*/
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.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;
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;
* 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<String> 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();
+ String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
+ sequenceURLLinks = new Vector<String>();
try
{
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("/=$") == -1)
{
url = url + "|" + st.nextToken();
}
{
// upgrade old SRS link
- int srsPos = sequenceURLLinks
- .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$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);
}
}
* .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.
*/
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;
}
});
+ 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<String>();
+ urlLinks = new Vector<String>();
for (int i = 0; i < sequenceURLLinks.size(); i++)
{
String link = sequenceURLLinks.elementAt(i).toString();
/*
* 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());
*
* @param e
*/
+ @Override
public void ok_actionPerformed(ActionEvent e)
{
if (!validateSettings())
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 (nameLinks.size() > 0)
{
StringBuffer links = new StringBuffer();
- sequenceURLLinks = new Vector();
+ sequenceURLLinks = new Vector<String>();
for (int i = 0; i < nameLinks.size(); i++)
{
sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
else
{
Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ sequenceURLLinks.clear();
}
Cache.applicationProperties.setProperty("USE_PROXY",
/**
* DOCUMENT ME!
*/
+ @Override
public void startupFileTextfield_mouseClicked()
{
JalviewFileChooser chooser = new JalviewFileChooser(
* @param e
* DOCUMENT ME!
*/
+ @Override
public void cancel_actionPerformed(ActionEvent e)
{
try
* @param e
* DOCUMENT ME!
*/
+ @Override
public void annotations_actionPerformed(ActionEvent e)
{
conservation.setEnabled(annotations.isSelected());
&& (identity.isSelected() || showGroupConsensus.isSelected()));
}
+ @Override
public void newLink_actionPerformed(ActionEvent e)
{
}
}
+ @Override
public void editLink_actionPerformed(ActionEvent e)
{
GSequenceLink link = new GSequenceLink();
}
}
+ @Override
public void deleteLink_actionPerformed(ActionEvent e)
{
int index = linkNameList.getSelectedIndex();
linkURLList.setListData(urlLinks);
}
+ @Override
public void defaultBrowser_mouseClicked(MouseEvent e)
{
JFileChooser chooser = new JFileChooser(".");
* 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<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();
+ }
+ }
}