import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
-import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
-import jalview.util.Format;
+import jalview.util.ColorUtils;
+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.TreeMap;
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
+ Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
+ ssm, files, sequence, sr, fr, alignment);
- ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+ List<String> colourCommands = buildColourCommands(colourMap);
+ StructureMappingcommandSet cs = new StructureMappingcommandSet(
+ ChimeraCommands.class, null,
+ colourCommands.toArray(new String[0]));
+
+ return new StructureMappingcommandSet[]
+ { cs };
+ }
+
+ /**
+ * 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
+ *
+ * <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
+ * #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ *
+ * @see http
+ * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
+ * .html </pre>
+ *
+ * @param colourMap
+ * @return
+ */
+ protected static List<String> buildColourCommands(
+ Map<Color, Map<Integer, Map<String, List<int[]>>>> 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<String>();
+ StringBuilder sb = new StringBuilder(256);
+ boolean firstColour = true;
+ for (Color colour : colourMap.keySet())
+ {
+ String colourCode = ColorUtils.toTkCode(colour);
+ if (!firstColour)
+ {
+ sb.append("; ");
+ }
+ sb.append("color ").append(colourCode).append(" ");
+ firstColour = false;
+ boolean firstModelForColour = true;
+ final Map<Integer, Map<String, List<int[]>>> colourData = colourMap.get(colour);
+ for (Integer model : colourData.keySet())
+ {
+ boolean firstPositionForModel = true;
+ if (!firstModelForColour)
+ {
+ sb.append("|");
+ }
+ firstModelForColour = false;
+ sb.append("#").append(model).append(":");
+
+ final Map<String, List<int[]>> modelData = colourData.get(model);
+ for (String chain : modelData.keySet())
+ {
+ 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]);
+ }
+ sb.append(".").append(chain);
+ firstPositionForModel = false;
+ }
+ }
+ }
+ }
+ commands.add(sb.toString());
+ return commands;
+ }
+
+ /**
+ * <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.
+ * 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>
+ */
+ protected static Map<Color, Map<Integer, Map<String, List<int[]>>>> buildColoursMap(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment)
+ {
+ Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
+ Color lastColour = null;
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- float cols[] = new float[4];
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
- StringBuffer command = new StringBuffer();
- StructureMappingcommandSet smc;
- ArrayList<String> str = new ArrayList<String>();
if (mapping == null || mapping.length < 1)
+ {
continue;
+ }
- int startPos = -1, lastPos = -1, startModel = -1, lastModel = -1;
- String startChain = "", lastChain = "";
- Color lastCol = null;
+ 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++)
{
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+ final SequenceI seq = sequence[pdbfnum][s];
+ if (mapping[m].getSequence() == seq
+ && (sp = alignment.findIndex(seq)) > -1)
{
SequenceI asp = alignment.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ if (Comparison.isGap(asp.getCharAt(r)))
{
continue;
}
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
+ {
continue;
+ }
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+ Color colour = sr.getResidueColour(seq, r, fr);
+ final String chain = mapping[m].getChain();
- if (fr != null)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
- if (lastCol != col || lastPos + 1 != pos
- || pdbfnum != lastModel
- || !mapping[m].getChain().equals(lastChain))
+ /*
+ * 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 (lastCol != null)
+ if (startPos != -1)
{
-
- lastCol.getRGBComponents(cols);
- String newSelcom = "color " + cols[0] + "," + cols[1]
- + "," + cols[2] + " #" + startModel + ":"
- + startPos + "-" + lastPos + "." + lastChain;
- if (str.size() > 0
- && (str.get(str.size() - 1).length() + newSelcom
- .length()) < 4096)
- {
- str.set(str.size() - 1, str.get(str.size() - 1) + ";"
- + newSelcom);
- }
- else
- {
- str.add(newSelcom);
- }
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
+ lastPos, lastChain);
}
- lastCol = null;
startPos = pos;
- startModel = pdbfnum;
- startChain = mapping[m].getChain();
}
- lastCol = col;
+ lastColour = colour;
lastPos = pos;
- lastModel = pdbfnum;
- lastChain = mapping[m].getChain();
+ lastChain = chain;
}
// final colour range
- if (lastCol != null)
+ if (lastColour != null)
{
-
- lastCol.getRGBComponents(cols);
- String newSelcom = "color " + cols[0] + "," + cols[1] + ","
- + cols[2] + " #" + startModel + ":" + startPos + "-"
- + lastPos + "." + lastChain;
- if (str.size() > 0
- && (str.get(str.size() - 1).length() + newSelcom
- .length()) < 4096)
- {
- str.set(str.size() - 1, str.get(str.size() - 1) + ";"
- + newSelcom);
- }
- else
- {
- str.add(newSelcom);
- }
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
+ lastPos, lastChain);
}
break;
}
}
}
- // Finally, add the command set ready to be returned.
- cset.add(new StructureMappingcommandSet(ChimeraCommands.class,
- files[pdbfnum], str.toArray(new String[str.size()])));
}
- return cset.toArray(new StructureMappingcommandSet[cset.size()]);
+ return colourMap;
+ }
+
+ /**
+ * Helper method to add one contiguous colour range to the colour map.
+ *
+ * @param colourMap
+ * @param colour
+ * @param model
+ * @param startPos
+ * @param endPos
+ * @param chain
+ */
+ protected static void addColourRange(
+ Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap,
+ Color colour, int model, int startPos, int endPos, String chain)
+ {
+ /*
+ * Get/initialize map of data for the colour
+ */
+ Map<Integer, Map<String, List<int[]>>> colourData = colourMap
+ .get(colour);
+ if (colourData == null)
+ {
+ colourMap
+ .put(colour,
+ colourData = new TreeMap<Integer, Map<String, List<int[]>>>());
+ }
+
+ /*
+ * Get/initialize map of data for the colour and model
+ */
+ Map<String, List<int[]>> modelData = colourData.get(model);
+ if (modelData == null)
+ {
+ colourData.put(model, modelData = new TreeMap<String, List<int[]>>());
+ }
+
+ /*
+ * Get/initialize map of data for colour, model and chain
+ */
+ List<int[]> chainData = modelData.get(chain);
+ if (chainData == null)
+ {
+ modelData.put(chain, chainData = new ArrayList<int[]>());
+ }
+
+ /*
+ * Add the start/end positions
+ */
+ chainData.add(new int[]
+ { startPos, endPos });
}
}
git://source.jalview.org / jalview.git / blobdiff