X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=03ab5364b4d54f20362ca306c0706af6e3b5476f;hb=HEAD;hp=e6b28db3ee5f829c04a4dd4e9c9fadfb20fa9220;hpb=1c757dc1e6ee864277825c1ebd9c6a9fbe0da7b2;p=jalview.git diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index e6b28db..03ab536 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -20,62 +20,64 @@ */ package jalview.schemes; -import jalview.analysis.Conservation; -import jalview.analysis.Profile; import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.SequenceCollectionI; +import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.util.MessageManager; import java.awt.Color; import java.util.Map; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * Base class for residue-based colour schemes */ -public class ResidueColourScheme implements ColourSchemeI +public abstract class ResidueColourScheme implements ColourSchemeI { - final int[] symbolIndex; - - boolean conservationColouring = false; + public static final String NONE = "None"; - Color[] colors = null; - - int threshold = 0; + /* + * default display name for a user defined colour scheme + */ + public static final String USER_DEFINED = "User Defined"; - /* Set when threshold colouring to either pid_gaps or pid_nogaps */ - protected boolean ignoreGaps = false; + /* + * name for (new) "User Defined.." colour scheme menu item + */ + public static final String USER_DEFINED_MENU = "*User Defined*"; - /** Consenus as a hashtable array */ - Profile[] consensus; + /* + * the canonical name of the annotation colour scheme + * (may be used to identify it in menu items) + */ + public static final String ANNOTATION_COLOUR = "Annotation"; - /** Conservation string as a char array */ - char[] conservation; + /* + * lookup up by character value e.g. 'G' to the colors array index + * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K + */ + final int[] symbolIndex; - int conservationLength = 0; + /* + * colour for residue characters as indexed by symbolIndex + */ + Color[] colors = null; - /** DOCUMENT ME!! */ - int inc = 30; + /* Set when threshold colouring to either pid_gaps or pid_nogaps */ + protected boolean ignoreGaps = false; /** * Creates a new ResidueColourScheme object. * - * @param final int[] index table into colors (ResidueProperties.naIndex or - * ResidueProperties.aaIndex) + * @param final + * int[] index table into colors (ResidueProperties.naIndex or + * ResidueProperties.aaIndex) * @param colors * colours for symbols in sequences - * @param threshold - * threshold for conservation shading */ - public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours, - int threshold) + public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours) { symbolIndex = aaOrnaIndex; this.colors = colours; - this.threshold = threshold; } /** @@ -99,233 +101,127 @@ public class ResidueColourScheme implements ColourSchemeI /** * Find a colour without an index in a sequence */ - @Override public Color findColour(char c) { - return colors == null ? Color.white : colors[symbolIndex[c]]; - } + Color colour = Color.white; - @Override - public Color findColour(char c, int j, SequenceI seq) - { - Color currentColour; - - if (colors != null && symbolIndex != null && (threshold == 0) - || aboveThreshold(c, j)) - { - currentColour = colors[symbolIndex[c]]; - } - else + if (colors != null && symbolIndex != null && c < symbolIndex.length + && symbolIndex[c] < colors.length) { - currentColour = Color.white; + colour = colors[symbolIndex[c]]; } - if (conservationColouring) - { - currentColour = applyConservation(currentColour, j); - } - - return currentColour; + return colour; } /** - * Get the percentage threshold for this colour scheme - * - * @return Returns the percentage threshold + * Default is to call the overloaded method that ignores consensus. A colour + * scheme that depends on consensus (for example, Blosum62), should override + * this method instead. */ @Override - public int getThreshold() + public Color findColour(char c, int j, SequenceI seq, + String consensusResidue, float pid) { - return threshold; + return findColour(c, j, seq); } /** - * DOCUMENT ME! + * Default implementation looks up the residue colour in a fixed scheme, or + * returns White if not found. Override this method for a colour scheme that + * depends on the column position or sequence. * - * @param ct - * DOCUMENT ME! + * @param c + * @param j + * @param seq + * @return */ + protected Color findColour(char c, int j, SequenceI seq) + { + return findColour(c); + } + @Override - public void setThreshold(int