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JAL-2361 Blosum is enabled for peptide
[jalview.git]
/
src
/
jalview
/
schemes
/
UserColourScheme.java
diff --git
a/src/jalview/schemes/UserColourScheme.java
b/src/jalview/schemes/UserColourScheme.java
index
7bf02c1
..
09cef92
100755
(executable)
--- a/
src/jalview/schemes/UserColourScheme.java
+++ b/
src/jalview/schemes/UserColourScheme.java
@@
-24,9
+24,11
@@
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
+import jalview.util.StringUtils;
import java.awt.Color;
import java.util.ArrayList;
import java.awt.Color;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@
-54,7
+56,7
@@
public class UserColourScheme extends ResidueColourScheme
}
@Override
}
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
UserColourScheme usc = new UserColourScheme(colors);
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
UserColourScheme usc = new UserColourScheme(colors);
@@
-292,7
+294,7
@@
public class UserColourScheme extends ResidueColourScheme
{
return schemeName;
}
{
return schemeName;
}
- return JalviewColourScheme.UserDefined.toString();
+ return "User Defined";
}
/**
}
/**
@@
-302,6
+304,9
@@
public class UserColourScheme extends ResidueColourScheme
*/
public String toAppletParameter()
{
*/
public String toAppletParameter()
{
+ /*
+ * step 1: build a map from colours to the symbol(s) that have the colour
+ */
Map<Color, List<String>> colours = new HashMap<Color, List<String>>();
for (char symbol = 'A'; symbol <= 'Z'; symbol++)
Map<Color, List<String>> colours = new HashMap<Color, List<String>>();
for (char symbol = 'A'; symbol <= 'Z'; symbol++)
@@
-331,14
+336,15
@@
public class UserColourScheme extends ResidueColourScheme
}
}
}
}
}
}
- StringBuilder sb = new StringBuilder();
+
+ /*
+ * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
+ */
+ List<String> residueColours = new ArrayList<String>();
for (Entry<Color, List<String>> cols : colours.entrySet())
{
for (Entry<Color, List<String>> cols : colours.entrySet())
{
- if (sb.length() > 0)
- {
- sb.append(";");
- }
boolean first = true;
boolean first = true;
+ StringBuilder sb = new StringBuilder();
for (String residue : cols.getValue())
{
if (!first)
for (String residue : cols.getValue())
{
if (!first)
@@
-355,8
+361,13
@@
public class UserColourScheme extends ResidueColourScheme
String hexString = Integer.toHexString(cols.getKey().getRGB())
.substring(2);
sb.append(hexString);
String hexString = Integer.toHexString(cols.getKey().getRGB())
.substring(2);
sb.append(hexString);
+ residueColours.add(sb.toString());
}
}
- return sb.toString();
+ /*
+ * sort and output
+ */
+ Collections.sort(residueColours);
+ return StringUtils.listToDelimitedString(residueColours, ";");
}
}
}
}