+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
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;
/**
- * A class that wraps either a simple colour or a graduated colour
+ * A class that represents a colour scheme for a feature type. Options supported
+ * are currently
+ * <ul>
+ * <li>a simple colour e.g. Red</li>
+ * <li>colour by label - a colour is generated from the feature description</li>
+ * <li>graduated colour by feature score</li>
+ * <ul>
+ * <li>minimum and maximum score range must be provided</li>
+ * <li>minimum and maximum value colours should be specified</li>
+ * <li>a colour for 'no value' may optionally be provided</li>
+ * <li>colours for intermediate scores are interpolated RGB values</li>
+ * <li>there is an optional threshold above/below which to colour values</li>
+ * <li>the range may be the full value range, or may be limited by the threshold
+ * value</li>
+ * </ul>
+ * <li>colour by (text) value of a named attribute</li> <li>graduated colour by
+ * (numeric) value of a named attribute</li> </ul>
*/
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";
+
+ private static final String BELOW = "below";
+
+ /*
+ * constants used to read or write a Jalview Features file
+ */
+ private static final String LABEL = "label";
+
+ private static final String SCORE = "score";
+
+ private static final String ATTRIBUTE = "attribute";
+
+ private static final String NO_VALUE_MIN = "noValueMin";
+
+ private static final String NO_VALUE_MAX = "noValueMax";
+
+ private static final String NO_VALUE_NONE = "noValueNone";
+
+ static final Color DEFAULT_NO_COLOUR = null;
+
+ private static final String BAR = "|";
+
final private Color colour;
final private Color minColour;
final private Color maxColour;
+ /*
+ * colour to use for colour by attribute when the
+ * attribute value is absent
+ */
+ final private Color noColour;
+
+ /*
+ * if true, then colour has a gradient based on a numerical
+ * range (either feature score, or an attribute value)
+ */
private boolean graduatedColour;
+ /*
+ * if true, colour values are generated from a text string,
+ * either feature description, or an attribute value
+ */
private boolean colourByLabel;
+ /*
+ * if not null, the value of [attribute, [sub-attribute] ...]
+ * is used for colourByLabel or graduatedColour
+ */
+ private String[] attributeName;
+
private float threshold;
private float base;
private boolean aboveThreshold;
- private boolean thresholdIsMinOrMax;
-
private boolean isHighToLow;
private boolean autoScaled;
final private float deltaBlue;
/**
+ * Parses a Jalview features file format colour descriptor
+ * <p>
+ * <code>
+ * [label|score|[attribute|attributeName]|][mincolour|maxcolour|
+ * [absolute|]minvalue|maxvalue|[noValueOption|]thresholdtype|thresholdvalue]</code>
+ * <p>
+ * 'Score' is optional (default) for a graduated colour. An attribute with
+ * sub-attribute should be written as (for example) CSQ:Consequence.
+ * noValueOption is one of <code>noValueMin, noValueMax, noValueNone</code>
+ * with default noValueMin.
+ * <p>
+ * Examples:
+ * <ul>
+ * <li>red</li>
+ * <li>a28bbb</li>
+ * <li>25,125,213</li>
+ * <li>label</li>
+ * <li>attribute|CSQ:PolyPhen</li>
+ * <li>label|||0.0|0.0|above|12.5</li>
+ * <li>label|||0.0|0.0|below|12.5</li>
+ * <li>red|green|12.0|26.0|none</li>
+ * <li>score|red|green|12.0|26.0|none</li>
+ * <li>attribute|AF|red|green|12.0|26.0|none</li>
+ * <li>attribute|AF|red|green|noValueNone|12.0|26.0|none</li>
+ * <li>a28bbb|3eb555|12.0|26.0|above|12.5</li>
+ * <li>a28bbb|3eb555|abso|12.0|26.0|below|12.5</li>
+ * </ul>
+ *
+ * @param descriptor
+ * @return
+ * @throws IllegalArgumentException
+ * if not parseable
+ */
+ public static FeatureColourI parseJalviewFeatureColour(String descriptor)
+ {
+ StringTokenizer gcol = new StringTokenizer(descriptor, BAR, true);
+ float min = Float.MIN_VALUE;
+ float max = Float.MAX_VALUE;
+ boolean byLabel = false;
+ boolean byAttribute = false;
+ String attName = null;
+ String mincol = null;
+ String maxcol = null;
+
+ /*
+ * first token should be 'label', or 'score', or an
+ * attribute name, or simple colour, or minimum colour
+ */
+ String nextToken = gcol.nextToken();
+ if (nextToken == BAR)
+ {
+ throw new IllegalArgumentException(
+ "Expected either 'label' or a colour specification in the line: "
+ + descriptor);
+ }
+ if (nextToken.toLowerCase().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))
+ {
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+ else if (nextToken.toLowerCase().startsWith(ATTRIBUTE))
+ {
+ byAttribute = true;
+ attName = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ attName = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+ else
+ {
+ mincol = nextToken;
+ }
+
+ /*
+ * if only one token, it can validly be label, attributeName,
+ * or a plain colour value
+ */
+ if (!gcol.hasMoreTokens())
+ {
+ if (byLabel || byAttribute)
+ {
+ FeatureColourI fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ if (byAttribute)
+ {
+ fc.setAttributeName(
+ FeatureMatcher.fromAttributeDisplayName(attName));
+ }
+ return fc;
+ }
+
+ Color colour = ColorUtils.parseColourString(descriptor);
+ if (colour == null)
+ {
+ throw new IllegalArgumentException(
+ "Invalid colour descriptor: " + descriptor);
+ }
+ return new FeatureColour(colour);
+ }
+
+ /*
+ * continue parsing for min/max/no colour (if graduated)
+ * and for threshold (colour by text or graduated)
+ */
+
+ /*
+ * autoScaled == true: colours range over actual score range
+ * autoScaled == false ('abso'): colours range over min/max range
+ */
+ boolean autoScaled = true;
+ String tok = null, minval, maxval;
+ String noValueColour = NO_VALUE_MIN;
+
+ if (mincol != null)
+ {
+ // at least four more tokens
+ if (mincol.equals(BAR))
+ {
+ mincol = null;
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ maxcol = gcol.nextToken();
+ if (maxcol.equals(BAR))
+ {
+ maxcol = null;
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ tok = gcol.nextToken();
+
+ /*
+ * check for specifier for colour for no attribute value
+ * (new in 2.11, defaults to minColour if not specified)
+ */
+ if (tok.equalsIgnoreCase(NO_VALUE_MIN))
+ {
+ tok = gcol.nextToken();
+ tok = gcol.nextToken();
+ }
+ else if (tok.equalsIgnoreCase(NO_VALUE_MAX))
+ {
+ noValueColour = NO_VALUE_MAX;
+ tok = gcol.nextToken();
+ tok = gcol.nextToken();
+ }
+ else if (tok.equalsIgnoreCase(NO_VALUE_NONE))
+ {
+ noValueColour = NO_VALUE_NONE;
+ tok = gcol.nextToken();
+ tok = gcol.nextToken();
+ }
+
+ gcol.nextToken(); // skip next '|'
+ if (tok.toLowerCase().startsWith(ABSOLUTE))
+ {
+ minval = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ autoScaled = false;
+ }
+ else
+ {
+ minval = tok;
+ }
+ maxval = gcol.nextToken();
+ if (gcol.hasMoreTokens())
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ try
+ {
+ if (minval.length() > 0)
+ {
+ min = new Float(minval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(
+ "Couldn't parse the minimum value for graduated colour ('"
+ + minval + "')");
+ }
+ try
+ {
+ if (maxval.length() > 0)
+ {
+ max = new Float(maxval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(
+ "Couldn't parse the maximum value for graduated colour ("
+ + descriptor + ")");
+ }
+ }
+ else
+ {
+ /*
+ * dummy min/max colours for colour by text
+ * (label or attribute value)
+ */
+ mincol = "white";
+ maxcol = "black";
+ byLabel = true;
+ }
+
+ /*
+ * construct the FeatureColour!
