From be5a6a44e9eb355110f3b414d6b0fd5419f5936c Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 30 Mar 2010 17:48:15 +0000 Subject: [PATCH] group autoannotation and consensus display settings --- help/html/menus/alwview.html | 23 ++++++++++++ src/jalview/bin/Cache.java | 8 +++- src/jalview/gui/AlignFrame.java | 30 +++++++++++++-- src/jalview/gui/AlignViewport.java | 46 +++++++++++++++++++++++ src/jalview/gui/AlignmentPanel.java | 18 ++++++++- src/jalview/gui/AnnotationLabels.java | 55 +++++++++++++++++++++++---- src/jalview/gui/Preferences.java | 24 ++++++++---- src/jalview/jbgui/GAlignFrame.java | 66 +++++++++++++++++++++++++++++++-- src/jalview/jbgui/GPreferences.java | 54 +++++++++++++++++++++++++++ 9 files changed, 299 insertions(+), 25 deletions(-) diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 4cc5c15..10ab511 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -22,6 +22,29 @@ If this is selected the "Annotation Panel" will be displayed below the alignment. The default setting is to display the conservation calculation, quality calculation and consensus values as bar charts. +
  • Autocalculated Annotation
    Settings for the display of autocalculated annotation. + +
  • Automatic Scrolling
    When selected, the view will automatically scroll to display the highlighted sequence position corresponding to the position under the mouse diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 621ded0..d5c54b2 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -115,8 +115,12 @@ import org.biojava.dasobert.dasregistry.Das1Source; *
  • SORT_BY_TREE (false) sort the current alignment view according to the * order of a newly displayed tree
    • *
  • DBFETCH_USEPICR (false) use PICR to recover valid DB references from sequence ID strings before attempting retrieval from any datasource
    • - *
  • - *
    • + *
  • SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the alignment.
    • + *
  • SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups in the alignment.
    • + *
  • SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's histogram.
    • + *
  • SHOW_CONSENSUS_PROFILE (false) Show consensus annotation row's sequence logo.
    • + * + *
  • * *
  • * diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index dcb4b21..1bccb66 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -610,7 +610,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showTranslation.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); - + showGroupConservation.setEnabled(!nucleotide); // Remember AlignFrame always starts as protein if (!nucleotide) { @@ -655,6 +655,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showUnconservedMenuItem.setSelected(av.showUnconserved); showGroupConsensus.setSelected(av.showGroupConsensus); showGroupConservation.setSelected(av.showGroupConservation); + showConsensusHistogram.setSelected(av.showConsensusHistogram); + showConsensusProfile.setSelected(av.showConsensusProfile); setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); @@ -4480,7 +4482,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showGroupConsensus_actionPerformed(ActionEvent e) { viewport.setShowGroupConsensus(showGroupConsensus.getState()); - alignPanel.updateAnnotation(); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } @@ -4494,7 +4496,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showGroupConservation_actionPerformed(ActionEvent e) { viewport.setShowGroupConservation(showGroupConservation.getState()); - alignPanel.updateAnnotation(); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* (non-Javadoc) + * @see jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt.event.ActionEvent) + */ + protected void showConsensusHistogram_actionPerformed(ActionEvent e) + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* (non-Javadoc) + * @see jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt.event.ActionEvent) + */ + protected void showConsensusProfile_actionPerformed(ActionEvent e) + { + viewport.setShowConsensusProfile(showConsensusProfile.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } /* diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 289fab7..159acb1 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -349,7 +349,15 @@ public class AlignViewport implements SelectionSource alignment.addAnnotation(quality); } + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", false); + + { + + } } + showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true); + showConsensusProfile = Cache.getDefault("SHOW_CONSENSUS_PROFILE", false); + showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); // TODO: add menu option action that nulls or creates consensus object depending on if the user wants to see the annotation or not in a specific alignment consensus = new AlignmentAnnotation("Consensus", "PID", new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); @@ -2086,6 +2094,35 @@ public class AlignViewport implements SelectionSource * should consensus rows be shown