/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
import jalview.bin.*;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class Preferences
- extends GPreferences
+public class Preferences extends GPreferences
{
- /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
+
+ /**
+ * Holds name and link separated with | character. Sequence ID must be
+ * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
+ */
public static Vector sequenceURLLinks;
+
+ /**
+ * Holds name and link separated with | character. Sequence IDS and Sequences
+ * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
+ * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
+ * for first and second token specified after a pipe character at end |,|.
+ * (TODO: proper escape for using | to separate ids or sequences
+ */
+
+ public static Vector groupURLLinks;
static
{
- String string = Cache.getDefault("SEQUENCE_LINKS",
- "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ 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())
{
- sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
+ String name = st.nextToken();
+ String url = st.nextToken();
+ // check for '|' within a regex
+ int rxstart = url.indexOf("$SEQUENCE_ID$");
+ while (rxstart == -1 && url.indexOf("/=$") == -1)
+ {
+ url = url + "|" + st.nextToken();
+ }
+ sequenceURLLinks.addElement(name + "|" + url);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.out.println(ex + "\nError parsing sequence links");
}
+ {
+ // upgrade old SRS link
+ int srsPos = sequenceURLLinks
+ .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$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$",
+ srsPos);
+ }
+ }
+
+ /**
+ * TODO: reformulate groupURL encoding so two or more can be stored in the
+ * .properties file as '|' separated strings
+ */
+
+ groupURLLinks = new Vector();
+ // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$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;
DasSourceBrowser dasSource;
+ private WsPreferences wsPrefs;
+
/**
* Creates a new Preferences object.
*/
frame.setContentPane(this);
dasSource = new DasSourceBrowser();
dasPanel.add(dasSource, BorderLayout.CENTER);
-
+ wsPrefs = new WsPreferences();
+ wsPanel.add(wsPrefs, BorderLayout.CENTER);
int width = 500, height = 420;
- if (System.getProperty("os.name").startsWith("Mac"))
+ if (new jalview.util.Platform().isAMac())
{
width = 570;
height = 460;
fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
- conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
- quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
- identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
-
- for (int i = 0; i < 13; i++)
+ showUnconserved
+ .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ showNpTooltip.setSelected(Cache
+ .getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
+ true));
+ sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+ for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
{
colour.addItem(ColourSchemeProperty.getColourName(i));
}
colour.setSelectedItem(string);
- String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
+ /**
+ * default min-max colours for annotation shading
+ */
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
+
+ String[] fonts = java.awt.GraphicsEnvironment
+ .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
for (int i = 0; i < fonts.length; i++)
{
fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
- fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
+ fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
+ + ""));
smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
- startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+ startupCheckbox
+ .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- "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");
epsRendering.addItem("Lineart");
epsRendering.addItem("Text");
epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
- "Prompt each time"));
-
+ "Prompt each time"));
+ autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+ 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));
clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
- autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ autoCalculateConsCheck.setSelected(Cache.getDefault(
+ "AUTO_CALC_CONSENSUS", true));
+ showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
+ false));
+ showGroupConservation.setSelected(Cache.getDefault(
+ "SHOW_GROUP_CONSERVATION", false));
+ showConsensHistogram.setSelected(Cache.getDefault(
+ "SHOW_CONSENSUS_HISTOGRAM", true));
+ showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
+ false));
+
padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
- /****************************************************
+ /***************************************************************************
* Set up Connections
*/
nameLinks = new Vector();
proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
+
+ usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+ questionnaire
+ .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
+ // antisense
+ // here
+ versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
+ // is
+ // true
+ annotations_actionPerformed(null); // update the display of the annotation
+ // settings
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void ok_actionPerformed(ActionEvent e)
{
Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
- Boolean.toString(seqLimit.
- isSelected()));
+ Boolean.toString(seqLimit.isSelected()));
Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
- Boolean.toString(rightAlign.
- isSelected()));
+ Boolean.toString(rightAlign.isSelected()));
Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
- Boolean.toString(fullScreen.
- isSelected()));
+ Boolean.toString(fullScreen.isSelected()));
Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
- Boolean.toString(openoverv.
- isSelected()));
+ Boolean.toString(openoverv.isSelected()));
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
- Boolean.
- toString(annotations.isSelected()));
+ Boolean.toString(annotations.isSelected()));
Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
- Boolean.
