*/
package jalview.ext.jmol;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
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 jalview.util.Platform;
/**
* Routines for generating Jmol commands for Jalview/Jmol binding
*/
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";
+ private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
+ "select *; cartoons off; backbone");
+
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand("zoom 0");
- private static final String CMD_COLOUR_BY_CHAIN = "select *;color chain";
+ private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
+ "select *;color white;");
+
+ private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
+ "select *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow");
+
+ private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
+ "select *;color chain");
private static final String PIPE = "|";
c.getBlue());
}
-
- public String[] colourBySequence(StructureSelectionManager ssm,
- String[] files,
- SequenceI[][] sequence, SequenceRenderer sr,
- AlignmentViewPanel viewPanel)
- {
- // TODO delete method
-
- FeatureRenderer fr = viewPanel.getFeatureRenderer();
- FeatureColourFinder finder = new FeatureColourFinder(fr);
- AlignViewportI viewport = viewPanel.getAlignViewport();
- HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
- AlignmentI al = viewport.getAlignment();
- List<String> cset = new ArrayList<>();
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
- StringBuilder command = new StringBuilder(128);
- List<String> str = new ArrayList<>();
-
- if (mapping == null || mapping.length < 1)
- {
- continue;
- }
-
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
- {
- int lastPos = StructureMapping.UNASSIGNED_VALUE;
- SequenceI asp = al.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos == lastPos)
- {
- continue;
- }
- if (pos == StructureMapping.UNASSIGNED_VALUE)
- {
- // terminate current colour op
- if (command.length() > 0
- && command.charAt(command.length() - 1) != ';')
- {
- command.append(";");
- }
- // reset lastPos
- lastPos = StructureMapping.UNASSIGNED_VALUE;
- continue;
- }
-
- lastPos = pos;
-
- Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
- finder);
-
- /*
- * shade hidden regions darker
- */
- if (!cs.isVisible(r))
- {
- col = Color.GRAY;
- }
-
- String newSelcom = (mapping[m].getChain() != " "
- ? ":" + mapping[m].getChain()
- : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
- + getColourString(col);
- if (command.length() > newSelcom.length() && command
- .substring(command.length() - newSelcom.length())
- .equals(newSelcom))
- {
- command = JmolCommands.condenseCommand(command, pos);
- continue;
- }
- // TODO: deal with case when buffer is too large for Jmol to parse
- // - execute command and flush
-
- if (command.length() > 0
- && command.charAt(command.length() - 1) != ';')
- {
- command.append(";");
- }
-
- if (command.length() > 51200)
- {
- // add another chunk
- str.add(command.toString());
- command.setLength(0);
- }
- command.append("select " + pos);
- command.append(newSelcom);
- }
- // break;
- }
- }
- }
- {
- // add final chunk
- str.add(command.toString());
- command.setLength(0);
- }
- cset.addAll(str);
-
- }
- return cset.toArray(new String[cset.size()]);
- }
-
- public static StringBuilder condenseCommand(StringBuilder command,
- int pos)
- {
-
- // work back to last 'select'
- int p = command.length(), q = p;
- do
- {
- p -= 6;
- if (p < 1)
- {
- p = 0;
- }
- ;
- } while ((q = command.indexOf("select", p)) == -1 && p > 0);
-
- StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
-
- command = command.delete(0, q + 7);
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
@Override
- public String colourByChain()
+ public StructureCommandI colourByChain()
{
- return CMD_COLOUR_BY_CHAIN;
+ return COLOUR_BY_CHAIN;
}
@Override
- public String colourByCharge()
+ public List<StructureCommandI> colourByCharge()
{
- return CMD_COLOUR_BY_CHARGE;
+ return Arrays.asList(COLOUR_BY_CHARGE);
}
@Override
- public String colourByResidues(Map<String, Color> colours)
+ public List<StructureCommandI> colourByResidues(Map<String, Color> colours)
{
- StringBuilder cmd = new StringBuilder(128);
- cmd.append("select *;color white;");
- cmd.append(super.colourByResidues(colours));
-
- return cmd.toString();
+ List<StructureCommandI> cmds = super.colourByResidues(colours);
+ cmds.add(0, COLOUR_ALL_WHITE);
+ return cmds;
}
@Override
- public String setBackgroundColour(Color col)
+ public StructureCommandI setBackgroundColour(Color col)
{
- return "background " + getColourString(col);
+ return new StructureCommand("background " + getColourString(col));
}
@Override
- public String focusView()
+ public StructureCommandI focusView()
{
- return "zoom 0";
+ return FOCUS_VIEW;
}
@Override
- public String showChains(List<String> toShow)
+ public List<StructureCommandI> showChains(List<String> toShow)
{
StringBuilder atomSpec = new StringBuilder(128);
boolean first = true;
String spec = atomSpec.toString();
String command = "select *;restrict " + spec + ";cartoon;center "
+ spec;
- return command;
+ return Arrays.asList(new StructureCommand(command));
}
/**
* @see https://chemapps.stolaf.edu/jmol/docs/#compare
*/
@Override
- public String superposeStructures(AtomSpecModel refAtoms,
+ public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
AtomSpecModel atomSpec)
{
StringBuilder sb = new StringBuilder(64);
- int refModel = refAtoms.getModels().iterator().next();
- int model2 = atomSpec.getModels().iterator().next();
