import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
+import jalview.util.IntRangeComparator;
import java.awt.Color;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashMap;
+import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
*/
public class ChimeraCommands
{
-
public static final String NAMESPACE_PREFIX = "jv_";
+ /*
+ * colour for residues shown in structure but hidden in alignment
+ */
+ private static final String COLOR_GRAY_HEX = "color "
+ + ColorUtils.toTkCode(Color.GRAY);
+
/**
* Constructs Chimera commands to colour residues as per the Jalview alignment
*
- * @param ssm
- * @param files
- * @param sequence
- * @param sr
- * @param fr
- * @param viewPanel
+ * @param colourMap
+ * @param binding
* @return
*/
- public static StructureMappingcommandSet[] getColourBySequenceCommand(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr,
- AlignmentViewPanel viewPanel)
+ public static String[] getColourBySequenceCommand(
+ Map<Object, AtomSpecModel> colourMap,
+ AAStructureBindingModel binding)
{
- Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
- sequence, sr, viewPanel);
-
- List<String> colourCommands = buildColourCommands(colourMap);
-
- StructureMappingcommandSet cs = new StructureMappingcommandSet(
- ChimeraCommands.class, null,
- colourCommands.toArray(new String[colourCommands.size()]));
+ List<String> colourCommands = buildColourCommands(colourMap, binding);
- return new StructureMappingcommandSet[] { cs };
+ return colourCommands.toArray(new String[colourCommands.size()]);
}
/**
* </pre>
*
* @param colourMap
+ * @param binding
* @return
*/
protected static List<String> buildColourCommands(
- Map<Object, AtomSpecModel> colourMap)
+ Map<Object, AtomSpecModel> colourMap,
+ AAStructureBindingModel binding)
{
/*
* This version concatenates all commands into a single String (semi-colon
*/
List<String> commands = new ArrayList<>();
StringBuilder sb = new StringBuilder(256);
- boolean firstColour = true;
+ sb.append(COLOR_GRAY_HEX);
+
for (Object key : colourMap.keySet())
{
Color colour = (Color) key;
String colourCode = ColorUtils.toTkCode(colour);
- if (!firstColour)
- {
- sb.append("; ");
- }
+ sb.append("; ");
sb.append("color ").append(colourCode).append(" ");
- firstColour = false;
final AtomSpecModel colourData = colourMap.get(colour);
- sb.append(colourData.getAtomSpec());
+ sb.append(getAtomSpec(colourData, binding));
}
commands.add(sb.toString());
return commands;
}
/**
- * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and
- * builds a Chimera format atom spec
+ * Build a data structure which records contiguous subsequences for each colour.
+ * From this we can easily generate the Chimera command for colour by sequence.
*
- * @param modelAndChainRanges
- */
- protected static String getAtomSpec(
- Map<Integer, Map<String, List<int[]>>> modelAndChainRanges)
- {
- StringBuilder sb = new StringBuilder(128);
- boolean firstModelForColour = true;
- for (Integer model : modelAndChainRanges.keySet())
- {
- boolean firstPositionForModel = true;
- if (!firstModelForColour)
- {
- sb.append("|");
- }
- firstModelForColour = false;
- sb.append("#").append(model).append(":");
-
- final Map<String, List<int[]>> modelData = modelAndChainRanges
- .get(model);
- for (String chain : modelData.keySet())
- {
- boolean hasChain = !"".equals(chain.trim());
- for (int[] range : modelData.get(chain))
- {
- if (!firstPositionForModel)
- {
- sb.append(",");
- }
- if (range[0] == range[1])
- {
- sb.append(range[0]);
- }
- else
- {
- sb.append(range[0]).append("-").append(range[1]);
- }
- if (hasChain)
- {
- sb.append(".").append(chain);
- }
- firstPositionForModel = false;
- }
- }
- }
- return sb.toString();
- }
-
- /**
* <pre>
- * 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
* list of start/end ranges
- * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
* </pre>
+ *
+ * Ordering is by order of addition (for colours and positions), natural
+ * ordering (for models and chains)
+ *
+ * @param ssm
+ * @param files
+ * @param sequence
+ * @param sr
+ * @param hideHiddenRegions
+ * @param viewPanel
+ * @return
*/
protected static Map<Object, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr,
- AlignmentViewPanel viewPanel)
+ boolean hideHiddenRegions, AlignmentViewPanel viewPanel)
{
FeatureRenderer fr = viewPanel.getFeatureRenderer();
FeatureColourFinder finder = new FeatureColourFinder(fr);
Color colour = sr.getResidueColour(seq, r, finder);
/*
- * darker colour for hidden regions
+ * hidden regions are shown gray or, optionally, ignored
*/
if (!cs.isVisible(r))
{
- colour = Color.GRAY;
+ if (hideHiddenRegions)
+ {
+ continue;
+ }
+ else
+ {
+ colour = Color.GRAY;
+ }
}
final String chain = mapping[m].getChain();
* @param endPos
* @param chain
*/
- protected static void addAtomSpecRange(Map<Object, AtomSpecModel> map,
+ public static void addAtomSpecRange(Map<Object, AtomSpecModel> map,
Object value, int model, int startPos, int endPos, String chain)
{
/*
/**
* Constructs and returns Chimera commands to set attributes on residues
- * corresponding to features in Jalview. Attribute names are the Jalview
- * feature type, with a "jv_" prefix.
