import java.util.List;
import javax.help.HelpSetException;
+import javax.swing.JButton;
import javax.swing.JColorChooser;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+ public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
private static final int MIN_FONT_SIZE = 1;
private static final int MAX_FONT_SIZE = 30;
* .properties file as '|' separated strings
*/
- groupURLLinks = new ArrayList<String>();
+ groupURLLinks = new ArrayList<>();
}
JInternalFrame frame;
openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
showUnconserved
.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
- showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
- false));
- showGroupConservation.setSelected(Cache.getDefault(
- "SHOW_GROUP_CONSERVATION", false));
- showConsensHistogram.setSelected(Cache.getDefault(
- "SHOW_CONSENSUS_HISTOGRAM", true));
- showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
- false));
- showNpTooltip.setSelected(Cache
- .getDefault("SHOW_NPFEATS_TOOLTIP", true));
- showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
- true));
+ showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
+ showGroupConsensus
+ .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+ showGroupConservation.setSelected(
+ Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+ showConsensHistogram.setSelected(
+ Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+ showConsensLogo
+ .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showNpTooltip
+ .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ showDbRefTooltip
+ .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
- fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
- + ""));
+ fontStyleCB.setSelectedItem(
+ Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
- scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
- false));
+ scaleProteinToCdna
+ .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
protColour.setSelectedItem(newProp != null ? newProp : oldProp);
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ gapColour.setBackground(
+ Cache.getDefaultColour("GAP_COLOUR", Color.lightGray));
+ hiddenColour.setBackground(
+ Cache.getDefaultColour("HIDDEN_COLOUR", Color.darkGray));
/*
* Set Structure tab defaults.
addSecondaryStructure.setEnabled(structSelected);
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
addTempFactor.setEnabled(structSelected);
- structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
- ViewerType.JMOL.name()));
+ structViewer.setSelectedItem(
+ Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
SortOrder.DESCENDING));
sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
SortOrder.DESCENDING));
- sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
- SortOrder.ASCENDING));
+ sortKeys.add(
+ new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
sorter.setSortKeys(sortKeys);
sorter.sort();
-
+
// set up filtering
ActionListener onReset;
onReset = new ActionListener()
@Override
public void changedUpdate(DocumentEvent e)
{
- sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
- + filterTB.getText()));
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
}
@Override
public void removeUpdate(DocumentEvent e)
{
- sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
- + filterTB.getText()));
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
}
@Override
public void insertUpdate(DocumentEvent e)
{
- sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
- + filterTB.getText()));
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
}
});
// set up list selection functionality
- linkUrlTable.getSelectionModel().addListSelectionListener(
- new UrlListSelectionHandler());
+ linkUrlTable.getSelectionModel()
+ .addListSelectionListener(new UrlListSelectionHandler());
// set up radio buttons
int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
.getPrimaryColumn();
String onClickName = linkUrlTable.getColumnName(onClickCol);
- linkUrlTable.getColumn(onClickName).setCellRenderer(
- new RadioButtonRenderer());
+ linkUrlTable.getColumn(onClickName)
+ .setCellRenderer(new RadioButtonRenderer());
linkUrlTable.getColumn(onClickName)
.setCellEditor(new RadioButtonEditor());
if (linkUrlTable.getModel().getColumnClass(column)
.equals(Boolean.class))
{
- TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
- column);
+ TableColumn tableColumn = linkUrlTable.getColumnModel()
+ .getColumn(column);
int preferredWidth = tableColumn.getMinWidth();
TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
- embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
- true));
+ embbedBioJSON
+ .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
/*
* Set Editing tab defaults
*/
- autoCalculateConsCheck.setSelected(Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
+ autoCalculateConsCheck
+ .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("GAP_SYMBOL",
+ gapSymbolCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
- .getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
- .getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_NAME",
+ fontNameCB.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_STYLE",
+ fontStyleCB.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_SIZE",
+ fontSizeCB.getSelectedItem().toString());
Cache.applicationProperties.setProperty("ID_ITALICS",
Boolean.toString(idItalics.isSelected()));
Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
Boolean.toString(showUnconserved.isSelected()));
+ Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
+ Boolean.toString(showOccupancy.isSelected()));
Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
Boolean.toString(showGroupConsensus.isSelected()));
Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
Boolean.toString(startupCheckbox.isSelected()));
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+ sortby.getSelectedItem().toString());
// convert description of sort order to enum name for save
SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
- .valueOf(showAutocalcFirst).toString());
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+ Boolean.valueOf(showAutocalcFirst).toString());
/*
* Save Colours settings
*/
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
- .getSelectedItem().toString());
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+ protColour.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+ nucColour.getSelectedItem().toString());
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
Boolean.toString(useRnaView.isSelected()));
Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
- Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
+ structViewer.getSelectedItem().toString());
Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
Boolean.toString(siftsMapping.isSelected()));
public void startupFileTextfield_mouseClicked()
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser.forRead(
- Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ JalviewFileChooser chooser = JalviewFileChooser
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.select_startup_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_startup_file"));
int value = chooser.showOpenDialog(this);
Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
format.getName());
}
- startupFileTextfield.setText(chooser.getSelectedFile()
- .getAbsolutePath());
+ startupFileTextfield
+ .setText(chooser.getSelectedFile().getAbsolutePath());
}
}
conservation.setEnabled(annotations.isSelected());
quality.setEnabled(annotations.isSelected());
identity.setEnabled(annotations.isSelected());
+ showOccupancy.setEnabled(annotations.isSelected());
showGroupConsensus.setEnabled(annotations.isSelected());
showGroupConservation.setEnabled(annotations.isSelected());
showConsensHistogram.setEnabled(annotations.isSelected()
{
if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.new_sequence_url_link"),
- JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
if (((UrlLinkTableModel) linkUrlTable.getModel())
.isUniqueName(link.getName()))
{
- ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
- link.getName(), link.getURL());
+ ((UrlLinkTableModel) linkUrlTable.getModel())
+ .insertRow(link.getName(), link.getURL());
valid = true;
}
else
{
if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.edit_sequence_url_link"),
- JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
}
-
@Override
public void defaultBrowser_mouseClicked(MouseEvent e)
{
JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle(MessageManager
- .getString("label.select_default_browser"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_default_browser"));
int value = chooser.showOpenDialog(this);
}
@Override
+ public void gapColour_actionPerformed(JButton btn)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_gap_colour"),
+ gapColour.getForeground());
+ if (col != null)
+ {
+ btn.setForeground(col);
+ }
+ btn.repaint();
+ }
+
+ @Override
+ public void hiddenColour_actionPerformed(JButton btn)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_hidden_colour"),
+ hiddenColour.getForeground());
+ if (col != null)
+ {
+ btn.setForeground(col);
+ }
+ btn.repaint();
+ }
+
+ @Override
protected void userIdWidth_actionPerformed()
{
try
}
} catch (NumberFormatException x)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .getString("warn.user_defined_width_requirements"),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
JvOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
if (!found)
{
String[] options = { "OK", "Help" };
- int showHelp = JvOptionPane.showInternalOptionDialog(
- Desktop.desktop,
+ int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
return name.hashCode() + code.hashCode();
}
}
-
+
private class UrlListSelectionHandler implements ListSelectionListener
{
editLink.setEnabled(false);
}
}
-}
+ }
}
git://source.jalview.org / jalview.git / blobdiff