git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
9a0f8bd
)
showUnconserved view and group setting
author
jprocter
<Jim Procter>
Fri, 6 Feb 2009 14:53:55 +0000
(14:53 +0000)
committer
jprocter
<Jim Procter>
Fri, 6 Feb 2009 14:53:55 +0000
(14:53 +0000)
src/jalview/gui/AlignFrame.java
patch
|
blob
|
history
src/jalview/gui/AlignViewport.java
patch
|
blob
|
history
src/jalview/gui/Jalview2XML.java
patch
|
blob
|
history
src/jalview/gui/PopupMenu.java
patch
|
blob
|
history
src/jalview/gui/Preferences.java
patch
|
blob
|
history
src/jalview/gui/SequenceRenderer.java
patch
|
blob
|
history
src/jalview/jbgui/GAlignFrame.java
patch
|
blob
|
history
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
1feffa5
..
33ac298
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-600,7
+600,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
annotationPanelMenuItem.setState(av.showAnnotation);
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
annotationPanelMenuItem.setState(av.showAnnotation);
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
-
+ showUnconservedMenuItem.setSelected(av.showUnconserved);
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
@@
-3764,7
+3764,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
final Alignment ds = dataset;
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
final Alignment ds = dataset;
- String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection,
+ String[] ptypes = (selection==null || selection.length==0) ? null
+ : CrossRef.findSequenceXrefTypes(dna, selection,
dataset);
// Object[] prods =
// CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
dataset);
// Object[] prods =
// CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
@@
-4332,6
+4333,14
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
showSeqFeatures.setSelected(true);
viewport.setShowSequenceFeatures(true);
}
showSeqFeatures.setSelected(true);
viewport.setShowSequenceFeatures(true);
}
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
}
class PrintThread extends Thread
}
class PrintThread extends Thread
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
0536f8d
..
d07b010
100755
(executable)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-373,6
+373,7
@@
public class AlignViewport implements SelectionSource
}
wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
}
wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+ showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", false);
}
/**
}
/**
@@
-2197,5
+2198,13
@@
public class AlignViewport implements SelectionSource
{
return showSeqFeaturesHeight;
}
{
return showSeqFeaturesHeight;
}
-
+ boolean showUnconserved=false;
+ public boolean getShowUnconserved()
+ {
+ return showUnconserved;
+ }
+ public void setShowUnconserved(boolean showunconserved)
+ {
+ showUnconserved=showunconserved;
+ }
}
}
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
115477d
..
db53d00
100755
(executable)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-915,7
+915,7
@@
public class Jalview2XML
groups[i].setTextCol1(sg.textColour.getRGB());
groups[i].setTextCol2(sg.textColour2.getRGB());
groups[i].setTextColThreshold(sg.thresholdTextColour);
groups[i].setTextCol1(sg.textColour.getRGB());
groups[i].setTextCol2(sg.textColour2.getRGB());
groups[i].setTextColThreshold(sg.thresholdTextColour);
-
+ groups[i].setShowUnconserved(sg.getShowunconserved());
for (int s = 0; s < sg.getSize(); s++)
{
jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
for (int s = 0; s < sg.getSize(); s++)
{
jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
@@
-1022,6
+1022,7
@@
public class Jalview2XML
view.setRightAlignIds(av.rightAlignIds);
view.setShowSequenceFeatures(av.showSequenceFeatures);
view.setShowText(av.getShowText());
view.setRightAlignIds(av.rightAlignIds);
view.setShowSequenceFeatures(av.showSequenceFeatures);
view.setShowText(av.getShowText());
+ view.setShowUnconserved(av.getShowUnconserved());
view.setWrapAlignment(av.getWrapAlignment());
view.setTextCol1(av.textColour.getRGB());
view.setTextCol2(av.textColour2.getRGB());
view.setWrapAlignment(av.getWrapAlignment());
view.setTextCol1(av.textColour.getRGB());
view.setTextCol2(av.textColour2.getRGB());
@@
-2130,6
+2131,7
@@
public class Jalview2XML
sg.textColour = new java.awt.Color(groups[i].getTextCol1());
sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
sg.textColour = new java.awt.Color(groups[i].getTextCol1());
sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
+ sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i].isShowUnconserved() : false);
sg.thresholdTextColour = groups[i].getTextColThreshold();
if (groups[i].getConsThreshold() != 0)
sg.thresholdTextColour = groups[i].getTextColThreshold();
if (groups[i].getConsThreshold() != 0)
@@
-2531,7
+2533,7
@@
public class Jalview2XML
af.viewport.textColour = new java.awt.Color(view.getTextCol1());
af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
af.viewport.thresholdTextColour = view.getTextColThreshold();
af.viewport.textColour = new java.awt.Color(view.getTextCol1());
af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
af.viewport.thresholdTextColour = view.getTextColThreshold();
-
+ af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view.isShowUnconserved() : false);
af.viewport.setStartRes(view.getStartRes());
af.viewport.setStartSeq(view.getStartSeq());
af.viewport.setStartRes(view.getStartRes());
af.viewport.setStartSeq(view.getStartSeq());
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
f16e647
..
