-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
- 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 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
- int colIndex =\r
- ( (Integer) ResidueProperties.aaHash.\r
- get(st2.nextToken())).intValue();\r
-\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+import java.util.StringTokenizer;
+
+public class UserColourScheme extends ResidueColourScheme
+{
+ Color[] lowerCaseColours;
+
+ protected String schemeName;
+
+ public UserColourScheme()
+ {
+ super(ResidueProperties.aaIndex);
+ }
+
+ public UserColourScheme(Color[] newColors)
+ {
+ super(ResidueProperties.aaIndex);
+ colors = newColors;
+ }
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ UserColourScheme usc = new UserColourScheme(colors);
+ if (lowerCaseColours != null)
+ {
+ usc.schemeName = new String(schemeName);
+ usc.lowerCaseColours = new Color[lowerCaseColours.length];
+ System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
+ lowerCaseColours.length);
+ }
+ return usc;
+ }
+
+ public UserColourScheme(String colour)
+ {
+ super(ResidueProperties.aaIndex);
+ Color col = getColourFromString(colour);
+
+ if (col == null)
+ {
+ System.out.println("Unknown colour!! " + colour);
+ col = createColourFromName(colour);
+ }
+
+ colors = new Color[24];
+ for (int i = 0; i < 24; i++)
+ {
+ colors[i] = col;
+ }
+ schemeName = colour;
+ }
+
+ public Color[] getColours()
+ {
+ return colors;
+ }
+
+ public Color[] getLowerCaseColours()
+ {
+ return lowerCaseColours;
+ }
+
+ public void setName(String name)
+ {
+ schemeName = name;
+ }
+
+ public String getName()
+ {
+ return schemeName;
+ }
+
+ public Color getColourFromString(String colour)
+ {
+ 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 Color createColourFromName(String name)
+ {
+ 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;
+ }
+
+ 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;
+ 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())
+ {
+ token = st2.nextToken();
+
+ if (ResidueProperties.aaIndex[token.charAt(0)] == -1)
+ {
+ continue;
+ }
+
+ int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
+
+ if (token.equalsIgnoreCase("lowerCase"))
+ {
+ if (lowerCaseColours == null)
+ {
+ lowerCaseColours = new Color[23];
+ }
+ for (int i = 0; i < 23; i++)
+ {
+ if (lowerCaseColours[i] == null)
+ {
+ lowerCaseColours[i] = getColourFromString(colour);
+ }
+ }
+
+ continue;
+ }
+
+ if (token.equals(token.toLowerCase()))
+ {
+ if (lowerCaseColours == null)
+ {
+ lowerCaseColours = new Color[23];
+ }
+ lowerCaseColours[colIndex] = getColourFromString(colour);
+ }
+ else
+ {
+ colors[colIndex] = getColourFromString(colour);
+ }
+ }
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error parsing userDefinedColours:\n" + token
+ + "\n" + ex);
+ }
+
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color currentColour;
+ int index = ResidueProperties.aaIndex[c];
+
+ if ((threshold == 0) || aboveThreshold(c, j))
+ {
+ if (lowerCaseColours != null && 'a' <= c && c <= 'z')
+ {
+ currentColour = lowerCaseColours[index];
+ }
+ else
+ {
+ currentColour = colors[index];
+ }
+ }
+ else
+ {
+ currentColour = Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+
+ public void setLowerCaseColours(Color[] lcolours)
+ {
+ lowerCaseColours = lcolours;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff