X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=4777c85c8aeb76cd4530c9da52a385d421e9b350;hb=b0cee3aaf7d8873910939f97b6acb217d518968d;hp=2e8aa890d0b3cb19e451c27f1f646a80e600a93b;hpb=6a1564abce042be6eb37fd3ae883921e00a2bd0c;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 2e8aa89..4777c85 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,32 +20,47 @@ */ package jalview.gui; +import static jalview.util.UrlConstants.DB_ACCESSION; +import static jalview.util.UrlConstants.EMBLEBI_STRING; +import static jalview.util.UrlConstants.SEQUENCE_ID; +import static jalview.util.UrlConstants.SRS_STRING; + import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.bin.Cache; -import jalview.gui.StructureViewer.Viewer; +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.JalviewColourScheme; +import jalview.schemes.ResidueColourScheme; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.sifts.SiftsSettings; 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.util.Collection; +import java.io.File; +import java.util.ArrayList; +import java.util.List; import java.util.StringTokenizer; import java.util.Vector; +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 ext.edu.ucsf.rbvi.strucviz2.StructureManager; + /** * DOCUMENT ME! * @@ -54,6 +69,15 @@ import javax.swing.JPanel; */ public class Preferences extends GPreferences { + public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; + + public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; + + public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR"; + + public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT"; + + public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC"; public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN"; @@ -65,6 +89,8 @@ public class Preferences extends GPreferences 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"; @@ -77,7 +103,7 @@ public class Preferences extends GPreferences * Holds name and link separated with | character. Sequence ID must be * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$ */ - public static Vector sequenceURLLinks; + public static Vector sequenceURLLinks; /** * Holds name and link separated with | character. Sequence IDS and Sequences @@ -87,14 +113,11 @@ public class Preferences extends GPreferences * (TODO: proper escape for using | to separate ids or sequences */ - public static Vector groupURLLinks; + public static List groupURLLinks; static { - String string = Cache - .getDefault( - "SEQUENCE_LINKS", - "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"); - sequenceURLLinks = new Vector(); + String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING); + sequenceURLLinks = new Vector(); try { @@ -104,7 +127,11 @@ public class Preferences extends GPreferences String name = st.nextToken(); String url = st.nextToken(); // check for '|' within a regex - int rxstart = url.indexOf("$SEQUENCE_ID$"); + int rxstart = url.indexOf("$" + DB_ACCESSION + "$"); + if (rxstart == -1) + { + rxstart = url.indexOf("$" + SEQUENCE_ID + "$"); + } while (rxstart == -1 && url.indexOf("/=$") == -1) { url = url + "|" + st.nextToken(); @@ -117,14 +144,10 @@ public class Preferences extends GPreferences } { // upgrade old SRS link - int srsPos = sequenceURLLinks - .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); + int srsPos = sequenceURLLinks.indexOf(SRS_STRING); if (srsPos > -1) { - sequenceURLLinks - .setElementAt( - "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$", - srsPos); + sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos); } } @@ -133,10 +156,10 @@ public class Preferences extends GPreferences * .properties file as '|' separated strings */ - groupURLLinks = new Vector(); + groupURLLinks = new ArrayList(); } - Vector nameLinks, urlLinks; + Vector nameLinks, urlLinks; JInternalFrame frame; @@ -144,6 +167,16 @@ public class Preferences extends GPreferences private WsPreferences wsPrefs; + private OptionsParam promptEachTimeOpt = new OptionsParam( + MessageManager.getString("label.prompt_each_time"), + "Prompt each time"); + + private OptionsParam lineArtOpt = new OptionsParam( + MessageManager.getString("label.lineart"), "Lineart"); + + private OptionsParam textOpt = new OptionsParam( + MessageManager.getString("action.text"), "Text"); + /** * Creates a new Preferences object. */ @@ -156,11 +189,12 @@ public class Preferences extends GPreferences dasTab.add(dasSource, BorderLayout.CENTER); wsPrefs = new WsPreferences(); wsTab.add(wsPrefs, BorderLayout.CENTER); - int width = 500, height = 420; - if (new jalview.util.Platform().isAMac()) + int width = 500, height = 450; + new jalview.util.Platform(); + if (Platform.isAMac()) { width = 570; - height = 460; + height = 480; } Desktop.addInternalFrame(frame, @@ -216,6 +250,8 @@ public class Preferences extends GPreferences + "")); smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false)); + scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, + false)); idItalics.setSelected(Cache.getDefault("ID_ITALICS", true)); @@ -243,8 +279,7 @@ public class Preferences extends GPreferences sortAutocalc.addItem("Autocalculated first"); sortAutocalc.addItem("Autocalculated last"); - final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, - true); + final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true); sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0) : sortAutocalc.getItemAt(1)); startupCheckbox @@ -256,12 +291,22 @@ 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 (JalviewColourScheme cs : JalviewColourScheme.values()) { - colour.addItem(ColourSchemeProperty.getColourName(i)); + if (cs != JalviewColourScheme.UserDefined) + { + protColour.addItem(cs.toString()); + nucColour.addItem(cs.toString()); + } } - String string = Cache.getDefault("DEFAULT_COLOUR", "None"); - colour.setSelectedItem(string); + 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); + nucColour.setSelectedItem(newProp != null ? newProp : oldProp); minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", @@ -274,19 +319,39 @@ public class Preferences extends GPreferences structFromPdb.setSelected(structSelected); useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false)); useRnaView.setEnabled(structSelected); - addSecondaryStructure - .setSelected(Cache.getDefault(ADD_SS_ANN, false)); + 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())); + ViewerType.JMOL.name())); + chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, "")); + chimeraPath.