X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FCovariationColourScheme.java;h=4884283aa1024b9636932482a37f3cafa2489214;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=fe533ed690184a8d2105b9dd86ff99a0a8a9c9be;hpb=323a457c9d0643be2406b6661246e8e988c0d0f6;p=jalview.git
diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index fe533ed..4884283 100644
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -1,26 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+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
@@ -30,15 +37,26 @@ 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(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
+ }
+
+ /**
* Creates a new CovariationColourScheme object.
*/
public CovariationColourScheme(AlignmentAnnotation annotation)
@@ -47,9 +65,9 @@ public class CovariationColourScheme extends ResidueColourScheme
for (int x = 0; x < this.annotation._rnasecstr.length; x++)
{
- // System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+ // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
// this.annotation._rnasecstr[x].getBegin());
- // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+ // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
// pairs.put(this.annotation._rnasecstr[x].getBegin(),
// this.annotation._rnasecstr[x].getEnd());
@@ -58,18 +76,19 @@ 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));
}
}
@@ -82,9 +101,10 @@ public class CovariationColourScheme extends ResidueColourScheme
*
* @return DOCUMENT ME!
*/
+ @Override
public Color findColour(char c)
{
- // System.out.println("called"); log.debug
+ // jalview.bin.Console.outPrintln("called"); log.debug
// Generate a random pastel color
return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];// jalview.util.ColorUtils.generateRandomColor(Color.white);
@@ -104,18 +124,35 @@ public class CovariationColourScheme extends ResidueColourScheme
{
Color currentColour = Color.white;
String currentHelix = null;
- // System.out.println(c + " " + j);
- currentHelix = (String) positionsToHelix.get(j);
- // System.out.println(positionsToHelix.get(j));
+ // jalview.bin.Console.outPrintln(c + " " + j);
+ currentHelix = positionsToHelix.get(j);
+ // jalview.bin.Console.outPrintln(positionsToHelix.get(j));
if (currentHelix != null)
{
- currentColour = (Color) helixcolorhash.get(currentHelix);
+ currentColour = helixcolorhash.get(currentHelix);
}
- // System.out.println(c + " " + j + " helix " + currentHelix + " " +
+ // jalview.bin.Console.outPrintln(c + " " + j + " helix " + currentHelix + " " +
// currentColour);
return currentColour;
}
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Covariation";
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}