X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FCovariationColourScheme.java;h=923bd852d1ca56c9a335304c09470d1680d67ad5;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=223b24998c1b94380d323168de911a7127901a74;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index 223b249..923bd85 100644
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -1,27 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * 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 java.awt.*;
-import java.util.Hashtable;
-
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
/**
* Became RNAHelicesColour.java. Placeholder for true covariation color scheme
@@ -31,15 +38,26 @@ import jalview.datamodel.AlignmentAnnotation;
*/
public class CovariationColourScheme extends ResidueColourScheme
{
- public Hashtable helixcolorhash = new Hashtable();
+ public Map helixcolorhash = new Hashtable();
- public Hashtable positionsToHelix = new Hashtable();
+ public Map positionsToHelix = new Hashtable();
int numHelix = 0;
public AlignmentAnnotation annotation;
/**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map hrs)
+ {
+ return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
+ }
+
+ /**
* Creates a new CovariationColourScheme object.
*/
public CovariationColourScheme(AlignmentAnnotation annotation)
@@ -59,18 +77,19 @@ public class CovariationColourScheme extends ResidueColourScheme
positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
this.annotation._rnasecstr[x].getFeatureGroup());
- if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
+ if (Integer.parseInt(
+ this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
{
- numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup());
+ numHelix = Integer
+ .parseInt(this.annotation._rnasecstr[x].getFeatureGroup());
}
}
for (int j = 0; j <= numHelix; j++)
{
- helixcolorhash.put(Integer.toString(j),
- jalview.util.ColorUtils.generateRandomColor(Color.white));
+ helixcolorhash.put(String.valueOf(j),
+ ColorUtils.generateRandomColor(Color.white));
}
}
@@ -83,6 +102,7 @@ public class CovariationColourScheme extends ResidueColourScheme
*
* @return DOCUMENT ME!
*/
+ @Override
public Color findColour(char c)
{
// System.out.println("called"); log.debug
@@ -106,12 +126,12 @@ public class CovariationColourScheme extends ResidueColourScheme
Color currentColour = Color.white;
String currentHelix = null;
// System.out.println(c + " " + j);
- currentHelix = (String) positionsToHelix.get(j);
+ currentHelix = positionsToHelix.get(j);
// System.out.println(positionsToHelix.get(j));
if (currentHelix != null)
{
- currentColour = (Color) helixcolorhash.get(currentHelix);
+ currentColour = helixcolorhash.get(currentHelix);
}
// System.out.println(c + " " + j + " helix " + currentHelix + " " +
@@ -119,4 +139,21 @@ public class CovariationColourScheme extends ResidueColourScheme
return currentColour;
}
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Covariation";
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}