import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
import java.awt.Color;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
/**
- * Routines for generating Jmol commands for Jalview/Jmol binding another
- * cruisecontrol test.
+ * Routines for generating Jmol commands for Jalview/Jmol binding
*
* @author JimP
*
*/
-public class JmolCommands
+public class JmolCommands extends StructureCommandsBase
{
+ private static final String CMD_COLOUR_BY_CHARGE = "select *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow";
- /**
- * Jmol utility which constructs the commands to colour chains by the given
- * alignment
- *
- * @returns Object[] { Object[] { <model being coloured>,
- *
- */
- public static StructureMappingcommandSet[] getColourBySequenceCommand(
+ private static final String CMD_COLOUR_BY_CHAIN = "select *;color chain";
+
+ private static String formatRGB(Color c) {
+ return c == null ? null
+ : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
+ c.getBlue());
+ }
+
+ @Override
+ public String[] colourBySequence(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr,
AlignmentViewPanel viewPanel)
{
+ // TODO refactor to call buildColoursMap() first...
+
FeatureRenderer fr = viewPanel.getFeatureRenderer();
FeatureColourFinder finder = new FeatureColourFinder(fr);
AlignViewportI viewport = viewPanel.getAlignViewport();
HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
AlignmentI al = viewport.getAlignment();
- List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+ List<String> cset = new ArrayList<>();
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
- StringBuffer command = new StringBuffer();
- StructureMappingcommandSet smc;
- ArrayList<String> str = new ArrayList<String>();
+ StringBuilder command = new StringBuilder(128);
+ List<String> str = new ArrayList<>();
if (mapping == null || mapping.length < 1)
{
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ if (Comparison.isGap(asp.getCharAt(r)))
{
continue;
}
str.add(command.toString());
command.setLength(0);
}
- // Finally, add the command set ready to be returned.
- cset.add(new StructureMappingcommandSet(JmolCommands.class,
- files[pdbfnum], str.toArray(new String[str.size()])));
+ cset.addAll(str);
}
- return cset.toArray(new StructureMappingcommandSet[cset.size()]);
+ return cset.toArray(new String[cset.size()]);
}
- public static StringBuffer condenseCommand(StringBuffer command, int pos)
+ public static StringBuilder condenseCommand(StringBuilder command,
+ int pos)
{
// work back to last 'select'
;
} while ((q = command.indexOf("select", p)) == -1 && p > 0);
- StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
+ StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
command = command.delete(0, q + 7);
return sb;
}
+ @Override
+ public String colourByChain()
+ {
+ return CMD_COLOUR_BY_CHAIN;
+ }
+
+ @Override
+ public String colourByCharge()
+ {
+ return CMD_COLOUR_BY_CHARGE;
+ }
+
+ @Override
+ public String colourByResidues(Map<String, Color> colours)
+ {
+ StringBuilder cmd = new StringBuilder(128);
+ cmd.append("select *;color white;");
+
+ /*
+ * concatenate commands like
+ * select VAL;color[100,215,55]
+ */
+ for (Entry<String, Color> entry : colours.entrySet())
+ {
+ Color col = entry.getValue();
+ String resCode = entry.getKey();
+ cmd.append("select ").append(resCode).append(";");
+ cmd.append("color[");
+ cmd.append(formatRGB(col));
+ cmd.append("];");
+ }
+
+ return cmd.toString();
+ }
+
+ @Override
+ public String setBackgroundColour(Color col)
+ {
+ return "background " + formatRGB(col);
+ }
+
+ @Override
+ public String focusView()
+ {
+ return "zoom 0";
+ }
+
+ @Override
+ public String showChains(List<String> toShow)
+ {
+ StringBuilder atomSpec = new StringBuilder(128);
+ boolean first = true;
+ for (String chain : toShow)
+ {
+ String[] tokens = chain.split(":");
+ if (tokens.length == 2)
+ {
+ if (!first)
+ {
+ atomSpec.append(" or ");
+ }
+ first = false;
+ atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
+ }
+ }
+
+ String spec = atomSpec.toString();
+ String command = "select *;restrict " + spec + ";cartoon;center "
+ + spec;
+ return command;
+ }
+
}