X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=3259909f6805c98cee95942e15f3056444001c8c;hb=f37c3fd4fe12799de498de5f397252e9f457fee9;hp=7af3abcebb8437d74a3daab8fc2a07d5b89eb2fa;hpb=cef7be0f9008ff15318e3479a5de35e127071ef3;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 7af3abc..3259909 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -22,14 +22,9 @@ package jalview.gui; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.bin.Cache; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenMarkovModel; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceI; import jalview.gui.Help.HelpId; import jalview.gui.StructureViewer.ViewerType; -import jalview.hmmer.HMMBuildThread; +import jalview.hmmer.HmmerCommand; import jalview.io.FileFormatI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; @@ -42,6 +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; @@ -54,17 +50,19 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; import java.awt.event.MouseEvent; import java.io.File; import java.util.ArrayList; import java.util.List; -import java.util.Scanner; import javax.help.HelpSetException; 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; @@ -88,6 +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"; @@ -112,12 +119,24 @@ public class Preferences extends GPreferences public static final String HMMER_PATH = "HMMER_PATH"; + public static final String CYGWIN_PATH = "CYGWIN_PATH"; + + public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS"; + public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; 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; @@ -210,30 +229,59 @@ public class Preferences extends GPreferences /* * Set HMMER tab defaults */ - trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false)); - isHMMERInstalled - .setSelected(Cache.getDefault("HMMER_INSTALLED", false)); - if (Cache.getDefault("USE_UNIPROT", false)) + hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false)); + if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false)) { - uniprot.setSelected(true); + hmmerBackgroundUniprot.setSelected(true); } else { - alignment.setSelected(true); + hmmerBackgroundAlignment.setSelected(true); } - numberOfSequencesToKeepField - .setText(Cache.getProperty("SEQUENCES_TO_KEEP")); - installationLocation.setEnabled(isHMMERInstalled.isSelected()); - hmmerPath.setEnabled(isHMMERInstalled.isSelected()); + hmmerSequenceCount + .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT)); hmmerPath.setText(Cache.getProperty(HMMER_PATH)); hmmerPath.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - validateHMMERPath(); + validateHmmerPath(); } }); + hmmerPath.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) + { + 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 @@ -349,6 +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); @@ -542,8 +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)); @@ -677,42 +742,50 @@ public class Preferences extends GPreferences /* * Save HMMER settings */ - Cache.applicationProperties.setProperty("TRIM_TERMINI", - Boolean.toString(trimTermini.isSelected())); - Cache.applicationProperties.setProperty("USE_UNIPROT", - Boolean.toString(uniprot.isSelected())); - Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP", - numberOfSequencesToKeepField.getText()); - Cache.applicationProperties.setProperty(HMMER_PATH, - hmmerPath.getText()); - boolean hmmerInstalled = isHMMERInstalled.isSelected(); - Cache.applicationProperties.setProperty("HMMER_INSTALLED", - Boolean.toString(hmmerInstalled)); - boolean hmmerFunctioning = validateHMMERPath(false); - Cache.applicationProperties.setProperty("HMMER_FUNCTIONING", - Boolean.toString(hmmerFunctioning)); + Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI, + Boolean.toString(hmmrTrimTermini.isSelected())); + Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND, + Boolean.toString(hmmerBackgroundUniprot.isSelected())); + Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT, + hmmerSequenceCount.getText()); + Cache.setOrRemove(HMMER_PATH, hmmerPath.getText()); + if (cygwinPath != null) + { + Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText()); + } AlignFrame[] frames = Desktop.getAlignFrames(); - boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false; - for (AlignFrame frame : frames) + if (frames != null && frames.length > 0) { - frame.updateHMMERStatus(hmmerStatus); + for (AlignFrame f : frames) + { + f.updateHMMERStatus(); + } } - - trimTermini.