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JAL-1264 reinstate Show annotations menu item
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 1 Apr 2015 13:57:24 +0000
(14:57 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 1 Apr 2015 13:57:24 +0000
(14:57 +0100)
src/jalview/appletgui/AlignFrame.java
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src/jalview/appletgui/SplitFrame.java
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src/jalview/gui/Jalview2XML.java
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src/jalview/viewmodel/AlignmentViewport.java
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diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
3e919f6
..
93bd155
100644
(file)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-113,9
+113,10
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
public AlignViewport viewport;
public AlignViewport viewport;
- int DEFAULT_WIDTH = 700;
+ // width and height may be overridden by applet parameters
+ int frameWidth = 700;
- int DEFAULT_HEIGHT = 500;
+ int frameHeight = 500;
String jalviewServletURL;
String jalviewServletURL;
@@
-176,13
+177,13
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (param != null)
{
int width = Integer.parseInt(param);
if (param != null)
{
int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
+ frameWidth = width;
}
param = applet.getParameter("windowHeight");
if (param != null)
{
int height = Integer.parseInt(param);
}
param = applet.getParameter("windowHeight");
if (param != null)
{
int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
+ frameHeight = height;
}
} catch (Exception ex)
{
}
} catch (Exception ex)
{
@@
-203,6
+204,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
showSequenceLogo.setState(viewport.isShowSequenceLogo());
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
showSequenceLogo.setState(viewport.isShowSequenceLogo());
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+ annotationPanelMenuItem.setState(viewport.isShowAnnotation());
showAlignmentAnnotations.setState(viewport.isShowAnnotation());
showSequenceAnnotations.setState(viewport.isShowAnnotation());
showAlignmentAnnotations.setState(viewport.isShowAnnotation());
showSequenceAnnotations.setState(viewport.isShowAnnotation());
@@
-1964,8
+1966,8
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
}
}
}
- jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+ frameHeight);
}
else
{
}
else
{
@@
-3596,8
+3598,8
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
/*
* Annotations menu
*/
/*
* Annotations menu
*/
- // annotationsMenu.add(annotationPanelMenuItem);
- // annotationsMenu.addSeparator();
+ annotationsMenu.add(annotationPanelMenuItem);
+ annotationsMenu.addSeparator();
annotationsMenu.add(showAlignmentAnnotations);
annotationsMenu.add(showSequenceAnnotations);
annotationsMenu.add(sortAnnBySequence);
annotationsMenu.add(showAlignmentAnnotations);
annotationsMenu.add(showSequenceAnnotations);
annotationsMenu.add(sortAnnBySequence);
@@
-3771,8
+3773,8
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
- DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ frameWidth,
+ frameHeight);
}
}
}
}
diff --git
a/src/jalview/appletgui/SplitFrame.java
b/src/jalview/appletgui/SplitFrame.java
index
cdd1605
..
59b66c6
100644
(file)
--- a/
src/jalview/appletgui/SplitFrame.java
+++ b/
src/jalview/appletgui/SplitFrame.java
@@
-1,16
+1,17
@@
package jalview.appletgui;
package jalview.appletgui;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.Panel;
+
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
import jalview.structure.StructureSelectionManager;
import jalview.api.ViewStyleI;
import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
import jalview.structure.StructureSelectionManager;
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-import java.awt.Panel;
-
public class SplitFrame extends EmbmenuFrame
{
private static final long serialVersionUID = 1L;
public class SplitFrame extends EmbmenuFrame
{
private static final long serialVersionUID = 1L;
@@
-65,6
+66,14
@@
public class SplitFrame extends EmbmenuFrame
ssm.addCommandListener(protein);
}
ssm.addCommandListener(protein);
}
+ /*
+ * Now mappings exist, can compute cDNA consensus on protein alignment
+ */
+ protein.initComplementConsensus();
+ AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel
+ : topFrame.alignPanel;
+ protein.updateConsensus(ap);
+
adjustLayout();
}
adjustLayout();
}
@@
-178,9
+187,9
@@
public class SplitFrame extends EmbmenuFrame
else
{
this.add(outermost);
else
{
this.add(outermost);
- int width = Math.max(topFrame.DEFAULT_WIDTH,
- bottomFrame.DEFAULT_WIDTH);
- int height = topFrame.DEFAULT_HEIGHT + bottomFrame.DEFAULT_HEIGHT;
+ int width = Math.max(topFrame.frameWidth,
+ bottomFrame.frameWidth);
+ int height = topFrame.frameHeight + bottomFrame.frameHeight;
jalview.bin.JalviewLite
.addFrame(this, this.getTitle(), width, height);
}
jalview.bin.JalviewLite
.addFrame(this, this.getTitle(), width, height);
}
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
5317d4c
..
2528841
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-2263,6
+2263,13
@@
public class Jalview2XML
int height = (int) (dnaFrame.getBounds().getHeight()
+ proteinFrame.getBounds().getHeight() + 50);
Desktop.addInternalFrame(splitFrame, title, width, height);
int height = (int) (dnaFrame.getBounds().getHeight()
+ proteinFrame.getBounds().getHeight() + 50);
Desktop.addInternalFrame(splitFrame, title, width, height);
+
+ /*
+ * And compute cDNA consensus (couldn't do earlier with consensus as
+ * mappings were not yet present)
+ */
+ proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
+
return splitFrame;
}
return splitFrame;
}
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
7054ed3
..
1270c15
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-1731,7
+1731,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
* If this is a protein alignment and there are mappings to cDNA, add the cDNA
* consensus annotation.
*/
* If this is a protein alignment and there are mappings to cDNA, add the cDNA
* consensus annotation.
*/
- protected void initComplementConsensus()
+ public void initComplementConsensus()
{
if (!alignment.isNucleotide())
{
{
if (!alignment.isNucleotide())
{