/*
- * 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
- * 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.
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
*/
package jalview.schemes;
/** DOCUMENT ME!! */
public static final int USER_DEFINED = 11;
- /** DOCUMENT ME!! */
+ /** No Colourscheme Index */
public static final int NONE = 12;
+ /** Undefined Colourscheme Index */
+ public static final int UNDEFINED = 13;
+
/**
* DOCUMENT ME!
*
* @param name
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
public static int getColourIndexFromName(String name)
{
- int ret = 12;
+ int ret = UNDEFINED;
if (name.equalsIgnoreCase("Clustal"))
{
{
ret = USER_DEFINED;
}
+ else if (name.equalsIgnoreCase("None"))
+ {
+ ret = NONE;
+ }
return ret;
}
* DOCUMENT ME!
*
* @param cs
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
public static String getColourName(ColourSchemeI cs)
{
- int index = 12;
+ int index = NONE;
if (cs instanceof ClustalxColourScheme)
{
* DOCUMENT ME!
*
* @param index
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param al
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param name
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
}
/**
- * DOCUMENT ME!
+ * retrieve or create colourscheme associated with name
*
* @param seqs
- * DOCUMENT ME!
+ * sequences to colour
* @param width
- * DOCUMENT ME!
+ * range of sequences to colour
* @param name
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * colourscheme name, applet colour parameter specification, or
+ * string to parse as colour for new coloursheme
+ * @return Valid Colourscheme
*/
public static ColourSchemeI getColour(java.util.Vector seqs, int width,
String name)
{
int colindex = getColourIndexFromName(name);
- if (colindex > USER_DEFINED)
+ if (colindex == UNDEFINED)
{
- try
+ if (name.indexOf('=') == -1)
{
- return new UserColourScheme(name);
- } catch (Exception e)
+ // try to build a colour from the string directly
+ try
+ {
+ return new UserColourScheme(name);
+ } catch (Exception e)
+ {
+ // System.err.println("Ignoring unknown colourscheme name");
+ }
+ }
+ else
{
- // System.err.println("Ignoring unknown colourscheme name");
+ // try to parse the string as a residue colourscheme
+ try
+ {
+ // fix the launchApp user defined coloursheme transfer bug
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ "white");
+ ucs.parseAppletParameter(name);
+
+ } catch (Exception e)
+ {
+ // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
+ }
}
}
return getColour(seqs, width, getColourIndexFromName(name));
* DOCUMENT ME!
*
* @param seqs
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param index
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/