ct, boolean ignoreGaps) + public void alignmentChanged(AnnotatedCollectionI alignment, + Map hiddenReps) { - threshold = ct; - this.ignoreGaps = ignoreGaps; } /** - * DOCUMENT ME! - * - * @param s - * DOCUMENT ME! - * @param j - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Answers false if the colour scheme is nucleotide or peptide specific, and + * the data does not match, else true. Override to modify or extend this test + * as required. */ - public boolean aboveThreshold(char c, int j) + @Override + public boolean isApplicableTo(AnnotatedCollectionI ac) { - if ('a' <= c && c <= 'z') + if (!isPeptideSpecific() && !isNucleotideSpecific()) { - // TO UPPERCASE !!! - // Faster than toUpperCase - c -= ('a' - 'A'); + return true; } - - if (consensus == null || consensus.length < j || consensus[j] == null) + if (ac == null) { - return false; + return true; } - - if (consensus[j].getMaxCount() > 0) // != -1)) + /* + * pop-up menu on selection group before group created + * (no alignment context) + */ + // TODO: add nucleotide flag to SequenceGroup? + if (ac instanceof SequenceGroup && ac.getContext() == null) { - if (consensus[j].getPercentageIdentity(ignoreGaps) >= threshold) - { - return true; - } + return true; } - return false; - } - - @Override - public boolean conservationApplied() - { - return conservationColouring; - } - - @Override - public void setConservationApplied(boolean conservationApplied) - { - conservationColouring = conservationApplied; - } - - @Override - public void setConservationInc(int i) - { - inc = i; - } + /* + * inspect the data context (alignment) for residue type + */ + boolean nucleotide = ac.isNucleotide(); - @Override - public int getConservationInc() - { - return inc; + /* + * does data type match colour scheme type? + */ + return (nucleotide && isNucleotideSpecific()) + || (!nucleotide && isPeptideSpecific()); } /** - * DOCUMENT ME! + * Answers true if the colour scheme is normally only for peptide data * - * @param consensus - * DOCUMENT ME! + * @return */ - @Override - public void setConsensus(Profile[] consensus) + public boolean isPeptideSpecific() { - if (consensus == null) - { - return; - } - - this.consensus = consensus; - } - - @Override - public void setConservation(Conservation cons) - { - if (cons == null) - { - conservationColouring = false; - conservation = null; - } - else - { - conservationColouring = true; - int i, iSize = cons.getConsSequence().getLength(); - conservation = new char[iSize]; - for (i = 0; i < iSize; i++) - { - conservation[i] = cons.getConsSequence().getCharAt(i); - } - conservationLength = conservation.length; - } - + return false; } /** - * DOCUMENT ME! - * - * @param s - * DOCUMENT ME! - * @param i - * DOCUMENT ME! + * Answers true if the colour scheme is normally only for nucleotide data * - * @return DOCUMENT ME! + * @return */ - - Color applyConservation(Color currentColour, int i) + public boolean isNucleotideSpecific() { - - if ((conservationLength > i) && (conservation[i] != '*') - && (conservation[i] != '+')) - { - if (jalview.util.Comparison.isGap(conservation[i])) - { - currentColour = Color.white; - } - else - { - float t = 11 - (conservation[i] - '0'); - if (t == 0) - { - return Color.white; - } - - int red = currentColour.getRed(); - int green = currentColour.getGreen(); - int blue = currentColour.getBlue(); - - int dr = 255 - red; - int dg = 255 - green; - int db = 255 - blue; - - dr *= t / 10f; - dg *= t / 10f; - db *= t / 10f; - - red += (inc / 20f) * dr; - green += (inc / 20f) * dg; - blue += (inc / 20f) * db; - - if (red > 255 || green > 255 || blue > 255) - { - currentColour = Color.white; - } - else - { - currentColour = new Color(red, green, blue); - } - } - } - return currentColour; + return false; } + /** + * Default method returns true. Override this to return false in colour + * schemes that are not determined solely by the sequence symbol. + */ @Override - public void alignmentChanged(AnnotatedCollectionI alignment, - Map hiddenReps) + public boolean isSimple() { + return true; } + /** + * Default method returns false. Override this to return true in colour + * schemes that have a colour associated with gap residues. + */ @Override - public ColourSchemeI applyTo(AnnotatedCollectionI sg, - Map hiddenRepSequences) + public boolean hasGapColour() { - try - { - return getClass().newInstance(); - } catch (Exception q) - { - throw new Error(MessageManager.formatMessage( - "error.implementation_error_cannot_duplicate_colour_scheme", - new String[] { getClass().getName() }), q); - } + return false; } }