X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;fp=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=8e58c209b1642492beb6183b39a56a020425b0e4;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=9ae14cac7145a2897e3ced7a7b226fa8b0ea301f;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index 9ae14ca..8e58c20 100755 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -23,13 +23,23 @@ package jalview.schemes; import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceI; +import jalview.util.ColorUtils; +import jalview.util.StringUtils; import java.awt.Color; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; import java.util.Map; +import java.util.Map.Entry; import java.util.StringTokenizer; public class UserColourScheme extends ResidueColourScheme { + /* + * lookup (by symbol index) of lower case colours (if configured) + */ Color[] lowerCaseColours; protected String schemeName; @@ -46,37 +56,86 @@ public class UserColourScheme extends ResidueColourScheme } @Override - public ColourSchemeI applyTo(AnnotatedCollectionI sg, + public ColourSchemeI getInstance(AnnotatedCollectionI sg, Map hiddenRepSequences) { - UserColourScheme usc = new UserColourScheme(colors); - if (lowerCaseColours != null) + return new UserColourScheme(this); + } + + /** + * Copy constructor + * + * @return + */ + protected UserColourScheme(UserColourScheme from) + { + this(from.colors); + schemeName = from.schemeName; + if (from.lowerCaseColours != null) { - usc.schemeName = new String(schemeName); - usc.lowerCaseColours = new Color[lowerCaseColours.length]; - System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0, - lowerCaseColours.length); + lowerCaseColours = new Color[from.lowerCaseColours.length]; + System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0, + from.lowerCaseColours.length); } - return usc; } + /** + * Constructor for an animino acid colour scheme. The colour specification may + * be one of + * + * + * @param colour + */ public UserColourScheme(String colour) { super(ResidueProperties.aaIndex); - Color col = getColourFromString(colour); + + if (colour.contains("=")) + { + /* + * a list of colours per residue(s) + */ + parseAppletParameter(colour); + return; + } + + Color col = ColorUtils.parseColourString(colour); if (col == null) { System.out.println("Making colour from name: " + colour); - col = createColourFromName(colour); + col = ColorUtils.createColourFromName(colour); } - colors = new Color[24]; - for (int i = 0; i < 24; i++) + setAll(col); + schemeName = colour; + } + + /** + * Sets all symbols to the specified colour + * + * @param col + */ + protected void setAll(Color col) + { + if (symbolIndex == null) + { + return; + } + int max = 0; + for (int index : symbolIndex) + { + max = Math.max(max, index); + } + colors = new Color[max + 1]; + for (int i = 0; i <= max; i++) { colors[i] = col; } - schemeName = colour; } public Color[] getColours() @@ -99,77 +158,25 @@ public class UserColourScheme extends ResidueColourScheme return schemeName; } - public static Color getColourFromString(String colour) - { - if (colour == null) - { - return null; - } - colour = colour.trim(); - - Color col = null; - try - { - int value = Integer.parseInt(colour, 16); - col = new Color(value); - } catch (NumberFormatException ex) - { - } - - if (col == null) - { - col = ColourSchemeProperty.getAWTColorFromName(colour); - } - - if (col == null) - { - try - { - java.util.StringTokenizer st = new java.util.StringTokenizer( - colour, ","); - int r = Integer.parseInt(st.nextToken()); - int g = Integer.parseInt(st.nextToken()); - int b = Integer.parseInt(st.nextToken()); - col = new Color(r, g, b); - } catch (Exception ex) - { - } - } - - return col; - - } - - public static Color createColourFromName(String name) + /** + * Parse and save residue colours specified as (for example) + * + * 
+   *     D,E=red; K,R,H=0022FF; c=100,50,75
+   *
+ * + * This should be a semi-colon separated list of colours, which may be defined + * by colour name, hex value or comma-separated RGB triple. Each colour is + * defined for a comma-separated list of amino acid single letter codes. (Note + * that this also allows a colour scheme to be defined for ACGT, but not for + * U.) + * + * @param paramValue + */ + void parseAppletParameter(String paramValue) { - int r, g, b; - - int lsize = name.length(); - int start = 0, end = lsize / 3; - - int rgbOffset = Math.abs(name.hashCode() % 10) * 15; - - r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20; - start = end; - end += lsize / 3; - if (end > lsize) - { - end = lsize; - } + setAll(Color.white); - g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20; - - b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20; - - Color