* @param end
* end column position
*/
- public Conservation(String name, int threshold,
- List<SequenceI> sequences, int start, int end)
+ public Conservation(String name, int threshold, List<SequenceI> sequences,
+ int start, int end)
{
this.name = name;
this.threshold = threshold;
else
{
// JBPNote INFO level debug
- System.err
- .println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
+ System.err.println(
+ "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
}
}
continue;
}
- char c = sequences[i].getCharAt(column); // gaps do not have upper/lower case
+ char c = sequences[i].getCharAt(column); // gaps do not have upper/lower
+ // case
if (Comparison.isGap((c)))
{
* @param endCol
* @param scoreMatrix
*/
- protected void findQuality(int startCol, int endCol, ScoreMatrix scoreMatrix)
+ protected void findQuality(int startCol, int endCol,
+ ScoreMatrix scoreMatrix)
{
quality = new Vector<Double>();
public void completeAnnotations(AlignmentAnnotation conservation,
AlignmentAnnotation quality2, int istart, int alWidth)
{
- char[] sequence = getConsSequence().getSequence();
- float minR;
- float minG;
- float minB;
- float maxR;
- float maxG;
- float maxB;
- minR = 0.3f;
- minG = 0.0f;
- minB = 0f;
- maxR = 1.0f - minR;
- maxG = 0.9f - minG;
- maxB = 0f - minB; // scalable range for colouring both Conservation and
- // Quality
+ SequenceI cons = getConsSequence();
+
+ /*
+ * colour scale for Conservation and Quality;
+ */
+ float minR = 0.3f;
+ float minG = 0.0f;
+ float minB = 0f;
+ float maxR = 1.0f - minR;
+ float maxG = 0.9f - minG;
+ float maxB = 0f - minB;
float min = 0f;
float max = 11f;
float qmin = 0f;
float qmax = 0f;
- char c;
-
if (conservation != null && conservation.annotations != null
&& conservation.annotations.length < alWidth)
{
{
float value = 0;
- c = sequence[i];
+ char c = cons.getCharAt(i);
if (Character.isDigit(c))
{
float vprop = value - min;
vprop /= max;
int consp = i - start;
- String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
- : "";
+ String conssym = (value > 0 && consp > -1
+ && consp < consSymbs.length) ? consSymbs[consp] : "";
conservation.annotations[i] = new Annotation(String.valueOf(c),
- conssym, ' ', value, new Color(minR + (maxR * vprop), minG
- + (maxG * vprop), minB + (maxB * vprop)));
+ conssym, ' ', value, new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop), minB + (maxB * vprop)));
}
// Quality calc
value = quality.elementAt(i).floatValue();
float vprop = value - qmin;
vprop /= qmax;
- quality2.annotations[i] = new Annotation(" ",
- String.valueOf(value), ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
+ quality2.annotations[i] = new Annotation(" ", String.valueOf(value),
+ ' ', value, new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop), minB + (maxB * vprop)));
}
}
}
*/
String getTooltip(int column)
{
- char[] sequence = getConsSequence().getSequence();
- char val = column < sequence.length ? sequence[column] : '-';
+ SequenceI cons = getConsSequence();
+ char val = column < cons.getLength() ? cons.getCharAt(column) : '-';
boolean hasConservation = val != '-' && val != '0';
int consp = column - start;
- String tip = (hasConservation && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ String tip = (hasConservation && consp > -1 && consp < consSymbs.length)
+ ? consSymbs[consp]
: "";
return tip;
}