import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
-import java.util.HashMap;
import java.util.List;
import java.util.Map;
private static final int SIXTY = 60;
- /*
- * Map from conventional colour names to Clustal version of the same
- */
- private static Map<Color, Color> colhash = new HashMap<Color, Color>();
+ enum ClustalColour
+ {
+ RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
+ ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
+ PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), YELLOW(0.8f, 0.8f,
+ 0.0f);
+
+ final Color colour;
+
+ ClustalColour(float r, float g, float b)
+ {
+ colour = new Color(r, g, b);
+ }
+ }
+ private class ConsensusColour
+ {
+ Consensus[] cons;
+
+ Color c;
+
+ public ConsensusColour(ClustalColour col, Consensus[] conses)
+ {
+ this.cons = conses;
+ this.c = col.colour;
+ }
+ }
private int[][] cons2;
private boolean includeGaps = true;
- static
+ /**
+ * Default constructor (required for Class.newInstance())
+ */
+ public ClustalxColourScheme()
{
- colhash.put(Color.RED, new Color(0.9f, 0.2f, 0.1f));
- colhash.put(Color.BLUE, new Color(0.5f, 0.7f, 0.9f));
- colhash.put(Color.GREEN, new Color(0.1f, 0.8f, 0.1f));
- colhash.put(Color.ORANGE, new Color(0.9f, 0.6f, 0.3f));
- colhash.put(Color.CYAN, new Color(0.1f, 0.7f, 0.7f));
- colhash.put(Color.PINK, new Color(0.9f, 0.5f, 0.5f));
- colhash.put(Color.MAGENTA, new Color(0.8f, 0.3f, 0.8f));
- colhash.put(Color.YELLOW, new Color(0.8f, 0.8f, 0.0f));
+
}
public ClustalxColourScheme(AnnotatedCollectionI alignment,
alignmentChanged(alignment, hiddenReps);
}
+ @Override
public void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
// get the current setting of the
// includeGaps param.
- int start = 0;
-
- // Initialize the array
- for (int j = 0; j < 24; j++)
- {
- for (int i = 0; i < maxWidth; i++)
- {
- cons2[i][j] = 0;
- }
- }
-
- int res;
- int i;
- int j = 0;
- char[] seq;
+ int res = 0;
for (SequenceI sq : seqs)
{
- seq = sq.getSequence();
+ char[] seq = sq.getSequence();
int end_j = seq.length - 1;
- for (i = start; i <= end_j; i++)
+ for (int i = 0; i <= end_j; i++)
{
if ((seq.length - 1) < i)
{
{
res = ResidueProperties.aaIndex[seq[i]];
}
-
cons2[i][res]++;
}
-
- j++;
}
this.size = seqs.size();
makeColours();
}
- public void makeColours()
+ void makeColours()
{
conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
Consensus[] tmp8 = new Consensus[1];
tmp8[0] = conses[30]; // G
- colours[7] = new ConsensusColour(colhash.get(Color.ORANGE), tmp8);
+ colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8);
Consensus[] tmp9 = new Consensus[1];
tmp9[0] = conses[31]; // P
- colours[8] = new ConsensusColour(colhash.get(Color.YELLOW), tmp9);
+ colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9);
Consensus[] tmp10 = new Consensus[1];
tmp10[0] = conses[27]; // C
- colours[9] = new ConsensusColour(colhash.get(Color.PINK), tmp8);
+ colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8);
Consensus[] tmp1 = new Consensus[14];
tmp1[0] = conses[0]; // %
tmp1[11] = conses[25]; // Y
tmp1[12] = conses[18]; // P
tmp1[13] = conses[19]; // p
- colours[0] = new ConsensusColour(colhash.get(Color.BLUE), tmp1);
+ colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1);
- colours[10] = new ConsensusColour(colhash.get(Color.CYAN), tmp1);
+ colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1);
Consensus[] tmp2 = new Consensus[5];
tmp2[0] = conses[8]; // t
