From: jprocter Date: Sun, 6 Jun 2010 14:57:31 +0000 (+0000) Subject: patch for JAL-542 X-Git-Tag: Release_2_5_1~24 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=de87ceaadf42025516d3201bb8f1ba1ea1776fd1;p=jalview.git patch for JAL-542 --- diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 4d58689..13390d9 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -151,7 +151,7 @@ public class APopupMenu extends java.awt.PopupMenu implements showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); - displayNonconserved.setState(sg.getShowunconserved()); + displayNonconserved.setState(sg.getShowNonconserved()); if (!ap.av.alignment.getGroups().contains(sg)) { groupMenu.remove(unGroupMenuItem); @@ -992,7 +992,7 @@ public class APopupMenu extends java.awt.PopupMenu implements public void showNonconserved_itemStateChanged() { - getGroup().setShowunconserved(this.displayNonconserved.getState()); + getGroup().setShowNonconserved(this.displayNonconserved.getState()); refresh(); } diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 56948e3..b8ed2f1 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -2866,7 +2866,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, annotationPanelMenuItem.addItemListener(this); colourTextMenuItem.setLabel("Colour Text"); colourTextMenuItem.addItemListener(this); - displayNonconservedMenuItem.setLabel("Show non-conserved"); + displayNonconservedMenuItem.setLabel("Show nonconserved"); displayNonconservedMenuItem.addItemListener(this); alProperties.addActionListener(this); overviewMenuItem.setLabel("Overview Window"); diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index a954e7b..85c8ab5 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1578,7 +1578,7 @@ public class AlignViewport } /** - * @param showUnconserved + * @param showNonconserved * the showUnconserved to set */ public void setShowunconserved(boolean displayNonconserved) diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index 822e906..e8508b6 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -219,7 +219,7 @@ public class SequenceRenderer getBoxColour(currentSequenceGroup.cs, seq, i); graphics.setColor(resBoxColour.darker()); } - if (currentSequenceGroup.getShowunconserved()) + if (currentSequenceGroup.getShowNonconserved()) { // cheat - use this if we have a consensus for each group: s = // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.'); diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 9d3e6db..cc71e4a 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -49,7 +49,7 @@ public class SequenceGroup /** * after Olivier's non-conserved only character display */ - boolean showUnconserved = false; + boolean showNonconserved = false; /** * group members @@ -957,18 +957,18 @@ public class SequenceGroup /** * @return the showUnconserved */ - public boolean getShowunconserved() + public boolean getShowNonconserved() { - return showUnconserved; + return showNonconserved; } /** - * @param showUnconserved + * @param showNonconserved * the showUnconserved to set */ - public void setShowunconserved(boolean displayNonconserved) + public void setShowNonconserved(boolean displayNonconserved) { - this.showUnconserved = displayNonconserved; + this.showNonconserved = displayNonconserved; } AlignmentAnnotation consensus = null, conservation = null; diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 2e6ea52..22647a3 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -588,7 +588,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, annotationPanelMenuItem.setState(av.showAnnotation); viewBoxesMenuItem.setSelected(av.showBoxes); viewTextMenuItem.setSelected(av.showText); - showUnconservedMenuItem.setSelected(av.showUnconserved); + showNonconservedMenuItem.setSelected(av.showUnconserved); showGroupConsensus.setSelected(av.showGroupConsensus); showGroupConservation.setSelected(av.showGroupConservation); showConsensusHistogram.setSelected(av.showConsensusHistogram); @@ -4555,7 +4555,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { - viewport.setShowUnconserved(showUnconservedMenuItem.getState()); + viewport.setShowUnconserved(showNonconservedMenuItem.getState()); alignPanel.paintAlignment(true); } @@ -4638,7 +4638,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // set view properties for each group for (int g = 0; g < gps.length; g++) { - gps[g].setShowunconserved(viewport.getShowUnconserved()); + gps[g].setShowNonconserved(viewport.getShowUnconserved()); gps[g].setIncludeAllConsSymbols(viewport .isIncludeAllConsensusSymbols()); viewport.alignment.addGroup(gps[g]); diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index ba3cef2..8de14b1 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -946,7 +946,7 @@ public class Jalview2XML groups[i].setTextCol1(sg.textColour.getRGB()); groups[i].setTextCol2(sg.textColour2.getRGB()); groups[i].setTextColThreshold(sg.thresholdTextColour); - groups[i].setShowUnconserved(sg.getShowunconserved()); + groups[i].setShowUnconserved(sg.getShowNonconserved()); groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram()); groups[i].setShowSequenceLogo(sg.isShowSequenceLogo()); @@ -2233,7 +2233,7 @@ public class Jalview2XML 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] + sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i] .isShowUnconserved() : false); sg.thresholdTextColour = groups[i].getTextColThreshold(); if (groups[i].hasShowConsensusHistogram()) diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 92e24bf..899a3f8 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -395,7 +395,7 @@ public class PopupMenu extends JPopupMenu { conservationMenuItem.setSelected(true); } - displayNonconserved.setSelected(sg.getShowunconserved()); + displayNonconserved.setSelected(sg.getShowNonconserved()); showText.setSelected(sg.getDisplayText()); showColourText.setSelected(sg.getColourText()); showBoxes.setSelected(sg.getDisplayBoxes()); @@ -1139,7 +1139,7 @@ public class PopupMenu extends JPopupMenu protected void showNonconserved_actionPerformed() { - getGroup().setShowunconserved(displayNonconserved.isSelected()); + getGroup().setShowNonconserved(displayNonconserved.isSelected()); refresh(); } diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 86c8490..db66993 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -325,7 +325,7 @@ public class SequenceRenderer { graphics.setColor(currentSequenceGroup.textColour); } - if (currentSequenceGroup.getShowunconserved()) // todo optimize + if (currentSequenceGroup.getShowNonconserved()) // todo optimize { // todo - use sequence group consensus s = getDisplayChar(av.consensus, i, s, '.'); diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 2721fb2..ae5bb46 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -416,7 +416,7 @@ public class AnnotationFile text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t"); text.append("displayText=" + sg.getDisplayText() + "\t"); text.append("colourText=" + sg.getColourText() + "\t"); - text.append("showUnconserved=" + sg.getShowunconserved() + "\t"); + text.append("showUnconserved=" + sg.getShowNonconserved() + "\t"); if (sg.textColour != java.awt.Color.black) { text.append("textCol1=" @@ -1253,7 +1253,7 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("showUnconserved")) { - sg.setShowunconserved(Boolean.valueOf(value).booleanValue()); + sg.setShowNonconserved(Boolean.valueOf(value).booleanValue()); } else if (key.equalsIgnoreCase("displayText")) { diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 067b3d2..8342609 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -121,7 +121,7 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); JMenuItem htmlMenuItem = new JMenuItem(); @@ -656,9 +656,9 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); - showUnconservedMenuItem.setText("Show Unconserved"); - showUnconservedMenuItem.setState(false); - showUnconservedMenuItem + showNonconservedMenuItem.setText("Show nonconserved"); + showNonconservedMenuItem.setState(false); + showNonconservedMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1794,7 +1794,7 @@ public class GAlignFrame extends JInternalFrame formatMenu.add(colourTextMenuItem); formatMenu.add(renderGapsMenuItem); formatMenu.add(centreColumnLabelsMenuItem); - formatMenu.add(showUnconservedMenuItem); + formatMenu.add(showNonconservedMenuItem); selectMenu.add(findMenuItem); selectMenu.addSeparator(); selectMenu.add(selectAllSequenceMenuItem);