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)) { - uniprot.setSelected(true); + hmmerBackgroundUniprot.setSelected(true); } else { - alignment.setSelected(true); + hmmerBackgroundAlignment.setSelected(true); } - numberOfSequencesToKeepField - .setText(Cache.getProperty("SEQUENCES_TO_KEEP")); + hmmerSequenceCount + .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, @@ -831,7 +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()); /* @@ -869,14 +942,6 @@ public class Preferences extends GPreferences structureTab.requestFocusInWindow(); return false; } - if (isHMMERInstalled.isSelected()) - { - if (!validateHMMER()) - { - hmmerTab.requestFocusInWindow(); - return false; - } - } return true; } @@ -887,13 +952,6 @@ public class Preferences extends GPreferences } - @Override - protected boolean validateHMMER() - { - return validateHMMERPath(); - - } - /** * DOCUMENT ME! */ @@ -1134,6 +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 @@ -1188,94 +1303,31 @@ public class Preferences extends GPreferences } /** - * Returns true if hmmer path contains the necessary valid executables, else - * show an error dialog (if showing 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 */ - private boolean validateHMMERPath(boolean showDialog) + protected boolean validateExecutablePath(JTextField textField, String executable) { - int missing = 0; - String message = ""; - String folder = hmmerPath.getText().trim(); + String folder = textField.getText().trim(); + + if (FileUtils.getExecutable(executable, folder) != null) + { + return true; + } if (folder.length() > 0) { - File f = new File(folder); - if (!f.exists()) - { - if (showDialog) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.folder_not_exists"), - MessageManager.getString("label.invalid_folder"), - JvOptionPane.ERROR_MESSAGE); - } - return false; - } - AlignmentI alignment = new Alignment( - new SequenceI[] - { new Sequence("test", "WLWL", 0, 3) }); - if (canExecute(folder + "/hmmbuild")) - { - validateHMMBuild(alignment); - } - else - { - message += MessageManager.getString("label.hmmbuild_not_found") - + "\n"; - missing++; - } - - - if (canExecute(folder + "/hmmalign")) - { - - } - else - { - message += MessageManager.getString("label.hmmalign_not_found") - + "\n"; - missing++; - } - - - if (canExecute(folder + "/hmmsearch")) - { - - } - else - { - message += MessageManager.getString("label.hmmsearch_not_found") - + "\n"; - missing++; - } - } - - if (missing > 0) - { - if (missing < 3) - { - if (showDialog) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, message, - MessageManager.getString("label.invalid_folder"), - JvOptionPane.ERROR_MESSAGE); - } - return false; - } - else - { - if (showDialog) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.no_binaries"), - MessageManager.getString("label.invalid_folder"), - JvOptionPane.ERROR_MESSAGE); - } - - return false; - } - } - - return true; + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage("label.executable_not_found", + executable), + MessageManager.getString("label.invalid_folder"), + JvOptionPane.ERROR_MESSAGE); + } + return false; } /** @@ -1302,57 +1354,6 @@ public class Preferences extends GPreferences } /** - * Runs hmmbuild to check if it is working. While doing this it parses the - * version of HMMER. - * - * @param frame - * @return - */ - public boolean validateHMMBuild(AlignmentI alignment) - { - HMMBuildThread hmmbuild = new HMMBuildThread(alignment); - hmmbuild.hmmbuildWaitTillComplete(); - SequenceI hmmSeq = alignment.getSequenceAt(1); - HiddenMarkovModel hmm; - if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null) - { - hmm = hmmSeq.getHMM(); - - if (hmm.getNumberOfSymbols() < 1) - { - return false; - } - } - else - { - return false; - } - - String header = hmm.getFileHeader(); - if (header == null) - { - return false; - } - else - { - Scanner scanner = new Scanner(header); - scanner.next(); - String string = scanner.next(); - String version = string.substring(1); - Cache.setProperty("HMMER_VERSION", version); - scanner.close(); - - } - return true; - } - - - private boolean validateHMMERPath() - { - return validateHMMERPath(true); - } - - /** * If Chimera is selected, check it can be found on default or user-specified * path, if not show a warning/help dialog. */ @@ -1399,6 +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;