for groups */ boolean showGroupConsensus = false; + /** + * should consensus profile be rendered by default + */ + public boolean showConsensusProfile = false; + /** + * should consensus histograms be rendered by default + */ + public boolean showConsensusHistogram = true; + /** + * @return the showConsensusProfile + */ + public boolean isShowConsensusProfile() + { + return showConsensusProfile; + } + /** + * @param showConsensusProfile the showConsensusProfile to set + */ + public void setShowConsensusProfile(boolean showConsensusProfile) + { + this.showConsensusProfile = showConsensusProfile; + } + /** + * @param showConsensusHistogram the showConsensusHistogram to set + */ + public void setShowConsensusHistogram(boolean showConsensusHistogram) + { + this.showConsensusHistogram = showConsensusHistogram; + } /** * @return the showGroupConservation @@ -2130,4 +2167,13 @@ public class AlignViewport implements SelectionSource this.includeAllConsensusSymbols = includeAllConsensusSymbols; } + /** + * + * @return flag to indicate if the consensus histogram should be rendered by default + */ + public boolean isShowConsensusHistogram() + { + return this.showConsensusHistogram; + } + } diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 4e3db27..99c7c72 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,6 +20,7 @@ package jalview.gui; import java.beans.*; import java.io.*; +import java.util.Hashtable; import java.util.Vector; import java.awt.*; @@ -1321,9 +1322,16 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void updateAnnotation() { + updateAnnotation(false); + } + public void updateAnnotation(boolean applyGlobalSettings) + { boolean updateCalcs = false; boolean conv = av.isShowGroupConservation(); boolean cons = av.isShowGroupConsensus(); + boolean showprf = av.isShowConsensusProfile(); + boolean showConsHist = av.isShowConsensusHistogram(); + boolean sortg = true; // remove old automatic annotation @@ -1333,10 +1341,12 @@ public class AlignmentPanel extends GAlignmentPanel implements // intersect alignment annotation with alignment groups AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation(); + Hashtable oldrfs = new Hashtable(); for (int an = 0; an < aan.length; an++) { if (aan[an].autoCalculated && aan[an].groupRef != null) { + oldrfs.put(aan[an].groupRef, aan[an].groupRef); av.alignment.deleteAnnotation(aan[an]); aan[an] = null; } @@ -1346,7 +1356,12 @@ public class AlignmentPanel extends GAlignmentPanel implements { updateCalcs = false; sg = (SequenceGroup) gr.elementAt(g); - + if (applyGlobalSettings || !oldrfs.containsKey(sg)) + { + // set defaults for this group's conservation/consensus + sg.setIncludeAllConsSymbols(showprf); + sg.setShowConsensusHistogram(showConsHist); + } if (conv) { updateCalcs = true; @@ -1363,6 +1378,7 @@ public class AlignmentPanel extends GAlignmentPanel implements sg.recalcConservation(); } } + oldrfs.clear(); adjustAnnotationHeight(); } } diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 3bf915a..61b9c31 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -432,12 +432,15 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (aa[selectedRow].groupRef!=null) { - ap.seqPanel.ap.idPanel.highlightSearchResults(aa[selectedRow].groupRef.getSequences(null)); if (evt.getClickCount()>=2) { // todo: make the ap scroll to the selection - ap.av.setSelectionGroup(new SequenceGroup(aa[selectedRow].groupRef)); + ap.seqPanel.ap.idPanel.highlightSearchResults(null); + ap.av.setSelectionGroup(//new SequenceGroup( + aa[selectedRow].groupRef); // ); ap.paintAlignment(false); + } else { + ap.seqPanel.ap.idPanel.highlightSearchResults(aa[selectedRow].groupRef.getSequences(null)); } return; } else @@ -541,8 +544,27 @@ public class AnnotationLabels extends JPanel implements MouseListener, // av and sequencegroup need to implement same interface for if (aaa.groupRef != null) { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + "Show Group Histogram", aa[selectedRow].groupRef + .isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setShowConsensusHistogram(chist.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - "Show Full Profile", aa[selectedRow].groupRef + "Show Group Logo", aa[selectedRow].groupRef .isIncludeAllConsSymbols()); cprof.addActionListener(new ActionListener() { @@ -561,9 +583,26 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprof); } else { -/* final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - "Show Full Profile", aa[selectedRow].groupRef - .isIncludeAllConsSymbols()); + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + "Show Histogram", av.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowConsensusHistogram(chist.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( + "Show Logo", av.isShowConsensusProfile()); cprof.