X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=e2a8cb31425ababfe725c11473bc4f7314894217;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=570787602460a082845bc3a6f6a94bad17ecc09f;hpb=dfb3daaf3d75deda32e7622713ffb759aaadd18c;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 5707876..e2a8cb3 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,16 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
-import jalview.binding.JalviewUserColours;
+import java.util.LinkedHashMap;
+import java.util.Locale;
+import java.util.Map;
+
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
-import java.awt.Color;
-import java.io.FileInputStream;
-import java.io.InputStreamReader;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
public class ColourSchemes
{
/*
@@ -19,7 +37,7 @@ public class ColourSchemes
private static ColourSchemes instance = new ColourSchemes();
/*
- * a map from scheme name to an instance of it
+ * a map from scheme name (lower-cased) to an instance of it
*/
private Map schemes;
@@ -49,17 +67,22 @@ public class ColourSchemes
* store in an order-preserving map, so items can be added to menus
* in the order in which they are 'discovered'
*/
- schemes = new LinkedHashMap();
+ schemes = new LinkedHashMap<>();
for (JalviewColourScheme cs : JalviewColourScheme.values())
{
try
{
- registerColourScheme(cs.getSchemeClass().newInstance());
+ registerColourScheme(
+ cs.getSchemeClass().getDeclaredConstructor().newInstance());
} catch (InstantiationException | IllegalAccessException e)
{
- System.err.println("Error instantiating colour scheme for "
+ jalview.bin.Console.errPrintln("Error instantiating colour scheme for "
+ cs.toString() + " " + e.getMessage());
+ e.printStackTrace();
+ } catch (ReflectiveOperationException roe)
+ {
+ roe.printStackTrace();
}
}
}
@@ -74,7 +97,7 @@ public class ColourSchemes
String name = cs.getSchemeName();
if (name == null)
{
- System.err.println("ColourScheme name may not be null");
+ jalview.bin.Console.errPrintln("ColourScheme name may not be null");
return;
}
@@ -82,7 +105,7 @@ public class ColourSchemes
* name is lower-case for non-case-sensitive lookup
* (name in the colour keeps its true case)
*/
- String lower = name.toLowerCase();
+ String lower = getColourSchemeShortName(cs);
if (schemes.containsKey(lower))
{
System.err
@@ -91,6 +114,19 @@ public class ColourSchemes
schemes.put(lower, cs);
}
+ private String getColourSchemeShortName(ColourSchemeI cs)
+ {
+ return getColourSchemeShortName(cs.getSchemeName());
+ }
+
+ private String getColourSchemeShortName(String name)
+ {
+ if (name == null)
+ return null;
+ return name.toLowerCase(Locale.ROOT).replaceAll("%", "pc")
+ .replaceAll("[^a-z0-9]", "-").replaceAll("--+", "-");
+ }
+
/**
* Removes a colour scheme by name
*
@@ -98,15 +134,19 @@ public class ColourSchemes
*/
public void removeColourScheme(String name)
{
- schemes.remove(name);
+ if (name != null)
+ {
+ schemes.remove(getColourSchemeShortName(name));
+ }
}
-
+
/**
* Returns an instance of the colour scheme with which the given view may be
* coloured
*
* @param name
* name of the colour scheme
+ * @param viewport
* @param forData
* the data to be coloured
* @param optional
@@ -114,7 +154,7 @@ public class ColourSchemes
* represent
* @return
*/
- public ColourSchemeI getColourScheme(String name,
+ public ColourSchemeI getColourScheme(String name, AlignViewportI viewport,
AnnotatedCollectionI forData,
Map hiddenRepSequences)
{
@@ -122,8 +162,8 @@ public class ColourSchemes
{
return null;
}
- ColourSchemeI cs = schemes.get(name.toLowerCase());
- return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
+ ColourSchemeI cs = schemes.get(getColourSchemeShortName(name));
+ return cs == null ? null : cs.getInstance(viewport, forData);
}
/**
@@ -139,7 +179,7 @@ public class ColourSchemes
public ColourSchemeI getColourScheme(String name,
AnnotatedCollectionI forData)
{
- return getColourScheme(name, forData, null);
+ return getColourScheme(name, null, forData, null);
}
/**
@@ -166,123 +206,6 @@ public class ColourSchemes
{
return false;
}
- name = name.toLowerCase();
- for (ColourSchemeI scheme : getColourSchemes())
- {
- if (name.equals(scheme.getSchemeName().toLowerCase()))
- {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Loads a user defined colour scheme from file. The file should contain a
- * definition of residue colours in XML format as defined in
- * JalviewUserColours.xsd.
- *
- * @param file
- *
- * @return
- */
- public static UserColourScheme loadColourScheme(String file)
- {
- UserColourScheme ucs = null;
- Color[] newColours = null;
- try
- {
- InputStreamReader in = new InputStreamReader(
- new FileInputStream(file), "UTF-8");
-
- jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-
- org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
- jucs);
- jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
- .unmarshal(in);
-
- /*
- * non-case-sensitive colours are for 20 amino acid codes,
- * B, Z, X and Gap
- * optionally, lower-case alternatives for all except Gap
- */
- newColours = new Color[24];
- Color[] lowerCase = new Color[23];
- boolean caseSensitive = false;
-
- String name;
- int index;
- for (int i = 0; i < jucs.getColourCount(); i++)
- {
- name = jucs.getColour(i).getName();
- if (ResidueProperties.aa3Hash.containsKey(name))
- {
- index = ResidueProperties.aa3Hash.get(name).intValue();
- }
- else
- {
- index = ResidueProperties.aaIndex[name.charAt(0)];
- }
- if (index == -1)
- {
- continue;
- }
-
- Color color = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
- if (name.toLowerCase().equals(name))
- {
- caseSensitive = true;
- lowerCase[index] = color;
- }
- else
- {
- newColours[index] = color;
- }
- }
-
- /*
- * instantiate the colour scheme
- */
- ucs = new UserColourScheme(newColours);
- ucs.setName(jucs.getSchemeName());
- if (caseSensitive)
- {
- ucs.setLowerCaseColours(lowerCase);
- }
- } catch (Exception ex)
- {
- // Could be old Jalview Archive format
- try
- {
- InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
-
- jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-
- jucs = JalviewUserColours.unmarshal(in);
-
- newColours = new Color[jucs.getColourCount()];
-
- for (int i = 0; i < 24; i++)
- {
- newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
- }
- ucs = new UserColourScheme(newColours);
- ucs.setName(jucs.getSchemeName());
- } catch (Exception ex2)
- {
- ex2.printStackTrace();
- }
-
- if (newColours == null)
- {
- System.out.println("Error loading User ColourFile\n" + ex);
- }
- }
-
- return ucs;
+ return schemes.containsKey(getColourSchemeShortName(name));
}
}