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JAL-2536 tweak javadoc wording
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationPanel.java
diff --git
a/src/jalview/gui/AnnotationPanel.java
b/src/jalview/gui/AnnotationPanel.java
index
7450555
..
919356f
100755
(executable)
--- a/
src/jalview/gui/AnnotationPanel.java
+++ b/
src/jalview/gui/AnnotationPanel.java
@@
-23,6
+23,7
@@
package jalview.gui;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
@@
-55,7
+56,6
@@
import java.util.List;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.Scrollable;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.Scrollable;
@@
-123,8
+123,6
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
boolean mouseDragging = false;
boolean mouseDragging = false;
- boolean MAC = false;
-
// for editing cursor
int cursorX = 0;
// for editing cursor
int cursorX = 0;
@@
-142,9
+140,6
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
*/
public AnnotationPanel(AlignmentPanel ap)
{
*/
public AnnotationPanel(AlignmentPanel ap)
{
-
- MAC = jalview.util.Platform.isAMac();
-
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
@@
-296,7
+291,7
@@
public class AnnotationPanel extends JPanel 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;
}
@@
-305,7
+300,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
else if (action.equals(LABEL))
{
String exMesg = collectAnnotVals(anot, LABEL);
else if (action.equals(LABEL))
{
String exMesg = collectAnnotVals(anot, LABEL);
- String label = JOptionPane.showInputDialog(this,
+ String label = JvOptionPane.showInputDialog(this,
MessageManager.getString("label.enter_label"), exMesg);
if (label == null)
MessageManager.getString("label.enter_label"), exMesg);
if (label == null)
@@
-320,7
+315,7
@@
public class AnnotationPanel extends JPanel 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;
}
@@
-343,7
+338,7
@@
public class AnnotationPanel extends JPanel 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;
}
@@
-385,7
+380,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
aa[activeRow].hasIcons = true;
}
aa[activeRow].hasIcons = true;
}
- String label = JOptionPane.showInputDialog(MessageManager
+ String label = JvOptionPane.showInputDialog(MessageManager
.getString("label.enter_label_for_the_structure"), symbol);
if (label == null)
.getString("label.enter_label_for_the_structure"), symbol);
if (label == null)
@@
-403,7
+398,7
@@
public class AnnotationPanel extends JPanel 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;
}
@@
-446,6
+441,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
/*
* the selection list (read-only view) is in selection order, not
/*
* the selection list (read-only view) is in selection order, not
@@
-456,15
+452,15
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
for (int index : selected)
{
// always check for current display state - just in case
for (int index : selected)
{
// always check for current display state - just in case
- if (!viscols.isVisible(index))
+ if (!hidden.isVisible(index))
{
continue;
}
String tlabel = null;
if (anots[index] != null)
{ // LML added stem code
{
continue;
}
String tlabel = null;
if (anots[index] != null)
{ // LML added stem code
- if (type.equals(HELIX) || type.equals(SHEET)
- || type.equals(STEM) || type.equals(LABEL))
+ if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+ || type.equals(LABEL))
{
tlabel = anots[index].description;
if (tlabel == null || tlabel.length() < 1)
{
tlabel = anots[index].description;
if (tlabel == null || tlabel.length() < 1)
@@
-713,11
+709,13
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
return;
}
return;
}
- 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);
}
AlignmentAnnotation ann = aa[row];
}
AlignmentAnnotation ann = aa[row];
@@
-819,8
+817,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
{
text.append(", ")
.append(MessageManager.getString("label.sequence"))
{
text.append(", ")
.append(MessageManager.getString("label.sequence"))
- .append(" ")
- .append(seqIndex + 1);
+ .append(" ").append(seqIndex + 1);
char residue = seqref.getCharAt(column);
if (!Comparison.isGap(residue))
{
char residue = seqref.getCharAt(column);
if (!Comparison.isGap(residue))
{
@@
-911,7
+908,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
return;
}
}
return;
}
}
- imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
+ imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1)
+ * av.getCharWidth();
if (imgWidth < 1)
{
return;
if (imgWidth < 1)
{
return;
@@
-952,7
+950,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
imageFresh = true;
}
imageFresh = true;
}
- drawComponent(gg, av.startRes, av.endRes + 1);
+ drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+ .getEndRes() + 1);
imageFresh = false;
g.drawImage(image, 0, 0, this);
}
imageFresh = false;
g.drawImage(image, 0, 0, this);
}
@@
-982,8
+981,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
gg.copyArea(0, 0, imgWidth, getHeight(),
-horizontal * av.getCharWidth(), 0);
long mtime = System.currentTimeMillis();
gg.copyArea(0, 0, imgWidth, getHeight(),
-horizontal * av.getCharWidth(), 0);
long mtime = System.currentTimeMillis();
- int sr = av.startRes;
- int er = av.endRes + 1;
+ int sr = av.getRanges().getStartRes();
+ int er = av.getRanges().getEndRes() + 1;
int transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
int transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
@@
-1139,4
+1138,25
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
return null;
}
}
return null;
}
}
+
+ /**
+ * Try to ensure any references held are nulled
+ */
+ public void dispose()
+ {
+ av = null;
+ ap = null;
+ image = null;
+ fadedImage = null;
+ gg = null;
+ _mwl = null;
+
+ /*
+ * I created the renderer so I will dispose of it
+ */
+ if (renderer != null)
+ {
+ renderer.dispose();
+ }
+ }
}
}