- sb.append(String.format("compare {%d.1} {%d.1}", model2, refModel));
+ String refModel = refAtoms.getModels().iterator().next();
+ String model2 = atomSpec.getModels().iterator().next();
+ sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
/*
sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
.append("cartoons");
- return sb.toString();
+ return Arrays.asList(new StructureCommand(sb.toString()));
}
@Override
- public String openCommandFile(String path)
+ public StructureCommandI openCommandFile(String path)
{
/*
* https://chemapps.stolaf.edu/jmol/docs/#script
* not currently used in Jalview
*/
- return "script " + path;
+ return new StructureCommand("script " + path);
}
@Override
- public String saveSession(String filepath)
+ public StructureCommandI saveSession(String filepath)
{
/*
- * https://chemapps.stolaf.edu/jmol/docs/#write
- * not currently used in Jalview
+ * https://chemapps.stolaf.edu/jmol/docs/#writemodel
*/
- return "write \"" + filepath + "\"";
+ return new StructureCommand("write STATE \"" + filepath + "\"");
}
@Override
- protected String getColourCommand(String atomSpec, Color colour)
+ protected StructureCommandI colourResidues(String atomSpec, Color colour)
{
StringBuilder sb = new StringBuilder(atomSpec.length()+20);
sb.append("select ").append(atomSpec).append(getCommandSeparator())
.append("color").append(getColourString(colour));
- return sb.toString();
+ return new StructureCommand(sb.toString());
}
@Override
StringBuilder sb = new StringBuilder(128);
boolean first = true;
- for (int modelNo : model.getModels())
+ for (String modelNo : model.getModels())
{
for (String chain : model.getChains(modelNo))
{
}
@Override
- public String showBackbone()
+ public List<StructureCommandI> showBackbone()
+ {
+ return Arrays.asList(SHOW_BACKBONE);
+ }
+
+ @Override
+ public StructureCommandI loadFile(String file)
+ {
+ // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
+ return new StructureCommand("load FILES \"" +
+ Platform.escapeBackslashes(file) + "\"");
+ }
+
+ /**
+ * Obsolete method, only referenced from
+ * jalview.javascript.MouseOverStructureListener
+ *
+ * @param ssm
+ * @param files
+ * @param sequence
+ * @param sr
+ * @param viewPanel
+ * @return
+ */
+ @Deprecated
+ public String[] colourBySequence(StructureSelectionManager ssm,
+ String[] files, SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
+ {
+ // TODO delete method
+
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
+ AlignmentI al = viewport.getAlignment();
+ List<String> cset = new ArrayList<>();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ StringBuilder command = new StringBuilder(128);
+ List<String> str = new ArrayList<>();
+
+ if (mapping == null || mapping.length < 1)
+ {
+ continue;
+ }
+
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
+ {
+ for (int sp, m = 0; m < mapping.length; m++)
+ {
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
+ {
+ int lastPos = StructureMapping.UNASSIGNED_VALUE;
+ SequenceI asp = al.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
+ {
+ // no mapping to gaps in sequence
+ if (Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+
+ if (pos == lastPos)
+ {
+ continue;
+ }
+ if (pos == StructureMapping.UNASSIGNED_VALUE)
+ {
+ // terminate current colour op
+ if (command.length() > 0
+ && command.charAt(command.length() - 1) != ';')
+ {
+ command.append(";");
+ }
+ // reset lastPos
+ lastPos = StructureMapping.UNASSIGNED_VALUE;
+ continue;
+ }
+
+ lastPos = pos;
+
+ Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+ finder);
+
+ /*
+ * shade hidden regions darker
+ */
+ if (!cs.isVisible(r))
+ {
+ col = Color.GRAY;
+ }
+
+ String newSelcom = (mapping[m].getChain() != " "
+ ? ":" + mapping[m].getChain()
+ : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
+ + getColourString(col);
+ if (command.length() > newSelcom.length() && command
+ .substring(command.length() - newSelcom.length())
+ .equals(newSelcom))
+ {
+ command = JmolCommands.condenseCommand(command, pos);
+ continue;
+ }
+ // TODO: deal with case when buffer is too large for Jmol to parse
+ // - execute command and flush
+
+ if (command.length() > 0
+ && command.charAt(command.length() - 1) != ';')
+ {
+ command.append(";");
+ }
+
+ if (command.length() > 51200)
+ {
+ // add another chunk
+ str.add(command.toString());
+ command.setLength(0);
+ }
+ command.append("select " + pos);
+ command.append(newSelcom);
+ }
+ // break;
+ }
+ }
+ }
+ {
+ // add final chunk
+ str.add(command.toString());
+ command.setLength(0);
+ }
+ cset.addAll(str);
+
+ }
+ return cset.toArray(new String[cset.size()]);
+ }
+
+ /**
+ * Helper method
+ *
+ * @param command
+ * @param pos
+ * @return
+ */
+ @Deprecated
+ private static StringBuilder condenseCommand(
+ StringBuilder command,
+ int pos)
+ {
+
+ // work back to last 'select'
+ int p = command.length(), q = p;
+ do
+ {
+ p -= 6;
+ if (p < 1)
+ {
+ p = 0;
+ }
+ ;
+ } while ((q = command.indexOf("select", p)) == -1 && p > 0);
+
+ StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
+
+ command = command.delete(0, q + 7);
+
+ String start;
+
+ if (command.indexOf("-") > -1)
+ {
+ start = command.substring(0, command.indexOf("-"));
+ }
+ else
+ {
+ start = command.substring(0, command.indexOf(":"));
+ }
+
+ sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
+
+ return sb;
+ }
+
+ @Override
+ public StructureCommandI openSession(String filepath)
{
- return "select *; cartoons off; backbone";
+ return loadFile(filepath);
}
}
git://source.jalview.org / jalview.git / blobdiff