*/
package jalview.ext.jmol;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.AtomSpecModel;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
import java.awt.Color;
import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
/**
* Routines for generating Jmol commands for Jalview/Jmol binding another
public class JmolCommands
{
+ private static final String COMMA = ",";
+
/**
* Jmol utility which constructs the commands to colour chains by the given
* alignment
*/
public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ AAStructureBindingModel binding, AlignmentViewPanel viewPanel)
{
+ SequenceRenderer sr = binding.getSequenceRenderer(viewPanel);
+ SequenceI[][] sequence = binding.getSequence();
+ return getColourBySequenceCommand(ssm, files, sequence, sr, viewPanel);
+ }
- ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+ public static StructureMappingcommandSet[] getColourBySequenceCommand(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
+ {
+ 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<>();
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>();
+ ArrayList<String> str = new ArrayList<>();
if (mapping == null || mapping.length < 1)
{
continue;
}
- int lastPos = -1;
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 = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+ && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
{
- SequenceI asp = alignment.getSequenceAt(sp);
+ int lastPos = StructureMapping.UNASSIGNED_VALUE;
+ SequenceI asp = al.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
}
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
- if (pos < 1 || pos == lastPos)
+ 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.getResidueBoxColour(sequence[pdbfnum][s], r);
+ Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+ finder);
- if (fr != null)
+ /*
+ * shade hidden regions darker
+ */
+ if (!cs.isVisible(r))
{
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+ col = Color.GRAY;
}
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
+
+ String newSelcom = (mapping[m].getChain() != " "
+ ? ":" + mapping[m].getChain()
+ : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
+ + col.getRed() + COMMA + col.getGreen() + COMMA
+ col.getBlue() + "]";
- if (command.length() > newSelcom.length()
- && command.substring(
- command.length() - newSelcom.length())
- .equals(newSelcom))
+ 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
- command.append(";");
+ if (command.length() > 0
+ && command.charAt(command.length() - 1) != ';')
+ {
+ command.append(";");
+ }
+
if (command.length() > 51200)
{
// add another chunk
return sb;
}
+ /**
+ * Answers a Jmol 'color' command to colour residues as described by the given
+ * map of {@code <Color, AtomSpecModel>}
+ *
+ * @param map
+ * @return
+ */
+ public static String[] getColourBySequenceCommand(
+ Map<Object, AtomSpecModel> map)
+ {
+ String[] cmds = new String[map.keySet().size()];
+
+ int i = 0;
+ for (Object o : map.keySet())
+ {
+ StringBuilder cmd = new StringBuilder(128);
+ Color c = (Color) o;
+ String atomSpec = getAtomSpec(map.get(o));
+ cmd.append("select ").append(atomSpec).append(";color[")
+ .append(c.getRed()).append(COMMA).append(c.getGreen())
+ .append(COMMA).append(c.getBlue()).append("];");
+ cmds[i] = cmd.toString();
+ i++;
+ }
+
+ return cmds;
+ }
+
+ /**
+ * Builds a Jmol syntax selection expression from the given model, for example
+ *
+ * <pre>
+ * 61-64,70:A/1.1,12-25,41-44:B/1.1,12:A/2.1
+ * for model 1, chain A, residues 61-64 and 70, chain B residues 12-25 and 41-44, model 2 chain A residue 12
+ * </pre>
+ *
+ * @param atomSpecModel
+ * @return
+ */
+ public static String getAtomSpec(AtomSpecModel atomSpecModel)
+ {
+ StringBuilder sb = new StringBuilder(64);
+ for (int model : atomSpecModel.getModels())
+ {
+ for (String chain : atomSpecModel.getChains(model))
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(COMMA);
+ }
+ boolean firstRange = true;
+ for (int[] range : atomSpecModel.getRanges(model, chain))
+ {
+ if (!firstRange)
+ {
+ sb.append(COMMA);
+ }
+ firstRange = false;
+ sb.append(range[0]);
+ if (range[1] != range[0])
+ {
+ sb.append("-").append(range[1]);
+ }
+ }
+ sb.append(":").append(chain).append("/")
+ .append(String.valueOf(model + 1))
+ .append(".1");
+ }
+ }
+
+ return sb.toString();
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff