<xs:attribute name="showUnconserved" type="xs:boolean" use="optional"/>
<xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
<xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showConsensusProfile" type="xs:boolean" use="optional" default="false"/>
+ <xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
<xs:attribute name="id" type="xs:string" use="optional"><xs:annotation>
<xs:documentation>
Optional sequence group ID (only needs to be unique for this alignment)
<xs:attribute name="showGroupConservation" type="xs:boolean" use="optional" default="false"/>
<xs:attribute name="showGroupConsensus" type="xs:boolean" use="optional" default="false"/>
<xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
- <xs:attribute name="showConsensusProfile" type="xs:boolean" use="optional" default="false"/>
+ <xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
<xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
<xs:attribute name="xpos" type="xs:int"/>
* <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the alignment.</li>
* <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups in the alignment.</li>
* <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's histogram.</li>
- * <li>SHOW_CONSENSUS_PROFILE (false) Show consensus annotation row's sequence logo.</li>
+ * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence logo.</li>
*
* <li></li>
*
/**
* consensus calculation property
*/
- private boolean showConsensusProfile=false;
+ private boolean showSequenceLogo=false;
/**
* @return the includeAllConsSymbols
*/
- public boolean isIncludeAllConsSymbols()
+ public boolean isShowSequenceLogo()
{
- return showConsensusProfile;
+ return showSequenceLogo;
}
try
{
- Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, endRes + 1, showConsensusProfile);
+ Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, endRes + 1, showSequenceLogo);
if (consensus != null)
{
_updateConsensusRow(cnsns);
consensus.annotations = null;
consensus.annotations = new Annotation[aWidth]; // should be alignment width
- AAFrequency.completeConsensus(consensus,cnsns,startRes,endRes+1,ignoreGapsInConsensus, showConsensusProfile); // TODO: setting container for ignoreGapsInConsensusCalculation);
+ AAFrequency.completeConsensus(consensus,cnsns,startRes,endRes+1,ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container for ignoreGapsInConsensusCalculation);
}
/**
*/
public void setIncludeAllConsSymbols(boolean includeAllConsSymbols)
{
- if (this.showConsensusProfile!=includeAllConsSymbols && consensus!=null) {
- this.showConsensusProfile = includeAllConsSymbols;
+ if (this.showSequenceLogo!=includeAllConsSymbols && consensus!=null) {
+ this.showSequenceLogo = includeAllConsSymbols;
recalcConservation();
}
- this.showConsensusProfile = includeAllConsSymbols;
+ this.showSequenceLogo = includeAllConsSymbols;
}
showGroupConsensus.setSelected(av.showGroupConsensus);
showGroupConservation.setSelected(av.showGroupConservation);
showConsensusHistogram.setSelected(av.showConsensusHistogram);
- showConsensusProfile.setSelected(av.showConsensusProfile);
+ showSequenceLogo.setSelected(av.showSequenceLogo);
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
/* (non-Javadoc)
* @see jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt.event.ActionEvent)
*/
- protected void showConsensusProfile_actionPerformed(ActionEvent e)
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
- viewport.setShowConsensusProfile(showConsensusProfile.getState());
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
}
}
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true);
- showConsensusProfile = Cache.getDefault("SHOW_CONSENSUS_PROFILE", false);
+ showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", 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",
/**
* should consensus profile be rendered by default
*/
- public boolean showConsensusProfile = false;
+ public boolean showSequenceLogo = false;
/**
* should consensus histograms be rendered by default
*/
/**
* @return the showConsensusProfile
*/
- public boolean isShowConsensusProfile()
+ public boolean isShowSequenceLogo()
{
- return showConsensusProfile;
+ return showSequenceLogo;
}
/**
- * @param showConsensusProfile the showConsensusProfile to set
+ * @param showSequenceLogo the new value
*/
- public void setShowConsensusProfile(boolean showConsensusProfile)
+ public void setShowSequenceLogo(boolean showSequenceLogo)
{
- this.showConsensusProfile = showConsensusProfile;
+ this.showSequenceLogo = showSequenceLogo;
}
/**
* @param showConsensusHistogram the showConsensusHistogram to set
boolean updateCalcs = false;
boolean conv = av.isShowGroupConservation();
boolean cons = av.isShowGroupConsensus();
- boolean showprf = av.isShowConsensusProfile();
+ boolean showprf = av.isShowSequenceLogo();
boolean showConsHist = av.isShowConsensusHistogram();
boolean sortg = true;
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
"Show Group Logo", aa[selectedRow].groupRef
- .isIncludeAllConsSymbols());
+ .isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- "Show Logo", av.isShowConsensusProfile());
+ "Show Logo", av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
// view
// can be
// updated.
- av.setShowConsensusProfile(cprof.getState());
+ av.setShowSequenceLogo(cprof.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
if (aa.groupRef!=null)
{
renderHistogram = aa.groupRef.isShowConsensusHistogram();
- renderProfile = aa.groupRef.isIncludeAllConsSymbols();
+ renderProfile = aa.groupRef.isShowSequenceLogo();
} else {
renderHistogram = av.isShowConsensusHistogram();
- renderProfile = av.isShowConsensusProfile();
+ renderProfile = av.isShowSequenceLogo();
}
}
while (x < eRes - sRes)
private int[] getProfileFor(AlignmentAnnotation aa, int column)
{
if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
- if (aa.groupRef!=null && aa.groupRef.consensusData!=null && aa.groupRef.isIncludeAllConsSymbols()) {
+ if (aa.groupRef!=null && aa.groupRef.consensusData!=null && aa.groupRef.isShowSequenceLogo()) {
return AAFrequency.extractProfile(aa.groupRef.consensusData[column],aa.groupRef.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to be stored
- if (aa.groupRef==null && aa.sequenceRef==null && av.isShowConsensusProfile())
+ if (aa.groupRef==null && aa.sequenceRef==null && av.isShowSequenceLogo())
{
return AAFrequency.extractProfile(av.hconsensus[column],av.getIgnoreGapsConsensus());
}
groups[i].setShowUnconserved(sg.getShowunconserved());
groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
- groups[i].setShowConsensusProfile(sg.isIncludeAllConsSymbols());
+ groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
for (int s = 0; s < sg.getSize(); s++)
{
jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
view.setTextCol2(av.textColour2.getRGB());
view.setTextColThreshold(av.thresholdTextColour);
view.setShowConsensusHistogram(av.isShowConsensusHistogram());
- view.setShowConsensusProfile(av.isShowConsensusProfile());
+ view.setShowSequenceLogo(av.isShowSequenceLogo());
view.setShowGroupConsensus(av.isShowGroupConsensus());
view.setShowGroupConservation(av.isShowGroupConservation());
view.setShowNPfeatureTooltip(av.isShowNpFeats());
if (groups[i].hasShowConsensusHistogram()) {
sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
};
- if (groups[i].hasShowConsensusProfile()) {
- sg.setIncludeAllConsSymbols(groups[i].isShowConsensusProfile());
+ if (groups[i].hasShowSequenceLogo()) {
+ sg.setIncludeAllConsSymbols(groups[i].isShowSequenceLogo());
}
if (groups[i].hasIgnoreGapsinConsensus())
{
if (view.hasShowConsensusHistogram())
{
af.viewport.setShowConsensusHistogram(view.getShowConsensusHistogram());
+ } else {
+ af.viewport.setShowConsensusHistogram(true);
}
- if (view.hasShowConsensusProfile())
+ if (view.hasShowSequenceLogo())
{
- af.viewport.setShowConsensusProfile(view.getShowConsensusProfile());
+ af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
+ } else {
+ af.viewport.setShowSequenceLogo(false);
}
if (view.hasShowDbRefTooltip())
{
if (view.hasShowGroupConsensus())
{
af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
+ } else {
+ af.viewport.setShowGroupConsensus(false);
}
if (view.hasShowGroupConservation())
{
af.viewport.setShowGroupConservation(view.getShowGroupConservation());
+ } else {
+ af.viewport.setShowGroupConservation(false);
}
// recover featre settings
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));
+ showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",false));
padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
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("SHOW_CONSENSUS_LOGO",Boolean.toString(showConsensLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
.toString(smoothFont.isSelected()));
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());
+ showConsensHistogram.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
+ showConsensLogo.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
}
public void newLink_actionPerformed(ActionEvent e)
protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem showConsensusProfile=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showSequenceLogo=new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
private JMenuItem grpsFromSelection = new JMenuItem();
}
});
- showConsensusProfile.setText("Show Consensus Logo");
- showConsensusProfile.addActionListener(new ActionListener()
+ showSequenceLogo.setText("Show Consensus Logo");