tmp2[2] = conses[22]; // T
tmp2[3] = conses[0]; // %
tmp2[4] = conses[1]; // #
- colours[1] = new ConsensusColour(colhash.get(Color.GREEN), tmp2);
+ colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2);
Consensus[] tmp3 = new Consensus[3];
tmp3[0] = conses[17]; // N
tmp3[1] = conses[29]; // D
tmp3[2] = conses[5]; // n
- colours[2] = new ConsensusColour(colhash.get(Color.GREEN), tmp3);
+ colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3);
Consensus[] tmp4 = new Consensus[6];
tmp4[0] = conses[6]; // q = QE
tmp4[3] = conses[3]; // +
tmp4[4] = conses[28]; // K
tmp4[5] = conses[20]; // R
- colours[3] = new ConsensusColour(colhash.get(Color.GREEN), tmp4);
+ colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4);
Consensus[] tmp5 = new Consensus[4];
tmp5[0] = conses[3]; // +
tmp5[1] = conses[28]; // K
tmp5[2] = conses[20]; // R
tmp5[3] = conses[19]; // Q
- colours[4] = new ConsensusColour(colhash.get(Color.RED), tmp5);
+ colours[4] = new ConsensusColour(ClustalColour.RED, tmp5);
Consensus[] tmp6 = new Consensus[6];
tmp6[0] = conses[3]; // -
tmp6[3] = conses[6]; // QE
tmp6[4] = conses[19]; // Q
tmp6[5] = conses[2]; // DE
- colours[5] = new ConsensusColour(colhash.get(Color.MAGENTA), tmp6);
+ colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6);
Consensus[] tmp7 = new Consensus[5];
tmp7[0] = conses[3]; // -
tmp7[2] = conses[10]; // E
tmp7[3] = conses[17]; // N
tmp7[4] = conses[2]; // DE
- colours[6] = new ConsensusColour(colhash.get(Color.MAGENTA), tmp7);
+ colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7);
// Now attach the ConsensusColours to the residue letters
residueColour = new ConsensusColour[20];
}
@Override
- public Color findColour(char c, int j, SequenceI seq)
+ protected Color findColour(char c, int j, SequenceI seq)
{
- Color currentColour;
-
- if (cons2.length <= j
- || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+ // TODO why the test for includeGaps here?
+ if (cons2.length <= j || Comparison.isGap(c)
+ /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
{
return Color.white;
}
int i = ResidueProperties.aaIndex[c];
- currentColour = Color.white;
+ Color colour = Color.white;
if (i > 19)
{
- return currentColour;
+ return colour;
}
- for (int k = 0; k < residueColour[i].conses.length; k++)
+ for (int k = 0; k < residueColour[i].cons.length; k++)
{
- if (residueColour[i].conses[k].isConserved(cons2, j, size,
+ if (residueColour[i].cons[k].isConserved(cons2, j, size,
includeGaps))
{
- currentColour = residueColour[i].c;
+ colour = residueColour[i].c;
}
}
if (i == 4)
{
+ /*
+ * override to colour C pink if >85% conserved
+ */
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
- currentColour = colhash.get(Color.PINK);
+ colour = ClustalColour.PINK.colour;
}
}
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return colour;
}
/**
}
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
ClustalxColourScheme css = new ClustalxColourScheme(sg,
css.includeGaps = includeGaps;
return css;
}
-}
-class ConsensusColour
-{
- Consensus[] conses;
-
- Color c;
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
- public ConsensusColour(Color c, Consensus[] conses)
+ @Override
+ public String getSchemeName()
{
- this.conses = conses;
+ return JalviewColourScheme.Clustal.toString();
+ }
- // this.list = list;
- this.c = c;
+ @Override
+ public boolean isSimple()
+ {
+ return false;
}
}
git://source.jalview.org / jalview.git / blobdiff