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Merge remote-tracking branch
[jalview.git]
/
src
/
jalview
/
appletgui
/
AnnotationPanel.java
diff --git
a/src/jalview/appletgui/AnnotationPanel.java
b/src/jalview/appletgui/AnnotationPanel.java
index
6bae9d9
..
5026ee4
100755
(executable)
--- a/
src/jalview/appletgui/AnnotationPanel.java
+++ b/
src/jalview/appletgui/AnnotationPanel.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-165,7
+165,7
@@
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
{
for (int index : av.getColumnSelection().getSelected())
{
{
for (int index : av.getColumnSelection().getSelected())
{
- if (av.getColumnSelection().isVisible(index))
+ if (av.getAlignment().getHiddenColumns().isVisible(index))
{
anot[index] = null;
}
{
anot[index] = null;
}
@@
-189,7
+189,7
@@
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
{
// TODO: JAL-2001 - provide a fast method to list visible selected
// columns
{
// TODO: JAL-2001 - provide a fast method to list visible selected
// columns
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
{
continue;
}
@@
-211,7
+211,7
@@
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
for (int index : av.getColumnSelection().getSelected())
{
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
{
continue;
}
@@
-271,7
+271,7
@@
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
for (int index : av.getColumnSelection().getSelected())
{
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
{
continue;
}
@@
-462,11
+462,13
@@
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
}
}
}
}
- int column = evt.getX() / av.getCharWidth() + av.getStartRes();
+ int column = evt.getX() / av.getCharWidth()
+ + av.getRanges().getStartRes();
if (av.hasHiddenColumns())
{
if (av.hasHiddenColumns())
{
- column = av.getColumnSelection().adjustForHiddenColumns(column);
+ column = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(column);
}
if (row > -1 && column < aa[row].annotations.length
}
if (row > -1 && column < aa[row].annotations.length
@@
-618,7
+620,8
@@
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
gg.setColor(Color.white);
gg.fillRect(0, 0, getSize().width, getSize().height);
gg.setColor(Color.white);
gg.fillRect(0, 0, getSize().width, getSize().height);
- drawComponent(gg, av.startRes, av.endRes + 1);
+ drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+ .getEndRes() + 1);
g.drawImage(image, 0, 0, this);
}
g.drawImage(image, 0, 0, this);
}
@@
-635,7
+638,7
@@
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
gg.copyArea(0, 0, imgWidth, getSize().height,
-horizontal * av.getCharWidth(), 0);
gg.copyArea(0, 0, imgWidth, getSize().height,
-horizontal * av.getCharWidth(), 0);
- int sr = av.startRes, er = av.endRes + 1, transX = 0;
+ int sr = av.getRanges().getStartRes(), er = av.getRanges().getEndRes() + 1, transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
if (horizontal > 0) // scrollbar pulled right, image to the left
{