+ showSequenceLogo.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- showConsensusProfile_actionPerformed(e);
+ showSequenceLogo_actionPerformed(e);
}
});
viewMenu.add(annotationPanelMenuItem);
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
- autoAnnMenu.add(showConsensusProfile);
+ autoAnnMenu.add(showSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
}
- protected void showConsensusProfile_actionPerformed(ActionEvent e)
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
GridLayout gridLayout2 = new GridLayout();
- JPanel jPanel3 = new JPanel();
+ JPanel annsettingsPanel = new JPanel();
JPanel autoAnnotSettings1 = new JPanel();
-
JPanel autoAnnotSettings2 = new JPanel();
+ JPanel autoAnnotSettings3 = new JPanel();
JPanel exportTab = new JPanel();
protected JCheckBox versioncheck = new JCheckBox();
protected JLabel showGroupbits = new JLabel();
protected JLabel showConsensbits = new JLabel();
- protected JCheckBox showConsensProfile = new JCheckBox();
+ protected JCheckBox showConsensLogo = new JCheckBox();
protected JCheckBox showConsensHistogram = new JCheckBox();
protected JCheckBox showGroupConsensus = new JCheckBox();
protected JCheckBox showGroupConservation = new JCheckBox();
+ protected JCheckBox shareSelections = new JCheckBox();
+ protected JCheckBox followHighlight = new JCheckBox();
+
/**
* Creates a new GPreferences object.
showGroupbits.setFont(verdana11);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText("Group:");
+ showGroupbits.setText("Show group:");
showConsensbits.setFont(verdana11);
showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
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");
+ showConsensLogo.setEnabled(false);
+ showConsensLogo.setFont(verdana11);
+ showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensLogo.setSelected(true);
+ showConsensLogo.setText("Logo");
showGroupConsensus.setEnabled(false);
showGroupConsensus.setFont(verdana11);
showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setText("Conservation");
annotations.setFont(verdana11);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
- annotations.setHorizontalTextPosition(SwingConstants.LEFT);
+ annotations.setHorizontalTextPosition(SwingConstants.LEADING);
annotations.setSelected(true);
annotations.setText("Show Annotations");
+ annotations.setBounds(new Rectangle(169, 16, 200, 23));
annotations.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
annotations_actionPerformed(e);
}
});
+ identity.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
showUnconserved.setFont(verdana11);
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
showunconserved_actionPerformed(e);
}
});
+ shareSelections.setFont(verdana11);
+ shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
+ shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
+ //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ shareSelections.setSelected(true);
+ shareSelections.setText("Share selection across views");
+ followHighlight.setFont(verdana11);
+ followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
+ followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
+ //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ followHighlight.setSelected(true);
+ followHighlight.setText("Scroll to highlighted regions");
gapLabel.setFont(verdana11);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
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));
+ // jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
+ //jPanel3.setBounds(new Rectangle(173, 35, 274, 78));
+ //jPanel3.setLayout(new GridLayout(3,3));
+// 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);
openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
openoverv.setActionCommand("Open Overview");
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
- openoverv.setHorizontalTextPosition(SwingConstants.LEADING);
- openoverv.setText("Open Overview Window");
- openoverv.setBounds(new Rectangle(169, 17, 200, 23));
+ openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
+ openoverv.setText("Open Overview");
jPanel2.add(fullScreen);
- jPanel2.add(annotations);
+ jPanel2.add(openoverv);
jPanel2.add(seqLimit);
jPanel2.add(rightAlign);
jPanel2.add(fontLabel);
jPanel2.add(colourLabel);