- toString(conservation.isSelected()));
+ Boolean.toString(conservation.isSelected()));
Cache.applicationProperties.setProperty("SHOW_QUALITY",
- Boolean.toString(quality.isSelected()));
+ Boolean.toString(quality.isSelected()));
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
- Boolean.toString(identity.
- isSelected()));
-
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR",
- colour.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("GAP_SYMBOL",
- gapSymbolCB.getSelectedItem().
- toString());
-
- Cache.applicationProperties.setProperty("FONT_NAME",
- fontNameCB.getSelectedItem().
- toString());
- Cache.applicationProperties.setProperty("FONT_STYLE",
- fontStyleCB.getSelectedItem().
- toString());
- Cache.applicationProperties.setProperty("FONT_SIZE",
- fontSizeCB.getSelectedItem().
- toString());
+ Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("ID_ITALICS",
- Boolean.toString(idItalics.
- isSelected()));
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
+ .getSelectedItem().toString());
+
+ Cache.applicationProperties.setProperty("ID_ITALICS",
+ Boolean.toString(idItalics.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+ Boolean.toString(showUnconserved.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+ Boolean.toString(showGroupConsensus.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
+ Boolean.toString(showGroupConservation.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
+ Boolean.toString(showConsensHistogram.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+ Boolean.toString(showConsensLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS",
- Boolean.toString(smoothFont.
- isSelected()));
+ Boolean.toString(smoothFont.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+ Boolean.toString(showNpTooltip.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+ Boolean.toString(showDbRefTooltip.isSelected()));
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
- Boolean.toString(wrap.isSelected()));
+ Boolean.toString(wrap.isSelected()));
Cache.applicationProperties.setProperty("STARTUP_FILE",
- startupFileTextfield.getText());
+ startupFileTextfield.getText());
Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
- Boolean.
- toString(startupCheckbox.isSelected()));
+ Boolean.toString(startupCheckbox.isSelected()));
+
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
+ .getSelectedItem().toString());
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
- sortby.getSelectedItem().toString());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ minColour.getBackground());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ maxColour.getBackground());
if (epsRendering.getSelectedItem().equals("Prompt each time"))
{
}
else
{
- Cache.applicationProperties.setProperty("EPS_RENDERING",
- epsRendering.getSelectedItem().
- toString());
+ Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
+ .getSelectedItem().toString());
}
if (defaultBrowser.getText().trim().length() < 1)
else
{
Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
- defaultBrowser.getText());
+ defaultBrowser.getText());
}
jalview.util.BrowserLauncher.resetBrowser();
sequenceURLLinks = new Vector();
for (int i = 0; i < nameLinks.size(); i++)
{
- sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" +
- urlLinks.elementAt(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.setProperty("SEQUENCE_LINKS",
+ links.toString());
}
else
{
}
Cache.applicationProperties.setProperty("USE_PROXY",
- Boolean.toString(useProxy.
- isSelected()));
+ Boolean.toString(useProxy.isSelected()));
if (proxyServerTB.getText().trim().length() < 1)
{
else
{
Cache.applicationProperties.setProperty("PROXY_SERVER",
- proxyServerTB.getText());
+ proxyServerTB.getText());
}
if (proxyPortTB.getText().trim().length() < 1)
}
else
{
- Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+ Cache.applicationProperties.setProperty("PROXY_PORT",
+ proxyPortTB.getText());
}
if (useProxy.isSelected())
System.setProperty("http.proxyHost", "");
System.setProperty("http.proxyPort", "");
}
-
+ Cache.setProperty("VERSION_CHECK",
+ Boolean.toString(versioncheck.isSelected()));
+ if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
+ {
+ // default is false - we only set this if the user has actively agreed
+ Cache.setProperty("USAGESTATS",
+ Boolean.toString(usagestats.isSelected()));
+ }
+ if (!questionnaire.isSelected())
+ {
+ Cache.setProperty("NOQUESTIONNAIRES", "true");
+ }
+ else
+ {
+ // special - made easy to edit a property file to disable questionnaires
+ // by just adding the given line
+ Cache.removeProperty("NOQUESTIONNAIRES");
+ }
Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
- Boolean.toString(blcjv.isSelected()));
+ Boolean.toString(blcjv.isSelected()));
Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
- Boolean.
- toString(clustaljv.isSelected()));
+ Boolean.toString(clustaljv.isSelected()));
Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
- Boolean.toString(fastajv.isSelected()));
+ Boolean.toString(fastajv.isSelected()));
Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
- Boolean.toString(msfjv.isSelected()));
+ Boolean.toString(msfjv.isSelected()));
Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
- Boolean.toString(pfamjv.isSelected()));
+ Boolean.toString(pfamjv.isSelected()));
Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
- Boolean.toString(pileupjv.
