X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=cccdd2e2a0878b612f307c7cce6828e5a2c38b07;hb=ef39fb4e4ab6c38dd20255f4a60609a6af581dcf;hp=b46ae10f6fc609dc8a4ebc8bc1ca7ed9a8cde436;hpb=4d22590f9c429fe89f4e44b2045e6741acb27fa5;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index b46ae10..cccdd2e 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -24,11 +24,14 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.bin.Cache; import jalview.gui.Help.HelpId; import jalview.gui.StructureViewer.ViewerType; +import jalview.io.FileFormatI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GPreferences; import jalview.jbgui.GSequenceLink; -import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemes; +import jalview.schemes.ResidueColourScheme; import jalview.urls.UrlLinkTableModel; import jalview.urls.api.UrlProviderFactoryI; import jalview.urls.api.UrlProviderI; @@ -54,7 +57,6 @@ import javax.help.HelpSetException; import javax.swing.JColorChooser; import javax.swing.JFileChooser; import javax.swing.JInternalFrame; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.ListSelectionModel; import javax.swing.RowFilter; @@ -105,6 +107,8 @@ public class Preferences extends GPreferences 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; @@ -208,6 +212,7 @@ public class Preferences extends GPreferences openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false)); showUnconserved .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false)); + showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false)); showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false)); showGroupConservation.setSelected(Cache.getDefault( @@ -284,12 +289,16 @@ public class Preferences extends GPreferences /* * Set Colours tab defaults */ - for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++) + protColour.addItem(ResidueColourScheme.NONE); + nucColour.addItem(ResidueColourScheme.NONE); + for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes()) { - protColour.addItem(ColourSchemeProperty.getColourName(i)); - nucColour.addItem(ColourSchemeProperty.getColourName(i)); + String name = cs.getSchemeName(); + protColour.addItem(name); + nucColour.addItem(name); } - String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None"); + String oldProp = Cache.getDefault(DEFAULT_COLOUR, + ResidueColourScheme.NONE); String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null); protColour.setSelectedItem(newProp != null ? newProp : oldProp); newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null); @@ -346,7 +355,7 @@ public class Preferences extends GPreferences List sortKeys = new ArrayList<>(); UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel(); - sortKeys.add(new RowSorter.SortKey(m.getDefaultColumn(), + sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(), SortOrder.DESCENDING)); sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(), SortOrder.DESCENDING)); @@ -429,7 +438,7 @@ public class Preferences extends GPreferences // set up radio buttons int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel()) - .getDefaultColumn(); + .getPrimaryColumn(); String onClickName = linkUrlTable.getColumnName(onClickCol); linkUrlTable.getColumn(onClickName).setCellRenderer( new RadioButtonRenderer()); @@ -459,8 +468,6 @@ public class Preferences extends GPreferences useProxy.setSelected(Cache.getDefault("USE_PROXY", false)); useProxy_actionPerformed(); // make sure useProxy is correctly initialised - proxyServerTB.setEnabled(useProxy.isSelected()); - proxyPortTB.setEnabled(useProxy.isSelected()); proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", "")); proxyPortTB.setText(Cache.getDefault("PROXY_PORT", "")); @@ -568,6 +575,8 @@ public class Preferences extends GPreferences 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", @@ -676,7 +685,7 @@ public class Preferences extends GPreferences } Cache.applicationProperties.setProperty("DEFAULT_URL", - sequenceUrlLinks.getDefaultUrlId()); + sequenceUrlLinks.getPrimaryUrlId()); Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected())); @@ -794,12 +803,9 @@ public class Preferences extends GPreferences @Override public void startupFileTextfield_mouseClicked() { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { - "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", - "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF", - "PIR", "BLC", "Jalview" }, - jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser chooser = JalviewFileChooser.forRead( + Cache.getProperty("LAST_DIRECTORY"), fileFormat); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager .getString("label.select_startup_file")); @@ -808,8 +814,12 @@ public class Preferences extends GPreferences if (value == JalviewFileChooser.APPROVE_OPTION) { - jalview.bin.Cache.applicationProperties.setProperty( - "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat()); + FileFormatI format = chooser.getSelectedFormat(); + if (format != null) + { + Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", + format.getName()); + } startupFileTextfield.setText(chooser.getSelectedFile() .getAbsolutePath()); } @@ -846,6 +856,7 @@ public class Preferences extends GPreferences 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() @@ -861,9 +872,9 @@ public class Preferences extends GPreferences boolean valid = false; while (!valid) { - if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, MessageManager.getString("label.new_sequence_url_link"), - JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { @@ -901,23 +912,29 @@ public class Preferences extends GPreferences return; } - link.setName(linkUrlTable.getValueAt(index, 0).toString()); - link.setURL(linkUrlTable.getValueAt(index, 1).toString()); + int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getNameColumn(); + int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getUrlColumn(); + String oldName = linkUrlTable.getValueAt(index, nameCol).toString(); + link.setName(oldName); + link.setURL(linkUrlTable.getValueAt(index, urlCol).toString()); boolean valid = false; while (!valid) { - if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, MessageManager.getString("label.edit_sequence_url_link"), - JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { - if (((UrlLinkTableModel) linkUrlTable.getModel()) - .isUniqueName(link.getName())) + if ((oldName.equals(link.getName())) + || (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName()))) { - linkUrlTable.setValueAt(link.getName(), index, 0); - linkUrlTable.setValueAt(link.getURL(), index, 1); + linkUrlTable.setValueAt(link.getName(), index, nameCol); + linkUrlTable.setValueAt(link.getURL(), index, urlCol); valid = true; } else @@ -1033,10 +1050,10 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("warn.user_defined_width_requirements"), MessageManager.getString("label.invalid_id_column_width"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); userIdWidth.setText(""); } } @@ -1059,10 +1076,10 @@ public class Preferences extends GPreferences File f = new File(chimeraPath.getText()); if (!f.canExecute()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.invalid_chimera_path"), MessageManager.getString("label.invalid_name"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); return false; } } @@ -1098,13 +1115,13 @@ public class Preferences extends GPreferences if (!found) { String[] options = { "OK", "Help" }; - int showHelp = JOptionPane.showInternalOptionDialog( + int showHelp = JvOptionPane.showInternalOptionDialog( Desktop.desktop, JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.chimera_missing")), - "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE, + "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, null, options, options[0]); - if (showHelp == JOptionPane.NO_OPTION) + if (showHelp == JvOptionPane.NO_OPTION) { try {