jPanel2.add(sortLabel);
jPanel2.add(startupCheckbox);
- visualTab.add(openoverv);
+ visualTab.add(annotations);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
visualTab.add(colour);
visualTab.add(gapSymbolCB);
- visualTab.add(jPanel3);
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);
+ annsettingsPanel.setBounds(new Rectangle(173,39,300,62));
+ annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT,0,0));
+ annsettingsPanel.add(autoAnnotSettings1);
+ annsettingsPanel.add(autoAnnotSettings2);
+ annsettingsPanel.add(autoAnnotSettings3);
+ autoAnnotSettings1.setLayout(new GridLayout(3,1,0,0));
+// autoAnnotSettings1.setPreferredSize(new Dimensions())
+ autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
+ autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
+ visualTab.add(annsettingsPanel);
+ //visualTab.add(autoAnnotSettings1);
+ //visualTab.add(autoAnnotSettings2);
+ Border jb = new EmptyBorder(1,1,4,5);
+ quality.setBorder(jb);
+ conservation.setBorder(jb);
+ identity.setBorder(jb);
+ showConsensbits.setBorder(jb);
+ showGroupbits.setBorder(jb);
+ showGroupConsensus.setBorder(jb);
+ showGroupConservation.setBorder(jb);
+ showConsensHistogram.setBorder(jb);
+ showConsensLogo.setBorder(jb);
+
+ autoAnnotSettings2.add(conservation);
+ autoAnnotSettings1.add(quality);
+ autoAnnotSettings3.add(identity);
+
+ /*FlowLayout fl = new FlowLayout();
+ fl.setAlignment(FlowLayout.LEFT);
+ autoAnnotSettings1.setLayout(fl);
+ fl = new FlowLayout();
+ fl.setAlignment(FlowLayout.LEFT);
+ autoAnnotSettings2.setLayout(fl); */
+ autoAnnotSettings1.add(showGroupbits);
+ autoAnnotSettings3.add(showGroupConsensus);
autoAnnotSettings2.add(showGroupConservation);
+ autoAnnotSettings1.add(showConsensbits);
+ autoAnnotSettings2.add(showConsensHistogram);
+ autoAnnotSettings3.add(showConsensLogo);
visualTab.add(jPanel2);
linkPanel.add(editLinkButtons, BorderLayout.EAST);
-#Mon Apr 05 11:52:37 BST 2010\r
+#Wed Apr 14 11:41:13 BST 2010\r
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor\r
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor\r
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor\r
jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor\r
jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor\r
jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor\r
-jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor\r
-jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor\r
jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor\r
+jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor\r
+jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor\r
jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor\r
jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor\r
-jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor\r
jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor\r
+jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor\r
jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor\r
jalview.schemabinding.version2.MappingChoiceItem=jalview.schemabinding.version2.descriptors.MappingChoiceItemDescriptor\r
private boolean _has_showConsensusHistogram;\r
\r
/**\r
- * Field _showConsensusProfile.\r
+ * Field _showSequenceLogo.\r
*/\r
- private boolean _showConsensusProfile = false;\r
+ private boolean _showSequenceLogo = false;\r
\r
/**\r
- * keeps track of state for field: _showConsensusProfile\r
+ * keeps track of state for field: _showSequenceLogo\r
*/\r
- private boolean _has_showConsensusProfile;\r
+ private boolean _has_showSequenceLogo;\r
\r
/**\r
* Optional sequence group ID (only needs to be unique for this\r
\r
/**\r
*/\r
- public void deleteShowConsensusProfile(\r
+ public void deleteShowSequenceLogo(\r
) {\r
- this._has_showConsensusProfile= false;\r
+ this._has_showSequenceLogo= false;\r
}\r
\r
/**\r
}\r
\r
/**\r
- * Returns the value of field 'showConsensusProfile'.\r
+ * Returns the value of field 'showSequenceLogo'.\r
* \r
- * @return the value of field 'ShowConsensusProfile'.\r
+ * @return the value of field 'ShowSequenceLogo'.\r
*/\r
- public boolean getShowConsensusProfile(\r
+ public boolean getShowSequenceLogo(\r
) {\r
- return this._showConsensusProfile;\r
+ return this._showSequenceLogo;\r
}\r
\r
/**\r
}\r
\r
/**\r
- * Method hasShowConsensusProfile.\r
+ * Method hasShowSequenceLogo.\r
* \r
- * @return true if at least one ShowConsensusProfile has been\r
- * added\r
+ * @return true if at least one ShowSequenceLogo has been added\r
*/\r
- public boolean hasShowConsensusProfile(\r
+ public boolean hasShowSequenceLogo(\r
) {\r
- return this._has_showConsensusProfile;\r
+ return this._has_showSequenceLogo;\r
}\r
\r
/**\r
}\r
\r
/**\r
- * Returns the value of field 'showConsensusProfile'.\r
+ * Returns the value of field 'showSequenceLogo'.\r
* \r
- * @return the value of field 'ShowConsensusProfile'.\r
+ * @return the value of field 'ShowSequenceLogo'.\r
*/\r
- public boolean isShowConsensusProfile(\r
+ public boolean isShowSequenceLogo(\r
) {\r
- return this._showConsensusProfile;\r
+ return this._showSequenceLogo;\r
}\r
\r
/**\r
}\r
\r
/**\r
- * Sets the value of field 'showConsensusProfile'.\r
+ * Sets the value of field 'showSequenceLogo'.\r
* \r
- * @param showConsensusProfile the value of field\r
- * 'showConsensusProfile'.\r
+ * @param showSequenceLogo the value of field 'showSequenceLogo'\r
*/\r
- public void setShowConsensusProfile(\r
- final boolean showConsensusProfile) {\r
- this._showConsensusProfile = showConsensusProfile;\r
- this._has_showConsensusProfile = true;\r
+ public void setShowSequenceLogo(\r
+ final boolean showSequenceLogo) {\r
+ this._showSequenceLogo = showSequenceLogo;\r
+ this._has_showSequenceLogo = true;\r
}\r
\r
/**\r
private boolean _has_showConsensusHistogram;\r
\r
/**\r
- * Field _showConsensusProfile.\r
+ * Field _showSequenceLogo.\r
*/\r
- private boolean _showConsensusProfile = false;\r
+ private boolean _showSequenceLogo = false;\r
\r
/**\r
- * keeps track of state for field: _showConsensusProfile\r
+ * keeps track of state for field: _showSequenceLogo\r
*/\r
- private boolean _has_showConsensusProfile;\r
+ private boolean _has_showSequenceLogo;\r
\r
/**\r
* Field _ignoreGapsinConsensus.\r
\r
/**\r
*/\r
- public void deleteShowConsensusProfile(\r
- ) {\r
- this._has_showConsensusProfile= false;\r
- }\r
-\r
- /**\r
- */\r
public void deleteShowDbRefTooltip(\r
) {\r
this._has_showDbRefTooltip= false;\r
\r
/**\r
*/\r
+ public void deleteShowSequenceLogo(\r
+ ) {\r
+ this._has_showSequenceLogo= false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteShowText(\r
) {\r
this._has_showText= false;\r
}\r
\r
/**\r
- * Returns the value of field 'showConsensusProfile'.\r
- * \r
- * @return the value of field 'ShowConsensusProfile'.\r
- */\r
- public boolean getShowConsensusProfile(\r
- ) {\r
- return this._showConsensusProfile;\r
- }\r
-\r
- /**\r
* Returns the value of field 'showDbRefTooltip'.\r
* \r
* @return the value of field 'ShowDbRefTooltip'.\r
}\r
\r
/**\r
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean getShowSequenceLogo(\r
+ ) {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'showText'.\r
* \r
* @return the value of field 'ShowText'.\r
}\r
\r
/**\r
- * Method hasShowConsensusProfile.\r
- * \r
- * @return true if at least one ShowConsensusProfile has been\r
- * added\r
- */\r
- public boolean hasShowConsensusProfile(\r
- ) {\r
- return this._has_showConsensusProfile;\r
- }\r
-\r
- /**\r
* Method hasShowDbRefTooltip.\r
* \r
* @return true if at least one ShowDbRefTooltip has been added\r
}\r
\r
/**\r
+ * Method hasShowSequenceLogo.\r
+ * \r
+ * @return true if at least one ShowSequenceLogo has been added\r
+ */\r
+ public boolean hasShowSequenceLogo(\r
+ ) {\r
+ return this._has_showSequenceLogo;\r
+ }\r
+\r
+ /**\r
* Method hasShowText.\r
* \r
* @return true if at least one ShowText has been added\r
}\r
\r
/**\r
- * Returns the value of field 'showConsensusProfile'.\r
- * \r
- * @return the value of field 'ShowConsensusProfile'.\r
- */\r
- public boolean isShowConsensusProfile(\r
- ) {\r
- return this._showConsensusProfile;\r
- }\r
-\r
- /**\r
* Returns the value of field 'showDbRefTooltip'.\r
* \r
* @return the value of field 'ShowDbRefTooltip'.\r
}\r
\r
/**\r
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean isShowSequenceLogo(\r
+ ) {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'showText'.\r
* \r
* @return the value of field 'ShowText'.\r
}\r
\r
/**\r
- * Sets the value of field 'showConsensusProfile'.\r
