*/
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.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
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;
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=$SEQUENCE_ID$");
+ 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);
}
}
/*
* Set Colours tab defaults
*/
- for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ protColour.addItem(ResidueColourScheme.NONE);
+ nucColour.addItem(ResidueColourScheme.NONE);
+ for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
{
- protColour.addItem(ColourSchemeProperty.getColourName(i));
- nucColour.addItem(ColourSchemeProperty.getColourName(i));
+ String name = cs.getSchemeName();
+ protColour.addItem(name);
+ nucColour.addItem(name);
}
- String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+ 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);
/*
* Save Output settings
*/
- Cache.applicationProperties.setProperty("EPS_RENDERING",
- ((OptionsParam) epsRendering.getSelectedItem()).getCode());
+ Cache.applicationProperties.setProperty("EPS_RENDERING",
+ ((OptionsParam) epsRendering.getSelectedItem()).getCode());
/*
* Save Connections settings
else
{
Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ sequenceURLLinks.clear();
}
Cache.applicationProperties.setProperty("USE_PROXY",
@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"));
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.getName());
+ }
startupFileTextfield.setText(chooser.getSelectedFile()
.getAbsolutePath());
}
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())
{
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;
}
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())
{
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);
}
} 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("");
}
}
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;
}
}
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
{
}
@Override
- public int hashCode(){
+ public int hashCode()
+ {
return name.hashCode() + code.hashCode();
}
}