X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureColourI.java;h=93773ccb283fb31bf16c5650ee8df139ef2cde2e;hb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;hp=0a333caf761a51499a313c7f2cecf91798574bc9;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java index 0a333ca..93773cc 100644 --- a/src/jalview/api/FeatureColourI.java +++ b/src/jalview/api/FeatureColourI.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.api; import jalview.datamodel.SequenceFeature; @@ -14,8 +34,6 @@ public interface FeatureColourI */ boolean isGraduatedColour(); - void setGraduatedColour(boolean b); - /** * Returns the feature colour (when isGraduatedColour answers false) * @@ -38,6 +56,14 @@ public interface FeatureColourI Color getMaxColour(); /** + * Returns the 'no value' colour (used when a feature lacks score, or the + * attribute, being used for colouring) + * + * @return + */ + Color getNoColour(); + + /** * Answers true if the feature has a single colour, i.e. if isColourByLabel() * and isGraduatedColour() both answer false * @@ -95,6 +121,13 @@ public interface FeatureColourI void setThreshold(float f); + /** + * Answers true if the colour varies between the actual minimum and maximum + * score values of the feature, or false if between absolute minimum and + * maximum values (or if not a graduated colour). + * + * @return + */ boolean isAutoScaled(); void setAutoScaled(boolean b); @@ -121,7 +154,9 @@ public interface FeatureColourI boolean hasThreshold(); /** - * Returns the computed colour for the given sequence feature + * Returns the computed colour for the given sequence feature. Answers null if + * the score of this feature instance is outside the range to render (if any), + * i.e. lies below or above a configured threshold. * * @param feature * @return @@ -129,21 +164,43 @@ public interface FeatureColourI Color getColor(SequenceFeature feature); /** - * 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. + * Update the min-max range for a graduated colour scheme. Note that the + * colour scheme may be configured to colour by feature score, or a + * (numeric-valued) attribute - the caller should ensure that the correct + * range is being set. + * + * @param min + * @param max + */ + void updateBounds(float min, float max); + + /** + * Returns the colour in Jalview features file format * - * @param feature * @return */ - boolean isColored(SequenceFeature feature); + String toJalviewFormat(String featureType); /** - * Update the min-max range for a graduated colour scheme + * Answers true if colour is by attribute text or numerical value * - * @param min - * @param max + * @return */ - void updateBounds(float min, float max); + boolean isColourByAttribute(); + + /** + * Answers the name of the attribute (and optional sub-attribute...) used for + * colouring if any, or null + * + * @return + */ + String[] getAttributeName(); + + /** + * Sets the name of the attribute (and optional sub-attribute...) used for + * colouring if any, or null to remove this property + * + * @return + */ + void setAttributeName(String... name); }