X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FFeatureColour.java;h=e5bda58f853bb16173a6a21765b69e8fec7760e1;hb=c5dc8281494c9cf96f6736fc326653f782fa5dbd;hp=f34478cf0abefd63b2f6f082c99496c8280696df;hpb=aa8a696f0a53363346ac8d41f5501c5ad34497a5;p=jalview.git diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java index f34478c..e5bda58 100644 --- a/src/jalview/schemes/FeatureColour.java +++ b/src/jalview/schemes/FeatureColour.java @@ -20,11 +20,14 @@ */ package jalview.schemes; +import java.util.Locale; + import jalview.api.FeatureColourI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.features.FeatureMatcher; import jalview.util.ColorUtils; import jalview.util.Format; +import jalview.util.MessageManager; import java.awt.Color; import java.util.StringTokenizer; @@ -50,6 +53,12 @@ import java.util.StringTokenizer; */ public class FeatureColour implements FeatureColourI { + private static final String I18N_LABEL = MessageManager + .getString("label.label"); + + private static final String I18N_SCORE = MessageManager + .getString("label.score"); + private static final String ABSOLUTE = "abso"; private static final String ABOVE = "above"; @@ -187,19 +196,19 @@ public class FeatureColour implements FeatureColourI "Expected either 'label' or a colour specification in the line: " + descriptor); } - if (nextToken.toLowerCase().startsWith(LABEL)) + if (nextToken.toLowerCase(Locale.ROOT).startsWith(LABEL)) { byLabel = true; // get the token after the next delimiter: mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); } - else if (nextToken.toLowerCase().startsWith(SCORE)) + else if (nextToken.toLowerCase(Locale.ROOT).startsWith(SCORE)) { mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); } - else if (nextToken.toLowerCase().startsWith(ATTRIBUTE)) + else if (nextToken.toLowerCase(Locale.ROOT).startsWith(ATTRIBUTE)) { byAttribute = true; attName = (gcol.hasMoreTokens() ? gcol.nextToken() : null); @@ -297,7 +306,7 @@ public class FeatureColour implements FeatureColourI } gcol.nextToken(); // skip next '|' - if (tok.toLowerCase().startsWith(ABSOLUTE)) + if (tok.toLowerCase(Locale.ROOT).startsWith(ABSOLUTE)) { minval = gcol.nextToken(); gcol.nextToken(); // skip next '|' @@ -316,7 +325,7 @@ public class FeatureColour implements FeatureColourI { if (minval.length() > 0) { - min = new Float(minval).floatValue(); + min = Float.valueOf(minval).floatValue(); } } catch (Exception e) { @@ -328,7 +337,7 @@ public class FeatureColour implements FeatureColourI { if (maxval.length() > 0) { - max = new Float(maxval).floatValue(); + max = Float.valueOf(maxval).floatValue(); } } catch (Exception e) { @@ -358,8 +367,8 @@ 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) @@ -373,17 +382,17 @@ public class FeatureColour implements FeatureColourI { // threshold type and possibly a threshold value ttype = gcol.nextToken(); - if (ttype.toLowerCase().startsWith(BELOW)) + if (ttype.toLowerCase(Locale.ROOT).startsWith(BELOW)) { featureColour.setBelowThreshold(true); } - else if (ttype.toLowerCase().startsWith(ABOVE)) + else if (ttype.toLowerCase(Locale.ROOT).startsWith(ABOVE)) { featureColour.setAboveThreshold(true); } else { - if (!ttype.toLowerCase().startsWith("no")) + if (!ttype.toLowerCase(Locale.ROOT).startsWith("no")) { System.err.println( "Ignoring unrecognised threshold type : " + ttype); @@ -396,7 +405,7 @@ public class FeatureColour implements FeatureColourI { gcol.nextToken(); tval = gcol.nextToken(); - featureColour.setThreshold(new Float(tval).floatValue()); + featureColour.setThreshold(Float.valueOf(tval).floatValue()); } catch (Exception e) { System.err.println("Couldn't parse threshold value as a float: (" @@ -429,36 +438,25 @@ 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); } /** @@ -491,29 +489,23 @@ 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)
{
@@ -523,10 +515,10 @@ 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;
@@ -558,7 +550,7 @@ 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)
@@ -833,9 +825,20 @@ 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())
{
@@ -921,4 +924,50 @@ public class FeatureColour implements FeatureColourI
|| (isBelowThreshold() && scr >= threshold));
}
+ @Override
+ public String getDescription()
+ {
+ if (isSimpleColour())
+ {
+ return "r=" + colour.getRed() + ",g=" + colour.getGreen() + ",b="
+ + colour.getBlue();
+ }
+ StringBuilder tt = new StringBuilder();
+ String by = null;
+
+ if (getAttributeName() != null)
+ {
+ by = FeatureMatcher.toAttributeDisplayName(getAttributeName());
+ }
+ else if (isColourByLabel())
+ {
+ by = I18N_LABEL;
+ }
+ else
+ {
+ by = I18N_SCORE;
+ }
+ tt.append(MessageManager.formatMessage("action.by_title_param", by));
+
+ /*
+ * add threshold if any
+ */
+ if (isAboveThreshold() || isBelowThreshold())
+ {
+ tt.append(" (");
+ if (isColourByLabel())
+ {
+ /*
+ * Jalview features file supports the combination of
+ * colour by label or attribute text with score threshold
+ */
+ tt.append(I18N_SCORE).append(" ");
+ }
+ tt.append(isAboveThreshold() ? "> " : "< ");
+ tt.append(getThreshold()).append(")");
+ }
+
+ return tt.toString();
+ }
+
}