")
  98                       + "/"
  99                       + (pdbfnum + 1)
 100                       + ".1"
 101                       + ";color["
 102                       + col.getRed()
 103                       + ","
 104                       + col.getGreen()
 105                       + ","
 106                       + col.getBlue() + "]";
 107               if (command.length() > newSelcom.length()
 108                       && command.substring(
 109                               command.length() - newSelcom.length())
 110                               .equals(newSelcom))
 111               {
 112                 command = VarnaCommands.condenseCommand(command, pos);
 113                 continue;
 114               }
 115               // TODO: deal with case when buffer is too large for Jmol to parse
 116               // - execute command and flush
 117
 118               command.append(";");
 119               if (command.length() > 51200)
 120               {
 121                 // add another chunk
 122                 str.add(command.toString());
 123                 command.setLength(0);
 124               }
 125               command.append("select " + pos);
 126               command.append(newSelcom);
 127             }
 128             break;
 129           }
 130         }
 131       }
 132     }
 133     {
 134       // add final chunk
 135       str.add(command.toString());
 136       command.setLength(0);
 137     }
 138     return str.toArray(new String[str.size()]);
 139   }
 140
 141   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 142   {
 143
 144     // work back to last 'select'
 145     int p = command.length(), q = p;
 146     do
 147     {
 148       p -= 6;
 149       if (p < 1)
 150       {
 151         p = 0;
 152       }
 153       ;
 154     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 155
 156     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 157
 158     command = command.delete(0, q + 7);
 159
 160     String start;
 161
 162     if (command.indexOf("-") > -1)
 163     {
 164       start = command.substring(0, command.indexOf("-"));
 165     }
 166     else
 167     {
 168       start = command.substring(0, command.indexOf(":"));
 169     }
 170
 171     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 172
 173     return sb;
 174   }
 175
 176 }