/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*/
package jalview.schemes;
-import java.util.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
-import java.awt.*;
-
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
public class ClustalxColourScheme extends ResidueColourScheme // implements
// IParameterizable
colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
- colhash
- .put("MAGENTA",
- new Color((float) 0.8, (float) 0.3, (float) 0.8));
+ colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
}
- public ClustalxColourScheme(Vector seqs, int maxWidth)
+ public ClustalxColourScheme(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps)
{
- resetClustalX(seqs, maxWidth);
+ alignmentChanged(alignment,hiddenReps);
}
-
- public void resetClustalX(Vector seqs, int maxWidth)
- {
+ public void alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps) {
+ int maxWidth=alignment.getWidth();
+ List<SequenceI> seqs=alignment.getSequences(hiddenReps);
cons2 = new int[maxWidth][24];
includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
// get the current setting of the
int j = 0;
char[] seq;
- while (j < seqs.size())
+ for (SequenceI sq: seqs)
{
- seq = ((SequenceI) seqs.elementAt(j)).getSequence();
+ seq = sq.getSequence();
int end_j = seq.length - 1;
tmp6[0] = conses[3]; // -
tmp6[1] = conses[29]; // D
tmp6[2] = conses[10]; // E
- tmp6[3] = conses[6]; // QE
+ tmp6[3] = conses[6]; // QE
tmp6[4] = conses[19]; // Q
tmp6[5] = conses[2]; // DE
colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
ResidueColour[19] = colours[0]; // V
}
+ @Override
public Color findColour(char c)
{
return Color.pink;
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;