X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=aad07764d1ee3dc246e2ed8c56c62878bf6a666f;hb=6c31e8ed324bd6d62441119e6548952880f68a08;hp=235747c9d2fe231c8037bceb5eb78bfff9be7a06;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 235747c..aad0776 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,29 +1,39 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 java.awt.*;
-import java.awt.image.*;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.image.BufferedImage;
import java.util.List;
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import javax.swing.JPanel;
/**
* DOCUMENT ME!
@@ -57,7 +67,7 @@ public class IdCanvas extends JPanel
AnnotationPanel ap;
- Font idfont;
+ private Font idfont;
/**
* Creates a new IdCanvas object.
@@ -77,6 +87,8 @@ public class IdCanvas extends JPanel
*
* @param gg
* DOCUMENT ME!
+ * @param hiddenRows
+ * true - check and display hidden row marker if need be
* @param s
* DOCUMENT ME!
* @param i
@@ -86,12 +98,12 @@ public class IdCanvas extends JPanel
* @param ypos
* DOCUMENT ME!
*/
- public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
- int ypos)
+ public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+ int i, int starty, int ypos)
{
int xPos = 0;
int panelWidth = getWidth();
- int charHeight = av.charHeight;
+ int charHeight = av.getCharHeight();
if ((searchResults != null) && searchResults.contains(s))
{
@@ -116,7 +128,7 @@ public class IdCanvas extends JPanel
gg.setColor(Color.black);
}
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
xPos = panelWidth
- fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
@@ -125,7 +137,7 @@ public class IdCanvas extends JPanel
gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
- if (av.hasHiddenRows() && av.showHiddenMarkers)
+ if (hiddenRows)
{
drawMarker(i, starty, ypos);
}
@@ -147,32 +159,35 @@ public class IdCanvas extends JPanel
return;
}
- gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+ ViewportRanges ranges = av.getRanges();
+
+ gg.copyArea(0, 0, getWidth(), imgHeight, 0,
+ -vertical * av.getCharHeight());
- int ss = av.startSeq;
- int es = av.endSeq;
+ int ss = ranges.getStartSeq();
+ int es = ranges.getEndSeq();
int transY = 0;
if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.startSeq)
+ if (ss < ranges.getStartSeq())
{ // ie scrolling too fast, more than a page at a time
- ss = av.startSeq;
+ ss = ranges.getStartSeq();
}
else
{
- transY = imgHeight - (vertical * av.charHeight);
+ transY = imgHeight - ((vertical + 1) * av.getCharHeight());
}
}
- else if (vertical < 0)
+ else if (vertical < 0) // scroll up
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > ranges.getEndSeq())
{
- es = av.endSeq;
+ es = ranges.getEndSeq();
}
}
@@ -192,6 +207,7 @@ public class IdCanvas extends JPanel
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
g.setColor(Color.white);
@@ -208,7 +224,7 @@ public class IdCanvas extends JPanel
int oldHeight = imgHeight;
imgHeight = getHeight();
- imgHeight -= (imgHeight % av.charHeight);
+ imgHeight -= (imgHeight % av.getCharHeight());
if (imgHeight < 1)
{
@@ -227,7 +243,7 @@ public class IdCanvas extends JPanel
gg.setColor(Color.white);
gg.fillRect(0, 0, getWidth(), imgHeight);
- drawIds(av.getStartSeq(), av.endSeq);
+ drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
g.drawImage(image, 0, 0, this);
}
@@ -242,17 +258,17 @@ public class IdCanvas extends JPanel
*/
void drawIds(int starty, int endy)
{
- if (av.seqNameItalics)
+ if (av.isSeqNameItalics())
{
- idfont = new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
- .getSize());
+ setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
+ .getSize()));
}
else
{
- idfont = av.getFont();
+ setIdfont(av.getFont());
}
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
fm = gg.getFontMetrics();
if (av.antiAlias)
@@ -264,6 +280,9 @@ public class IdCanvas extends JPanel
Color currentColor = Color.white;
Color currentTextColor = Color.black;
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows();
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
@@ -276,7 +295,7 @@ public class IdCanvas extends JPanel
int annotationHeight = 0;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
