X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=bcbebbdda70739269fa59687fcb51b128b54e01a;hb=ae216fceddd8539d20fa5425cdaef3da73aba8f0;hp=b15851c89620e82a63ad80fe2d10706d6c2a9791;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index b15851c..bcbebbd 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,26 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.gui;
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
/**
* DOCUMENT ME!
@@ -80,7 +87,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
public Color getResidueBoxColour(SequenceI seq, int i)
{
- allGroups = av.alignment.findAllGroups(seq);
+ allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
{
@@ -91,7 +98,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
return resBoxColour;
@@ -111,7 +118,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (cs != null)
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i);
+ resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -205,7 +212,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
}
@@ -328,7 +335,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
if (currentSequenceGroup.getShowNonconserved()) // todo optimize
{
// todo - use sequence group consensus
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+ '.');
}
@@ -343,7 +351,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
if (av.getShowBoxes())
{
@@ -359,7 +367,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (!getboxColour)
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
@@ -368,9 +376,10 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
graphics.setColor(av.textColour2);
}
}
- if (av.showUnconserved)
+ if (av.getShowUnconserved())
{
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+ '.');
}