5cf06b2
100755
(executable)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-94,6
+94,8
@@
public class PopupMenu extends JPopupMenu
JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+ JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
+
JMenu editMenu = new JMenu();
JMenuItem cut = new JMenuItem();
JMenu editMenu = new JMenu();
JMenuItem cut = new JMenuItem();
@@
-378,7
+380,7
@@
public class PopupMenu extends JPopupMenu
{
conservationMenuItem.setSelected(true);
}
{
conservationMenuItem.setSelected(true);
}
-
+ displayNonconserved.setSelected(sg.getShowunconserved());
showText.setSelected(sg.getDisplayText());
showColourText.setSelected(sg.getColourText());
showBoxes.setSelected(sg.getDisplayBoxes());
showText.setSelected(sg.getDisplayText());
showColourText.setSelected(sg.getColourText());
showBoxes.setSelected(sg.getDisplayBoxes());
@@
-616,6
+618,15
@@
public class PopupMenu extends JPopupMenu
showColourText_actionPerformed();
}
});
showColourText_actionPerformed();
}
});
+ displayNonconserved.setText("Show Nonconserved");
+ displayNonconserved.setState(true);
+ displayNonconserved.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showNonconserved_actionPerformed();
+ }
+ });
editMenu.setText("Edit");
cut.setText("Cut");
cut.addActionListener(new ActionListener()
editMenu.setText("Edit");
cut.setText("Cut");
cut.addActionListener(new ActionListener()
@@
-781,6
+792,7
@@
public class PopupMenu extends JPopupMenu
jMenu1.add(showText);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(showText);
jMenu1.add(showColourText);
jMenu1.add(outline);
+ jMenu1.add(displayNonconserved);
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
@@
-901,8
+913,14
@@
public class PopupMenu extends JPopupMenu
});
}
});
}
+ protected void showNonconserved_actionPerformed()
+ {
+ getGroup().setShowunconserved(displayNonconserved.isSelected());
+ refresh();
+ }
+
/**
/**
- * DOCUMENT ME!
+ * call to refresh view after settings change
*/
void refresh()
{
*/
void refresh()
{
diff --git
a/src/jalview/gui/Preferences.java
b/src/jalview/gui/Preferences.java
index
bd4c900
..
aa4d193
100755
(executable)
--- a/
src/jalview/gui/Preferences.java
+++ b/
src/jalview/gui/Preferences.java
@@
-22,6
+22,7
@@
import java.util.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
import jalview.bin.*;
import javax.swing.*;
import jalview.bin.*;
@@
-37,6
+38,7
@@
import jalview.schemes.*;
*/
public class Preferences extends GPreferences
{
*/
public class Preferences extends GPreferences
{
+
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
@@
-111,6
+113,7
@@
public class Preferences extends GPreferences
quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
+ showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
for (int i = 0; i < 13; i++)
{
for (int i = 0; i < 13; i++)
{
@@
-255,7
+258,7
@@
public class Preferences extends GPreferences
Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
.toString(idItalics.isSelected()));
Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
.toString(idItalics.isSelected()));
-
+ Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
.toString(smoothFont.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
.toString(smoothFont.isSelected()));
@@
-535,6
+538,14
@@
public class Preferences extends GPreferences
}
}
}
}
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void showunconserved_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+ super.showunconserved_actionPerformed(e);
+ }
private void jbInit() throws Exception
{
private void jbInit() throws Exception
{
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
a3dd5a6
..
