X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=0b65c1bcc126c4ae8af0123445183f709e5ac537;hb=18a91cf8bf71500b0bfa020c8348227cce2fc279;hp=1b274a8b751e53216694838585db0e9501e88472;hpb=2526066acdc3faf3a178e50672c78e428287e9ef;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 1b274a8..0b65c1b 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,16 +20,24 @@ */ 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.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.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.sifts.SiftsSettings; import java.awt.BorderLayout; import java.awt.Color; @@ -39,7 +47,7 @@ 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.ArrayList; import java.util.List; import java.util.StringTokenizer; import java.util.Vector; @@ -48,7 +56,6 @@ 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 ext.edu.ucsf.rbvi.strucviz2.StructureManager; @@ -95,7 +102,7 @@ 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 @@ -105,14 +112,11 @@ 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 { @@ -122,7 +126,11 @@ 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("/=$") == -1) { url = url + "|" + st.nextToken(); @@ -135,14 +143,10 @@ public class Preferences extends GPreferences } { // upgrade old SRS link - int srsPos = sequenceURLLinks - .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$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); } } @@ -151,10 +155,10 @@ public class Preferences extends GPreferences * .properties file as '|' separated strings */ - groupURLLinks = new Vector(); + groupURLLinks = new ArrayList(); } - Vector nameLinks, urlLinks; + Vector nameLinks, urlLinks; JInternalFrame frame; @@ -162,6 +166,16 @@ 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. */ @@ -175,7 +189,8 @@ public class Preferences extends GPreferences wsPrefs = new WsPreferences(); wsTab.add(wsPrefs, BorderLayout.CENTER); int width = 500, height = 450; - if (new jalview.util.Platform().isAMac()) + new jalview.util.Platform(); + if (Platform.isAMac()) { width = 570; height = 480; @@ -263,8 +278,7 @@ 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 @@ -298,8 +312,7 @@ 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); @@ -315,11 +328,23 @@ public class Preferences extends GPreferences } }); + 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(); @@ -346,15 +371,26 @@ 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)); @@ -386,6 +422,7 @@ public class Preferences extends GPreferences * * @param e */ + @Override public void ok_actionPerformed(ActionEvent e) { if (!validateSettings()) @@ -465,8 +502,8 @@ 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 @@ -494,19 +531,15 @@ public class Preferences extends GPreferences 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 @@ -518,7 +551,7 @@ public class Preferences extends GPreferences 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) + "|" @@ -534,6 +567,7 @@ public class Preferences extends GPreferences else { Cache.applicationProperties.remove("SEQUENCE_LINKS"); + sequenceURLLinks.clear(); } Cache.applicationProperties.setProperty("USE_PROXY", @@ -645,27 +679,30 @@ public class Preferences extends GPreferences 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()); } @@ -677,6 +714,7 @@ public class Preferences extends GPreferences * @param e * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try @@ -695,6 +733,7 @@ public class Preferences extends GPreferences * @param e * DOCUMENT ME! */ + @Override public void annotations_actionPerformed(ActionEvent e) { conservation.setEnabled(annotations.isSelected()); @@ -708,6 +747,7 @@ public class Preferences extends GPreferences && (identity.isSelected() || showGroupConsensus.isSelected())); } + @Override public void newLink_actionPerformed(ActionEvent e) { @@ -715,9 +755,9 @@ 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()) { @@ -734,6 +774,7 @@ public class Preferences extends GPreferences } } + @Override public void editLink_actionPerformed(ActionEvent e) { GSequenceLink link = new GSequenceLink(); @@ -741,10 +782,10 @@ 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; } @@ -755,9 +796,9 @@ 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()) { @@ -775,15 +816,16 @@ 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); @@ -797,10 +839,12 @@ 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); @@ -818,13 +862,14 @@ 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; } @@ -833,7 +878,8 @@ 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); @@ -845,7 +891,8 @@ 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); @@ -870,12 +917,10 @@ 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(""); } } @@ -898,10 +943,10 @@ 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; } } @@ -936,15 +981,14 @@ public class Preferences extends GPreferences } if (!found) { - String[] options = - { "OK", "Help" }; - int showHelp = JOptionPane.showInternalOptionDialog( + String[] options = { "OK", "Help" }; + int showHelp = JvOptionPane.showInternalOptionDialog( Desktop.desktop, JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.chimera_missing")), - "", JOptionPane.YES_NO_OPTION, - JOptionPane.WARNING_MESSAGE, null, options, options[0]); - if (showHelp == JOptionPane.NO_OPTION) + "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, + null, options, options[0]); + if (showHelp == JvOptionPane.NO_OPTION) { try { @@ -957,4 +1001,58 @@ public class Preferences extends GPreferences } } + 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(); + } + } }