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Edit and annotate wrapped alignment
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignFrame.java
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
f1ecd6a
..
fae50d9
100755
(executable)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-46,8
+46,18
@@
public class AlignFrame
alignPanel = new AlignmentPanel(this, viewport);
\r
add(alignPanel);
\r
alignPanel.validate();
\r
alignPanel = new AlignmentPanel(this, viewport);
\r
add(alignPanel);
\r
alignPanel.validate();
\r
+
\r
+ this.addWindowListener(new WindowAdapter()
\r
+ {
\r
+ public void windowClosing(WindowEvent e)
\r
+ {
\r
+ closeMenuItem_actionPerformed(null);
\r
+ }
\r
+ });
\r
+
\r
}
\r
\r
}
\r
\r
+
\r
public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
\r
{
\r
this.applet = applet;
\r
public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
\r
{
\r
this.applet = applet;
\r
@@
-57,7
+67,6
@@
public class AlignFrame
alignPanel.validate();
\r
\r
String treeFile = applet.getParameter("treeFile");
\r
alignPanel.validate();
\r
\r
String treeFile = applet.getParameter("treeFile");
\r
- TreePanel treepanel = null;
\r
if (treeFile != null)
\r
{
\r
try
\r
if (treeFile != null)
\r
{
\r
try
\r
@@
-82,6
+91,15
@@
public class AlignFrame
}
\r
}
\r
\r
}
\r
}
\r
\r
+ this.addWindowListener(new WindowAdapter()
\r
+ {
\r
+ public void windowClosing(WindowEvent e)
\r
+ {
\r
+ closeMenuItem_actionPerformed(null);
\r
+ }
\r
+ });
\r
+
\r
+
\r
\r
}
\r
\r
\r
}
\r
\r
@@
-108,6
+126,7
@@
public class AlignFrame
\r
public void closeMenuItem_actionPerformed(ActionEvent e)
\r
{
\r
\r
public void closeMenuItem_actionPerformed(ActionEvent e)
\r
{
\r
+ PaintRefresher.components.remove(viewport.alignment);
\r
dispose();
\r
}
\r
\r
dispose();
\r
}
\r
\r
@@
-488,10
+507,10
@@
public class AlignFrame
{
\r
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
}
\r
{
\r
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
}
\r
- sg.setEndRes(viewport.alignment.getWidth());
\r
+ sg.setEndRes(viewport.alignment.getWidth()-1);
\r
viewport.setSelectionGroup(sg);
\r
alignPanel.repaint();
\r
viewport.setSelectionGroup(sg);
\r
alignPanel.repaint();
\r
- PaintRefresher.Refresh(null);
\r
+ PaintRefresher.Refresh(null, viewport.alignment);
\r
}
\r
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
}
\r
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
@@
-499,7
+518,7
@@
public class AlignFrame
viewport.setSelectionGroup(null);
\r
viewport.getColumnSelection().clear();
\r
viewport.setSelectionGroup(null);
\r
viewport.setSelectionGroup(null);
\r
viewport.getColumnSelection().clear();
\r
viewport.setSelectionGroup(null);
\r
- PaintRefresher.Refresh(null);
\r
+ PaintRefresher.Refresh(null, viewport.alignment);
\r
}
\r
\r
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
}
\r
\r
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
@@
-510,7
+529,7
@@
public class AlignFrame
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
}
\r
\r
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
}
\r
\r
- PaintRefresher.Refresh(null);
\r
+ PaintRefresher.Refresh(null, viewport.alignment);
\r
}
\r
\r
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
}
\r
\r
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
@@
-804,53
+823,48
@@
public class AlignFrame
{
\r
int threshold = 0;
\r
\r
{
\r
int threshold = 0;
\r
\r
- if (viewport.getAbovePIDThreshold())
\r
+ if(cs!=null)
\r
{
\r
{
\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
-
\r
- if (cs instanceof ResidueColourScheme)
\r
+ if (viewport.getAbovePIDThreshold())
\r
{
\r
{
\r
- ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
- }
\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
\r
\r
- viewport.setGlobalColourScheme(cs);
\r
- }
\r
- else if (cs instanceof ResidueColourScheme)
\r
- {
\r
- ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
- }
\r
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
\r
\r
- if (viewport.getConservationSelected())
\r
- {
\r
- ConservationColourScheme ccs = null;
\r
+ viewport.setGlobalColourScheme(cs);
\r
+ }
\r
+ else
\r
+ {
\r
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
+ }
\r
\r
\r
- Alignment al = (Alignment) viewport.alignment;
\r
- Conservation c = new Conservation("All",
\r
- ResidueProperties.propHash, 3,
\r
- al.getSequences(), 0,
\r
- al.getWidth() - 1);
\r
+ if (viewport.getConservationSelected())
\r
+ {
\r
\r
\r
- c.calculate();
\r
- c.verdict(false, viewport.ConsPercGaps);
\r
+ Alignment al = (Alignment) viewport.alignment;
\r
+ Conservation c = new Conservation("All",
\r
+ ResidueProperties.propHash, 3,
\r
+ al.getSequences(), 0,
\r
+ al.getWidth() - 1);
\r
\r
\r
- ccs = new ConservationColourScheme(c, cs);
\r
+ c.calculate();
\r
