X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=9b91066e191fded769148b291ae9d68a71993fa0;hb=b0cee3aaf7d8873910939f97b6acb217d518968d;hp=0da773bb3502a152974dfb5acd7a56ef0f697b53;hpb=9d15a20b1f34c76427da5ec9274ff97a1ca49393;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 0da773b..9b91066 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -21,6 +21,7 @@ package jalview.schemes; import jalview.datamodel.AnnotatedCollectionI; +import jalview.util.ColorUtils; import java.awt.Color; @@ -38,566 +39,72 @@ import java.awt.Color; */ public class ColourSchemeProperty { - /** Undefined Colourscheme Index */ - public static final int UNDEFINED = -1; - - /** for schemes defined on the fly */ - public static final int USER_DEFINED = 0; - - /** No Colourscheme Index */ - public static final int NONE = 1; - - /** DOCUMENT ME!! */ - public static final int CLUSTAL = 2; - - /** DOCUMENT ME!! */ - public static final int BLOSUM = 3; - - /** DOCUMENT ME!! */ - public static final int PID = 4; - - /** DOCUMENT ME!! */ - public static final int ZAPPO = 5; - - /** DOCUMENT ME!! */ - public static final int TAYLOR = 6; - - /** DOCUMENT ME!! */ - public static final int HYDROPHOBIC = 7; - - /** DOCUMENT ME!! */ - public static final int HELIX = 8; - - /** DOCUMENT ME!! */ - public static final int STRAND = 9; - - /** DOCUMENT ME!! */ - public static final int TURN = 10; - - /** DOCUMENT ME!! */ - public static final int BURIED = 11; - - /** DOCUMENT ME!! */ - public static final int NUCLEOTIDE = 12; /** - * purine/pyrimidine - */ - public static final int PURINEPYRIMIDINE = 13; - - public static final int COVARIATION = 14; - - public static final int TCOFFEE = 15; - - public static final int RNAHELIX = 16; - - public static final int RNAINTERACTION = 17; - - /** - * index of first colourscheme (includes 'None') - */ - public static final int FIRST_COLOUR = NONE; - - public static final int LAST_COLOUR = RNAINTERACTION; - - /** - * DOCUMENT ME! + * Returns a colour scheme for the given name, with which the given data may + * be coloured. The name may be one of + * + * If none of these formats is matched, the string is converted to a colour + * using a hashing algorithm. * + * @param forData * @param name - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @return */ - public static int getColourIndexFromName(String name) + public static ColourSchemeI getColour(AnnotatedCollectionI forData, + String name) { - int ret = UNDEFINED; - - if (name.equalsIgnoreCase("Clustal")) - { - ret = CLUSTAL; - } - else if (name.equalsIgnoreCase("Blosum62")) - { - ret = BLOSUM; - } - else if (name.equalsIgnoreCase("% Identity")) - { - ret = PID; - } - else if (name.equalsIgnoreCase("Zappo")) - { - ret = ZAPPO; - } - else if (name.equalsIgnoreCase("Taylor")) - { - ret = TAYLOR; - } - else if (name.equalsIgnoreCase("Hydrophobic")) - { - ret = HYDROPHOBIC; - } - else if (name.equalsIgnoreCase("Helix Propensity")) - { - ret = HELIX; - } - else if (name.equalsIgnoreCase("Strand Propensity")) - { - ret = STRAND; - } - else if (name.equalsIgnoreCase("Turn Propensity")) - { - ret = TURN; - } - else if (name.equalsIgnoreCase("Buried Index")) - { - ret = BURIED; - } - else if (name.equalsIgnoreCase("Nucleotide")) - { - ret = NUCLEOTIDE; - } - else if (name.equalsIgnoreCase("T-Coffee Scores")) - { - ret = TCOFFEE; - } - - else if (name.equalsIgnoreCase("User Defined")) + JalviewColourScheme scheme = JalviewColourScheme.forName(name); + if (scheme != null) { - ret = USER_DEFINED; + // note JalviewColourScheme.None returns null here + return scheme.getColourScheme(forData); } - else if (name.equalsIgnoreCase("None")) - { - ret = NONE; - } - else if (name.equalsIgnoreCase("Purine/Pyrimidine")) - { - ret = PURINEPYRIMIDINE; - } - else if (name.equalsIgnoreCase("RNA Interaction type")) - { - ret = RNAINTERACTION; - } - else if (name.equalsIgnoreCase("RNA Helices")) - { - ret = RNAHELIX; - } - // else if (name.equalsIgnoreCase("Covariation")) - // { - // ret = COVARIATION; - // } - - return ret; - } - /** - * DOCUMENT ME! - * - * @param cs - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static String getColourName(ColourSchemeI cs) - { - - int index = NONE; - - if (cs instanceof ClustalxColourScheme) - { - index = CLUSTAL; - } - else if (cs instanceof Blosum62ColourScheme) - { - index = BLOSUM; - } - else if (cs instanceof PIDColourScheme) - { - index = PID; - } - else if (cs instanceof ZappoColourScheme) - { - index = ZAPPO; - } - else if (cs instanceof TaylorColourScheme) + if (name.indexOf('=') == -1) { - index = TAYLOR; + /* + * parse the name as a colour specification + * e.g. "red" or "ff00ed", + * or failing that hash the name to a colour + */ + return new UserColourScheme(name); } - else if (cs instanceof HydrophobicColourScheme) - { - index = HYDROPHOBIC; - } - else if (cs instanceof HelixColourScheme) - { - index = HELIX; - } - else if (cs instanceof StrandColourScheme) - { - index = STRAND; - } - else if (cs instanceof TurnColourScheme) - { - index = TURN; - } - else if (cs instanceof BuriedColourScheme) - { - index = BURIED; - } - else if (cs instanceof NucleotideColourScheme) - { - index = NUCLEOTIDE; - } - else if (cs instanceof PurinePyrimidineColourScheme) - { - index = PURINEPYRIMIDINE; - } - else if (cs instanceof TCoffeeColourScheme) - { - index = TCOFFEE; - } - else if (cs instanceof RNAHelicesColour) - { - index = RNAHELIX; - } - /* - * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; } - */ - else if (cs instanceof UserColourScheme) - { - if ((((UserColourScheme) cs).getName() != null) - && (((UserColourScheme) cs).getName().length() > 0)) - { - return ((UserColourScheme) cs).getName(); - } - // get default colourscheme name - index = USER_DEFINED; - } - - return getColourName(index); - } - - /** - * DOCUMENT ME! - * - * @param index - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static String getColourName(int index) - { - String ret = null; - - switch (index) - { - case CLUSTAL: - ret = "Clustal"; - - break; - - case BLOSUM: - ret = "Blosum62"; - - break; - - case PID: - ret = "% Identity"; - - break; - - case ZAPPO: - ret = "Zappo"; - - break; - - case TAYLOR: - ret = "Taylor"; - break; - - case HYDROPHOBIC: - ret = "Hydrophobic"; - - break; - - case HELIX: - ret = "Helix Propensity"; - - break; - - case STRAND: - ret = "Strand Propensity"; - - break; - - case TURN: - ret = "Turn Propensity"; - - break; - - case BURIED: - ret = "Buried Index"; - - break; - - case NUCLEOTIDE: - ret = "Nucleotide"; - - break; - - case PURINEPYRIMIDINE: - ret = "Purine/Pyrimidine"; - break; - - case TCOFFEE: - ret = "T-Coffee Scores"; - - break; - - case RNAINTERACTION: - ret = "RNA Interaction type"; - - break; - case RNAHELIX: - ret = "RNA Helices"; - - break; /* - * case COVARIATION: ret = "Covariation"; - * - * break; + * try to parse the string as a residues colour scheme + * e.g. A=red;T,G=blue etc */ - case USER_DEFINED: - ret = "User Defined"; - - break; - - default: - ret = "None"; - - break; - } - - return ret; - } - - /** - * retrieve or create colourscheme associated with name - * - * @param seqs - * sequences to colour - * @param width - * range of sequences to colour - * @param name - * colourscheme name, applet colour parameter specification, or - * string to parse as colour for new coloursheme - * @return Valid Colourscheme - */ - public static ColourSchemeI getColour(AnnotatedCollectionI alignment, - String name) - { - int colindex = getColourIndexFromName(name); - if (colindex == UNDEFINED) - { - if (name.indexOf('=') == -1) - { - // try to build a colour from the string directly - try - { - return new UserColourScheme(name); - } catch (Exception e) - { - // System.err.println("Ignoring unknown colourscheme name"); - } - } - else - { - // try to parse the string as a residue colourscheme - try - { - // fix the launchApp user defined coloursheme transfer bug - UserColourScheme ucs = new UserColourScheme("white"); - ucs.parseAppletParameter(name); - - } catch (Exception e) - { - // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter"); - } - } - } - return getColour(alignment, colindex); - } - - /** - * Construct an instance of ColourSchemeI corresponding to the given - * colourscheme index - * - * @param seqs - * sequences to be coloured by colourscheme - * @param width - * geometry of alignment - * @param index - * colourscheme number - * - * @return null or an instance of the colourscheme configured to colour given - * sequence set - */ - public static ColourSchemeI getColour( - jalview.datamodel.AnnotatedCollectionI coll, int index) - { - // TODO 3.0 2.8 refactor signature to take an alignmentI like container so - // colourschemes based on annotation can be initialised - ColourSchemeI cs = null; - - switch (index) + UserColourScheme ucs = null; + try { - case CLUSTAL: - cs = new ClustalxColourScheme(coll, null); - - break; - - case BLOSUM: - cs = new Blosum62ColourScheme(); - - break; - - case PID: - cs = new PIDColourScheme(); - - break; - - case ZAPPO: - cs = new ZappoColourScheme(); - - break; - - case TAYLOR: - cs = new TaylorColourScheme(); - break; - - case HYDROPHOBIC: - cs = new HydrophobicColourScheme(); - - break; - - case HELIX: - cs = new HelixColourScheme(); - - break; - - case STRAND: - cs = new StrandColourScheme(); - - break; - - case TURN: - cs = new TurnColourScheme(); - - break; - - case BURIED: - cs = new BuriedColourScheme(); - - break; - - case NUCLEOTIDE: - cs = new NucleotideColourScheme(); - - break; - - case PURINEPYRIMIDINE: - cs = new PurinePyrimidineColourScheme(); - - break; - - case TCOFFEE: - cs = new TCoffeeColourScheme(coll); - break; - - case RNAHELIX: - cs = new RNAHelicesColour(coll); - break; - - // case COVARIATION: - // cs = new CovariationColourScheme(annotation); - // break; - - case USER_DEFINED: - Color[] col = new Color[24]; - for (int i = 0; i < 24; i++) - { - col[i] = Color.white; - } - cs = new UserColourScheme(col); - break; - - default: - break; - } - - return cs; - } - - /** - * Returns the Color constant for a given colour name e.g. "pink", or null if - * the name is not recognised - * - * @param name - * @return - */ - public static Color getAWTColorFromName(String name) - { - if (name == null) + // fix the launchApp user defined colourscheme transfer bug + ucs = new UserColourScheme("white"); + ucs.parseAppletParameter(name); + } catch (Exception e) { - return null; + // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter"); } - Color col = null; - name = name.toLowerCase(); - - // or make a static map; or use reflection on the field name - switch (name) - { - case "black": - col = Color.black; - break; - case "blue": - col = Color.blue; - break; - case "cyan": - col = Color.cyan; - break; - case "darkgray": - col = Color.darkGray; - break; - case "gray": - col = Color.gray; - break; - case "green": - col = Color.green; - break; - case "lightgray": - col = Color.lightGray; - break; - case "magenta": - col = Color.magenta; - break; - case "orange": - col = Color.orange; - break; - case "pink": - col = Color.pink; - break; - case "red": - col = Color.red; - break; - case "white": - col = Color.white; - break; - case "yellow": - col = Color.yellow; - break; - } - - return col; + return ucs; } public static Color rnaHelices[] = null; @@ -623,17 +130,28 @@ public class ColourSchemeProperty // Generate random colors and store for (; j <= n; j++) { - rnaHelices[j] = jalview.util.ColorUtils - .generateRandomColor(Color.white); + rnaHelices[j] = ColorUtils.generateRandomColor(Color.white); } } /** - * delete the existing cached RNA helces colours + * delete the existing cached RNA helices colours */ public static void resetRnaHelicesShading() { rnaHelices = null; } + /** + * Returns the name of the colour scheme (or "None" if it is null) + * + * @param cs + * @return + */ + public static String getColourName(ColourSchemeI cs) + { + return cs == null ? ResidueColourScheme.NONE : cs + .getSchemeName(); + } + }