X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=27c455e40ef284484e37808b297c99de5c20bf1b;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=8868832d12108bb402ac4a9b49ab1c7f10c0dc7d;hpb=743075ad19dc11ae8456491c51a0c8808b996dc1;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 8868832..27c455e 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview. * - * 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 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. * - * 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 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 . */ package jalview.gui; @@ -29,6 +28,7 @@ import jalview.bin.*; import jalview.io.*; import jalview.jbgui.*; import jalview.schemes.*; +import jalview.ws.EnfinEnvision2OneWay; /** * DOCUMENT ME! @@ -44,10 +44,12 @@ public class Preferences extends GPreferences * $SEQUENCE_ID$ 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 |,|. + * 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 */ @@ -59,7 +61,7 @@ public class Preferences extends GPreferences "SEQUENCE_LINKS", "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); sequenceURLLinks = new Vector(); - + try { StringTokenizer st = new StringTokenizer(string, "|"); @@ -80,13 +82,14 @@ public class Preferences extends GPreferences System.out.println(ex + "\nError parsing sequence links"); } /** - * TODO: reformulate groupURL encoding so two or more can be stored in the .properties file as '|' separated strings + * 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?workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); - groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); - + // 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; @@ -95,6 +98,8 @@ public class Preferences extends GPreferences DasSourceBrowser dasSource; + private WsPreferences wsPrefs; + /** * Creates a new Preferences object. */ @@ -105,7 +110,8 @@ public class Preferences extends GPreferences 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 (new jalview.util.Platform().isAMac()) { @@ -121,17 +127,18 @@ public class Preferences extends GPreferences 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)); - showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", 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)); } @@ -140,6 +147,12 @@ public class Preferences extends GPreferences colour.setSelectedItem(string); + /** + * 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(); @@ -176,7 +189,7 @@ public class Preferences extends GPreferences 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"); @@ -201,6 +214,15 @@ public class Preferences extends GPreferences 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)); /*************************************************************************** @@ -224,11 +246,17 @@ public class Preferences extends GPreferences 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 + 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(); @@ -243,27 +271,27 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void ok_actionPerformed(ActionEvent e) { - Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean - .toString(seqLimit.isSelected())); - Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean - .toString(rightAlign.isSelected())); - Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean - .toString(fullScreen.isSelected())); - Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean - .toString(openoverv.isSelected())); - Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean - .toString(annotations.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean - .toString(conservation.isSelected())); - Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean - .toString(quality.isSelected())); - Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean - .toString(identity.isSelected())); + Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", + Boolean.toString(seqLimit.isSelected())); + Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", + Boolean.toString(rightAlign.isSelected())); + Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", + Boolean.toString(fullScreen.isSelected())); + Cache.applicationProperties.setProperty("SHOW_OVERVIEW", + Boolean.toString(openoverv.isSelected())); + Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Boolean.toString(annotations.isSelected())); + Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Boolean.toString(conservation.isSelected())); + Cache.applicationProperties.setProperty("SHOW_QUALITY", + Boolean.toString(quality.isSelected())); + Cache.applicationProperties.setProperty("SHOW_IDENTITY", + Boolean.toString(identity.isSelected())); Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour .getSelectedItem().toString()); @@ -277,23 +305,39 @@ public class Preferences extends GPreferences 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("ANTI_ALIAS", Boolean - .toString(smoothFont.isSelected())); - - Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean - .toString(wrap.isSelected())); + 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())); + 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())); Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText()); - Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean - .toString(startupCheckbox.isSelected())); + Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", + Boolean.toString(startupCheckbox.isSelected())); 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")) { Cache.applicationProperties.remove("EPS_RENDERING"); @@ -329,16 +373,16 @@ public class Preferences extends GPreferences } // 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"); } - Cache.applicationProperties.setProperty("USE_PROXY", Boolean - .toString(useProxy.isSelected())); + Cache.applicationProperties.setProperty("USE_PROXY", + Boolean.toString(useProxy.isSelected())); if (proxyServerTB.getText().trim().length() < 1) { @@ -346,8 +390,8 @@ public class Preferences extends GPreferences } else { - Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB - .getText()); + Cache.applicationProperties.setProperty("PROXY_SERVER", + proxyServerTB.getText()); } if (proxyPortTB.getText().trim().length() < 1) @@ -356,8 +400,8 @@ public class Preferences extends GPreferences } else { - Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB - .getText()); + Cache.applicationProperties.setProperty("PROXY_PORT", + proxyPortTB.getText()); } if (useProxy.isSelected()) @@ -370,45 +414,51 @@ public class Preferences extends GPreferences System.setProperty("http.proxyHost", ""); System.setProperty("http.proxyPort", ""); } - Cache.setProperty("VERSION_CHECK", Boolean - .toString(versioncheck.isSelected())); - if (Cache.getProperty("USAGESTATS")!=null || usagestats.isSelected()) { + 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())); + 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 + } + 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())); - Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean - .toString(clustaljv.isSelected())); - Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean - .toString(fastajv.isSelected())); - Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean - .toString(msfjv.isSelected())); - Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean - .toString(pfamjv.isSelected())); - Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean - .toString(pileupjv.isSelected())); - Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean - .toString(pirjv.isSelected())); - Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean - .toString(modellerOutput.isSelected())); + Cache.applicationProperties.setProperty("BLC_JVSUFFIX", + Boolean.toString(blcjv.isSelected())); + Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", + Boolean.toString(clustaljv.isSelected())); + Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", + Boolean.toString(fastajv.isSelected())); + Cache.applicationProperties.setProperty("MSF_JVSUFFIX", + Boolean.toString(msfjv.isSelected())); + Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", + Boolean.toString(pfamjv.isSelected())); + Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", + Boolean.toString(pileupjv.isSelected())); + Cache.applicationProperties.setProperty("PIR_JVSUFFIX", + Boolean.toString(pirjv.isSelected())); + Cache.applicationProperties.setProperty("PIR_MODELLER", + Boolean.toString(modellerOutput.isSelected())); jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected(); - Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean - .toString(autoCalculateConsCheck.isSelected())); - Cache.applicationProperties.setProperty("PAD_GAPS", Boolean - .toString(padGaps.isSelected())); + Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", + Boolean.toString(autoCalculateConsCheck.isSelected())); + Cache.applicationProperties.setProperty("SORT_BY_TREE", + Boolean.toString(sortByTree.isSelected())); + Cache.applicationProperties.setProperty("PAD_GAPS", + Boolean.toString(padGaps.isSelected())); dasSource.saveProperties(Cache.applicationProperties); - + wsPrefs.updateAndRefreshWsMenuConfig(false); Cache.saveProperties(); try { @@ -423,9 +473,10 @@ public class Preferences extends GPreferences */ 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" }, + 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")); @@ -447,12 +498,14 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void cancel_actionPerformed(ActionEvent e) { try { + wsPrefs.updateWsMenuConfig(true); + wsPrefs.refreshWs_actionPerformed(e); frame.setClosed(true); } catch (Exception ex) { @@ -463,13 +516,19 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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) @@ -572,8 +631,13 @@ public class Preferences extends GPreferences } } - /* (non-Javadoc) - * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent) + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event + * .ActionEvent) */ protected void showunconserved_actionPerformed(ActionEvent e) { @@ -584,4 +648,31 @@ public class Preferences extends GPreferences 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(); + } + }