+ * corresponding to features in Jalview. Attribute names are the Jalview feature
+ * type, with a "jv_" prefix.
*
* @param ssm
* @param files
* @param seqs
* @param viewPanel
+ * @param binding
* @return
*/
public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
- StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
- AlignmentViewPanel viewPanel)
+ AlignmentViewPanel viewPanel, AAStructureBindingModel binding)
{
+ StructureSelectionManager ssm = binding.getSsm();
+ String[] files = binding.getStructureFiles();
+ SequenceI[][] seqs = binding.getSequence();
+
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
ssm, files, seqs, viewPanel);
- List<String> commands = buildSetAttributeCommands(featureMap);
+ List<String> commands = buildSetAttributeCommands(featureMap, binding);
StructureMappingcommandSet cs = new StructureMappingcommandSet(
ChimeraCommands.class, null,
* </pre>
*
* @param featureMap
+ * @param binding
* @return
*/
protected static List<String> buildSetAttributeCommands(
- Map<String, Map<Object, AtomSpecModel>> featureMap)
+ Map<String, Map<Object, AtomSpecModel>> featureMap,
+ AAStructureBindingModel binding)
{
List<String> commands = new ArrayList<>();
for (String featureType : featureMap.keySet())
featureValue = featureValue.replaceAll("\\'", "'");
sb.append("setattr r ").append(attributeName).append(" '")
.append(featureValue).append("' ");
- sb.append(values.get(value).getAtomSpec());
+ sb.append(getAtomSpec(values.get(value), binding));
commands.add(sb.toString());
}
}
return attName;
}
+ /**
+ * Returns the range(s) formatted as a Chimera atomspec
+ *
+ * @return
+ */
+ public static String getAtomSpec(AtomSpecModel atomSpec,
+ AAStructureBindingModel binding)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModel = true;
+ for (Integer model : atomSpec.getModels())
+ {
+ if (!firstModel)
+ {
+ sb.append("|");
+ }
+ firstModel = false;
+ // todo use JalviewChimeraBinding.getModelSpec(model)
+ // which means this cannot be static
+ sb.append(binding.getModelSpec(model)).append(":");
+
+ boolean firstPositionForModel = true;
+
+ for (String chain : atomSpec.getChains(model))
+ {
+ chain = " ".equals(chain) ? chain : chain.trim();
+
+ List<int[]> rangeList = atomSpec.getRanges(model, chain);
+
+ /*
+ * sort ranges into ascending start position order
+ */
+ Collections.sort(rangeList, IntRangeComparator.ASCENDING);
+
+ int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
+ int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
+
+ Iterator<int[]> iterator = rangeList.iterator();
+ while (iterator.hasNext())
+ {
+ int[] range = iterator.next();
+ if (range[0] <= end + 1)
+ {
+ /*
+ * range overlaps or is contiguous with the last one
+ * - so just extend the end position, and carry on
+ * (unless this is the last in the list)
+ */
+ end = Math.max(end, range[1]);
+ }
+ else
+ {
+ /*
+ * we have a break so append the last range
+ */
+ appendRange(sb, start, end, chain, firstPositionForModel);
+ firstPositionForModel = false;
+ start = range[0];
+ end = range[1];
+ }
+ }
+
+ /*
+ * and append the last range
+ */
+ if (!rangeList.isEmpty())
+ {
+ appendRange(sb, start, end, chain, firstPositionForModel);
+ firstPositionForModel = false;
+ }
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * A helper method that appends one start-end range to a Chimera atomspec
+ *
+ * @param sb
+ * @param start
+ * @param end
+ * @param chain
+ * @param firstPositionForModel
+ */
+ static void appendRange(StringBuilder sb, int start, int end,
+ String chain, boolean firstPositionForModel)
+ {
+ if (!firstPositionForModel)
+ {
+ sb.append(",");
+ }
+ if (end == start)
+ {
+ sb.append(start);
+ }
+ else
+ {
+ sb.append(start).append("-").append(end);
+ }
+
+ sb.append(".");
+ if (!" ".equals(chain))
+ {
+ sb.append(chain);
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff