From c640b1c17cbfbc41723b0441f049cd416267dcc3 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 1 Apr 2015 14:57:24 +0100 Subject: [PATCH] JAL-1264 reinstate Show annotations menu item --- src/jalview/appletgui/AlignFrame.java | 22 ++++++++++++---------- src/jalview/appletgui/SplitFrame.java | 25 +++++++++++++++++-------- src/jalview/gui/Jalview2XML.java | 7 +++++++ src/jalview/viewmodel/AlignmentViewport.java | 2 +- 4 files changed, 37 insertions(+), 19 deletions(-) diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 3e919f6..93bd155 100644 --- 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; - 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; @@ -176,13 +177,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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); - DEFAULT_HEIGHT = height; + frameHeight = height; } } 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()); + annotationPanelMenuItem.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 { @@ -3596,8 +3598,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, /* * Annotations menu */ - // annotationsMenu.add(annotationPanelMenuItem); - // annotationsMenu.addSeparator(); + annotationsMenu.add(annotationPanelMenuItem); + annotationsMenu.addSeparator(); 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(), - DEFAULT_WIDTH, - DEFAULT_HEIGHT); + frameWidth, + frameHeight); } } diff --git a/src/jalview/appletgui/SplitFrame.java b/src/jalview/appletgui/SplitFrame.java index cdd1605..59b66c6 100644 --- a/src/jalview/appletgui/SplitFrame.java +++ b/src/jalview/appletgui/SplitFrame.java @@ -1,16 +1,17 @@ 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.api.AlignmentViewPanel; 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; @@ -65,6 +66,14 @@ public class SplitFrame extends EmbmenuFrame 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(); } @@ -178,9 +187,9 @@ public class SplitFrame extends EmbmenuFrame 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); } diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 5317d4c..2528841 100644 --- 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); + + /* + * And compute cDNA consensus (couldn't do earlier with consensus as + * mappings were not yet present) + */ + proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel); + return splitFrame; } diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 7054ed3..1270c15 100644 --- 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. */ - protected void initComplementConsensus() + public void initComplementConsensus() { if (!alignment.isNucleotide()) { -- 1.7.10.2