+ */
+ FeatureColour featureColour;
+ try
+ {
+ Color minColour = ColorUtils.parseColourString(mincol);
+ 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.setColourByLabel(minColour == null);
+ featureColour.setAutoScaled(autoScaled);
+ if (byAttribute)
+ {
+ featureColour.setAttributeName(
+ FeatureMatcher.fromAttributeDisplayName(attName));
+ }
+ // add in any additional parameters
+ String ttype = null, tval = null;
+ if (gcol.hasMoreTokens())
+ {
+ // threshold type and possibly a threshold value
+ ttype = gcol.nextToken();
+ if (ttype.toLowerCase().startsWith(BELOW))
+ {
+ featureColour.setBelowThreshold(true);
+ }
+ else if (ttype.toLowerCase().startsWith(ABOVE))
+ {
+ featureColour.setAboveThreshold(true);
+ }
+ else
+ {
+ if (!ttype.toLowerCase().startsWith("no"))
+ {
+ System.err.println(
+ "Ignoring unrecognised threshold type : " + ttype);
+ }
+ }
+ }
+ if (featureColour.hasThreshold())
+ {
+ try
+ {
+ gcol.nextToken();
+ tval = gcol.nextToken();
+ featureColour.setThreshold(new Float(tval).floatValue());
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't parse threshold value as a float: ("
+ + tval + ")");
+ }
+ }
+ if (gcol.hasMoreTokens())
+ {
+ System.err.println(
+ "Ignoring additional tokens in parameters in graduated colour specification\n");
+ while (gcol.hasMoreTokens())
+ {
+ System.err.println(BAR + gcol.nextToken());
+ }
+ System.err.println("\n");
+ }
+ return featureColour;
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(e.getMessage());
+ }
+ }
+
+ /**
* Default constructor
*/
public FeatureColour()
*/
public FeatureColour(Color c)
{
- minColour = null;
- maxColour = null;
+ minColour = Color.WHITE;
+ maxColour = Color.BLACK;
+ noColour = DEFAULT_NO_COLOUR;
minRed = 0f;
minGreen = 0f;
minBlue = 0f;
}
/**
- * Constructor given a colour range and a score range
+ * Constructor given a colour range and a score range, defaulting 'no value
+ * colour' to be the same as minimum colour
*
* @param low
* @param high
*/
public FeatureColour(Color low, Color high, float min, float max)
{
- graduatedColour = true;
- colour = null;
- minColour = low;
- maxColour = high;
- threshold = Float.NaN;
- isHighToLow = min >= max;
- minRed = low.getRed() / 255f;
- minGreen = low.getGreen() / 255f;
- minBlue = low.getBlue() / 255f;
- deltaRed = (high.getRed() / 255f) - minRed;
- deltaGreen = (high.getGreen() / 255f) - minGreen;
- deltaBlue = (high.getBlue() / 255f) - minBlue;
- if (isHighToLow)
- {
- base = max;
- range = min - max;
- }
- else
- {
- base = min;
- range = max - min;
- }
+ this(low, high, low, min, max);
}
/**
*/
public FeatureColour(FeatureColour fc)
{
+ graduatedColour = fc.graduatedColour;
colour = fc.colour;
minColour = fc.minColour;
maxColour = fc.maxColour;
+ noColour = fc.noColour;
minRed = fc.minRed;
minGreen = fc.minGreen;
minBlue = fc.minBlue;
base = fc.base;
range = fc.range;
isHighToLow = fc.isHighToLow;
+ attributeName = fc.attributeName;
setAboveThreshold(fc.isAboveThreshold());
setBelowThreshold(fc.isBelowThreshold());
setThreshold(fc.getThreshold());
setAutoScaled(fc.isAutoScaled());
setColourByLabel(fc.isColourByLabel());
}
-
+
/**
* Copy constructor with new min/max ranges
+ *
* @param fc
* @param min
* @param max
public FeatureColour(FeatureColour fc, float min, float max)
{
this(fc);
- graduatedColour = true;
updateBounds(min, max);
}
+ /**
+ * Constructor for a graduated colour
+ *
+ * @param low
+ * @param high
+ * @param noValueColour
+ * @param min
+ * @param max
+ */
+ public FeatureColour(Color low, Color high, Color noValueColour,
+ float min, float max)
+ {
+ if (low == null)
+ {
+ low = Color.white;
+ }
+ if (high == null)
+ {
+ high = Color.black;
+ }
+ graduatedColour = true;
+ colour = null;
+ minColour = low;
+ maxColour = high;
+ noColour = noValueColour;
+ threshold = Float.NaN;
+ isHighToLow = min >= max;
+ minRed = low.getRed() / 255f;
+ minGreen = low.getGreen() / 255f;
+ minBlue = low.getBlue() / 255f;
+ deltaRed = (high.getRed() / 255f) - minRed;
+ deltaGreen = (high.getGreen() / 255f) - minGreen;
+ deltaBlue = (high.getBlue() / 255f) - minBlue;
+ if (isHighToLow)
+ {
+ base = max;
+ range = min - max;
+ }
+ else
+ {
+ base = min;
+ range = max - min;
+ }
+ }
+
@Override
public boolean isGraduatedColour()
{
* Sets the 'graduated colour' flag. If true, also sets 'colour by label' to
* false.
*/
- @Override
- public void setGraduatedColour(boolean b)
+ void setGraduatedColour(boolean b)
{
graduatedColour = b;
if (b)
}
@Override
+ public Color getNoColour()
+ {
+ return noColour;
+ }
+
+ @Override
public boolean isColourByLabel()
{
return colourByLabel;
setGraduatedColour(false);
}
}
+
@Override
public boolean isBelowThreshold()
{
}
@Override
- public boolean isThresholdMinMax()
- {
- return thresholdIsMinOrMax;
- }
-
- @Override
- public void setThresholdMinMax(boolean b)
- {
- thresholdIsMinOrMax = b;
- }
-
- @Override
public float getThreshold()
{
return threshold;
}
/**
- * Updates the base and range appropriately for the given minmax range
- *
- * @param min
- * @param max
+ * {@inheritDoc}
*/
@Override
public void updateBounds(float min, float max)
{
if (isColourByLabel())
{
- return UserColourScheme
- .createColourFromName(feature.getDescription());
+ String label = attributeName == null ? feature.getDescription()
+ : feature.getValueAsString(attributeName);
+ return label == null ? noColour : ColorUtils
+ .createColourFromName(label);
}
if (!isGraduatedColour())
return getColour();
}
- // todo should we check for above/below threshold here?
