X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=5dae17916d1e7821875d7880661d732760939c87;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=d1aa72c025aa1c912fa7c4ae71f4ff639cf2fdea;hpb=21192459d39a4ee022f47d5b1fdb28f726557426;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index d1aa72c..5dae179 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,20 +1,20 @@ /* - * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -22,6 +22,7 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; import jalview.bin.*; @@ -31,19 +32,34 @@ import jalview.schemes.*; /** * 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 @@ -51,13 +67,41 @@ public class Preferences 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; @@ -66,6 +110,8 @@ public class Preferences DasSourceBrowser dasSource; + private WsPreferences wsPrefs; + /** * Creates a new Preferences object. */ @@ -76,9 +122,10 @@ public class Preferences 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; @@ -92,16 +139,18 @@ public class Preferences 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)); } @@ -110,8 +159,16 @@ public class Preferences 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++) { @@ -129,7 +186,8 @@ 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)); @@ -142,9 +200,11 @@ public class Preferences 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"); @@ -155,8 +215,12 @@ public class Preferences 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)); @@ -167,10 +231,20 @@ public class Preferences 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(); @@ -191,11 +265,21 @@ public class Preferences 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(); } @@ -204,71 +288,76 @@ public class Preferences /** * 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")) { @@ -276,9 +365,8 @@ public class Preferences } else { - Cache.applicationProperties.setProperty("EPS_RENDERING", - epsRendering.getSelectedItem(). - toString()); + Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering + .getSelectedItem().toString()); } if (defaultBrowser.getText().trim().length() < 1) @@ -288,7 +376,7 @@ public class Preferences else { Cache.applicationProperties.setProperty("DEFAULT_BROWSER", - defaultBrowser.getText()); + defaultBrowser.getText()); } jalview.util.BrowserLauncher.resetBrowser(); @@ -299,14 +387,15 @@ public class Preferences 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 { @@ -314,8 +403,7 @@ public class Preferences } Cache.applicationProperties.setProperty("USE_PROXY", - Boolean.toString(useProxy. - isSelected())); + Boolean.toString(useProxy.isSelected())); if (proxyServerTB.getText().trim().length() < 1) { @@ -324,7 +412,7 @@ public class Preferences else { Cache.applicationProperties.setProperty("PROXY_SERVER", - proxyServerTB.getText()); + proxyServerTB.getText()); } if (proxyPortTB.getText().trim().length() < 1) @@ -333,7 +421,8 @@ public class Preferences } else { - Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText()); + Cache.applicationProperties.setProperty("PROXY_PORT", + proxyPortTB.getText()); } if (useProxy.isSelected()) @@ -346,42 +435,62 @@ 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"); + } 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) { } } @@ -391,18 +500,13 @@ public class Preferences */ 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"); @@ -410,39 +514,48 @@ public class Preferences 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) @@ -453,10 +566,8 @@ public class Preferences 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()) { @@ -481,9 +592,8 @@ public class Preferences 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; } @@ -495,10 +605,8 @@ public class Preferences { 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()) { @@ -522,9 +630,8 @@ public class Preferences 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); @@ -552,8 +659,82 @@ public class Preferences } - 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()); + } + }