X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FFeatureColour.java;h=6483b85eb67900b4abacd867dc25f675b4f6156c;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=71a3d51209827c16224b79973d775d19079007b6;hpb=dcfba29a940c44003581f28e6da481450aa86575;p=jalview.git diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java index 71a3d51..6483b85 100644 --- a/src/jalview/schemes/FeatureColour.java +++ b/src/jalview/schemes/FeatureColour.java @@ -365,8 +365,8 @@ public class FeatureColour implements FeatureColourI Color maxColour = ColorUtils.parseColourString(maxcol); Color noColour = noValueColour.equals(NO_VALUE_MAX) ? maxColour : (noValueColour.equals(NO_VALUE_NONE) ? null : minColour); - featureColour = new FeatureColour(minColour, maxColour, noColour, min, - max); + featureColour = new FeatureColour(maxColour, minColour, maxColour, + noColour, min, max); featureColour.setColourByLabel(minColour == null); featureColour.setAutoScaled(autoScaled); if (byAttribute) @@ -436,36 +436,25 @@ public class FeatureColour implements FeatureColourI } /** - * Constructor given a simple colour + * Constructor given a simple colour. This also 'primes' a graduated colour + * range, where the maximum colour is the given simple colour, and the minimum + * colour a paler shade of it. This is for convenience when switching from a + * simple colour to a graduated colour scheme. * * @param c */ public FeatureColour(Color c) { - minColour = Color.WHITE; - maxColour = Color.BLACK; - noColour = DEFAULT_NO_COLOUR; - minRed = 0f; - minGreen = 0f; - minBlue = 0f; - deltaRed = 0f; - deltaGreen = 0f; - deltaBlue = 0f; - colour = c; - } + /* + * set max colour to the simple colour, min colour to a paler shade of it + */ + this(c, c == null ? Color.white : ColorUtils.bleachColour(c, 0.9f), + c == null ? Color.black : c, DEFAULT_NO_COLOUR, 0, 0); - /** - * Constructor given a colour range and a score range, defaulting 'no value - * colour' to be the same as minimum colour - * - * @param low - * @param high - * @param min - * @param max - */ - public FeatureColour(Color low, Color high, float min, float max) - { - this(low, high, low, min, max); + /* + * but enforce simple colour for now! + */ + setGraduatedColour(false); } /** @@ -498,29 +487,23 @@ public class FeatureColour implements FeatureColourI } /** - * Copy constructor with new min/max ranges - * - * @param fc - * @param min - * @param max - */ - public FeatureColour(FeatureColour fc, float min, float max) - { - this(fc); - updateBounds(min, max); - } - - /** - * Constructor for a graduated colour + * Constructor that sets both simple and graduated colour values. This allows + * alternative colour schemes to be 'preserved' while switching between them + * to explore their effects on the visualisation. + *
+ * This sets the colour scheme to 'graduated' by default. Override this if
+ * wanted by calling setGraduatedColour(false)
for a simple
+ * colour, or setColourByLabel(true)
for colour by label.
*
+ * @param myColour
* @param low
* @param high
* @param noValueColour
* @param min
* @param max
*/
- public FeatureColour(Color low, Color high, Color noValueColour,
- float min, float max)
+ public FeatureColour(Color myColour, Color low, Color high,
+ Color noValueColour, float min, float max)
{
if (low == null)
{
@@ -530,10 +513,10 @@ public class FeatureColour implements FeatureColourI
{
high = Color.black;
}
- graduatedColour = true;
- colour = null;
+ colour = myColour;
minColour = low;
maxColour = high;
+ setGraduatedColour(true);
noColour = noValueColour;
threshold = Float.NaN;
isHighToLow = min >= max;
@@ -565,7 +548,7 @@ public class FeatureColour implements FeatureColourI
* Sets the 'graduated colour' flag. If true, also sets 'colour by label' to
* false.
*/
- void setGraduatedColour(boolean b)
+ public void setGraduatedColour(boolean b)
{
graduatedColour = b;
if (b)
@@ -696,9 +679,12 @@ public class FeatureColour implements FeatureColourI
/**
* Returns the colour for the given instance of the feature. This may be a
- * simple colour, a colour generated from the feature description (if
- * isColourByLabel()), or a colour derived from the feature score (if
- * isGraduatedColour()).
+ * simple colour, a colour generated from the feature description or other
+ * attribute (if isColourByLabel()), or a colour derived from the feature
+ * score or other attribute (if isGraduatedColour()).
+ *
+ * Answers null if feature score (or attribute) value lies outside a + * configured threshold. * * @param feature * @return @@ -837,9 +823,20 @@ public class FeatureColour implements FeatureColourI sb.append(BAR).append(Format.getHexString(getMinColour())) .append(BAR); sb.append(Format.getHexString(getMaxColour())).append(BAR); - String noValue = minColour.equals(noColour) ? NO_VALUE_MIN - : (maxColour.equals(noColour) ? NO_VALUE_MAX - : NO_VALUE_NONE); + + /* + * 'no value' colour should be null, min or max colour; + * if none of these, coerce to minColour + */ + String noValue = NO_VALUE_MIN; + if (maxColour.equals(noColour)) + { + noValue = NO_VALUE_MAX; + } + if (noColour == null) + { + noValue = NO_VALUE_NONE; + } sb.append(noValue).append(BAR); if (!isAutoScaled()) { @@ -898,6 +895,34 @@ public class FeatureColour implements FeatureColourI } @Override + public boolean isOutwithThreshold(SequenceFeature feature) + { + if (!isGraduatedColour()) + { + return false; + } + float scr = feature.getScore(); + if (attributeName != null) + { + try + { + String attVal = feature.getValueAsString(attributeName); + scr = Float.valueOf(attVal); + } catch (Throwable e) + { + scr = Float.NaN; + } + } + if (Float.isNaN(scr)) + { + return false; + } + + return ((isAboveThreshold() && scr <= threshold) + || (isBelowThreshold() && scr >= threshold)); + } + + @Override public String getDescription() { if (isSimpleColour())