- * \r
- * @param showConsensusProfile the value of field\r
- * 'showConsensusProfile'.\r
- */\r
- public void setShowConsensusProfile(\r
- final boolean showConsensusProfile) {\r
- this._showConsensusProfile = showConsensusProfile;\r
- this._has_showConsensusProfile = true;\r
- }\r
-\r
- /**\r
* Sets the value of field 'showDbRefTooltip'.\r
* \r
* @param showDbRefTooltip the value of field 'showDbRefTooltip'\r
}\r
\r
/**\r
+ * Sets the value of field 'showSequenceLogo'.\r
+ * \r
+ * @param showSequenceLogo the value of field 'showSequenceLogo'\r
+ */\r
+ public void setShowSequenceLogo(\r
+ final boolean showSequenceLogo) {\r
+ this._showSequenceLogo = showSequenceLogo;\r
+ this._has_showSequenceLogo = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'showText'.\r
* \r
* @param showText the value of field 'showText'.\r
fieldValidator.setValidator(typeValidator);\r
}\r
desc.setValidator(fieldValidator);\r
- //-- _showConsensusProfile\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusProfile", "showConsensusProfile", org.exolab.castor.xml.NodeType.Attribute);\r
+ //-- _showSequenceLogo\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);\r
handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
public java.lang.Object getValue( java.lang.Object object ) \r
throws IllegalStateException\r
{\r
JGroup target = (JGroup) object;\r
- if (!target.hasShowConsensusProfile()) { return null; }\r
- return (target.getShowConsensusProfile() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ if (!target.hasShowSequenceLogo()) { return null; }\r
+ return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
}\r
public void setValue( java.lang.Object object, java.lang.Object value) \r
throws IllegalStateException, IllegalArgumentException\r
JGroup target = (JGroup) object;\r
// if null, use delete method for optional primitives \r
if (value == null) {\r
- target.deleteShowConsensusProfile();\r
+ target.deleteShowSequenceLogo();\r
return;\r
}\r
- target.setShowConsensusProfile( ((java.lang.Boolean) value).booleanValue());\r
+ target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue());\r
} catch (java.lang.Exception ex) {\r
throw new IllegalStateException(ex.toString());\r
}\r
desc.setMultivalued(false);\r
addFieldDescriptor(desc);\r
\r
- //-- validation code for: _showConsensusProfile\r
+ //-- validation code for: _showSequenceLogo\r
fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
{ //-- local scope\r
org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
fieldValidator.setValidator(typeValidator);\r
}\r
desc.setValidator(fieldValidator);\r
- //-- _showConsensusProfile\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusProfile", "showConsensusProfile", org.exolab.castor.xml.NodeType.Attribute);\r
+ //-- _showSequenceLogo\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute);\r
handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
public java.lang.Object getValue( java.lang.Object object ) \r
throws IllegalStateException\r
{\r
Viewport target = (Viewport) object;\r
- if (!target.hasShowConsensusProfile()) { return null; }\r
- return (target.getShowConsensusProfile() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ if (!target.hasShowSequenceLogo()) { return null; }\r
+ return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
}\r
public void setValue( java.lang.Object object, java.lang.Object value) \r
throws IllegalStateException, IllegalArgumentException\r
Viewport target = (Viewport) object;\r
// if null, use delete method for optional primitives \r
if (value == null) {\r
- target.deleteShowConsensusProfile();\r
+ target.deleteShowSequenceLogo();\r
return;\r
}\r
- target.setShowConsensusProfile( ((java.lang.Boolean) value).booleanValue());\r
+ target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue());\r
} catch (java.lang.Exception ex) {\r
throw new IllegalStateException(ex.toString());\r
}\r
desc.setMultivalued(false);\r
addFieldDescriptor(desc);\r
\r
- //-- validation code for: _showConsensusProfile\r
+ //-- validation code for: _showSequenceLogo\r
fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
{ //-- local scope\r
org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
git://source.jalview.org / jalview.git / commitdiff