JAL-2844 line drawing at mouse click added on top of Aptx
[jalview.git] / src / jalview / ext / jmol / JmolCommands.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.jmol;
22
23 import jalview.api.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.api.FeatureRenderer;
26 import jalview.api.SequenceRenderer;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.SequenceI;
30 import jalview.renderer.seqfeatures.FeatureColourFinder;
31 import jalview.structure.StructureMapping;
32 import jalview.structure.StructureMappingcommandSet;
33 import jalview.structure.StructureSelectionManager;
34
35 import java.awt.Color;
36 import java.util.ArrayList;
37 import java.util.List;
38
39 /**
40  * Routines for generating Jmol commands for Jalview/Jmol binding another
41  * cruisecontrol test.
42  * 
43  * @author JimP
44  * 
45  */
46 public class JmolCommands
47 {
48
49   /**
50    * Jmol utility which constructs the commands to colour chains by the given
51    * alignment
52    * 
53    * @returns Object[] { Object[] { <model being coloured>,
54    * 
55    */
56   public static StructureMappingcommandSet[] getColourBySequenceCommand(
57           StructureSelectionManager ssm, String[] files,
58           SequenceI[][] sequence, SequenceRenderer sr,
59           AlignmentViewPanel viewPanel)
60   {
61     FeatureRenderer fr = viewPanel.getFeatureRenderer();
62     FeatureColourFinder finder = new FeatureColourFinder(fr);
63     AlignViewportI viewport = viewPanel.getAlignViewport();
64     HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
65     AlignmentI al = viewport.getAlignment();
66     List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
67
68     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
69     {
70       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
71       StringBuffer command = new StringBuffer();
72       StructureMappingcommandSet smc;
73       ArrayList<String> str = new ArrayList<String>();
74
75       if (mapping == null || mapping.length < 1)
76       {
77         continue;
78       }
79
80       int lastPos = -1;
81       for (int s = 0; s < sequence[pdbfnum].length; s++)
82       {
83         for (int sp, m = 0; m < mapping.length; m++)
84         {
85           if (mapping[m].getSequence() == sequence[pdbfnum][s]
86                   && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
87           {
88             SequenceI asp = al.getSequenceAt(sp);
89             for (int r = 0; r < asp.getLength(); r++)
90             {
91               // no mapping to gaps in sequence
92               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
93               {
94                 continue;
95               }
96               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
97
98               if (pos < 1 || pos == lastPos)
99               {
100                 continue;
101               }
102
103               lastPos = pos;
104
105               Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
106                       finder);
107
108               /*
109                * shade hidden regions darker
110                */
111               if (!cs.isVisible(r))
112               {
113                 col = Color.GRAY;
114               }
115
116               String newSelcom = (mapping[m].getChain() != " "
117                       ? ":" + mapping[m].getChain()
118                       : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
119                       + col.getRed() + "," + col.getGreen() + ","
120                       + col.getBlue() + "]";
121               if (command.length() > newSelcom.length() && command
122                       .substring(command.length() - newSelcom.length())
123                       .equals(newSelcom))
124               {
125                 command = JmolCommands.condenseCommand(command, pos);
126                 continue;
127               }
128               // TODO: deal with case when buffer is too large for Jmol to parse
129               // - execute command and flush
130
131               command.append(";");
132               if (command.length() > 51200)
133               {
134                 // add another chunk
135                 str.add(command.toString());
136                 command.setLength(0);
137               }
138               command.append("select " + pos);
139               command.append(newSelcom);
140             }
141             // break;
142           }
143         }
144       }
145       {
146         // add final chunk
147         str.add(command.toString());
148         command.setLength(0);
149       }
150       // Finally, add the command set ready to be returned.
151       cset.add(new StructureMappingcommandSet(JmolCommands.class,
152               files[pdbfnum], str.toArray(new String[str.size()])));
153
154     }
155     return cset.toArray(new StructureMappingcommandSet[cset.size()]);
156   }
157
158   public static StringBuffer condenseCommand(StringBuffer command, int pos)
159   {
160
161     // work back to last 'select'
162     int p = command.length(), q = p;
163     do
164     {
165       p -= 6;
166       if (p < 1)
167       {
168         p = 0;
169       }
170       ;
171     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
172
173     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
174
175     command = command.delete(0, q + 7);
176
177     String start;
178
179     if (command.indexOf("-") > -1)
180     {
181       start = command.substring(0, command.indexOf("-"));
182     }
183     else
184     {
185       start = command.substring(0, command.indexOf(":"));
186     }
187
188     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
189
190     return sb;
191   }
192
193 }