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -574,12 +613,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, // view // can be // updated. - aaa.groupRef.setIncludeAllConsSymbols(cprof.getState()); + av.setShowConsensusProfile(cprof.getState()); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } }); - pop.add(cprof); */ + pop.add(cprof); } final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); consclipbrd.addActionListener(this); diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 6d94687..6273fbc 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -84,9 +84,8 @@ public class Preferences extends GPreferences */ groupURLLinks = new Vector(); - groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); - // TODO: make sequence Group URL links more efficiently generated so popup menu does not take so long. - // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); + groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); + groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); } @@ -122,10 +121,6 @@ public class Preferences extends GPreferences fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false)); annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true)); - conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true)); - quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true)); - identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true)); - conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true)); quality.setSelected(Cache.getDefault("SHOW_QUALITY", true)); identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true)); @@ -202,6 +197,11 @@ public class Preferences extends GPreferences autoCalculateConsCheck.setSelected(Cache.getDefault( "AUTO_CALC_CONSENSUS", true)); + showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",false)); + showGroupConservation.setSelected(Cache.getDefault("SHOW_GROUP_CONSERVATION", false)); + showConsensHistogram.setSelected(Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",true)); + showConsensProfile.setSelected(Cache.getDefault("SHOW_CONSENSUS_PROFILE",false)); + padGaps.setSelected(Cache.getDefault("PAD_GAPS", false)); /*************************************************************************** @@ -229,7 +229,7 @@ public class Preferences extends GPreferences usagestats.setSelected(Cache.getDefault("USAGESTATS", false)); questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true - + annotations_actionPerformed(null); // update the display of the annotation settings try { jbInit(); @@ -281,6 +281,10 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("ID_ITALICS", Boolean .toString(idItalics.isSelected())); Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected())); + Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",Boolean.toString(showGroupConsensus.isSelected())); + Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",Boolean.toString(showGroupConservation.isSelected())); + Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",Boolean.toString(showConsensHistogram.isSelected())); + Cache.applicationProperties.setProperty("SHOW_CONSENSUS_PROFILE",Boolean.toString(showConsensProfile.isSelected())); Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean .toString(smoothFont.isSelected())); @@ -471,6 +475,10 @@ public class Preferences extends GPreferences conservation.setEnabled(annotations.isSelected()); quality.setEnabled(annotations.isSelected()); identity.setEnabled(annotations.isSelected()); + showConsensHistogram.setEnabled(annotations.isSelected()); + showConsensProfile.setEnabled(annotations.isSelected()); + showGroupConsensus.setEnabled(annotations.isSelected()); + showGroupConservation.setEnabled(annotations.isSelected()); } public void newLink_actionPerformed(ActionEvent e) diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 020e617..a89228e 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -284,9 +284,13 @@ public class GAlignFrame extends JInternalFrame private JMenuItem justifyLeftMenuItem=new JMenuItem(); private JMenuItem justifyRightMenuItem=new JMenuItem(); - + + JMenu autoAnnMenu = new JMenu(); protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showConsensusProfile=new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem(); private JMenuItem grpsFromSelection = new JMenuItem(); public GAlignFrame() @@ -1025,6 +1029,38 @@ public class GAlignFrame extends JInternalFrame } }); + showConsensusHistogram.setText("Show Consensus Histogram"); + showConsensusHistogram.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showConsensusHistogram_actionPerformed(e); + } + + }); + showConsensusProfile.setText("Show Consensus Logo"); + showConsensusProfile.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showConsensusProfile_actionPerformed(e); + } + + }); + applyAutoAnnotationSettings.setText("Apply to all groups"); + applyAutoAnnotationSettings.setState(false); + applyAutoAnnotationSettings.setVisible(true); + applyAutoAnnotationSettings.