X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=b293e6f98ce4ca3e35e31e40acc04ac56f0e09d9;hb=fee1b781ca14aadea5d112fc554fe14879c787c5;hp=d1aa72c025aa1c912fa7c4ae71f4ff639cf2fdea;hpb=21192459d39a4ee022f47d5b1fdb28f726557426;p=jalview.git
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index d1aa72c..b293e6f 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,124 +1,240 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+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.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+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.Dimension;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.help.HelpSetException;
+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;
/**
* 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 $SEQUENCE_ID$ */
- public static Vector sequenceURLLinks;
+ public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+
+ public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+ public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+ public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
+ public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+ public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ 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;
+
+ /**
+ * 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 List 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");
- sequenceURLLinks = new Vector();
+ String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
+ 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("$" + DB_ACCESSION + "$");
+ if (rxstart == -1)
+ {
+ 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_STRING);
+ if (srsPos > -1)
+ {
+ sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
+ }
+ }
+
+ /**
+ * TODO: reformulate groupURL encoding so two or more can be stored in the
+ * .properties file as '|' separated strings
+ */
+
+ groupURLLinks = new ArrayList();
}
- Vector nameLinks, urlLinks;
+ Vector nameLinks, urlLinks;
JInternalFrame frame;
DasSourceBrowser dasSource;
+ 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.
*/
public Preferences()
{
-
+ super();
frame = new JInternalFrame();
frame.setContentPane(this);
dasSource = new DasSourceBrowser();
- dasPanel.add(dasSource, BorderLayout.CENTER);
-
- int width = 500, height = 420;
- if (System.getProperty("os.name").startsWith("Mac"))
+ dasTab.add(dasSource, BorderLayout.CENTER);
+ wsPrefs = new WsPreferences();
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
+ int width = 500, height = 450;
+ new jalview.util.Platform();
+ if (Platform.isAMac())
{
width = 570;
- height = 460;
+ height = 480;
}
- Desktop.addInternalFrame(frame, "Preferences", width, height);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.preferences"), width, height);
frame.setMinimumSize(new Dimension(width, height));
+ /*
+ * Set Visual tab defaults
+ */
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
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++)
- {
- colour.addItem(ColourSchemeProperty.getColourName(i));
- }
-
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");
-
- colour.setSelectedItem(string);
-
- String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
-
+ showUnconserved
+ .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ 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));
+ showNpTooltip.setSelected(Cache
+ .getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
+ true));
+
+ String[] fonts = java.awt.GraphicsEnvironment
+ .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
for (int i = 0; i < fonts.length; i++)
{
fontNameCB.addItem(fonts[i]);
}
- for (int i = 1; i < 31; i++)
+ for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
{
fontSizeCB.addItem(i + "");
}
@@ -129,9 +245,12 @@ public class Preferences
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));
+ scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
+ false));
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
@@ -142,39 +261,90 @@ public class Preferences
gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
- startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
- startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- "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"));
+ sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
+ SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBy.setSelectedItem(savedSort.toString());
+
+ sortAutocalc.addItem("Autocalculated first");
+ sortAutocalc.addItem("Autocalculated last");
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
+ sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
+ : sortAutocalc.getItemAt(1));
+ 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"));
- blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
- clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
- fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
- msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
- pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
- pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
- pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
+ /*
+ * Set Colours tab defaults
+ */
+ for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ {
+ protColour.addItem(ColourSchemeProperty.getColourName(i));
+ nucColour.addItem(ColourSchemeProperty.getColourName(i));
+ }
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+ String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
+ protColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
+ nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
+
+ /*
+ * Set Structure tab defaults.
