X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=b293e6f98ce4ca3e35e31e40acc04ac56f0e09d9;hb=fee1b781ca14aadea5d112fc554fe14879c787c5;hp=c7e13324920417d097c6723c5881dbb1d6a964f9;hpb=bba03888565b5277a487f3186b6f6444477466e6;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index c7e1332..b293e6f 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,6 +20,11 @@ */ 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; @@ -30,6 +35,7 @@ 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; @@ -40,7 +46,7 @@ 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; @@ -96,7 +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 @@ -106,14 +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 { @@ -123,7 +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("/=$") == -1) { url = url + "|" + st.nextToken(); @@ -136,14 +143,10 @@ public class Preferences extends GPreferences } { // upgrade old SRS link - int srsPos = sequenceURLLinks - .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$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); } } @@ -152,10 +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; @@ -163,6 +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. */ @@ -176,7 +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; @@ -329,8 +343,8 @@ public class Preferences extends GPreferences /* * 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(); @@ -357,12 +371,23 @@ 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()); @@ -513,15 +538,8 @@ public class Preferences extends GPreferences /* * 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 @@ -533,7 +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) + "|" @@ -549,6 +567,7 @@ public class Preferences extends GPreferences else { Cache.applicationProperties.remove("SEQUENCE_LINKS"); + sequenceURLLinks.clear(); } Cache.applicationProperties.setProperty("USE_PROXY", @@ -735,9 +754,9 @@ 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()) { @@ -762,10 +781,10 @@ 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; } @@ -776,9 +795,9 @@ 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()) { @@ -802,10 +821,10 @@ 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; } nameLinks.removeElementAt(index); @@ -849,7 +868,7 @@ public class Preferences extends GPreferences super.showunconserved_actionPerformed(e); } - public static Collection getGroupURLLinks() + public static List getGroupURLLinks() { return groupURLLinks; } @@ -897,10 +916,10 @@ 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(""); } } @@ -923,10 +942,10 @@ 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; } } @@ -962,13 +981,13 @@ 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 { @@ -981,4 +1000,58 @@ 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(); + } + } }