/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
-import java.awt.*;
+import java.awt.Color;
+import java.util.Map;
+import java.util.StringTokenizer;
-public class UserColourScheme
- extends ResidueColourScheme
+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);
+ System.out.println("Making colour from name: " + colour);
col = createColourFromName(colour);
}
return schemeName;
}
- public Color getColourFromString(String colour)
+ public static Color getColourFromString(String colour)
{
+ if (colour == null)
+ {
+ return null;
+ }
colour = colour.trim();
Color col = null;
{
int value = Integer.parseInt(colour, 16);
col = new Color(value);
+ } catch (NumberFormatException ex)
+ {
}
- catch (NumberFormatException ex)
- {}
if (col == null)
{
{
try
{
- java.util.StringTokenizer st = new java.util.StringTokenizer(colour,
- ",");
+ 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)
+ {
}
- catch (Exception ex)
- {}
}
return col;
}
- public Color createColourFromName(String name)
+ public static Color createColourFromName(String name)
{
int r, g, b;
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;
}
}
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- System.out.println("Error parsing userDefinedColours:\n"
- + token + "\n" + ex);
+ System.out.println("Error parsing userDefinedColours:\n" + token
+ + "\n" + ex);
}
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
int index = ResidueProperties.aaIndex[c];
- if ( (threshold == 0) || aboveThreshold(c, j))
+ if ((threshold == 0) || aboveThreshold(c, j))
{
if (lowerCaseColours != null && 'a' <= c && c <= 'z')
{