X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=9ae14cac7145a2897e3ced7a7b226fa8b0ea301f;hb=8bb1df31c9d46763d2a3278d27d52ce69ba441b3;hp=9a781cbbc2449432b6d7fc83854c9afca3e7eba7;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 9a781cb..9ae14ca 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,26 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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 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 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 .
+ * 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
{
@@ -30,20 +36,38 @@ public class UserColourScheme extends ResidueColourScheme
public UserColourScheme()
{
+ super(ResidueProperties.aaIndex);
}
public UserColourScheme(Color[] newColors)
{
+ super(ResidueProperties.aaIndex);
colors = newColors;
}
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map 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);
}
@@ -75,8 +99,12 @@ public class UserColourScheme extends ResidueColourScheme
return schemeName;
}
- public Color getColourFromString(String colour)
+ public static Color getColourFromString(String colour)
{
+ if (colour == null)
+ {
+ return null;
+ }
colour = colour.trim();
Color col = null;
@@ -112,7 +140,7 @@ public class UserColourScheme extends ResidueColourScheme
}
- public Color createColourFromName(String name)
+ public static Color createColourFromName(String name)
{
int r, g, b;
@@ -140,6 +168,8 @@ public class UserColourScheme extends ResidueColourScheme
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;
@@ -202,7 +232,8 @@ public class UserColourScheme extends ResidueColourScheme
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
int index = ResidueProperties.aaIndex[c];