+ */
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ structFromPdb.setSelected(structSelected);
+ useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
+ useRnaView.setEnabled(structSelected);
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setEnabled(structSelected);
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setEnabled(structSelected);
+ structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
+ ViewerType.JMOL.name()));
+ chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+ chimeraPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateChimeraPath();
+ }
+ });
- modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+ if (Cache.getDefault("MAP_WITH_SIFTS", false))
+ {
+ siftsMapping.setSelected(true);
+ }
+ else
+ {
+ nwMapping.setSelected(true);
+ }
- autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
- padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
- /****************************************************
- * Set up Connections
+ /*
+ * Set Connections tab defaults
*/
- nameLinks = new Vector();
- urlLinks = new Vector();
+ nameLinks = new Vector();
+ urlLinks = new Vector();
for (int i = 0; i < sequenceURLLinks.size(); i++)
{
String link = sequenceURLLinks.elementAt(i).toString();
@@ -191,150 +361,221 @@ public class Preferences
proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
- try
+
+ usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+ // note antisense here: default is true
+ questionnaire
+ .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
+ versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
+
+ /*
+ * Set Output tab defaults
+ */
+ 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"))
{
- jbInit();
+ epsRendering.setSelectedItem(lineArtOpt);
}
- catch (Exception ex)
+ else
{
- ex.printStackTrace();
+ epsRendering.setSelectedItem(promptEachTimeOpt);
}
+ 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));
+ msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
+ pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
+ pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
+ pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
+ modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+ embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
+ true));
+ /*
+ * Set Editing tab defaults
+ */
+ autoCalculateConsCheck.setSelected(Cache.getDefault(
+ "AUTO_CALC_CONSENSUS", true));
+ padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+
+ annotations_actionPerformed(null); // update the display of the annotation
+ // settings
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Save user selections on the Preferences tabs to the Cache and write out to
+ * file.
+ *
+ * @param e
*/
+ @Override
public void ok_actionPerformed(ActionEvent e)
{
+ if (!validateSettings())
+ {
+ return;
+ }
+ /*
+ * Save Visual settings
+ */
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("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(SCALE_PROTEIN_TO_CDNA,
+ Boolean.toString(scaleProteinToCdna.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());
- if (epsRendering.getSelectedItem().equals("Prompt each time"))
+ // convert description of sort order to enum name for save
+ SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
+ .forDescription(sortAnnBy.getSelectedItem().toString());
+ if (annSortOrder != null)
{
- Cache.applicationProperties.remove("EPS_RENDERING");
- }
- else
- {
- Cache.applicationProperties.setProperty("EPS_RENDERING",
- epsRendering.getSelectedItem().
- toString());
+ Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
+ annSortOrder.name());
}
- if (defaultBrowser.getText().trim().length() < 1)
- {
- Cache.applicationProperties.remove("DEFAULT_BROWSER");
- }
- else
- {
- Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
- defaultBrowser.getText());
- }
+ final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
+ .valueOf(showAutocalcFirst).toString());
+
+ /*
+ * Save Colours settings
+ */
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
+ .getSelectedItem().toString());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ minColour.getBackground());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ maxColour.getBackground());
+
+ /*
+ * Save Structure settings
+ */
+ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Boolean.toString(addTempFactor.isSelected()));
+ Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Boolean.toString(addSecondaryStructure.isSelected()));
+ Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Boolean.toString(useRnaView.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Boolean.toString(structFromPdb.isSelected()));
+ 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
+ */
+ Cache.applicationProperties.setProperty("EPS_RENDERING",
+ ((OptionsParam) epsRendering.getSelectedItem()).getCode());
+
+ /*
+ * Save Connections settings
+ */
+ Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
jalview.util.BrowserLauncher.resetBrowser();
if (nameLinks.size() > 0)
{
StringBuffer links = new StringBuffer();
- sequenceURLLinks = new Vector();
+ 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.remove("SEQUENCE_LINKS");
+ sequenceURLLinks.clear();
}
Cache.applicationProperties.setProperty("USE_PROXY",
- Boolean.toString(useProxy.
- isSelected()));
+ Boolean.toString(useProxy.isSelected()));
- if (proxyServerTB.getText().trim().length() < 1)
- {
- Cache.applicationProperties.remove("PROXY_SERVER");
- }
- else
- {
- Cache.applicationProperties.setProperty("PROXY_SERVER",
- proxyServerTB.getText());
- }
+ Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
- if (proxyPortTB.getText().trim().length() < 1)
- {
- Cache.applicationProperties.remove("PROXY_PORT");
- }
- else
- {
- Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
- }
+ Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
if (useProxy.isSelected())
{
@@ -346,105 +587,166 @@ public class Preferences
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");
+ }
+ /*
+ * Save Output settings
+ */
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()));
+ Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+ Boolean.toString(embbedBioJSON.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());
+
+ /*
+ * Save Editing settings
+ */
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();
+ Desktop.instance.doConfigureStructurePrefs();
try
{
frame.setClosed(true);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
+ }
+
+ /**
+ * Do any necessary validation before saving settings. Return focus to the
+ * first tab which fails validation.