98329b4
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-324,6
+324,12
@@
public class SequenceRenderer
{
graphics.setColor(currentSequenceGroup.textColour);
}
{
graphics.setColor(currentSequenceGroup.textColour);
}
+ if (currentSequenceGroup.getShowunconserved()) // todo optimize
+ {
+ // todo - use sequence group consensus
+ s = getDisplayChar(av.consensus, i, s, '.');
+
+ }
}
else
}
else
@@
-361,6
+367,11
@@
public class SequenceRenderer
graphics.setColor(av.textColour2);
}
}
graphics.setColor(av.textColour2);
}
}
+ if (av.showUnconserved)
+ {
+ s = getDisplayChar(av.consensus, i, s, '.');
+
+ }
}
}
@@
-371,6
+382,15
@@
public class SequenceRenderer
}
}
}
}
}
}
+ private char getDisplayChar(AlignmentAnnotation consensus, int position, char s, char c)
+ {
+ char conschar = consensus.annotations[position].displayCharacter.charAt(0);
+ if (conschar!='-' && s==conschar)
+ {
+ s= c;
+ }
+ return s;
+ }
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
a4f0983
..
0249e76
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-122,6
+122,8
@@
public class GAlignFrame extends JInternalFrame
public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
+
JMenuItem htmlMenuItem = new JMenuItem();
JMenuItem overviewMenuItem = new JMenuItem();
JMenuItem htmlMenuItem = new JMenuItem();
JMenuItem overviewMenuItem = new JMenuItem();
@@
-621,6
+623,15
@@
public class GAlignFrame extends JInternalFrame
viewTextMenuItem_actionPerformed(e);
}
});
viewTextMenuItem_actionPerformed(e);
}
});
+ showUnconservedMenuItem.setText("Show Unconserved");
+ showUnconservedMenuItem.setState(false);
+ showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showUnconservedMenuItem_actionPerformed(e);
+ }
+ });
sortPairwiseMenuItem.setText("by Pairwise Identity");
sortPairwiseMenuItem
.addActionListener(new java.awt.event.ActionListener()
sortPairwiseMenuItem.setText("by Pairwise Identity");
sortPairwiseMenuItem
.addActionListener(new java.awt.event.ActionListener()
@@
-1552,9
+1563,9
@@
public class GAlignFrame extends JInternalFrame
editMenu.add(removeAllGapsMenuItem);
editMenu.add(removeRedundancyMenuItem);
editMenu.addSeparator();
editMenu.add(removeAllGapsMenuItem);
editMenu.add(removeRedundancyMenuItem);
editMenu.addSeparator();
- // dont add these yet - they cannot be undone!
- //editMenu.add(justifyLeftMenuItem);
- //editMenu.add(justifyRightMenuItem);
+ // dont add these yet in the CVS build - they cannot be undone!
+ editMenu.add(justifyLeftMenuItem);
+ editMenu.add(justifyRightMenuItem);
editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
viewMenu.add(newView);
editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
viewMenu.add(newView);
@@
-1651,6
+1662,7
@@
public class GAlignFrame extends JInternalFrame
formatMenu.add(colourTextMenuItem);
formatMenu.add(renderGapsMenuItem);
formatMenu.add(centreColumnLabelsMenuItem);
formatMenu.add(colourTextMenuItem);
formatMenu.add(renderGapsMenuItem);
formatMenu.add(centreColumnLabelsMenuItem);
+ formatMenu.add(showUnconservedMenuItem);
selectMenu.add(findMenuItem);
selectMenu.addSeparator();
selectMenu.add(selectAllSequenceMenuItem);
selectMenu.add(findMenuItem);
selectMenu.addSeparator();
selectMenu.add(selectAllSequenceMenuItem);
@@
-1660,6
+1672,12
@@
public class GAlignFrame extends JInternalFrame
selectMenu.add(deleteGroups);
}
selectMenu.add(deleteGroups);
}
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
protected void showSeqFeaturesHeight_actionPerformed(
ActionEvent actionEvent)
{
protected void showSeqFeaturesHeight_actionPerformed(
ActionEvent actionEvent)
{