package jalview.structure;
-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.renderer.seqfeatures.FeatureColourFinder;
-import jalview.util.Comparison;
-
import java.awt.Color;
import java.util.ArrayList;
-import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
*/
public abstract class StructureCommandsBase implements StructureCommandsI
{
+ public static final String NAMESPACE_PREFIX = "jv_";
+
private static final String CMD_SEPARATOR = ";";
/**
return CMD_SEPARATOR;
}
- @Override
- public String[] setAttributesForFeatures(StructureSelectionManager ssm,
- String[] files, SequenceI[][] sequence, AlignmentViewPanel avp)
- {
- // default does nothing, override where this is implemented
- return null;
- }
-
/**
* Returns the lowest model number used by the structure viewer
*
}
/**
- * <pre>
- * Build a data structure which records contiguous subsequences for each colour.
- * From this we can easily generate the viewer 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>
- *
- * @param ssm
- * @param files
- * @param sequence
- * @param sr
- * @param viewPanel
- * @return
- */
- protected Map<Object, AtomSpecModel> buildColoursMap(
- 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();
- Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
- Color lastColour = null;
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- final int modelNumber = pdbfnum + getModelStartNo();
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- {
- continue;
- }
-
- int startPos = -1, lastPos = -1;
- String lastChain = "";
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- final SequenceI seq = sequence[pdbfnum][s];
- if (mapping[m].getSequence() == seq
- && (sp = al.findIndex(seq)) > -1)
- {
- 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 < 1 || pos == lastPos)
- {
- continue;
- }
-
- 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();
-
- /*
- * Just keep incrementing the end position for this colour range
- * _unless_ colour, PDB model or chain has changed, or there is a
- * gap in the mapped residue sequence
- */
- final boolean newColour = !colour.equals(lastColour);
- final boolean nonContig = lastPos + 1 != pos;
- final boolean newChain = !chain.equals(lastChain);
- if (newColour || nonContig || newChain)
- {
- if (startPos != -1)
- {
- addAtomSpecRange(colourMap, lastColour, modelNumber,
- startPos, lastPos, lastChain);
- }
- startPos = pos;
- }
- lastColour = colour;
- lastPos = pos;
- lastChain = chain;
- }
- // final colour range
- if (lastColour != null)
- {
- addAtomSpecRange(colourMap, lastColour, modelNumber, startPos,
- lastPos, lastChain);
- }
- // break;
- }
- }
- }
- }
- return colourMap;
- }
-
- /**
* Helper method to add one contiguous range to the AtomSpec model for the given
* value (creating the model if necessary). As used by Jalview, {@code value} is
* <ul>
* @param chain
*/
public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
- Object value,
- int model, int startPos, int endPos, String chain)
+ Object value, String model, int startPos, int endPos,
+ String chain)
{
/*
* Get/initialize map of data for the colour
}
/**
- * Returns a colour formatted suitable for use in viewer command syntax
+ * Makes a structure viewer attribute name for a Jalview feature type by
+ * prefixing it with "jv_", and replacing any non-alphanumeric characters with
+ * an underscore
*
- * @param colour
+ * @param featureType
* @return
*/
- protected abstract String getColourString(Color colour);
+ protected String makeAttributeName(String featureType)
+ {
+ StringBuilder sb = new StringBuilder();
+ if (featureType != null)
+ {
+ for (char c : featureType.toCharArray())
+ {
+ sb.append(Character.isLetterOrDigit(c) ? c : '_');
+ }
+ }
+ String attName = NAMESPACE_PREFIX + sb.toString();
+ return attName;
+ }
/**
* Traverse the map of colours/models/chains/positions to construct a list of
* 'color' commands (one per distinct colour used). The format of each command
* is specific to the structure viewer.
+ * <p>
+ * The default implementation returns a single command containing one command
+ * per colour, concatenated.
*
* @param colourMap
* @return
*/
- public List<String> buildColourCommands(
+ @Override
+ public List<StructureCommandI> colourBySequence(
Map<Object, AtomSpecModel> colourMap)
{
- /*
- * This version concatenates all commands into a single String (semi-colon
- * delimited). If length limit issues arise, refactor to return one color
- * command per colour.
- */
- List<String> commands = new ArrayList<>();
- StringBuilder sb = new StringBuilder(256);
- boolean firstColour = true;
+ List<StructureCommandI> commands = new ArrayList<>();
+ StringBuilder sb = new StringBuilder(colourMap.size() * 20);
+ boolean first = true;
for (Object key : colourMap.keySet())
{
Color colour = (Color) key;
- if (!firstColour)
+ final AtomSpecModel colourData = colourMap.get(colour);
+ StructureCommandI command = getColourCommand(colourData, colour);
+ if (!first)
{
- sb.append(getCommandSeparator()).append(" ");
+ sb.append(getCommandSeparator());
}
- firstColour = false;
- final AtomSpecModel colourData = colourMap.get(colour);
- sb.append(getColourCommand(colourData, colour));
+ first = false;
+ sb.append(command.getCommand());
}
- commands.add(sb.toString());
+
+ commands.add(new StructureCommand(sb.toString()));
return commands;
}
* @param colour
* @return
*/
- protected String getColourCommand(AtomSpecModel atomSpecModel, Color colour)
+ protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
+ Color colour)
{
String atomSpec = getAtomSpec(atomSpecModel, false);
- return getColourCommand(atomSpec, colour);
+ return colourResidues(atomSpec, colour);
}
/**
* @param colour
* @return
*/
- protected abstract String getColourCommand(String atomSpec, Color colour);
+ protected abstract StructureCommandI colourResidues(String atomSpec,
+ Color colour);
@Override
- public String colourByResidues(Map<String, Color> colours)
+ public List<StructureCommandI> colourByResidues(
+ Map<String, Color> colours)
{
- StringBuilder cmd = new StringBuilder(12 * colours.size());
-
+ List<StructureCommandI> commands = new ArrayList<>();
for (Entry<String, Color> entry : colours.entrySet())
{
- String residue = entry.getKey();
- String atomSpec = getResidueSpec(residue);
- cmd.append(getColourCommand(atomSpec, entry.getValue()));
- cmd.append(getCommandSeparator());
+ commands.add(colourResidue(entry.getKey(), entry.getValue()));
}
- return cmd.toString();
+ return commands;
+ }
+
+ private StructureCommandI colourResidue(String resName, Color col)
+ {
+ String atomSpec = getResidueSpec(resName);
+ return colourResidues(atomSpec, col);
}
/**
* @return
*/
protected abstract String getResidueSpec(String residue);
+
+ @Override
+ public List<StructureCommandI> setAttributes(
+ Map<String, Map<Object, AtomSpecModel>> featureValues)
+ {
+ // default does nothing, override where this is implemented
+ return null;
+ }
+
+ @Override
+ public List<StructureCommandI> startNotifications(String uri)
+ {
+ return null;
+ }
+
+ @Override
+ public List<StructureCommandI> stopNotifications()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff