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HideSequences
[jalview.git]
/
src
/
jalview
/
schemes
/
ColourSchemeProperty.java
diff --git
a/src/jalview/schemes/ColourSchemeProperty.java
b/src/jalview/schemes/ColourSchemeProperty.java
index
d27dcf0
..
b586a0a
100755
(executable)
--- a/
src/jalview/schemes/ColourSchemeProperty.java
+++ b/
src/jalview/schemes/ColourSchemeProperty.java
@@
-40,28
+40,32
@@
public class ColourSchemeProperty
public static final int ZAPPO = 3;
\r
\r
/** DOCUMENT ME!! */
\r
public static final int ZAPPO = 3;
\r
\r
/** DOCUMENT ME!! */
\r
- public static final int HYDROPHOBIC = 4;
\r
+ public static final int TAYLOR = 4;
\r
\r
/** DOCUMENT ME!! */
\r
\r
/** DOCUMENT ME!! */
\r
- public static final int HELIX = 5;
\r
+ public static final int HYDROPHOBIC = 5;
\r
\r
/** DOCUMENT ME!! */
\r
\r
/** DOCUMENT ME!! */
\r
- public static final int STRAND = 6;
\r
+ public static final int HELIX = 6;
\r
\r
/** DOCUMENT ME!! */
\r
\r
/** DOCUMENT ME!! */
\r
- public static final int TURN = 7;
\r
+ public static final int STRAND = 7;
\r
\r
/** DOCUMENT ME!! */
\r
\r
/** DOCUMENT ME!! */
\r
- public static final int BURIED = 8;
\r
+ public static final int TURN = 8;
\r
\r
/** DOCUMENT ME!! */
\r
\r
/** DOCUMENT ME!! */
\r
- public static final int NUCLEOTIDE = 9;
\r
+ public static final int BURIED = 9;
\r
\r
/** DOCUMENT ME!! */
\r
\r
/** DOCUMENT ME!! */
\r
- public static final int USER_DEFINED = 10;
\r
+ public static final int NUCLEOTIDE = 10;
\r
\r
/** DOCUMENT ME!! */
\r
\r
/** DOCUMENT ME!! */
\r
- public static final int NONE = 11;
\r
+ public static final int USER_DEFINED = 11;
\r
+
\r
+
\r
+ /** DOCUMENT ME!! */
\r
+ public static final int NONE = 12;
\r
\r
/**
\r
* DOCUMENT ME!
\r
\r
/**
\r
* DOCUMENT ME!
\r
@@
-72,7
+76,7
@@
public class ColourSchemeProperty
*/
\r
public static int getColourIndexFromName(String name)
\r
{
\r
*/
\r
public static int getColourIndexFromName(String name)
\r
{
\r
- int ret = 11;
\r
+ int ret = 12;
\r
\r
if (name.equalsIgnoreCase("Clustal"))
\r
{
\r
\r
if (name.equalsIgnoreCase("Clustal"))
\r
{
\r
@@
-90,6
+94,10
@@
public class ColourSchemeProperty
{
\r
ret = ZAPPO;
\r
}
\r
{
\r
ret = ZAPPO;
\r
}
\r
+ else if (name.equalsIgnoreCase("Taylor"))
\r
+ {
\r
+ ret = TAYLOR;
\r
+ }
\r
else if (name.equalsIgnoreCase("Hydrophobic"))
\r
{
\r
ret = HYDROPHOBIC;
\r
else if (name.equalsIgnoreCase("Hydrophobic"))
\r
{
\r
ret = HYDROPHOBIC;
\r
@@
-131,12
+139,8
@@
public class ColourSchemeProperty
*/
\r
public static String getColourName(ColourSchemeI cs)
\r
{
\r
*/
\r
public static String getColourName(ColourSchemeI cs)
\r
{
\r
- if (cs instanceof ConservationColourScheme)
\r
- {
\r
- cs = ((ConservationColourScheme) cs).cs;
\r
- }
\r
\r
\r
- int index = 11;
\r
+ int index = 12;
\r
\r
if (cs instanceof ClustalxColourScheme)
\r
{
\r
\r
if (cs instanceof ClustalxColourScheme)
\r
{
\r
@@
-154,6
+158,10
@@
public class ColourSchemeProperty
{
\r
index = ZAPPO;
\r
}
\r
{
\r
index = ZAPPO;
\r
}
\r
+ else if (cs instanceof TaylorColourScheme)
\r
+ {
\r
+ index = TAYLOR;
\r
+ }
\r
else if (cs instanceof HydrophobicColourScheme)
\r
{
\r
index = HYDROPHOBIC;
\r
else if (cs instanceof HydrophobicColourScheme)
\r
{
\r
index = HYDROPHOBIC;
\r
@@
-219,6
+227,10
@@
public class ColourSchemeProperty
\r
break;
\r
\r
\r
break;
\r
\r
+ case TAYLOR:
\r
+ ret = "Taylor";
\r
+ break;
\r
+
\r
case HYDROPHOBIC:
\r
ret = "Hydrophobic";
\r
\r
case HYDROPHOBIC:
\r
ret = "Hydrophobic";
\r
\r
@@
-328,6
+340,10
@@
public class ColourSchemeProperty
\r
break;
\r
\r
\r
break;
\r
\r
+ case TAYLOR:
\r
+ cs = new TaylorColourScheme();
\r
+ break;
\r
+
\r
case HYDROPHOBIC:
\r
cs = new HydrophobicColourScheme();
\r
\r
case HYDROPHOBIC:
\r
cs = new HydrophobicColourScheme();
\r
\r
@@
-359,8
+375,10
@@
public class ColourSchemeProperty
break;
\r
\r
case USER_DEFINED:
\r
break;
\r
\r
case USER_DEFINED:
\r
- cs = new UserColourScheme(new Color[0]);
\r
-
\r
+ Color[] col = new Color[24];
\r
+ for (int i = 0; i < 24; i++)
\r
+ col[i] = Color.white;
\r
+ cs = new UserColourScheme(col);
\r
break;
\r
\r
default:
\r
break;
\r
\r
default:
\r