X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=c6a3df26bff6ca69a6d9af2ed304cc650789ee7a;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=a4325fe0305d610ce8960ba9da8cbf8b52390a50;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index a4325fe..c6a3df2 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,22 +1,26 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.gui;
+import jalview.api.FeatureRenderer;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
@@ -77,11 +81,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
// If EPS graphics, stringWidth will be a double, not an int
double dwidth = fm.getStringBounds("M", g).getWidth();
- monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && (float) av.charWidth == dwidth);
+ monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av.charWidth == dwidth);
this.renderGaps = renderGaps;
}
+ @Override
public Color getResidueBoxColour(SequenceI seq, int i)
{
allGroups = av.getAlignment().findAllGroups(seq);
@@ -102,6 +107,31 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
/**
+ * Get the residue colour at the given sequence position - as determined by
+ * the sequence group colour (if any), else the colour scheme, possibly
+ * overridden by a feature colour.
+ *
+ * @param seq
+ * @param position
+ * @param fr
+ * @return
+ */
+ @Override
+ public Color getResidueColour(final SequenceI seq, int position,
+ FeatureRenderer fr)
+ {
+ // TODO replace 8 or so code duplications with calls to this method
+ // (refactored as needed)
+ Color col = getResidueBoxColour(seq, position);
+
+ if (fr != null)
+ {
+ col = fr.findFeatureColour(col, seq, position);
+ }
+ return col;
+ }
+
+ /**
* DOCUMENT ME!
*
* @param cs
@@ -185,7 +215,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
int y1)
{
if (seq == null)
+ {
return; // fix for racecondition
+ }
int i = start;
int length = seq.getLength();
@@ -287,6 +319,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else
{
+ boolean srep = av.isDisplayReferenceSeq();
boolean getboxColour = false;
for (int i = start; i <= end; i++)
{
@@ -332,7 +365,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
if (currentSequenceGroup.getShowNonconserved()) // todo optimize
{
// todo - use sequence group consensus
- s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+ s = getDisplayChar(srep, i, s,
'.');
}
@@ -375,7 +408,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
if (av.getShowUnconserved())
{
- s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+ s = getDisplayChar(srep, i, s,
'.');
}
@@ -390,10 +423,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
}
- private char getDisplayChar(AlignmentAnnotation consensus, int position,
+ private char getDisplayChar(final boolean usesrep, int position,
char s, char c)
{
- char conschar = consensus.annotations[position].displayCharacter
+ // TODO - use currentSequenceGroup rather than alignemnt
+ // currentSequenceGroup.getConsensus()
+ char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
.charAt(0);
if (conschar != '-' && s == conschar)
{