X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FFeatureColour.java;h=e5bda58f853bb16173a6a21765b69e8fec7760e1;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=aa0b6406c93cdc072b27ed002e959ad7fe589548;hpb=a1073a1f85c1a0c3f57cc85b8a7c49d6ad09ef27;p=jalview.git diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java index aa0b640..e5bda58 100644 --- a/src/jalview/schemes/FeatureColour.java +++ b/src/jalview/schemes/FeatureColour.java @@ -20,10 +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; @@ -49,6 +53,33 @@ 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"; + + 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 = "|"; @@ -111,16 +142,29 @@ public class FeatureColour implements FeatureColourI /** * Parses a Jalview features file format colour descriptor - * [label|][mincolour|maxcolour - * |[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue] Examples: + *

+ * + * [label|score|[attribute|attributeName]|][mincolour|maxcolour| + * [absolute|]minvalue|maxvalue|[noValueOption|]thresholdtype|thresholdvalue] + *

+ * '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 noValueMin, noValueMax, noValueNone + * with default noValueMin. + *

+ * Examples: *

@@ -130,34 +174,71 @@ public class FeatureColour implements FeatureColourI * @throws IllegalArgumentException * if not parseable */ - public static FeatureColour parseJalviewFeatureColour(String descriptor) + public static FeatureColourI parseJalviewFeatureColour(String descriptor) { - StringTokenizer gcol = new StringTokenizer(descriptor, "|", true); + StringTokenizer gcol = new StringTokenizer(descriptor, BAR, true); float min = Float.MIN_VALUE; float max = Float.MAX_VALUE; - boolean labelColour = false; + boolean byLabel = false; + boolean byAttribute = false; + String attName = null; + String mincol = null; + String maxcol = null; - String mincol = gcol.nextToken(); - if (mincol == "|") + /* + * 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); } - String maxcol = null; - if (mincol.toLowerCase().indexOf("label") == 0) + if (nextToken.toLowerCase(Locale.ROOT).startsWith(LABEL)) { - labelColour = true; + byLabel = true; + // get the token after the next delimiter: mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); - // skip '|' mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); } + else if (nextToken.toLowerCase(Locale.ROOT).startsWith(SCORE)) + { + mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); + mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); + } + else if (nextToken.toLowerCase(Locale.ROOT).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 (!labelColour && !gcol.hasMoreTokens()) + /* + * if only one token, it can validly be label, attributeName, + * or a plain colour value + */ + if (!gcol.hasMoreTokens()) { - /* - * only a simple colour specification - parse it - */ + 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) { @@ -168,34 +249,64 @@ public class FeatureColour implements FeatureColourI } /* + * 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("|")) + if (mincol.equals(BAR)) { - mincol = ""; + mincol = null; } else { gcol.nextToken(); // skip next '|' } maxcol = gcol.nextToken(); - if (maxcol.equals("|")) + if (maxcol.equals(BAR)) { - maxcol = ""; + 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("abso")) + if (tok.toLowerCase(Locale.ROOT).startsWith(ABSOLUTE)) { minval = gcol.nextToken(); gcol.nextToken(); // skip next '|' @@ -214,19 +325,19 @@ public class FeatureColour implements FeatureColourI { if (minval.length() > 0) { - min = new Float(minval).floatValue(); + min = Float.valueOf(minval).floatValue(); } } catch (Exception e) { throw new IllegalArgumentException( - "Couldn't parse the minimum value for graduated colour (" - + descriptor + ")"); + "Couldn't parse the minimum value for graduated colour ('" + + minval + "')"); } try { if (maxval.length() > 0) { - max = new Float(maxval).floatValue(); + max = Float.valueOf(maxval).floatValue(); } } catch (Exception e) { @@ -237,40 +348,51 @@ public class FeatureColour implements FeatureColourI } else { - // add in some dummy min/max colours for the label-only - // colourscheme. - mincol = "FFFFFF"; - maxcol = "000000"; + /* + * dummy min/max colours for colour by text + * (label or attribute value) + */ + mincol = "white"; + maxcol = "black"; + byLabel = true; } /* - * construct the FeatureColour + * construct the FeatureColour! */ FeatureColour featureColour; try { Color minColour = ColorUtils.parseColourString(mincol); Color maxColour = ColorUtils.parseColourString(maxcol); - featureColour = new FeatureColour(minColour, maxColour, min, max); - featureColour.setColourByLabel(labelColour); + Color noColour = noValueColour.equals(NO_VALUE_MAX) ? maxColour + : (noValueColour.equals(NO_VALUE_NONE) ? null : minColour); + featureColour = new FeatureColour(maxColour, 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")) + 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); @@ -283,7 +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: (" @@ -296,7 +418,7 @@ public class FeatureColour implements FeatureColourI "Ignoring additional tokens in parameters in graduated colour specification\n"); while (gcol.hasMoreTokens()) { - System.err.println("|" + gcol.nextToken()); + System.err.println(BAR + gcol.nextToken()); } System.err.println("\n"); } @@ -316,36 +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); } /** @@ -378,29 +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) { @@ -410,10 +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; @@ -445,7 +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) @@ -576,9 +681,12 @@ 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 @@ -698,21 +806,54 @@ public class FeatureColour implements FeatureColourI else { StringBuilder sb = new StringBuilder(32); - if (isColourByLabel()) + if (isColourByAttribute()) { - sb.append("label"); - if (hasThreshold()) - { - sb.append(BAR).append(BAR).append(BAR); - } + sb.append(ATTRIBUTE).append(BAR); + sb.append( + FeatureMatcher.toAttributeDisplayName(getAttributeName())); + } + else if (isColourByLabel()) + { + sb.append(LABEL); + } + else + { + sb.append(SCORE); } if (isGraduatedColour()) { - sb.append(Format.getHexString(getMinColour())).append(BAR); + sb.append(BAR).append(Format.getHexString(getMinColour())) + .append(BAR); sb.append(Format.getHexString(getMaxColour())).append(BAR); + + /* + * '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()) { - sb.append("abso").append(BAR); + 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()) @@ -721,11 +862,11 @@ public class FeatureColour implements FeatureColourI sb.append(getMax()).append(BAR); if (isBelowThreshold()) { - sb.append("below").append(BAR).append(getThreshold()); + sb.append(BELOW).append(BAR).append(getThreshold()); } else if (isAboveThreshold()) { - sb.append("above").append(BAR).append(getThreshold()); + sb.append(ABOVE).append(BAR).append(getThreshold()); } else { @@ -755,4 +896,78 @@ public class FeatureColour implements FeatureColourI attributeName = name; } + @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()) + { + 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(); + } + }