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.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.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, 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         continue;
  62
  63       int lastPos = -1;
  64       for (int s = 0; s < sequence[pdbfnum].length; s++)
  65       {
  66         for (int sp, m = 0; m < mapping.length; m++)
  67         {
  68           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  69                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
  70           {
  71             SequenceI asp = alignment.getSequenceAt(sp);
  72             for (int r = 0; r < asp.getLength(); r++)
  73             {
  74               // no mapping to gaps in sequence
  75               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  76               {
  77                 continue;
  78               }
  79               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  80
  81               if (pos < 1 || pos == lastPos)
  82                 continue;
  83
  84               lastPos = pos;
  85
  86               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  87
  88               if (fr != null)
  89                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
  90               String newSelcom = (mapping[m].getChain() != " " ? ":"
  91                       + mapping[m].getChain() : "")
  92                       + "/"
  93                       + (pdbfnum + 1)
  94                       + ".1"
  95                       + ";color["
  96                       + col.getRed()
  97                       + ","
  98                       + col.getGreen()
  99                       + ","
 100                       + col.getBlue() + "]";
 101               if (command.length() > newSelcom.length()
 102                       && command.substring(
 103                               command.length() - newSelcom.length())
 104                               .equals(newSelcom))
 105               {
 106                 command = VarnaCommands.condenseCommand(command, pos);
 107                 continue;
 108               }
 109               // TODO: deal with case when buffer is too large for Jmol to parse
 110               // - execute command and flush
 111
 112               command.append(";");
 113               if (command.length() > 51200)
 114               {
 115                 // add another chunk
 116                 str.add(command.toString());
 117                 command.setLength(0);
 118               }
 119               command.append("select " + pos);
 120               command.append(newSelcom);
 121             }
 122             break;
 123           }
 124         }
 125       }
 126     }
 127     {
 128       // add final chunk
 129       str.add(command.toString());
 130       command.setLength(0);
 131     }
 132     return str.toArray(new String[str.size()]);
 133   }
 134
 135   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 136   {
 137
 138     // work back to last 'select'
 139     int p = command.length(), q = p;
 140     do
 141     {
 142       p -= 6;
 143       if (p < 1)
 144       {
 145         p = 0;
 146       }
 147       ;
 148     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 149
 150     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 151
 152     command = command.delete(0, q + 7);
 153
 154     String start;
 155
 156     if (command.indexOf("-") > -1)
 157     {
 158       start = command.substring(0, command.indexOf("-"));
 159     }
 160     else
 161     {
 162       start = command.substring(0, command.indexOf(":"));
 163     }
 164
 165     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 166
 167     return sb;
 168   }
 169
 170 }