X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=19b038ab609f78c287d1f4651a11c93f79f186d2;hb=c94c1390298db2e80abc04b371d3e7767f5e5968;hp=862dd825d783c69c3e099853d73f77e707499bd1;hpb=63a18b71aa3ed6503b6fbb8ec3543b5d66ed3f70;p=jalview.git
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 862dd82..19b038a 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,24 +1,26 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.appletgui;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
@@ -84,6 +86,31 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
return resBoxColour;
}
+ /**
+ * 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;
+ }
+
void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
{
if (cs != null)
@@ -133,7 +160,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
int length = seq.getLength();
int curStart = -1;
- int curWidth = av.charWidth;
+ int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av
+ .getCharHeight();
Color tempColour = null;
while (i <= end)
@@ -158,40 +186,41 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (tempColour != null)
{
- graphics.fillRect(av.charWidth * (curStart - start), y1,
- curWidth, av.charHeight);
+ graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+ avCharHeight);
}
graphics.setColor(resBoxColour);
curStart = i;
- curWidth = av.charWidth;
+ curWidth = avCharWidth;
tempColour = resBoxColour;
}
else
{
- curWidth += av.charWidth;
+ curWidth += avCharWidth;
}
i++;
}
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
- av.charHeight);
+ graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+ avCharHeight);
}
public void drawText(SequenceI seq, int start, int end, int y1)
{
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
Font boldFont = null;
boolean bold = false;
- if (av.upperCasebold)
+ if (av.isUpperCasebold())
{
- boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+ boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight);
graphics.setFont(av.getFont());
}
- y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+ y1 += avCharHeight - avCharHeight / 5; // height/5 replaces pady
int charOffset = 0;
@@ -258,7 +287,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
}
- if (av.upperCasebold)
+ if (av.isUpperCasebold())
{
fm = graphics.getFontMetrics();
if ('A' <= s && s <= 'Z')
@@ -278,8 +307,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+ charOffset = (avCharWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s), charOffset + avCharWidth
* (i - start), y1);
}
@@ -322,11 +351,11 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
public void drawHighlightedText(SequenceI seq, int start, int end,
int x1, int y1)
{
- int pady = av.charHeight / 5;
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+ int pady = avCharHeight / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
- av.charHeight);
+ graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight);
graphics.setColor(Color.white);
char s = '~';
@@ -340,19 +369,19 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
s = seq.getCharAt(i);
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (avCharWidth - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1
- + av.charWidth * (i - start), y1 + av.charHeight - pady);
+ + avCharWidth * (i - start), y1 + avCharHeight - pady);
}
}
}
public void drawCursor(SequenceI seq, int res, int x1, int y1)
{
- int pady = av.charHeight / 5;
+ int pady = av.getCharHeight() / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
graphics.setColor(Color.white);
graphics.setColor(Color.white);
@@ -361,9 +390,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.validCharWidth)
{
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.charHeight) - pady);
+ (y1 + av.getCharHeight()) - pady);
}
}