1 package jalview.schemes;
\r
3 import jalview.datamodel.*;
\r
7 public class PIDColourScheme extends ResidueColourScheme {
\r
8 public Color[] pidColours;
\r
9 public float[] thresholds;
\r
11 SequenceGroup group;
\r
13 public PIDColourScheme() {
\r
14 this.pidColours = ResidueProperties.pidColours;
\r
15 this.thresholds = ResidueProperties.pidThresholds;
\r
19 public Color findColour(SequenceI seq,String s, int j,Vector aa) {
\r
20 Color c = Color.white;
\r
21 Hashtable hash = null;
\r
25 hash = (Hashtable)aa.elementAt(j);
\r
29 String max = (String)hash.get("maxResidue");
\r
32 if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))
\r
35 sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;
\r
36 // MC Should be isGap
\r
37 if (!s.equals("-") && !s.equals(".") && !s.equals(" "))
\r
39 for (int i = 0; i < thresholds.length; i++)
\r
41 if (sc > thresholds[i])
\r