X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=3259909f6805c98cee95942e15f3056444001c8c;hb=f37c3fd4fe12799de498de5f397252e9f457fee9;hp=b0fd2150676590b9af1e73ce0b503123c12195cb;hpb=81c9c8d460d5e2261111f7bdced2a75f1af64f9a;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index b0fd215..3259909 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -37,6 +37,7 @@ import jalview.urls.UrlLinkTableModel; import jalview.urls.api.UrlProviderFactoryI; import jalview.urls.api.UrlProviderI; import jalview.urls.desktop.DesktopUrlProviderFactory; +import jalview.util.FileUtils; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.UrlConstants; @@ -61,6 +62,7 @@ import javax.swing.JColorChooser; import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JPanel; +import javax.swing.JTextField; import javax.swing.ListSelectionModel; import javax.swing.RowFilter; import javax.swing.RowSorter; @@ -84,6 +86,15 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; */ public class Preferences extends GPreferences { + // suggested list delimiter character + public static final String COMMA = ","; + + public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT"; + + public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND"; + + public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI"; + public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; @@ -108,7 +119,7 @@ public class Preferences extends GPreferences public static final String HMMER_PATH = "HMMER_PATH"; - public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS"; + public static final String CYGWIN_PATH = "CYGWIN_PATH"; public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS"; @@ -118,6 +129,14 @@ public class Preferences extends GPreferences public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY"; + public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START"; + + public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP"; + + public static final String GAP_COLOUR = "GAP_COLOUR"; + + public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR"; + private static final int MIN_FONT_SIZE = 1; private static final int MAX_FONT_SIZE = 30; @@ -210,8 +229,8 @@ public class Preferences extends GPreferences /* * Set HMMER tab defaults */ - hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false)); - if (Cache.getDefault("USE_UNIPROT", false)) + hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false)); + if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false)) { hmmerBackgroundUniprot.setSelected(true); } @@ -220,14 +239,14 @@ public class Preferences extends GPreferences hmmerBackgroundAlignment.setSelected(true); } hmmerSequenceCount - .setText(Cache.getProperty("SEQUENCES_TO_KEEP")); + .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT)); hmmerPath.setText(Cache.getProperty(HMMER_PATH)); hmmerPath.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - validateHMMERPath(true); + validateHmmerPath(); } }); hmmerPath.addFocusListener(new FocusAdapter() @@ -235,9 +254,34 @@ public class Preferences extends GPreferences @Override public void focusLost(FocusEvent e) { - validateHMMERPath(true); + validateHmmerPath(); } }); + if (cygwinPath != null) + { + String path = Cache.getProperty(CYGWIN_PATH); + if (path == null) + { + path = FileUtils.getPathTo("bash"); + } + cygwinPath.setText(path); + cygwinPath.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + validateCygwinPath(); + } + }); + cygwinPath.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) + { + validateCygwinPath(); + } + }); + } /* * Set Visual tab defaults @@ -353,6 +397,21 @@ public class Preferences extends GPreferences Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); /* + * Set overview panel defaults + */ + gapColour.setBackground( + Cache.getDefaultColour(GAP_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP)); + hiddenColour.setBackground( + Cache.getDefaultColour(HIDDEN_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN)); + useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false)); + gapLabel.setEnabled(!useLegacyGap.isSelected()); + gapColour.setEnabled(!useLegacyGap.isSelected()); + showHiddenAtStart + .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true)); + + /* * Set Structure tab defaults. */ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false); @@ -546,8 +605,10 @@ public class Preferences extends GPreferences autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); userIdWidth.setEnabled(!autoIdWidth.isSelected()); userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); - Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH"); + Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"); userIdWidth.setText(wi == null ? "" : wi.toString()); + // TODO: refactor to use common enum via FormatAdapter and allow extension + // for new flat file formats blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true)); clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true)); fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true)); @@ -681,14 +742,17 @@ public class Preferences extends GPreferences /* * Save HMMER settings */ - Cache.applicationProperties.setProperty("TRIM_TERMINI", + Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI, Boolean.toString(hmmrTrimTermini.isSelected())); - Cache.applicationProperties.setProperty("USE_UNIPROT", + Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND, Boolean.toString(hmmerBackgroundUniprot.isSelected())); - Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP", + Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT, hmmerSequenceCount.getText()); - Cache.applicationProperties.setProperty(HMMER_PATH, - hmmerPath.getText()); + Cache.setOrRemove(HMMER_PATH, hmmerPath.getText()); + if (cygwinPath != null) + { + Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText()); + } AlignFrame[] frames = Desktop.getAlignFrames(); if (frames != null && frames.length > 0) { @@ -698,8 +762,8 @@ public class Preferences extends GPreferences } } - hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false)); - if (Cache.getDefault("USE_UNIPROT", false)) + hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false)); + if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false)) { hmmerBackgroundUniprot.setSelected(true); } @@ -708,10 +772,20 @@ public class Preferences extends GPreferences hmmerBackgroundAlignment.setSelected(true); } hmmerSequenceCount - .setText(Cache.getProperty("SEQUENCES_TO_KEEP")); + .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT)); hmmerPath.setText(Cache.getProperty(HMMER_PATH)); /* + * Save Overview settings + */ + Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground()); + Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground()); + Cache.applicationProperties.setProperty(USE_LEGACY_GAP, + Boolean.toString(useLegacyGap.isSelected())); + Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START, + Boolean.toString(showHiddenAtStart.isSelected())); + + /* * Save Structure settings */ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN, @@ -830,7 +904,7 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", Boolean.toString(autoIdWidth.isSelected())); userIdWidth_actionPerformed(); - Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH", + Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH", userIdWidth.getText()); /* @@ -1118,6 +1192,63 @@ public class Preferences extends GPreferences } @Override + public void gapColour_actionPerformed(JPanel gap) + { + if (!useLegacyGap.isSelected()) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_gap_colour"), + gapColour.getBackground()); + if (col != null) + { + gap.setBackground(col); + } + gap.repaint(); + } + } + + @Override + public void hiddenColour_actionPerformed(JPanel hidden) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_hidden_colour"), + hiddenColour.getBackground()); + if (col != null) + { + hidden.setBackground(col); + } + hidden.repaint(); + } + + @Override + protected void useLegacyGaps_actionPerformed(ActionEvent e) + { + boolean enabled = useLegacyGap.isSelected(); + if (enabled) + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP); + } + else + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + } + gapColour.setEnabled(!enabled); + gapLabel.setEnabled(!enabled); + } + + @Override + protected void resetOvDefaults_actionPerformed(ActionEvent e) + { + useLegacyGap.setSelected(false); + useLegacyGaps_actionPerformed(null); + showHiddenAtStart.setSelected(true); + hiddenColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); + } + + @Override protected void userIdWidth_actionPerformed() { try @@ -1172,23 +1303,27 @@ public class Preferences extends GPreferences } /** - * Returns true if hmmer path is to a folder that contains an executable - * hmmbuild or hmmbuild.exe, else false (optionally after showing a warning - * dialog) + * Returns true if the given text field contains a path to a folder that + * contains an executable with the given name, else false (after showing a + * warning dialog). The executable name will be tried with .exe appended if not + * found. + * + * @param textField + * @param executable */ - @Override - protected boolean validateHMMERPath(boolean showWarning) + protected boolean validateExecutablePath(JTextField textField, String executable) { - String folder = hmmerPath.getText().trim(); + String folder = textField.getText().trim(); - if (HmmerCommand.getExecutable(HmmerCommand.HMMBUILD, folder) != null) + if (FileUtils.getExecutable(executable, folder) != null) { return true; } - if (showWarning && folder.length() > 0) + if (folder.length() > 0) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.hmmbuild_not_found"), + MessageManager.formatMessage("label.executable_not_found", + executable), MessageManager.getString("label.invalid_folder"), JvOptionPane.ERROR_MESSAGE); } @@ -1265,6 +1400,18 @@ public class Preferences extends GPreferences } } + @Override + protected void validateHmmerPath() + { + validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD); + } + + @Override + protected void validateCygwinPath() + { + validateExecutablePath(cygwinPath, "run"); + } + public class OptionsParam { private String name;