import jalview.jbgui.GSequenceLink;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.UrlProvider;
+import jalview.util.UrlProviderI;
import jalview.ws.sifts.SiftsSettings;
import java.awt.BorderLayout;
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;
import javax.help.HelpSetException;
public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
- public static final String HIDE_INTRONS = "HIDE_INTRONS";
-
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 $SEQUENCE_ID=/.possible | chars ./=$
*/
- public static Vector sequenceURLLinks;
+ public static UrlProviderI sequenceUrlLinks;
/**
* Holds name and link separated with | character. Sequence IDS and Sequences
* (TODO: proper escape for using | to separate ids or sequences
*/
- public static Vector groupURLLinks;
+ public static List<String> 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();
-
- try
- {
- StringTokenizer st = new StringTokenizer(string, "|");
- while (st.hasMoreElements())
- {
- String name = st.nextToken();
- String url = st.nextToken();
- // check for '|' within a regex
- int rxstart = url.indexOf("$SEQUENCE_ID$");
- while (rxstart == -1 && url.indexOf("/=$") == -1)
- {
- url = url + "|" + st.nextToken();
- }
- sequenceURLLinks.addElement(name + "|" + url);
- }
- } catch (Exception ex)
- {
- System.out.println(ex + "\nError parsing sequence links");
- }
- {
- // upgrade old SRS link
- int srsPos = sequenceURLLinks
- .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
- if (srsPos > -1)
- {
- sequenceURLLinks
- .setElementAt(
- "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
- srsPos);
- }
- }
+ String string = Cache.getDefault("SEQUENCE_LINKS",
+ UrlProviderI.DEFAULT_STRING);
+ sequenceUrlLinks = new UrlProvider(UrlProviderI.DEFAULT_LABEL, string);
/**
* TODO: reformulate groupURL encoding so two or more can be stored in the
* .properties file as '|' separated strings
*/
- groupURLLinks = new Vector();
+ groupURLLinks = new ArrayList<String>();
}
- Vector nameLinks, urlLinks;
+ Vector<String> nameLinks, urlLinks;
JInternalFrame frame;
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.
*/
dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
- int width = 500, height = 470;
- if (new jalview.util.Platform().isAMac())
+ int width = 500, height = 450;
+ new jalview.util.Platform();
+ if (Platform.isAMac())
{
width = 570;
- height = 500;
+ height = 480;
}
Desktop.addInternalFrame(frame,
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
- hideIntrons.setSelected(Cache.getDefault(HIDE_INTRONS, true));
gapSymbolCB.addItem("-");
gapSymbolCB.addItem(".");
/*
* Set Connections tab defaults
*/
- nameLinks = new Vector();
- urlLinks = new Vector();
- for (int i = 0; i < sequenceURLLinks.size(); i++)
- {
- String link = sequenceURLLinks.elementAt(i).toString();
- nameLinks.addElement(link.substring(0, link.indexOf("|")));
- urlLinks.addElement(link.substring(link.indexOf("|") + 1));
- }
+ nameLinks = new Vector<String>();
+ urlLinks = new Vector<String>();
+ resetStoredLinks();
updateLinkData();
useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
/*
* 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());
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
Boolean.toString(wrap.isSelected()));
- Cache.applicationProperties.setProperty(HIDE_INTRONS,
- Boolean.toString(hideIntrons.isSelected()));
Cache.applicationProperties.setProperty("STARTUP_FILE",
startupFileTextfield.getText());
/*
* 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
jalview.util.BrowserLauncher.resetBrowser();
- if (nameLinks.size() > 0)
+ // save user-defined and selected links
+ String links = sequenceUrlLinks.writeUrlsAsString();
+ if (links.isEmpty())
{
- StringBuffer links = new StringBuffer();
- sequenceURLLinks = new Vector();
- for (int i = 0; i < nameLinks.size(); i++)
- {
- sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
- + urlLinks.elementAt(i));
- links.append(sequenceURLLinks.elementAt(i).toString());
- links.append("|");
- }
- // remove last "|"
- links.setLength(links.length() - 1);
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
- links.toString());
+ Cache.applicationProperties.remove("SEQUENCE_LINKS");
}
else
{
- Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+ links.toString());
}
Cache.applicationProperties.setProperty("USE_PROXY",
{
nameLinks.addElement(link.getName());
urlLinks.addElement(link.getURL());
- updateLinkData();
- valid = true;
+ if (updateLinkData())
+ {
+ valid = true;
+ }
+ else
+ {
+ break;
+ }
}
}
else
{
nameLinks.setElementAt(link.getName(), index);
urlLinks.setElementAt(link.getURL(), index);
- updateLinkData();
- valid = true;
+ if (updateLinkData())
+ {
+ valid = true;
+ }
+ else
+ {
+ break;
+ }
}
}
updateLinkData();
}
- void updateLinkData()
+ private boolean updateLinkData()
+ {
+ try
+ {
+ sequenceUrlLinks.setUrlLinks(nameLinks, urlLinks);
+ linkNameList.setListData(nameLinks);
+ linkURLList.setListData(urlLinks);
+ } catch (IllegalArgumentException e)
+ {
+
+ // put back the old links
+ resetStoredLinks();
+
+ linkNameList.setListData(nameLinks);
+ linkURLList.setListData(urlLinks);
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ e.getMessage(), MessageManager.getString("label.link_name"),
+ JOptionPane.WARNING_MESSAGE);
+
+ return false;
+ }
+ return true;
+ }
+
+ private void resetStoredLinks()
{
- linkNameList.setListData(nameLinks);
- linkURLList.setListData(urlLinks);
+ Vector<String> nlinks = sequenceUrlLinks.getLinksForDisplay();
+
+ nameLinks.clear();
+ urlLinks.clear();
+ for (String entry : nlinks)
+ {
+ nameLinks.addElement(entry.split("\\|")[0]);
+ urlLinks.addElement(entry.split("\\|")[1]);
+ }
}
@Override
super.showunconserved_actionPerformed(e);
}
- public static Collection getGroupURLLinks()
+ public static List<String> getGroupURLLinks()
{
return groupURLLinks;
}
}
}
+ 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();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff