*/
package jalview.ext.rbvi.chimera;
+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.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import java.util.List;
import java.util.Map;
-import MCview.PDBChain;
-
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*
* @param sequence
* @param sr
* @param fr
- * @param alignment
+ * @param viewPanel
* @return
*/
- public static StructureMappingcommandSet getColourBySequenceCommand(
+ public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
- Map<Object, AtomSpecModel> colourMap = buildColoursMap(
- ssm, files, sequence, sr, fr, alignment);
+ Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
+ sequence, sr, viewPanel);
List<String> colourCommands = buildColourCommands(colourMap);
ChimeraCommands.class, null,
colourCommands.toArray(new String[colourCommands.size()]));
- return cs;
+ return new StructureMappingcommandSet[] { cs };
}
/**
}
sb.append("color ").append(colourCode).append(" ");
firstColour = false;
- final AtomSpecModel colourData = colourMap
- .get(colour);
+ final AtomSpecModel colourData = colourMap.get(colour);
sb.append(colourData.getAtomSpec());
}
commands.add(sb.toString());
/**
* <pre>
- * Build a data structure which maps contiguous subsequences for each colour.
- * This generates a data structure from which we can easily generate the
- * Chimera command for colour by sequence.
+ * Build a data structure which records contiguous subsequences for each colour.
+ * From this we can easily generate the Chimera command for colour by sequence.
* Color
* Model number
* Chain
*/
protected static Map<Object, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ 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();
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
Color lastColour = null;
+
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
{
final SequenceI seq = sequence[pdbfnum][s];
if (mapping[m].getSequence() == seq
- && (sp = alignment.findIndex(seq)) > -1)
+ && (sp = al.findIndex(seq)) > -1)
{
- SequenceI asp = alignment.getSequenceAt(sp);
+ SequenceI asp = al.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
continue;
}
- Color colour = sr.getResidueColour(seq, r, fr);
+ Color colour = sr.getResidueColour(seq, r, finder);
+
+ /*
+ * darker colour for hidden regions
+ */
+ if (!cs.isVisible(r))
+ {
+ colour = Color.GRAY;
+ }
+
final String chain = mapping[m].getChain();
/*
{
if (startPos != -1)
{
- addRange(colourMap, lastColour, pdbfnum, startPos,
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
lastPos, lastChain);
}
startPos = pos;
// final colour range
if (lastColour != null)
{
- addRange(colourMap, lastColour, pdbfnum, startPos,
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
lastPos, lastChain);
}
// break;
* @param endPos
* @param chain
*/
- protected static void addRange(Map<Object, AtomSpecModel> map,
+ protected static void addColourRange(Map<Object, AtomSpecModel> map,
Object key, int model, int startPos, int endPos, String chain)
{
/*
* @param ssm
* @param files
* @param seqs
- * @param fr
- * @param alignment
+ * @param viewPanel
* @return
*/
public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
- ssm, files, seqs, fr, alignment);
+ ssm, files, seqs, viewPanel);
List<String> commands = buildSetAttributeCommands(featureMap);
* @param ssm
* @param files
* @param seqs
- * @param fr
- * @param alignment
+ * @param viewPanel
* @return
*/
protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ if (fr == null)
+ {
+ return theMap;
+ }
+
List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
if (visibleFeatures.isEmpty())
{
return theMap;
}
-
+
+ AlignmentI alignment = viewPanel.getAlignment();
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
StructureMapping mapping, SequenceI seq,
Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
- SequenceFeature[] sfs = seq.getSequenceFeatures();
- if (sfs == null)
- {
- return;
- }
-
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+ visibleFeatures.toArray(new String[visibleFeatures.size()]));
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
*/
boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
.equals(sf.getFeatureGroup());
- if (isFromViewer || !visibleFeatures.contains(type)
- || suppressFeature(type))
+ if (isFromViewer)
{
continue;
}
}
for (int[] range : mappedRanges)
{
- addRange(featureValues, value, modelNumber, range[0], range[1],
- mapping.getChain());
+ addColourRange(featureValues, value, modelNumber, range[0],
+ range[1], mapping.getChain());
}
}
}
}
/**
- * Answers true if the feature type is one we don't wish to propagate to
- * Chimera - for now, RESNUM
- *
- * @param type
- * @return
- */
- static boolean suppressFeature(String type)
- {
- return PDBChain.RESNUM_FEATURE.equals(type);
- }
-
- /**
* Traverse the map of features/values/models/chains/positions to construct a
* list of 'setattr' commands (one per distinct feature type and value).
* <p>
/*
* for each distinct value recorded for this feature type,
* add a command to set the attribute on the mapped residues
+ * Put values in single quotes, encoding any embedded single quotes
*/
StringBuilder sb = new StringBuilder(128);
- sb.append("setattr r ").append(attributeName).append(" \"")
- .append(value.toString()).append("\" ");
+ String featureValue = value.toString();
+ featureValue = featureValue.replaceAll("\\'", "'");
+ sb.append("setattr r ").append(attributeName).append(" '")
+ .append(featureValue).append("' ");
sb.append(values.get(value).getAtomSpec());
commands.add(sb.toString());
}
* to an underscore.
*
* @param featureType
- * @return <pre>
- * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
- * </pre>
+ * @return
+ *
+ * <pre>
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+ * </pre>
*/
protected static String makeAttributeName(String featureType)
{
git://source.jalview.org / jalview.git / blobdiff