hiddenRepSequences)
+ {
+ return new UserColourScheme(this);
+ }
+
+ /**
+ * Copy constructor
+ *
+ * @return
+ */
+ protected UserColourScheme(UserColourScheme from)
+ {
+ this(from.colors);
+ schemeName = from.schemeName;
+ if (from.lowerCaseColours != null)
+ {
+ lowerCaseColours = new Color[from.lowerCaseColours.length];
+ System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0,
+ from.lowerCaseColours.length);
+ }
+ }
+
+ /**
+ * Constructor for an animino acid colour scheme. The colour specification may
+ * be one of
+ *
+ * - an AWT colour name e.g. red
+ * - an AWT hex rgb colour e.g. ff2288
+ * - residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow
+ *
+ *
+ * @param colour
+ */
+ public UserColourScheme(String colour)
+ {
+ super(ResidueProperties.aaIndex);
+
+ 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 = ColorUtils.createColourFromName(colour);
+ }
+
+ 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;
+ }
+ }
+
+ public Color[] getColours()
+ {
+ return colors;
+ }
+
+ public Color[] getLowerCaseColours()
+ {
+ return lowerCaseColours;
+ }
+
+ public void setName(String name)
+ {
+ schemeName = name;
+ }
+
+ public String getName()
+ {
+ return schemeName;
+ }
+
+ /**
+ * 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)
+ {
+ setAll(Color.white);
+
+ StringTokenizer st = new StringTokenizer(paramValue, ";");
+ StringTokenizer st2;
+ String token = null, colour, residues;
+ try
+ {
+ while (st.hasMoreElements())
+ {
+ token = st.nextToken().trim();
+ residues = token.substring(0, token.indexOf("="));
+ colour = token.substring(token.indexOf("=") + 1);
+
+ st2 = new StringTokenizer(residues, " ,");
+ while (st2.hasMoreTokens())
+ {
+ String residue = st2.nextToken();
+
+ int colIndex = ResidueProperties.aaIndex[residue.charAt(0)];
+ if (colIndex == -1)
+ {
+ continue;
+ }
+
+ if (residue.equalsIgnoreCase("lowerCase"))
+ {
+ if (lowerCaseColours == null)
+ {
+ lowerCaseColours = new Color[colors.length];
+ }
+ for (int i = 0; i < lowerCaseColours.length; i++)
+ {
+ if (lowerCaseColours[i] == null)
+ {
+ lowerCaseColours[i] = ColorUtils.parseColourString(colour);
+ }
+ }
+
+ continue;
+ }
+
+ if (residue.equals(residue.toLowerCase()))
+ {
+ if (lowerCaseColours == null)
+ {
+ lowerCaseColours = new Color[colors.length];
+ }
+ lowerCaseColours[colIndex] = ColorUtils
+ .parseColourString(colour);
+ }
+ else
+ {
+ colors[colIndex] = ColorUtils.parseColourString(colour);
+ }
+ }
+ }
+ } catch (Exception ex)
+ {
+ System.out.println(
+ "Error parsing userDefinedColours:\n" + token + "\n" + ex);
+ }
+
+ }
+
+ public void setLowerCaseColours(Color[] lcolours)
+ {
+ lowerCaseColours = lcolours;
+ }
+
+ /**
+ * 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)
+ {
+ Color colour = lowerCaseColours[symbolIndex[c]];
+ if (colour != null)
+ {
+ return colour;
+ }
+ }
+ 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)
+ {
+ return schemeName;
+ }
+ return ResidueColourScheme.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<>();
+
+ for (char symbol = 'A'; symbol <= 'Z'; symbol++)
+ {
+ 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);
+ }
+ }
+ }
+
+ /*
+ * 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());
+ }
+
+ /*
+ * sort and output
+ */
+ Collections.sort(residueColours);
+ return StringUtils.listToDelimitedString(residueColours, ";");
+ }
+
+ @Override
+ public boolean hasGapColour()
+ {
+ return (findColour(' ') != null);
+ }
+}