/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
* ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
* intelligently with mapping unknown names to user defined colourschemes (that
* exist or can be created from the string representation of the colourscheme
- * name - either a hex RGB triplet or a named colour under java.awt.color )
+ * name - either a hex RGB triplet or a named colour under java.awt.color ). The
+ * values of the colourscheme constants is important for callers of
+ * getColourName(int i), since it can be used to enumerate the set of built in
+ * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
*
* @author $author$
* @version $Revision$
*/
public class ColourSchemeProperty
{
- /** DOCUMENT ME!! */
- public static final int CLUSTAL = 0;
+ /** Undefined Colourscheme Index */
+ public static final int UNDEFINED = -1;
- /** DOCUMENT ME!! */
- public static final int BLOSUM = 1;
+ /** for schemes defined on the fly */
+ public static final int USER_DEFINED = 0;
+
+ /** No Colourscheme Index */
+ public static final int NONE = 1;
/** DOCUMENT ME!! */
- public static final int PID = 2;
+ public static final int CLUSTAL = 2;
/** DOCUMENT ME!! */
- public static final int ZAPPO = 3;
+ public static final int BLOSUM = 3;
/** DOCUMENT ME!! */
- public static final int TAYLOR = 4;
+ public static final int PID = 4;
/** DOCUMENT ME!! */
- public static final int HYDROPHOBIC = 5;
+ public static final int ZAPPO = 5;
/** DOCUMENT ME!! */
- public static final int HELIX = 6;
+ public static final int TAYLOR = 6;
/** DOCUMENT ME!! */
- public static final int STRAND = 7;
+ public static final int HYDROPHOBIC = 7;
/** DOCUMENT ME!! */
- public static final int TURN = 8;
+ public static final int HELIX = 8;
/** DOCUMENT ME!! */
- public static final int BURIED = 9;
+ public static final int STRAND = 9;
/** DOCUMENT ME!! */
- public static final int NUCLEOTIDE = 10;
+ public static final int TURN = 10;
/** DOCUMENT ME!! */
- public static final int USER_DEFINED = 11;
+ public static final int BURIED = 11;
/** DOCUMENT ME!! */
- public static final int NONE = 12;
+ public static final int NUCLEOTIDE = 12;
+
+ /**
+ * purine/pyrimidine
+ */
+ public static final int PURINEPYRIMIDINE = 13;
+
+ public static final int COVARIATION = 14;
+
+ /**
+ * index of first colourscheme (includes 'None')
+ */
+ public static final int FIRST_COLOUR = NONE;
+
+ public static final int LAST_COLOUR = NUCLEOTIDE;
/**
* 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;
+ }
+ else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
+ {
+ ret = PURINEPYRIMIDINE;
+ }
+ // else if (name.equalsIgnoreCase("Covariation"))
+ // {
+ // ret = COVARIATION;
+ // }
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)
{
{
index = NUCLEOTIDE;
}
+ else if (cs instanceof PurinePyrimidineColourScheme)
+ {
+ index = PURINEPYRIMIDINE;
+ }
+ /*
+ * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
+ */
else if (cs instanceof UserColourScheme)
{
if ((((UserColourScheme) cs).getName() != null)
* DOCUMENT ME!
*
* @param index
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
break;
+ case PURINEPYRIMIDINE:
+ ret = "Purine/Pyrimidine";
+
+ break;
+
+ /*
+ * case COVARIATION: ret = "Covariation";
+ *
+ * break;
+ */
case USER_DEFINED:
ret = "User Defined";
* 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!
*/
break;
+ case PURINEPYRIMIDINE:
+ cs = new PurinePyrimidineColourScheme();
+
+ break;
+
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
+
+ // break;
+
case USER_DEFINED:
Color[] col = new Color[24];
for (int i = 0; i < 24; i++)
git://source.jalview.org / jalview.git / blobdiff