color = new Color(r, g, b); - - return color; - } - - public void parseAppletParameter(String paramValue) - { - // TODO: need a function to generate appletParameter colour string from a - // UCS StringTokenizer st = new StringTokenizer(paramValue, ";"); StringTokenizer st2; String token = null, colour, residues; @@ -184,43 +191,42 @@ public class UserColourScheme extends ResidueColourScheme st2 = new StringTokenizer(residues, " ,"); while (st2.hasMoreTokens()) { - token = st2.nextToken(); + String residue = st2.nextToken(); - if (ResidueProperties.aaIndex[token.charAt(0)] == -1) + int colIndex = ResidueProperties.aaIndex[residue.charAt(0)]; + if (colIndex == -1) { continue; } - int colIndex = ResidueProperties.aaIndex[token.charAt(0)]; - - if (token.equalsIgnoreCase("lowerCase")) + if (residue.equalsIgnoreCase("lowerCase")) { if (lowerCaseColours == null) { - lowerCaseColours = new Color[23]; + lowerCaseColours = new Color[colors.length]; } - for (int i = 0; i < 23; i++) + for (int i = 0; i < lowerCaseColours.length; i++) { if (lowerCaseColours[i] == null) { - lowerCaseColours[i] = getColourFromString(colour); + lowerCaseColours[i] = ColorUtils.parseColourString(colour); } } continue; } - if (token.equals(token.toLowerCase())) + if (residue.equals(residue.toLowerCase())) { if (lowerCaseColours == null) { - lowerCaseColours = new Color[23]; + lowerCaseColours = new Color[colors.length]; } - lowerCaseColours[colIndex] = getColourFromString(colour); + lowerCaseColours[colIndex] = ColorUtils.parseColourString(colour); } else { - colors[colIndex] = getColourFromString(colour); + colors[colIndex] = ColorUtils.parseColourString(colour); } } } @@ -232,39 +238,115 @@ public class UserColourScheme extends ResidueColourScheme } - @Override - public Color findColour(char c, int j, SequenceI seq) + public void setLowerCaseColours(Color[] lcolours) { - Color currentColour; - int index = ResidueProperties.aaIndex[c]; + lowerCaseColours = lcolours; + } - if ((threshold == 0) || aboveThreshold(c, j)) + /** + * Returns the colour for the given residue character. If the residue is + * lower-case, and there is a specific colour defined for lower case, that + * colour is returned, else the colour for the upper case residue. + */ + @Override + public Color findColour(char c) + { + if ('a' <= c && c <= 'z' && lowerCaseColours != null) { - if (lowerCaseColours != null && 'a' <= c && c <= 'z') - { - currentColour = lowerCaseColours[index]; - } - else + Color colour = lowerCaseColours[symbolIndex[c]]; + if (colour != null) { - currentColour = colors[index]; + return colour; } } - else + return super.findColour(c); + } + + /** + * Answers the customised name of the colour scheme, if it has one, else + * "User Defined" + */ + @Override + public String getSchemeName() + { + if (schemeName != null && schemeName.length() > 0) { - currentColour = Color.white; + return schemeName; } + return "User Defined"; + } + + /** + * Generate an applet colour parameter like A,C,D=12ffe9;Q,W=2393fd;w=9178dd + * + * @return + */ + public String toAppletParameter() + { + /* + * step 1: build a map from colours to the symbol(s) that have the colour + */ + Map> colours = new HashMap>(); - if (conservationColouring) + for (char symbol = 'A'; symbol <= 'Z'; symbol++) { - currentColour = applyConservation(currentColour, j); + String residue = String.valueOf(symbol); + int index = symbolIndex[symbol]; + Color c = colors[index]; + if (c != null && !c.equals(Color.white)) + { + if (colours.get(c) == null) + { + colours.put(c, new ArrayList()); + } + colours.get(c).add(residue); + } + if (lowerCaseColours != null) + { + c = lowerCaseColours[index]; + if (c != null && !c.equals(Color.white)) + { + residue = residue.toLowerCase(); + if (colours.get(c) == null) + { + colours.put(c, new ArrayList()); + } + colours.get(c).add(residue); + } + } } - return currentColour; - } + /* + * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs + */ + List residueColours = new ArrayList(); + for (Entry> cols : colours.entrySet()) + { + boolean first = true; + StringBuilder sb = new StringBuilder(); + for (String residue : cols.getValue()) + { + if (!first) + { + sb.append(","); + } + sb.append(residue); + first = false; + } + sb.append("="); + /* + * get color as hex value, dropping the alpha (ff) part + */ + String hexString = Integer.toHexString(cols.getKey().getRGB()) + .substring(2); + sb.append(hexString); + residueColours.add(sb.toString()); + } - public void setLowerCaseColours(Color[] lcolours) - { - lowerCaseColours = lcolours; + /* + * sort and output + */ + Collections.sort(residueColours); + return StringUtils.listToDelimitedString(residueColours, ";"); } - }