+ *
+ * @return
+ */
+ private boolean validateSettings()
+ {
+ if (!validateStructure())
{
+ structureTab.requestFocusInWindow();
+ return false;
}
+ return true;
+ }
+
+ @Override
+ protected boolean validateStructure()
+ {
+ return validateChimeraPath();
+
}
/**
* DOCUMENT ME!
*/
+ @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"));
+ 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");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_startup_file"));
int value = chooser.showOpenDialog(this);
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!
*/
+ @Override
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!
*/
+ @Override
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()));
}
+ @Override
public void newLink_actionPerformed(ActionEvent e)
{
@@ -452,11 +754,9 @@ public class Preferences
boolean valid = false;
while (!valid)
{
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link",
- JOptionPane.OK_CANCEL_OPTION
- , -1, null)
- == JOptionPane.OK_OPTION)
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ MessageManager.getString("label.new_sequence_url_link"),
+ JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
@@ -473,6 +773,7 @@ public class Preferences
}
}
+ @Override
public void editLink_actionPerformed(ActionEvent e)
{
GSequenceLink link = new GSequenceLink();
@@ -480,10 +781,10 @@ public class Preferences
int index = linkNameList.getSelectedIndex();
if (index == -1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!"
- , "No link selected",
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.no_link_selected"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
@@ -494,11 +795,9 @@ public class Preferences
while (!valid)
{
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link",
- JOptionPane.OK_CANCEL_OPTION
- , -1, null)
- == JOptionPane.OK_OPTION)
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ MessageManager.getString("label.new_sequence_url_link"),
+ JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
@@ -516,15 +815,16 @@ public class Preferences
}
}
+ @Override
public void deleteLink_actionPerformed(ActionEvent e)
{
int index = linkNameList.getSelectedIndex();
if (index == -1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!"
- , "No link selected",
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.no_link_selected"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
nameLinks.removeElementAt(index);
@@ -538,10 +838,12 @@ public class Preferences
linkURLList.setListData(urlLinks);
}
+ @Override
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);
@@ -552,8 +854,204 @@ public class Preferences
}
- private void jbInit()
- throws Exception
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * 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 List getGroupURLLinks()
+ {
+ return groupURLLinks;
+ }
+
+ @Override
+ public void minColour_actionPerformed(JPanel panel)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_colour_minimum_value"),
+ minColour.getBackground());
+ if (col != null)
+ {
+ panel.setBackground(col);
+ }
+ panel.repaint();
+ }
+
+ @Override
+ public void maxColour_actionPerformed(JPanel panel)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_colour_maximum_value"),
+ maxColour.getBackground());
+ if (col != null)
+ {
+ panel.setBackground(col);
+ }
+ panel.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)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("warn.user_defined_width_requirements"),
+ MessageManager.getString("label.invalid_id_column_width"),
+ JvOptionPane.WARNING_MESSAGE);
+ userIdWidth.setText("");
+ }
+ }
+
+ @Override
+ protected void autoIdWidth_actionPerformed()
+ {
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+ }
+
+ /**
+ * Returns true if chimera path is to a valid executable, else show an error
+ * dialog.
+ */
+ private boolean validateChimeraPath()
+ {
+ if (chimeraPath.getText().trim().length() > 0)
+ {
+ File f = new File(chimeraPath.getText());
+ if (!f.canExecute())
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.invalid_chimera_path"),
+ MessageManager.getString("label.invalid_name"),
+ JvOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * If Chimera is selected, check it can be found on default or user-specified
+ * path, if not show a warning/help dialog.
+ */
+ @Override
+ protected void structureViewer_actionPerformed(String selectedItem)
+ {
+ if (!selectedItem.equals(ViewerType.CHIMERA.name()))
+ {
+ return;
+ }
+ boolean found = false;
+
+ /*
+ * Try user-specified and standard paths for Chimera executable.
+ */
+ List paths = StructureManager.getChimeraPaths();
+ paths.add(0, chimeraPath.getText());
+ for (String path : paths)
+ {
+ if (new File(path.trim()).canExecute())
+ {
+ found = true;
+ break;
+ }
+ }
+ if (!found)
+ {
+ String[] options = { "OK", "Help" };
+ int showHelp = JvOptionPane.showInternalOptionDialog(
+ Desktop.desktop,
+ JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_missing")),
+ "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
+ if (showHelp == JvOptionPane.NO_OPTION)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.StructureViewer);
+ } catch (HelpSetException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ 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();
+ }
}
}