X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=e5397bfdeb8a82c45b02784f4c19d1544001c43d;hb=d423f22792e47dbc800ae220a58677f988971d06;hp=88f438e6a72b366b49f134741326d13f275314b1;hpb=486e70a70e56b8ac23fd191c2ac9f8c7366f4fd7;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 88f438e..e5397bf 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 2.5) + * Copyright (C) 2010 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; @@ -45,10 +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 */ @@ -60,7 +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, "|"); @@ -81,13 +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?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|,"); - + // 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; @@ -126,7 +128,12 @@ public class Preferences extends GPreferences 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)); + showUnconserved + .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false)); + showNpTooltip.setSelected(Cache + .getDefault("SHOW_NPFEATS_TOOLTIP", true)); + showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", + true)); for (int i = 0; i < 13; i++) { @@ -198,11 +205,15 @@ 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)); - showConsensProfile.setSelected(Cache.getDefault("SHOW_CONSENSUS_PROFILE",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)); + padGaps.setSelected(Cache.getDefault("PAD_GAPS", false)); /*************************************************************************** @@ -226,11 +237,17 @@ 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 - annotations_actionPerformed(null); // update the display of the annotation settings + 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(); @@ -245,7 +262,7 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void ok_actionPerformed(ActionEvent e) { @@ -281,13 +298,22 @@ public class Preferences extends GPreferences 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_PROFILE",Boolean.toString(showConsensProfile.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())); @@ -376,18 +402,22 @@ 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 @@ -453,7 +483,7 @@ public class Preferences extends GPreferences * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void cancel_actionPerformed(ActionEvent e) { @@ -469,17 +499,19 @@ 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()); - showConsensHistogram.setEnabled(annotations.isSelected()); - showConsensProfile.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) @@ -582,8 +614,13 @@ 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) {