/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
-import jalview.ws.EnfinEnvision2OneWay;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
String string = Cache
.getDefault(
"SEQUENCE_LINKS",
- "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
sequenceURLLinks = new Vector();
try
{
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);
+ }
+ }
+
/**
* TODO: reformulate groupURL encoding so two or more can be stored in the
* .properties file as '|' separated strings
*/
groupURLLinks = new Vector();
- // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
- // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
-
}
Vector nameLinks, urlLinks;
height = 460;
}
- Desktop.addInternalFrame(frame, "Preferences", width, height);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.preferences"), width, height);
frame.setMinimumSize(new Dimension(width, height));
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
/**
* default min-max colours for annotation shading
*/
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
startupCheckbox
.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org","http://www.jalview.org")+"/examples/exampleFile_2_3.jar"));
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+ + "/examples/exampleFile_2_3.jar"));
sortby.addItem("No sort");
sortby.addItem("Id");
sortby.addItem("Pairwise Identity");
sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
- epsRendering.addItem("Prompt each time");
- epsRendering.addItem("Lineart");
- epsRendering.addItem("Text");
- epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
- "Prompt each time"));
+ epsRendering.addItem(MessageManager.getString("label.prompt_each_time"));
+ epsRendering.addItem(MessageManager.getString("label.lineart"));
+ epsRendering.addItem(MessageManager.getString("action.text"));
+ epsRendering.setSelectedIndex(0);
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));
Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
.getSelectedItem().toString());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", maxColour.getBackground());
-
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ minColour.getBackground());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ maxColour.getBackground());
+
if (epsRendering.getSelectedItem().equals("Prompt each time"))
{
Cache.applicationProperties.remove("EPS_RENDERING");
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
- userIdWidth.getText());
+ userIdWidth.getText());
Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
Boolean.toString(autoCalculateConsCheck.isSelected()));
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select startup file");
+ chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
int value = chooser.showOpenDialog(this);
while (!valid)
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
- null) == JOptionPane.OK_OPTION)
+ MessageManager.getString("label.new_sequence_url_link"),
+ JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
{
if (index == -1)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!", "No link selected",
+ MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
- null) == JOptionPane.OK_OPTION)
+ MessageManager.getString("label.new_sequence_url_link"),
+ JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
{
if (index == -1)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!", "No link selected",
+ MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
public void defaultBrowser_mouseClicked(MouseEvent e)
{
JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle("Select default web browser");
+ chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
int value = chooser.showOpenDialog(this);
{
return groupURLLinks;
}
+
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Minimum Value", minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
if (col != null)
{
minColour.setBackground(col);
public void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Maximum Value", maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
if (col != null)
{
maxColour.setBackground(col);
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.",
- "Invalid ID Column width",
+ MessageManager.getString("warn.user_defined_width_requirements"),
+ MessageManager.getString("label.invalid_id_column_width"),
JOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
}
git://source.jalview.org / jalview.git / blobdiff