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 java.awt.Color;
import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.Map;
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
{
ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
- Hashtable<String,StringBuffer> colranges=new Hashtable<String,StringBuffer>();
+
+ /*
+ * Map of { colour, positionSpecs}
+ */
+ Map<String, StringBuilder> colranges = new LinkedHashMap<String, StringBuilder>();
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 = "";
+ String lastChain = "";
Color lastCol = null;
for (int s = 0; s < sequence[pdbfnum].length; s++)
{
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
+ {
continue;
+ }
Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
if (fr != null)
+ {
col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+ }
if (lastCol != col || lastPos + 1 != pos
|| pdbfnum != lastModel
|| !mapping[m].getChain().equals(lastChain))
lastCol = null;
startPos = pos;
startModel = pdbfnum;
- startChain = mapping[m].getChain();
}
lastCol = col;
lastPos = pos;
}
}
// Finally, add the command set ready to be returned.
- StringBuffer coms=new StringBuffer();
+ StringBuilder coms = new StringBuilder(256);
for (String cr:colranges.keySet())
{
coms.append("color #"+cr+" "+colranges.get(cr)+";");
return cset.toArray(new StructureMappingcommandSet[cset.size()]);
}
- private static void addColourRange(Hashtable<String, StringBuffer> colranges, Color lastCol, int startModel,
- int startPos, int lastPos, String lastChain)
+ /**
+ * Helper method to record a range of positions of the same colour.
+ *
+ * @param colranges
+ * @param colour
+ * @param model
+ * @param startPos
+ * @param endPos
+ * @param chain
+ */
+ private static void addColourRange(Map<String, StringBuilder> colranges,
+ Color colour, int model,
+ int startPos, int endPos, String chain)
{
-
- String colstring = ((lastCol.getRed()< 16) ? "0":"")+Integer.toHexString(lastCol.getRed())
- + ((lastCol.getGreen()< 16) ? "0":"")+Integer.toHexString(lastCol.getGreen())
- + ((lastCol.getBlue()< 16) ? "0":"")+Integer.toHexString(lastCol.getBlue());
- StringBuffer currange = colranges.get(colstring);
- if (currange==null)
+ String colstring = ((colour.getRed()< 16) ? "0":"")+Integer.toHexString(colour.getRed())
+ + ((colour.getGreen()< 16) ? "0":"")+Integer.toHexString(colour.getGreen())
+ + ((colour.getBlue()< 16) ? "0":"")+Integer.toHexString(colour.getBlue());
+ StringBuilder currange = colranges.get(colstring);
+ if (currange == null)
{
- colranges.put(colstring,currange = new StringBuffer());
+ colranges.put(colstring, currange = new StringBuilder(256));
}
- if (currange.length()>0)
+ if (currange.length() > 0)
{
currange.append("|");
}
- currange.append("#" + startModel + ":" + ((startPos==lastPos) ? startPos : startPos + "-"
- + lastPos) + "." + lastChain);
+ currange.append("#" + model + ":" + ((startPos==endPos) ? startPos : startPos + "-"
+ + endPos) + "." + chain);
}
}