-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-import java.util.StringTokenizer;\r
-\r
-public class UserColourScheme\r
- extends ResidueColourScheme\r
-{\r
- Color [] lowerCaseColours;\r
-\r
- protected String schemeName;\r
-\r
- public UserColourScheme()\r
- { }\r
-\r
- public UserColourScheme(Color[] newColors)\r
- {\r
- colors = newColors;\r
- }\r
-\r
- public UserColourScheme(String colour)\r
- {\r
- Color col = getColourFromString(colour);\r
-\r
- if(col==null)\r
- {\r
- System.out.println("Unknown colour!! "+colour);\r
- col = createColourFromName(colour);\r
- }\r
-\r
- colors = new Color[24];\r
- for(int i=0; i<24; i++)\r
- colors[i] = col;\r
- }\r
-\r
- public Color[] getColours()\r
- {\r
- return colors;\r
- }\r
-\r
- public Color[] getLowerCaseColours()\r
- {\r
- return lowerCaseColours;\r
- }\r
-\r
- public void setName(String name)\r
- {\r
- schemeName = name;\r
- }\r
-\r
- public String getName()\r
- {\r
- return schemeName;\r
- }\r
-\r
- public Color getColourFromString(String colour)\r
- {\r
- colour = colour.trim();\r
-\r
- Color col = null;\r
- try\r
- {\r
- int value = Integer.parseInt(colour, 16);\r
- col = new Color(value);\r
- }\r
- catch (NumberFormatException ex)\r
- {}\r
-\r
- if (col == null)\r
- col = ColourSchemeProperty.getAWTColorFromName(colour);\r
-\r
- if (col == null)\r
- {\r
- try\r
- {\r
- java.util.StringTokenizer st = new java.util.StringTokenizer(colour,\r
- ",");\r
- int r = Integer.parseInt(st.nextToken());\r
- int g = Integer.parseInt(st.nextToken());\r
- int b = Integer.parseInt(st.nextToken());\r
- col = new Color(r, g, b);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
-\r
- return col;\r
-\r
- }\r
-\r
- public Color createColourFromName(String name)\r
- {\r
- int r, g, b;\r
-\r
- int lsize = name.length();\r
- int start = 0, end = lsize / 3;\r
-\r
- int rgbOffset = Math.abs(name.hashCode() % 10) * 15;\r
-\r
- r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;\r
- start = end;\r
- end += lsize / 3;\r
- if (end > lsize)\r
- end = lsize;\r
-\r
- g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;\r
-\r
- b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20;\r
-\r
- Color color = new Color(r, g, b);\r
-\r
- return color;\r
- }\r
-\r
- public void parseAppletParameter(String paramValue)\r
- {\r
- StringTokenizer st = new StringTokenizer(paramValue, ";");\r
- StringTokenizer st2;\r
- String token=null, colour, residues;\r
- try{\r
- while (st.hasMoreElements())\r
- {\r
- token = st.nextToken().trim();\r
- residues = token.substring(0, token.indexOf("="));\r
- colour = token.substring(token.indexOf("=") + 1);\r
-\r
- st2 = new StringTokenizer(residues, " ,");\r
- while (st2.hasMoreTokens())\r
- {\r
- token = st2.nextToken();\r
-\r
- if (ResidueProperties.aaIndex[token.charAt(0)]==-1)\r
- continue;\r
-\r
- int colIndex = ResidueProperties.aaIndex[token.charAt(0)];\r
-\r
- if(token.equalsIgnoreCase("lowerCase"))\r
- {\r
- if (lowerCaseColours == null)\r
- lowerCaseColours = new Color[23];\r
- for (int i = 0; i < 23; i++)\r
- if (lowerCaseColours[i] == null)\r
- lowerCaseColours[i] = getColourFromString(colour);\r
-\r
- continue;\r
- }\r
-\r
- if(token.equals(token.toLowerCase()))\r
- {\r
- if(lowerCaseColours==null)\r
- {\r
- lowerCaseColours = new Color[23];\r
- }\r
- lowerCaseColours[colIndex] = getColourFromString(colour);\r
- }\r
- else\r
- colors[colIndex] = getColourFromString(colour);\r
- }\r
- }\r
- }\r
- catch(Exception ex)\r
- {\r
- System.out.println("Error parsing userDefinedColours:\n"\r
- +token+"\n"+ex);\r
- }\r
-\r
- }\r
-\r
-\r
-\r
- public Color findColour(String s, int j)\r
- {\r
- Color currentColour;\r
- int index = ResidueProperties.aaIndex[s.charAt(0)];\r
-\r
- if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))\r
- {\r
- if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')\r
- currentColour = lowerCaseColours[index];\r
- else\r
- currentColour = colors[index];\r
- }\r
- else\r
- {\r
- currentColour = Color.white;\r
- }\r
-\r
- if(conservationColouring)\r
- currentColour = applyConservation(currentColour, j);\r
-\r
-\r
- return currentColour;\r
- }\r
-\r
- public void setLowerCaseColours(Color [] lcolours)\r
- {\r
- lowerCaseColours = lcolours;\r
- }\r
-\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import java.util.Locale;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+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;
+
+ public UserColourScheme()
+ {
+ super(ResidueProperties.aaIndex);
+ }
+
+ public UserColourScheme(Color[] newColors)
+ {
+ super(ResidueProperties.aaIndex);
+ colors = newColors;
+ }
+
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
+ {
+ 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
+ * <ul>
+ * <li>an AWT colour name e.g. red</li>
+ * <li>an AWT hex rgb colour e.g. ff2288</li>
+ * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
+ * </ul>
+ *
+ * @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)
+ *
+ * <pre>
+ * D,E=red; K,R,H=0022FF; c=100,50,75
+ * </pre>
+ *
+ * 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(Locale.ROOT)))
+ {
+ 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<Color, List<String>> 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<String>());
+ }
+ colours.get(c).add(residue);
+ }
+ if (lowerCaseColours != null)
+ {
+ c = lowerCaseColours[index];
+ if (c != null && !c.equals(Color.white))
+ {
+ residue = residue.toLowerCase(Locale.ROOT);
+ if (colours.get(c) == null)
+ {
+ colours.put(c, new ArrayList<String>());
+ }
+ colours.get(c).add(residue);
+ }
+ }
+ }
+
+ /*
+ * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
+ */
+ List<String> residueColours = new ArrayList<>();
+ for (Entry<Color, List<String>> 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);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff