X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=789799e16dedb8df5c2e22bc917922342bac3605;hb=7e538eabe7bc9b2905fac031165bf39c8963231c;hp=70f8f3e37bc385de4cd43526e12111e3bf26b98c;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 70f8f3e..789799e 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview. * @@ -137,7 +137,7 @@ public class Preferences extends GPreferences .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)); @@ -147,6 +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(); @@ -183,7 +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"); @@ -195,7 +201,11 @@ public class Preferences extends GPreferences epsRendering.addItem("Text"); epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING", "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)); @@ -329,6 +339,9 @@ public class Preferences extends GPreferences 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"); @@ -441,8 +454,16 @@ public class Preferences extends GPreferences 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())); + Cache.applicationProperties.setProperty("SORT_BY_TREE", + Boolean.toString(sortByTree.isSelected())); Cache.applicationProperties.setProperty("PAD_GAPS", Boolean.toString(padGaps.isSelected())); @@ -494,6 +515,7 @@ public class Preferences extends GPreferences try { wsPrefs.updateWsMenuConfig(true); + wsPrefs.refreshWs_actionPerformed(e); frame.setClosed(true); } catch (Exception ex) { @@ -641,4 +663,60 @@ public class Preferences extends GPreferences { 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()); + } + }