if (ap == null)
{
@@ -290,40 +309,41 @@ public class IdCanvas extends JPanel
}
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = alheight * av.charHeight + hgap + annotationHeight;
+ int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
- int rowSize = av.getEndRes() - av.getStartRes();
+ int rowSize = av.getRanges().getEndRes()
+ - av.getRanges().getStartRes();
// Draw the rest of the panels
- for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
+ for (int ypos = hgap, row = av.getRanges().getStartRes(); (ypos <= getHeight())
&& (row < maxwidth); ypos += cHeight, row += rowSize)
{
for (int i = starty; i < alheight; i++)
{
SequenceI s = av.getAlignment().getSequenceAt(i);
- if (av.hasHiddenRows())
+ if (doHiddenCheck)
{
setHiddenFont(s);
}
else
{
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
}
- drawIdString(gg, s, i, 0, ypos);
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
}
- if (labels != null && av.showAnnotation)
+ if (labels != null && av.isShowAnnotation())
{
- gg.translate(0, ypos + (alheight * av.charHeight));
+ gg.translate(0, ypos + (alheight * av.getCharHeight()));
labels.drawComponent(gg, getWidth());
- gg.translate(0, -ypos - (alheight * av.charHeight));
+ gg.translate(0, -ypos - (alheight * av.getCharHeight()));
}
}
}
@@ -338,7 +358,7 @@ public class IdCanvas extends JPanel
SequenceI sequence;
// Now draw the id strings
- for (int i = starty; i < endy; i++)
+ for (int i = starty; i <= endy; i++)
{
sequence = av.getAlignment().getSequenceAt(i);
@@ -347,7 +367,7 @@ public class IdCanvas extends JPanel
continue;
}
- if (av.hasHiddenRows())
+ if (doHiddenCheck)
{
setHiddenFont(sequence);
}
@@ -373,23 +393,23 @@ public class IdCanvas extends JPanel
gg.setColor(currentColor);
- gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
- av.charHeight);
+ gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
+ av.getCharHeight());
gg.setColor(currentTextColor);
String string = sequence.getDisplayId(av.getShowJVSuffix());
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
xPos = panelWidth - fm.stringWidth(string) - 4;
}
gg.drawString(string, xPos,
- (((i - starty) * av.charHeight) + av.charHeight)
- - (av.charHeight / 5));
+ (((i - starty) * av.getCharHeight()) + av.getCharHeight())
+ - (av.getCharHeight() / 5));
- if (av.hasHiddenRows() && av.showHiddenMarkers)
+ if (hiddenRows)
{
drawMarker(i, starty, 0);
}
@@ -437,25 +457,24 @@ public class IdCanvas extends JPanel
if (below)
{
gg.fillPolygon(
- new int[]
- { getWidth() - av.charHeight, getWidth() - av.charHeight,
- getWidth() }, new int[]
- {
- (i - starty) * av.charHeight + yoffset,
- (i - starty) * av.charHeight + yoffset + av.charHeight
- / 4, (i - starty) * av.charHeight + yoffset }, 3);
+ new int[] { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(), getWidth() },
+ new int[] {
+ (i - starty) * av.getCharHeight() + yoffset,
+ (i - starty) * av.getCharHeight() + yoffset
+ + av.getCharHeight() / 4,
+ (i - starty) * av.getCharHeight() + yoffset }, 3);
}
if (above)
{
gg.fillPolygon(
- new int[]
- { getWidth() - av.charHeight, getWidth() - av.charHeight,
- getWidth() }, new int[]
- {
- (i - starty + 1) * av.charHeight + yoffset,
- (i - starty + 1) * av.charHeight + yoffset
- - av.charHeight / 4,
- (i - starty + 1) * av.charHeight + yoffset }, 3);
+ new int[] { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(), getWidth() },
+ new int[] {
+ (i - starty + 1) * av.getCharHeight() + yoffset,
+ (i - starty + 1) * av.getCharHeight() + yoffset
+ - av.getCharHeight() / 4,
+ (i - starty + 1) * av.getCharHeight() + yoffset }, 3);
}
}
@@ -465,13 +484,13 @@ public class IdCanvas extends JPanel
Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
.getSize());
- if (av.isHiddenRepSequence(seq))
+ if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
{
gg.setFont(bold);
}
else
{
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
}
}
@@ -486,4 +505,14 @@ public class IdCanvas extends JPanel
searchResults = list;
repaint();
}
+
+ public Font getIdfont()
+ {
+ return idfont;
+ }
+
+ public void setIdfont(Font idfont)
+ {
+ this.idfont = idfont;
+ }
}