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + applyAutoAnnotationSettings_actionPerformed(e); + } + + }); nucleotideColour.setText("Nucleotide"); nucleotideColour.addActionListener(new java.awt.event.ActionListener() @@ -1560,6 +1596,7 @@ public class GAlignFrame extends JInternalFrame } }); tooltipSettingsMenu.setText("Sequence ID Tooltip"); + autoAnnMenu.setText("Autocalculated Annotation"); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(selectMenu); @@ -1613,8 +1650,13 @@ public class GAlignFrame extends JInternalFrame viewMenu.addSeparator(); viewMenu.add(followHighlightMenuItem); viewMenu.add(annotationPanelMenuItem); - viewMenu.add(showGroupConservation); - viewMenu.add(showGroupConsensus); + autoAnnMenu.add(applyAutoAnnotationSettings); + autoAnnMenu.add(showConsensusHistogram); + autoAnnMenu.add(showConsensusProfile); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); //viewMenu.add(showSeqFeaturesHeight); @@ -1711,6 +1753,24 @@ public class GAlignFrame extends JInternalFrame selectMenu.add(grpsFromSelection); } + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showConsensusHistogram_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showConsensusProfile_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 7b2e5c4..6b2c0f4 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -138,6 +138,10 @@ public class GPreferences extends JPanel JPanel jPanel3 = new JPanel(); + JPanel autoAnnotSettings1 = new JPanel(); + + JPanel autoAnnotSettings2 = new JPanel(); + JPanel exportTab = new JPanel(); JLabel epsLabel = new JLabel(); @@ -196,6 +200,12 @@ public class GPreferences extends JPanel protected JCheckBox usagestats = new JCheckBox(); protected JCheckBox questionnaire = new JCheckBox(); protected JCheckBox versioncheck = new JCheckBox(); + protected JLabel showGroupbits = new JLabel(); + protected JLabel showConsensbits = new JLabel(); + protected JCheckBox showConsensProfile = new JCheckBox(); + protected JCheckBox showConsensHistogram = new JCheckBox(); + protected JCheckBox showGroupConsensus = new JCheckBox(); + protected JCheckBox showGroupConservation = new JCheckBox(); /** * Creates a new GPreferences object. @@ -260,6 +270,38 @@ public class GPreferences extends JPanel identity.setHorizontalTextPosition(SwingConstants.LEFT); identity.setSelected(true); identity.setText("Consensus"); + showGroupbits.setFont(verdana11); + showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT); + showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT); + showGroupbits.setText("Group:"); + showConsensbits.setFont(verdana11); + showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT); + showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT); + showConsensbits.setText("Consensus:"); + showConsensHistogram.setEnabled(false); + showConsensHistogram.setFont(verdana11); + showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT); + showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT); + showConsensHistogram.setSelected(true); + showConsensHistogram.setText("Histogram"); + showConsensProfile.setEnabled(false); + showConsensProfile.setFont(verdana11); + showConsensProfile.setHorizontalAlignment(SwingConstants.RIGHT); + showConsensProfile.setHorizontalTextPosition(SwingConstants.LEFT); + showConsensProfile.setSelected(true); + showConsensProfile.setText("Profile"); + showGroupConsensus.setEnabled(false); + showGroupConsensus.setFont(verdana11); + showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT); + showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT); + showGroupConsensus.setSelected(true); + showGroupConsensus.setText("Consensus"); + showGroupConservation.setEnabled(false); + showGroupConservation.setFont(verdana11); + showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT); + showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT); + showGroupConservation.setSelected(true); + showGroupConservation.setText("Conservation"); annotations.setFont(verdana11); annotations.setHorizontalAlignment(SwingConstants.RIGHT); annotations.setHorizontalTextPosition(SwingConstants.LEFT); @@ -435,6 +477,8 @@ public class GPreferences extends JPanel jPanel2.setLayout(gridLayout2); gridLayout2.setRows(13); jPanel3.setBounds(new Rectangle(173, 35, 274, 26)); + autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78)); + autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26)); exportTab.setLayout(null); epsLabel.setFont(verdana11); epsLabel.setHorizontalAlignment(SwingConstants.RIGHT); @@ -533,9 +577,19 @@ public class GPreferences extends JPanel visualTab.add(fontNameCB); visualTab.add(fontSizeCB); visualTab.add(fontStyleCB); + visualTab.add(autoAnnotSettings1); + visualTab.add(autoAnnotSettings2); jPanel3.add(conservation); jPanel3.add(identity); jPanel3.add(quality); + autoAnnotSettings1.setLayout(new FlowLayout()); + autoAnnotSettings2.setLayout(new FlowLayout()); + autoAnnotSettings1.add(showConsensbits); + autoAnnotSettings1.add(showConsensHistogram); + autoAnnotSettings1.add(showConsensProfile); + autoAnnotSettings2.add(showGroupbits); + autoAnnotSettings2.add(showGroupConsensus); + autoAnnotSettings2.add(showGroupConservation); visualTab.add(jPanel2); linkPanel.add(editLinkButtons, BorderLayout.EAST); -- 1.7.10.2