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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationPanel.java
diff --git
a/src/jalview/gui/AnnotationPanel.java
b/src/jalview/gui/AnnotationPanel.java
index
e020701
..
3f4c92a
100755
(executable)
--- a/
src/jalview/gui/AnnotationPanel.java
+++ b/
src/jalview/gui/AnnotationPanel.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-139,7
+139,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
public AnnotationPanel(AlignmentPanel ap)
{
public AnnotationPanel(AlignmentPanel ap)
{
- MAC = new jalview.util.Platform().isAMac();
+ MAC = jalview.util.Platform.isAMac();
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
@@
-241,7
+241,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
public void adjustmentValueChanged(AdjustmentEvent evt)
{
// update annotation label display
public void adjustmentValueChanged(AdjustmentEvent evt)
{
// update annotation label display
- ap.alabels.setScrollOffset(-evt.getValue());
+ ap.getAlabels().setScrollOffset(-evt.getValue());
}
/**
}
/**
@@
-335,7
+335,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
else if (evt.getActionCommand().equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
else if (evt.getActionCommand().equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_foreground_colour"), Color.black);
+ MessageManager.getString("label.select_foreground_colour"),
+ Color.black);
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
@@
-412,7
+413,6
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
anot[index] = new Annotation(label, "", type, 0);
}
anot[index] = new Annotation(label, "", type, 0);
}
-
anot[index].secondaryStructure = type != 'S' ? type : label
.length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
anot[index].secondaryStructure = type != 'S' ? type : label
.length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
@@
-566,7
+566,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
return;
}
return;
}
- ap.scalePanel.mousePressed(evt);
+ ap.getScalePanel().mousePressed(evt);
}
}
@@
-582,7
+582,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
graphStretch = -1;
graphStretchY = -1;
mouseDragging = false;
graphStretch = -1;
graphStretchY = -1;
mouseDragging = false;
- ap.scalePanel.mouseReleased(evt);
+ ap.getScalePanel().mouseReleased(evt);
}
/**
}
/**
@@
-594,7
+594,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@Override
public void mouseEntered(MouseEvent evt)
{
@Override
public void mouseEntered(MouseEvent evt)
{
- ap.scalePanel.mouseEntered(evt);
+ ap.getScalePanel().mouseEntered(evt);
}
/**
}
/**
@@
-606,7
+606,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@Override
public void mouseExited(MouseEvent evt)
{
@Override
public void mouseExited(MouseEvent evt)
{
- ap.scalePanel.mouseExited(evt);
+ ap.getScalePanel().mouseExited(evt);
}
/**
}
/**
@@
-632,7
+632,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
else
{
}
else
{
- ap.scalePanel.mouseDragged(evt);
+ ap.getScalePanel().mouseDragged(evt);
}
}
}
}
@@
-709,8
+709,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
&& aa[row].annotations[res].description != null
&& aa[row].annotations[res].description.length() > 0)
{
&& aa[row].annotations[res].description != null
&& aa[row].annotations[res].description.length() > 0)
{
- this.setToolTipText(JvSwingUtils
- .wrapTooltip(true, aa[row].annotations[res].description));
+ this.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ aa[row].annotations[res].description));
}
else
{
}
else
{
@@
-757,10
+757,10
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
int y1)
{
public void drawCursor(Graphics graphics, 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);
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
if (av.validCharWidth)
{
if (av.validCharWidth)
{
@@
-768,9
+768,9
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
char s = seq.getCharAt(res);
char s = seq.getCharAt(res);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1,
graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.charHeight) - pady);
+ (y1 + av.getCharHeight()) - pady);
}
}
}
}
@@
-799,7
+799,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
return;
}
}
return;
}
}
- imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
+ imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
if (imgWidth < 1)
{
return;
if (imgWidth < 1)
{
return;
@@
-809,8
+809,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
{
try
{
{
try
{
- image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
- BufferedImage.TYPE_INT_RGB);
+ image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
+ .getHeight(), BufferedImage.TYPE_INT_RGB);
} catch (OutOfMemoryError oom)
{
try
} catch (OutOfMemoryError oom)
{
try
@@
-867,7
+867,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
return;
}
long stime = System.currentTimeMillis();
return;
}
long stime = System.currentTimeMillis();
- gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
+ gg.copyArea(0, 0, imgWidth, getHeight(),
+ -horizontal * av.getCharWidth(), 0);
long mtime = System.currentTimeMillis();
int sr = av.startRes;
int er = av.endRes + 1;
long mtime = System.currentTimeMillis();
int sr = av.startRes;
int er = av.endRes + 1;
@@
-875,7
+876,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
if (horizontal > 0) // scrollbar pulled right, image to the left
{
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * av.getCharWidth();
sr = er - horizontal;
}
else if (horizontal < 0)
sr = er - horizontal;
}
else if (horizontal < 0)
@@
-960,7
+961,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
g.setColor(Color.white);
}
g.setColor(Color.white);
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+ g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
g.setFont(av.getFont());
if (fm == null)
g.setFont(av.getFont());
if (fm == null)
@@
-1013,9
+1014,9
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@Override
public int[] getVisibleVRange()
{
@Override
public int[] getVisibleVRange()
{
- if (ap != null && ap.alabels != null)
+ if (ap != null && ap.getAlabels() != null)
{
{
- int sOffset = -ap.alabels.scrollOffset;
+ int sOffset = -ap.getAlabels().getScrollOffset();
int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
bounds[0] = sOffset;
bounds[1] = visHeight;
int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
bounds[0] = sOffset;
bounds[1] = visHeight;