X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=6810fed9e16f47ff76cbcf78dbf4b3b9d5cd5224;hb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;hp=7ccc3790f5a890e27c77aed439755f952c54c991;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 7ccc379..6810fed 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,25 +1,29 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 java.util.List;
+
import javax.swing.*;
import jalview.datamodel.*;
@@ -48,7 +52,7 @@ public class IdCanvas extends JPanel
boolean fastPaint = false;
- java.util.Vector searchResults;
+ List searchResults;
FontMetrics fm;
@@ -56,13 +60,13 @@ public class IdCanvas extends JPanel
AnnotationPanel ap;
- Font idfont;
+ private Font idfont;
/**
* Creates a new IdCanvas object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public IdCanvas(AlignViewport av)
{
@@ -75,15 +79,15 @@ public class IdCanvas extends JPanel
* DOCUMENT ME!
*
* @param gg
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param starty
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param ypos
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
int ypos)
@@ -115,7 +119,7 @@ public class IdCanvas extends JPanel
gg.setColor(Color.black);
}
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
xPos = panelWidth
- fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
@@ -124,7 +128,7 @@ 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 (av.hasHiddenRows() && av.showHiddenMarkers)
{
drawMarker(i, starty, ypos);
}
@@ -135,7 +139,7 @@ public class IdCanvas extends JPanel
* DOCUMENT ME!
*
* @param vertical
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void fastPaint(int vertical)
{
@@ -189,7 +193,7 @@ public class IdCanvas extends JPanel
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
@@ -235,23 +239,23 @@ public class IdCanvas extends JPanel
* DOCUMENT ME!
*
* @param starty
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param endy
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void drawIds(int starty, int endy)
{
if (av.seqNameItalics)
{
- 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)
@@ -265,17 +269,17 @@ public class IdCanvas extends JPanel
if (av.getWrapAlignment())
{
- int maxwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight();
+ int maxwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
int annotationHeight = 0;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
if (ap == null)
{
@@ -305,20 +309,20 @@ public class IdCanvas extends JPanel
{
for (int i = starty; i < alheight; i++)
{
- SequenceI s = av.alignment.getSequenceAt(i);
- if (av.hasHiddenRows)
+ SequenceI s = av.getAlignment().getSequenceAt(i);
+ if (av.hasHiddenRows())
{
setHiddenFont(s);
}
else
{
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
}
drawIdString(gg, s, i, 0, ypos);
}
- if (labels != null && av.showAnnotation)
+ if (labels != null && av.isShowAnnotation())
{
gg.translate(0, ypos + (alheight * av.charHeight));
labels.drawComponent(gg, getWidth());
@@ -339,14 +343,14 @@ public class IdCanvas extends JPanel
// Now draw the id strings
for (int i = starty; i < endy; i++)
{
- sequence = av.alignment.getSequenceAt(i);
+ sequence = av.getAlignment().getSequenceAt(i);
if (sequence == null)
{
continue;
}
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
setHiddenFont(sequence);
}
@@ -358,8 +362,8 @@ public class IdCanvas extends JPanel
currentTextColor = Color.white;
}
else if ((av.getSelectionGroup() != null)
- && av.getSelectionGroup().getSequences(null).contains(
- sequence))
+ && av.getSelectionGroup().getSequences(null)
+ .contains(sequence))
{
currentColor = Color.lightGray;
currentTextColor = Color.black;
@@ -379,7 +383,7 @@ public class IdCanvas extends JPanel
String string = sequence.getDisplayId(av.getShowJVSuffix());
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
xPos = panelWidth - fm.stringWidth(string) - 4;
}
@@ -388,7 +392,7 @@ public class IdCanvas extends JPanel
(((i - starty) * av.charHeight) + av.charHeight)
- (av.charHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.showHiddenMarkers)
{
drawMarker(i, starty, 0);
}
@@ -401,7 +405,7 @@ public class IdCanvas extends JPanel
void drawMarker(int i, int starty, int yoffset)
{
- SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+ SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
// Use this method here instead of calling hiddenSeq adjust
// 3 times.
int hSize = hseqs.length;
@@ -464,26 +468,35 @@ public class IdCanvas extends JPanel
Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
.getSize());
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.isHiddenRepSequence(seq))
{
gg.setFont(bold);
}
else
{
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
}
}
/**
* DOCUMENT ME!
*
- * @param found
- * DOCUMENT ME!
+ * @param list
+ * DOCUMENT ME!
*/
- public void setHighlighted(java.util.Vector found)
+ public void setHighlighted(List list)
{
- searchResults = found;
+ searchResults = list;
repaint();
}
+
+ public Font getIdfont()
+ {
+ return idfont;
+ }
+
+ public void setIdfont(Font idfont)
+ {
+ this.idfont = idfont;
+ }
}