- if (range == 0.0)
+ /*
+ * graduated colour case, optionally with threshold
+ * may be based on feature score on an attribute value
+ * Float.NaN, or no value, is assigned the 'no value' colour
+ */
+ float scr = feature.getScore();
+ if (attributeName != null)
{
- return getMaxColour();
+ try
+ {
+ String attVal = feature.getValueAsString(attributeName);
+ scr = Float.valueOf(attVal);
+ } catch (Throwable e)
+ {
+ scr = Float.NaN;
+ }
}
- float scr = feature.getScore();
if (Float.isNaN(scr))
{
- return getMinColour();
+ return noColour;
+ }
+
+ if (isAboveThreshold() && scr <= threshold)
+ {
+ return null;
+ }
+
+ if (isBelowThreshold() && scr >= threshold)
+ {
+ return null;
+ }
+ if (range == 0.0)
+ {
+ return getMaxColour();
}
float scl = (scr - base) / range;
if (isHighToLow)
{
scl = 1f;
}
- return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen, minBlue + scl * deltaBlue);
+ return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen,
+ minBlue + scl * deltaBlue);
}
/**
return (isHighToLow) ? (base + range) : base;
}
- /**
- * Answers true if the feature has a simple colour, or is coloured by label,
- * or has a graduated colour and the score of this feature instance is within
- * the range to render (if any), i.e. does not lie below or above any
- * threshold set.
- *
- * @param feature
- * @return
- */
@Override
- public boolean isColored(SequenceFeature feature)
+ public boolean isSimpleColour()
{
- if (isColourByLabel() || !isGraduatedColour())
- {
- return true;
- }
+ return (!isColourByLabel() && !isGraduatedColour());
+ }
- float val = feature.getScore();
- if (Float.isNaN(val))
- {
- return true;
- }
- if (Float.isNaN(this.threshold))
- {
- return true;
- }
+ @Override
+ public boolean hasThreshold()
+ {
+ return isAboveThreshold() || isBelowThreshold();
+ }
- if (isAboveThreshold() && val <= threshold)
+ @Override
+ public String toJalviewFormat(String featureType)
+ {
+ String colourString = null;
+ if (isSimpleColour())
{
- return false;
+ colourString = Format.getHexString(getColour());
}
- if (isBelowThreshold() && val >= threshold)
+ else
{
- return false;
+ StringBuilder sb = new StringBuilder(32);
+ if (isColourByAttribute())
+ {
+ sb.append(ATTRIBUTE).append(BAR);
+ sb.append(
+ FeatureMatcher.toAttributeDisplayName(getAttributeName()));
+ }
+ else if (isColourByLabel())
+ {
+ sb.append(LABEL);
+ }
+ else
+ {
+ sb.append(SCORE);
+ }
+ if (isGraduatedColour())
+ {
+ 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);
+ sb.append(noValue).append(BAR);
+ if (!isAutoScaled())
+ {
+ sb.append(ABSOLUTE).append(BAR);
+ }
+ }
+ else
+ {
+ /*
+ * colour by text with score threshold: empty fields for
+ * minColour and maxColour (not used)
+ */
+ if (hasThreshold())
+ {
+ sb.append(BAR).append(BAR).append(BAR);
+ }
+ }
+ if (hasThreshold() || isGraduatedColour())
+ {
+ sb.append(getMin()).append(BAR);
+ sb.append(getMax()).append(BAR);
+ if (isBelowThreshold())
+ {
+ sb.append(BELOW).append(BAR).append(getThreshold());
+ }
+ else if (isAboveThreshold())
+ {
+ sb.append(ABOVE).append(BAR).append(getThreshold());
+ }
+ else
+ {
+ sb.append("none");
+ }
+ }
+ colourString = sb.toString();
}
- return true;
+ return String.format("%s\t%s", featureType, colourString);
}
@Override
- public boolean isSimpleColour()
+ public boolean isColourByAttribute()
{
- return (!isColourByLabel() && !isGraduatedColour());
+ return attributeName != null;
}
@Override
- public boolean hasThreshold()
+ public String[] getAttributeName()
{
- return isAboveThreshold() || isBelowThreshold();
+ return attributeName;
+ }
+
+ @Override
+ public void setAttributeName(String... name)
+ {
+ attributeName = name;
+ }
+
+ @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();
}
}