+ c.verdict(false, viewport.ConsPercGaps);
\r
\r
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
- ccs.setConsensus(viewport.vconsensus);
\r
- viewport.setGlobalColourScheme(ccs);
\r
+ cs.setConservation(c);
\r
\r
\r
- SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
+ "Background"));
\r
\r
\r
- }
\r
- else
\r
- {
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
- if (cs != null)
\r
+ }
\r
+ else
\r
{
\r
{
\r
- cs.setConsensus(viewport.vconsensus);
\r
+ cs.setConservation(null);
\r
}
\r
}
\r
- viewport.setGlobalColourScheme(cs);
\r
+
\r
+ cs.setConsensus(viewport.vconsensus);
\r
+
\r
}
\r
}
\r
+ viewport.setGlobalColourScheme(cs);
\r
\r
if (viewport.getColourAppliesToAllGroups())
\r
{
\r
\r
if (viewport.getColourAppliesToAllGroups())
\r
{
\r
@@
-866,9
+880,7
@@
public class AlignFrame
}
\r
if (cs instanceof ClustalxColourScheme)
\r
{
\r
}
\r
if (cs instanceof ClustalxColourScheme)
\r
{
\r
- ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
\r
- cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
\r
- sg.cs = cxs;
\r
+ sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
@@
-883,15
+895,15
@@
public class AlignFrame
}
\r
}
\r
\r
}
\r
}
\r
\r
- if (viewport.getAbovePIDThreshold())
\r
+ if (viewport.getAbovePIDThreshold()
\r
+ || cs instanceof PIDColourScheme
\r
+ || cs instanceof Blosum62ColourScheme)
\r
{
\r
{
\r
- if (sg.cs instanceof ResidueColourScheme)
\r
- {
\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
- }
\r
-
\r
+ sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
}
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
}
\r
+ else
\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
\r
if (viewport.getConservationSelected())
\r
{
\r
\r
if (viewport.getConservationSelected())
\r
{
\r
@@
-901,22
+913,17
@@
public class AlignFrame
viewport.alignment.getWidth() - 1);
\r
c.calculate();
\r
c.verdict(false, viewport.ConsPercGaps);
\r
viewport.alignment.getWidth() - 1);
\r
c.calculate();
\r
c.verdict(false, viewport.ConsPercGaps);
\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
\r
-
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
- ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
- sg.cs = ccs;
\r
+ sg.cs.setConservation(c);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
+ sg.cs.setConservation(null);
\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
}
\r
\r
}
\r
}
\r
\r
}
\r
\r
}
\r
}
\r
\r
- updateCSConsensus();
\r
\r
if (alignPanel.getOverviewPanel() != null)
\r
{
\r
\r
if (alignPanel.getOverviewPanel() != null)
\r
{
\r
@@
-926,15
+933,11
@@
public class AlignFrame
alignPanel.repaint();
\r
}
\r
\r
alignPanel.repaint();
\r
}
\r
\r
- public void updateCSConsensus()
\r
- {
\r
- //Colour schemes must have their consensus updated
\r
\r
\r
- }
\r
\r
protected void modifyPID_actionPerformed(ActionEvent e)
\r
{
\r
\r
protected void modifyPID_actionPerformed(ActionEvent e)
\r
{
\r
- if (viewport.getAbovePIDThreshold())
\r
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
{
\r
SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
"Background");
\r
{
\r
SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
"Background");
\r
@@
-944,7
+947,7
@@
public class AlignFrame
\r
protected void modifyConservation_actionPerformed(ActionEvent e)
\r
{
\r
\r
protected void modifyConservation_actionPerformed(ActionEvent e)
\r
{
\r
- if (viewport.getConservationSelected())
\r
+ if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
{
\r
SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
"Background");
\r
{
\r
SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
"Background");
\r
@@
-959,15
+962,7
@@
public class AlignFrame
viewport.setAbovePIDThreshold(false);
\r
abovePIDThreshold.setState(false);
\r
\r
viewport.setAbovePIDThreshold(false);
\r
abovePIDThreshold.setState(false);
\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
- if (cs instanceof ConservationColourScheme)
\r
- {
\r
- changeColour( ( (ConservationColourScheme) cs).cs);
\r
- }
\r
- else
\r
- {
\r
- changeColour(cs);
\r
- }
\r
+ changeColour(viewport.getGlobalColourScheme());
\r
\r
modifyConservation_actionPerformed(null);
\r
}
\r
\r
modifyConservation_actionPerformed(null);
\r
}
\r
@@
-979,16
+974,7
@@
public class AlignFrame
conservationMenuItem.setState(false);
\r
viewport.setConservationSelected(false);
\r
\r
conservationMenuItem.setState(false);
\r
viewport.setConservationSelected(false);
\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
-
\r
- if (cs instanceof ConservationColourScheme)
\r
- {
\r
- changeColour( ( (ConservationColourScheme) cs).cs);
\r
- }
\r
- else
\r
- {
\r
- changeColour(cs);
\r
- }
\r
+ changeColour(viewport.getGlobalColourScheme());
\r
\r
modifyPID_actionPerformed(null);
\r
}
\r
\r
modifyPID_actionPerformed(null);
\r
}
\r