- isSelected()));
+ Boolean.toString(pileupjv.isSelected()));
Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
- Boolean.toString(pirjv.isSelected()));
+ Boolean.toString(pirjv.isSelected()));
Cache.applicationProperties.setProperty("PIR_MODELLER",
- Boolean.toString(modellerOutput.
- isSelected()));
+ Boolean.toString(modellerOutput.isSelected()));
jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+ Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+ Boolean.toString(autoIdWidth.isSelected()));
+ userIdWidth_actionPerformed();
+ Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ userIdWidth.getText());
+
Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
- Boolean.toString(
- autoCalculateConsCheck.isSelected()));
+ Boolean.toString(autoCalculateConsCheck.isSelected()));
+ Cache.applicationProperties.setProperty("SORT_BY_TREE",
+ Boolean.toString(sortByTree.isSelected()));
Cache.applicationProperties.setProperty("PAD_GAPS",
- Boolean.toString(padGaps.isSelected()));
+ Boolean.toString(padGaps.isSelected()));
dasSource.saveProperties(Cache.applicationProperties);
-
+ wsPrefs.updateAndRefreshWsMenuConfig(false);
Cache.saveProperties();
try
{
frame.setClosed(true);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
}
*/
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"));
+ 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"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Select startup file");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
- chooser.getSelectedFormat());
+ jalview.bin.Cache.applicationProperties.setProperty(
+ "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
startupFileTextfield.setText(chooser.getSelectedFile()
- .getAbsolutePath());
+ .getAbsolutePath());
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void cancel_actionPerformed(ActionEvent e)
{
try
{
+ wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
frame.setClosed(true);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void annotations_actionPerformed(ActionEvent e)
{
conservation.setEnabled(annotations.isSelected());
quality.setEnabled(annotations.isSelected());
identity.setEnabled(annotations.isSelected());
+ showGroupConsensus.setEnabled(annotations.isSelected());
+ showGroupConservation.setEnabled(annotations.isSelected());
+ showConsensHistogram.setEnabled(annotations.isSelected()
+ && (identity.isSelected() || showGroupConsensus.isSelected()));
+ showConsensLogo.setEnabled(annotations.isSelected()
+ && (identity.isSelected() || showGroupConsensus.isSelected()));
}
public void newLink_actionPerformed(ActionEvent e)
while (!valid)
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link",
- JOptionPane.OK_CANCEL_OPTION
- , -1, null)
- == JOptionPane.OK_OPTION)
+ "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",
- JOptionPane.WARNING_MESSAGE);
+ "No link selected!", "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)
+ "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",
- JOptionPane.WARNING_MESSAGE);
+ "No link selected!", "No link selected",
+ JOptionPane.WARNING_MESSAGE);
return;
}
nameLinks.removeElementAt(index);
}
- private void jbInit()
- throws Exception
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ protected void showunconserved_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+ super.showunconserved_actionPerformed(e);
+ }
+
+ private void jbInit() throws Exception
+ {
+ }
+
+ public static Collection getGroupURLLinks()
+ {
+ return groupURLLinks;
+ }
+
+ public void minColour_actionPerformed()
{
+ Color col = JColorChooser.showDialog(this,
+ "Select Colour for Minimum Value", minColour.getBackground());
+ if (col != null)
+ {
+ minColour.setBackground(col);
+ }
+ minColour.repaint();
}
+
+ public void maxColour_actionPerformed()
+ {
+ Color col = JColorChooser.showDialog(this,
+ "Select Colour for Maximum Value", maxColour.getBackground());
+ if (col != null)
+ {
+ maxColour.setBackground(col);
+ }
+ maxColour.repaint();
+ }
+
+ @Override
+ protected void userIdWidth_actionPerformed()
+ {
+ try
+ {
+ String val = userIdWidth.getText().trim();
+ if (val.length() > 0)
+ {
+ Integer iw = Integer.parseInt(val);
+ if (iw.intValue() < 12)
+ {
+ throw new NumberFormatException();
+ }
+ userIdWidth.setText(iw.toString());
+ }
+ } catch (NumberFormatException x)
+ {
+ 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",
+ JOptionPane.WARNING_MESSAGE);
+ userIdWidth.setText("");
+ }
+ }
+
+ @Override
+ protected void autoIdWidth_actionPerformed()
+ {
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff