X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;fp=src%2Fjalview%2Fgui%2FPreferences.java;h=b082bc68bec8b03d43eaa78a7e1d7a2249a9fa8f;hb=b8810711642d8473325c8a3d3e76cc5c3c9b5bbd;hp=e44915da79b359601d869fa57686ee9d1176d7c1;hpb=936d4dc095734df2b1e9f3bf9e0bd29b9c86434c;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index e44915d..b082bc6 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,19 +20,34 @@ */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; - -import jalview.bin.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; +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 jalview.jbgui.GSequenceLink; +import jalview.schemes.ColourSchemeProperty; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseEvent; +import java.io.File; +import java.util.Collection; +import java.util.StringTokenizer; +import java.util.Vector; + +import javax.swing.JColorChooser; +import javax.swing.JFileChooser; +import javax.swing.JInternalFrame; +import javax.swing.JOptionPane; +import javax.swing.JPanel; + /** * DOCUMENT ME! * @@ -42,6 +57,26 @@ import jalview.util.MessageManager; 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 CHIMERA_PATH = "CHIMERA_PATH"; + + 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 $SEQUENCE_ID=/.possible | chars ./=$ @@ -118,13 +153,13 @@ public class Preferences extends GPreferences */ 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()) { @@ -136,6 +171,9 @@ public class Preferences extends GPreferences 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)); @@ -147,37 +185,27 @@ public class Preferences extends GPreferences 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 + ""); } @@ -202,51 +230,73 @@ public class Preferences extends GPreferences 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"); sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort")); - 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)); + sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString()); + sortAnnBy + .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString()); + sortAnnBy + .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString()); + SequenceAnnotationOrder savedSort = SequenceAnnotationOrder + .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(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")); - 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)); + /* + * 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)); - padGaps.setSelected(Cache.getDefault("PAD_GAPS", false)); + /* + * 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())); + chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, "")); + chimeraPath.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + validateChimeraPath(); + } + }); - /*************************************************************************** - * Set up Connections + /* + * Set Connections tab defaults */ nameLinks = new Vector(); urlLinks = new Vector(); @@ -268,34 +318,62 @@ public class Preferences extends GPreferences 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) { + if (!validateSettings()) + { + return; + } + /* + * Save Visual settings + */ Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected())); Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", @@ -313,8 +391,6 @@ public class Preferences extends GPreferences 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()); @@ -355,11 +431,47 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby .getSelectedItem().toString()); + // convert description of sort order to enum name for save + SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder + .forDescription(sortAnnBy.getSelectedItem().toString()); + if (annSortOrder != null) + { + Cache.applicationProperties.setProperty(SORT_ANNOTATIONS, + annSortOrder.name()); + } + + final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0; + 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()); + Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText()); + + /* + * Save Output settings + */ if (epsRendering.getSelectedItem().equals("Prompt each time")) { Cache.applicationProperties.remove("EPS_RENDERING"); @@ -370,15 +482,10 @@ public class Preferences extends GPreferences .getSelectedItem().toString()); } - if (defaultBrowser.getText().trim().length() < 1) - { - Cache.applicationProperties.remove("DEFAULT_BROWSER"); - } - else - { - Cache.applicationProperties.setProperty("DEFAULT_BROWSER", - defaultBrowser.getText()); - } + /* + * Save Connections settings + */ + Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); jalview.util.BrowserLauncher.resetBrowser(); @@ -406,25 +513,9 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected())); - if (proxyServerTB.getText().trim().length() < 1) - { - Cache.applicationProperties.remove("PROXY_SERVER"); - } - else - { - Cache.applicationProperties.setProperty("PROXY_SERVER", - proxyServerTB.getText()); - } + Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText()); - if (proxyPortTB.getText().trim().length() < 1) - { - Cache.applicationProperties.remove("PROXY_PORT"); - } - else - { - Cache.applicationProperties.setProperty("PROXY_PORT", - proxyPortTB.getText()); - } + Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText()); if (useProxy.isSelected()) { @@ -454,6 +545,10 @@ public class Preferences extends GPreferences // 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", @@ -478,6 +573,9 @@ public class Preferences extends GPreferences 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", @@ -488,6 +586,7 @@ public class Preferences extends GPreferences dasSource.saveProperties(Cache.applicationProperties); wsPrefs.updateAndRefreshWsMenuConfig(false); Cache.saveProperties(); + Desktop.instance.doConfigureStructurePrefs(); try { frame.setClosed(true); @@ -497,6 +596,27 @@ public class Preferences extends GPreferences } /** + * Do any necessary validation before saving settings. + * + * @return + */ + private boolean validateSettings() + { + if (!validateStructure()) + { + structureTab.requestFocusInWindow(); + return false; + } + return true; + } + + @Override + protected boolean validateStructure() + { + return validateChimeraPath(); + + } + /** * DOCUMENT ME! */ public void startupFileTextfield_mouseClicked() @@ -675,35 +795,33 @@ public class Preferences extends GPreferences 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 @@ -740,4 +858,25 @@ public class Preferences extends GPreferences userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); } + /** + * Returns true if chimera path is to a valid executable, else show an error + * dialog. + */ + private boolean validateChimeraPath() + { + if (chimeraPath.getText().trim().length() > 0) + { + File f = new File(chimeraPath.getText()); + if (!f.canExecute()) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.invalid_chimera_path"), + MessageManager.getString("label.invalid_name"), + JOptionPane.ERROR_MESSAGE); + return false; + } + } + return true; + } + }