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + validateChimeraPath(); + } + }); + + if (Cache.getDefault("MAP_WITH_SIFTS", false)) + { + siftsMapping.setSelected(true); + } + else + { + nwMapping.setSelected(true); + } + + SiftsSettings + .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); /* * Set Connections tab defaults */ - nameLinks = new Vector(); - urlLinks = new Vector(); + nameLinks = new Vector(); + urlLinks = new Vector(); for (int i = 0; i < sequenceURLLinks.size(); i++) { String link = sequenceURLLinks.elementAt(i).toString(); @@ -313,15 +378,26 @@ public class Preferences extends GPreferences /* * 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")); + epsRendering.addItem(promptEachTimeOpt); + epsRendering.addItem(lineArtOpt); + epsRendering.addItem(textOpt); + String defaultEPS = Cache.getDefault("EPS_RENDERING", + "Prompt each time"); + if (defaultEPS.equalsIgnoreCase("Text")) + { + epsRendering.setSelectedItem(textOpt); + } + else if (defaultEPS.equalsIgnoreCase("Lineart")) + { + epsRendering.setSelectedItem(lineArtOpt); + } + else + { + epsRendering.setSelectedItem(promptEachTimeOpt); + } autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); - userIdWidth.setEnabled(autoIdWidth.isSelected()); - userIdWidthlabel.setEnabled(autoIdWidth.isSelected()); + 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)); @@ -332,6 +408,8 @@ public class Preferences extends GPreferences 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)); /* * Set Editing tab defaults @@ -351,8 +429,14 @@ public class Preferences extends GPreferences * * @param e */ + @Override public void ok_actionPerformed(ActionEvent e) { + if (!validateSettings()) + { + return; + } + /* * Save Visual settings */ @@ -397,6 +481,8 @@ public class Preferences extends GPreferences Boolean.toString(showConsensLogo.isSelected())); Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected())); + Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA, + Boolean.toString(scaleProteinToCdna.isSelected())); Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean.toString(showNpTooltip.isSelected())); Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", @@ -423,13 +509,15 @@ public class Preferences extends GPreferences } 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", colour + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour + .getSelectedItem().toString()); + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour .getSelectedItem().toString()); Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground()); @@ -449,39 +537,28 @@ public class Preferences extends GPreferences Boolean.toString(structFromPdb.isSelected())); Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer .getSelectedItem().toString()); + Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText()); + Cache.applicationProperties.setProperty("MAP_WITH_SIFTS", + Boolean.toString(siftsMapping.isSelected())); + SiftsSettings.setMapWithSifts(siftsMapping.isSelected()); /* * Save Output settings */ - if (epsRendering.getSelectedItem().equals("Prompt each time")) - { - Cache.applicationProperties.remove("EPS_RENDERING"); - } - else - { - Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering - .getSelectedItem().toString()); - } + Cache.applicationProperties.setProperty("EPS_RENDERING", + ((OptionsParam) epsRendering.getSelectedItem()).getCode()); /* * Save Connections settings */ - if (defaultBrowser.getText().trim().length() < 1) - { - Cache.applicationProperties.remove("DEFAULT_BROWSER"); - } - else - { - Cache.applicationProperties.setProperty("DEFAULT_BROWSER", - defaultBrowser.getText()); - } + Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); jalview.util.BrowserLauncher.resetBrowser(); if (nameLinks.size() > 0) { StringBuffer links = new StringBuffer(); - sequenceURLLinks = new Vector(); + sequenceURLLinks = new Vector(); for (int i = 0; i < nameLinks.size(); i++) { sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" @@ -497,30 +574,15 @@ public class Preferences extends GPreferences else { Cache.applicationProperties.remove("SEQUENCE_LINKS"); + sequenceURLLinks.clear(); } 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()) { @@ -570,6 +632,8 @@ public class Preferences extends GPreferences Boolean.toString(pirjv.isSelected())); Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected())); + Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON", + Boolean.toString(embbedBioJSON.isSelected())); jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected(); Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", @@ -590,9 +654,8 @@ public class Preferences extends GPreferences dasSource.saveProperties(Cache.applicationProperties); wsPrefs.updateAndRefreshWsMenuConfig(false); - Cache.saveProperties(); - + Desktop.instance.doConfigureStructurePrefs(); try { frame.setClosed(true); @@ -602,26 +665,51 @@ public class Preferences extends GPreferences } /** + * Do any necessary validation before saving settings. Return focus to the + * first tab which fails validation. + * + * @return + */ + private boolean validateSettings() + { + if (!validateStructure()) + { + structureTab.requestFocusInWindow(); + return false; + } + return true; + } + + @Override + protected boolean validateStructure() + { + return validateChimeraPath(); + + } + + /** * DOCUMENT ME! */ + @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")); + chooser.setDialogTitle(MessageManager + .getString("label.select_startup_file")); int value = chooser.showOpenDialog(this); 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.toString()); + } startupFileTextfield.setText(chooser.getSelectedFile() .getAbsolutePath()); } @@ -633,6 +721,7 @@ public class Preferences extends GPreferences * @param e * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try @@ -651,6 +740,7 @@ public class Preferences extends GPreferences * @param e * DOCUMENT ME! */ + @Override public void annotations_actionPerformed(ActionEvent e) { conservation.setEnabled(annotations.isSelected()); @@ -664,6 +754,7 @@ public class Preferences extends GPreferences && (identity.isSelected() || showGroupConsensus.isSelected())); } + @Override public void newLink_actionPerformed(ActionEvent e) { @@ -671,9 +762,9 @@ 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()) { @@ -690,6 +781,7 @@ public class Preferences extends GPreferences } } + @Override public void editLink_actionPerformed(ActionEvent e) { GSequenceLink link = new GSequenceLink(); @@ -697,10 +789,10 @@ public class Preferences extends GPreferences int index = linkNameList.getSelectedIndex(); if (index == -1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -711,9 +803,9 @@ public class Preferences extends GPreferences 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()) { @@ -731,15 +823,16 @@ public class Preferences extends GPreferences } } + @Override public void deleteLink_actionPerformed(ActionEvent e) { int index = linkNameList.getSelectedIndex(); if (index == -1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } nameLinks.removeElementAt(index); @@ -753,10 +846,12 @@ public class Preferences extends GPreferences linkURLList.setListData(urlLinks); } + @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); @@ -774,13 +869,14 @@ public class Preferences extends GPreferences * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event * .ActionEvent) */ + @Override protected void showunconserved_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub super.showunconserved_actionPerformed(e); } - public static Collection getGroupURLLinks() + public static List getGroupURLLinks() { return groupURLLinks; } @@ -789,7 +885,8 @@ public class Preferences extends GPreferences public void minColour_actionPerformed(JPanel panel) { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground()); + MessageManager.getString("label.select_colour_minimum_value"), + minColour.getBackground()); if (col != null) { panel.setBackground(col); @@ -801,7 +898,8 @@ public class Preferences extends GPreferences public void maxColour_actionPerformed(JPanel panel) { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground()); + MessageManager.getString("label.select_colour_maximum_value"), + maxColour.getBackground()); if (col != null) { panel.setBackground(col); @@ -826,12 +924,10 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - MessageManager.getString("warn.user_defined_width_requirements"), - MessageManager.getString("label.invalid_id_column_width"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .getString("warn.user_defined_width_requirements"), + MessageManager.getString("label.invalid_id_column_width"), + JvOptionPane.WARNING_MESSAGE); userIdWidth.setText(""); } } @@ -843,4 +939,127 @@ 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()) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.invalid_chimera_path"), + MessageManager.getString("label.invalid_name"), + JvOptionPane.ERROR_MESSAGE); + return false; + } + } + return true; + } + + /** + * If Chimera is selected, check it can be found on default or user-specified + * path, if not show a warning/help dialog. + */ + @Override + protected void structureViewer_actionPerformed(String selectedItem) + { + if (!selectedItem.equals(ViewerType.CHIMERA.name())) + { + return; + } + boolean found = false; + + /* + * Try user-specified and standard paths for Chimera executable. + */ + List paths = StructureManager.getChimeraPaths(); + paths.add(0, chimeraPath.getText()); + for (String path : paths) + { + if (new File(path.trim()).canExecute()) + { + found = true; + break; + } + } + if (!found) + { + String[] options = { "OK", "Help" }; + int showHelp = JvOptionPane.showInternalOptionDialog( + Desktop.desktop, + JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.chimera_missing")), + "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, + null, options, options[0]); + if (showHelp == JvOptionPane.NO_OPTION) + { + try + { + Help.showHelpWindow(HelpId.StructureViewer); + } catch (HelpSetException e) + { + e.printStackTrace(); + } + } + } + } + + public class OptionsParam + { + private String name; + + private String code; + + public OptionsParam(String name, String code) + { + this.name = name; + this.code = code; + } + + public String getName() + { + return name; + } + + public void setName(String name) + { + this.name = name; + } + + public String getCode() + { + return code; + } + + public void setCode(String code) + { + this.code = code; + } + + @Override + public String toString() + { + return name; + } + + @Override + public boolean equals(Object that) + { + if (!(that instanceof OptionsParam)) + { + return false; + } + return this.code.equalsIgnoreCase(((OptionsParam) that).code); + } + + @Override + public int hashCode() + { + return name.hashCode() + code.hashCode(); + } + } }