import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
+import jalview.gui.StructureViewer.Viewer;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GPreferences;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
import javax.swing.JOptionPane;
+import javax.swing.JPanel;
/**
* DOCUMENT ME!
public class Preferences extends GPreferences
{
+ public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ private static final int MIN_FONT_SIZE = 1;
+
+ private static final int MAX_FONT_SIZE = 30;
+
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
public Preferences()
{
-
+ super();
frame = new JInternalFrame();
frame.setContentPane(this);
dasSource = new DasSourceBrowser();
- dasPanel.add(dasSource, BorderLayout.CENTER);
+ dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
- wsPanel.add(wsPrefs, BorderLayout.CENTER);
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
int width = 500, height = 420;
if (new jalview.util.Platform().isAMac())
{
MessageManager.getString("label.preferences"), width, height);
frame.setMinimumSize(new Dimension(width, height));
+ /*
+ * Set Visual tab defaults
+ */
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
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));
- sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
- for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
- {
- colour.addItem(ColourSchemeProperty.getColourName(i));
- }
-
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");
-
- colour.setSelectedItem(string);
-
- /**
- * default min-max colours for annotation shading
- */
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-
for (int i = 0; i < fonts.length; i++)
{
fontNameCB.addItem(fonts[i]);
}
- for (int i = 1; i < 31; i++)
+ for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
{
fontSizeCB.addItem(i + "");
}
gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
- startupCheckbox
- .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
- startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_3.jar"));
-
sortby.addItem("No sort");
sortby.addItem("Id");
sortby.addItem("Pairwise Identity");
sortAnnBy
.addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
- .valueOf(Cache.getDefault(Cache.SORT_ANNOTATIONS,
+ .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name()));
sortAnnBy.setSelectedItem(savedSort.toString());
sortAutocalc.addItem("Autocalculated first");
sortAutocalc.addItem("Autocalculated last");
-
- final boolean showAbove = Cache.getDefault(Cache.SHOW_AUTOCALC_ABOVE,
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
true);
sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
: sortAutocalc.getItemAt(1));
+ startupCheckbox
+ .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+ startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+ + "/examples/exampleFile_2_3.jar"));
- epsRendering.addItem(MessageManager.getString("label.prompt_each_time"));
- epsRendering.addItem(MessageManager.getString("label.lineart"));
- epsRendering.addItem(MessageManager.getString("action.text"));
- epsRendering.setSelectedIndex(0);
- autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
- userIdWidth.setEnabled(autoIdWidth.isSelected());
- userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
- Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
- userIdWidth.setText(wi == null ? "" : wi.toString());
- blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
- clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
- fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
- msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
- pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
- pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
- pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
-
- modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
-
- 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));
- showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
- false));
-
- padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ /*
+ * Set Colours tab defaults
+ */
+ for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ {
+ colour.addItem(ColourSchemeProperty.getColourName(i));
+ }
+ String string = Cache.getDefault("DEFAULT_COLOUR", "None");
+ colour.setSelectedItem(string);
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
- /***************************************************************************
- * Set up Connections
+ /*
+ * Set Structure tab defaults.
+ */
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ structFromPdb.setSelected(structSelected);
+ useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
+ useRnaView.setEnabled(structSelected);
+ addSecondaryStructure
+ .setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setEnabled(structSelected);
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setEnabled(structSelected);
+ structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
+ Viewer.JMOL.name()));
+
+ /*
+ * Set Connections tab defaults
*/
nameLinks = new Vector();
urlLinks = new Vector();
defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+ // note antisense here: default is true
questionnaire
- .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
- // antisense
- // here
- versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
- // is
- // true
+ .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
+ versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
+
+ /*
+ * Set Output tab defaults
+ */
+ epsRendering
+ .addItem(MessageManager.getString("label.prompt_each_time"));
+ epsRendering.addItem(MessageManager.getString("label.lineart"));
+ epsRendering.addItem(MessageManager.getString("action.text"));
+ epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
+ "Prompt each time"));
+ autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+ userIdWidth.setEnabled(autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
+ Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+ userIdWidth.setText(wi == null ? "" : wi.toString());
+ blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
+ clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
+ fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
+ msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
+ pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
+ pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
+ pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
+ modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+
+ /*
+ * Set Editing tab defaults
+ */
+ autoCalculateConsCheck.setSelected(Cache.getDefault(
+ "AUTO_CALC_CONSENSUS", true));
+ padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+
annotations_actionPerformed(null); // update the display of the annotation
// settings
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
}
/**
- * DOCUMENT ME!
+ * Save user selections on the Preferences tabs to the Cache and write out to
+ * file.
*
* @param e
- * DOCUMENT ME!
*/
public void ok_actionPerformed(ActionEvent e)
{
-
+ /*
+ * Save Visual settings
+ */
Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
Boolean.toString(seqLimit.isSelected()));
Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
- .getSelectedItem().toString());
Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
.getSelectedItem().toString());
.forDescription(sortAnnBy.getSelectedItem().toString());
if (annSortOrder != null)
{
- Cache.applicationProperties.setProperty(Cache.SORT_ANNOTATIONS,
+ Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
annSortOrder.name());
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(Cache.SHOW_AUTOCALC_ABOVE,
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
Boolean.valueOf(showAutocalcFirst).toString());
+ /*
+ * Save Colours settings
+ */
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
+ .getSelectedItem().toString());
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
maxColour.getBackground());
+ /*
+ * Save Structure settings
+ */
+ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Boolean.toString(addTempFactor.isSelected()));
+ Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Boolean.toString(addSecondaryStructure.isSelected()));
+ Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Boolean.toString(useRnaView.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Boolean.toString(structFromPdb.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
+ .getSelectedItem().toString());
+
+ /*
+ * Save Output settings
+ */
if (epsRendering.getSelectedItem().equals("Prompt each time"))
{
Cache.applicationProperties.remove("EPS_RENDERING");
.getSelectedItem().toString());
}
+ /*
+ * Save Connections settings
+ */
if (defaultBrowser.getText().trim().length() < 1)
{
Cache.applicationProperties.remove("DEFAULT_BROWSER");
// by just adding the given line
Cache.removeProperty("NOQUESTIONNAIRES");
}
+
+ /*
+ * Save Output settings
+ */
Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
Boolean.toString(blcjv.isSelected()));
Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
userIdWidth.getText());
+ /*
+ * Save Editing settings
+ */
Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
Boolean.toString(autoCalculateConsCheck.isSelected()));
Cache.applicationProperties.setProperty("SORT_BY_TREE",
dasSource.saveProperties(Cache.applicationProperties);
wsPrefs.updateAndRefreshWsMenuConfig(false);
+
Cache.saveProperties();
+
try
{
frame.setClosed(true);
super.showunconserved_actionPerformed(e);
}
- private void jbInit() throws Exception
- {
- }
-
public static Collection getGroupURLLinks()
{
return groupURLLinks;
}
- public void minColour_actionPerformed()
+ @Override
+ public void minColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
if (col != null)
{
- minColour.setBackground(col);
+ panel.setBackground(col);
}
- minColour.repaint();
+ panel.repaint();
}
- public void maxColour_actionPerformed()
+ @Override
+ public void maxColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
if (col != null)
{
- maxColour.setBackground(col);
+ panel.setBackground(col);
}
- maxColour.repaint();
+ panel.repaint();
}
@Override
git://source.jalview.org / jalview.git / blobdiff