X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=04851e87374514a97dca49561c36b6dfbf247623;hb=586ade46bdcd05ff028a1cff82c3c527326d28ec;hp=4030afa83dacd504620fbf494a9229d91ebd0dda;hpb=54f6fe32b978af0932428981a56c9960b0df44a7;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 4030afa..04851e8 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -27,6 +27,8 @@ 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; @@ -37,6 +39,7 @@ import javax.swing.JComboBox; 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; @@ -50,6 +53,9 @@ import javax.swing.table.TableColumn; import javax.swing.table.TableModel; import javax.swing.table.TableRowSorter; +import jalview.hmmer.HmmerCommand; +import jalview.util.FileUtils; + import ext.edu.ucsf.rbvi.strucviz2.StructureManager; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.bin.Cache; @@ -82,6 +88,14 @@ import jalview.ws.sifts.SiftsSettings; */ 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 ADD_SS_ANN = "ADD_SS_ANN"; @@ -126,6 +140,12 @@ public class Preferences extends GPreferences public static final String FONT_SIZE = "FONT_SIZE"; public static final String FONT_STYLE = "FONT_STYLE"; + + 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 GAP_COLOUR = "GAP_COLOUR"; @@ -269,6 +289,8 @@ public class Preferences extends GPreferences private WsPreferences wsPrefs; + private SlivkaPreferences slivkaPrefs; + private OptionsParam promptEachTimeOpt = new OptionsParam( MessageManager.getString("label.prompt_each_time"), "Prompt each time"); @@ -296,6 +318,8 @@ public class Preferences extends GPreferences { wsPrefs = new WsPreferences(); wsTab.add(wsPrefs, BorderLayout.CENTER); + slivkaPrefs = new SlivkaPreferences(); + slivkaTab.add(slivkaPrefs, BorderLayout.CENTER); } int width = 500, height = 450; if (Platform.isAMacAndNotJS()) @@ -309,6 +333,63 @@ public class Preferences extends GPreferences frame.setMinimumSize(new Dimension(width, height)); /* + * Set HMMER tab defaults + */ + hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false)); + if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false)) + { + hmmerBackgroundUniprot.setSelected(true); + } + else + { + hmmerBackgroundAlignment.setSelected(true); + } + hmmerSequenceCount + .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT)); + hmmerPath.setText(Cache.getProperty(HMMER_PATH)); + hmmerPath.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + 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 */ seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true)); @@ -331,6 +412,9 @@ public class Preferences extends GPreferences Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true)); showConsensLogo .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false)); + showInformationHistogram.setSelected( + Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true)); + showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false)); showNpTooltip .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); showDbRefTooltip @@ -509,7 +593,7 @@ public class Preferences extends GPreferences doReset.addActionListener(onReset); // filter to display only custom urls - final RowFilter customUrlFilter = new RowFilter() + final RowFilter customUrlFilter = new RowFilter<>() { @Override public boolean include( @@ -741,6 +825,10 @@ public class Preferences extends GPreferences Boolean.toString(showConsensHistogram.isSelected())); Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO", Boolean.toString(showConsensLogo.isSelected())); + Cache.setPropertyNoSave("SHOW_INFORMATION_HISTOGRAM", + Boolean.toString(showConsensHistogram.isSelected())); + Cache.setPropertyNoSave("SHOW_HMM_LOGO", + Boolean.toString(showHMMLogo.isSelected())); Cache.setPropertyNoSave("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected())); Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA, @@ -787,6 +875,42 @@ public class Preferences extends GPreferences maxColour.getBackground()); /* + * Save HMMER settings + */ + Cache.setPropertyNoSave(HMMALIGN_TRIM_TERMINI, + Boolean.toString(hmmrTrimTermini.isSelected())); + Cache.setPropertyNoSave(HMMINFO_GLOBAL_BACKGROUND, + Boolean.toString(hmmerBackgroundUniprot.isSelected())); + Cache.setPropertyNoSave(HMMSEARCH_SEQCOUNT, + hmmerSequenceCount.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) + { + for (AlignFrame f : frames) + { + f.updateHMMERStatus(); + } + } + + hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false)); + if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false)) + { + hmmerBackgroundUniprot.setSelected(true); + } + else + { + hmmerBackgroundAlignment.setSelected(true); + } + hmmerSequenceCount + .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT)); + hmmerPath.setText(Cache.getProperty(HMMER_PATH)); + + /* * Save Overview settings */ Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground()); @@ -1101,6 +1225,8 @@ public class Preferences extends GPreferences && (identity.isSelected() || showGroupConsensus.isSelected())); showConsensLogo.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected())); + showInformationHistogram.setEnabled(annotations.isSelected()); + showHMMLogo.setEnabled(annotations.isSelected()); } @Override @@ -1370,6 +1496,57 @@ public class Preferences extends GPreferences } return true; } + + /** + * 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 + */ + protected boolean validateExecutablePath(JTextField textField, String executable) + { + String folder = textField.getText().trim(); + + if (FileUtils.getExecutable(executable, folder) != null) + { + return true; + } + if (folder.length() > 0) + { + JvOptionPane.showInternalMessageDialog(Desktop.getInstance(), + MessageManager.formatMessage("label.executable_not_found", + executable), + MessageManager.getString("label.invalid_folder"), + JvOptionPane.ERROR_MESSAGE); + } + return false; + } + + /** + * Checks if a file can be executed + * + * @param path + * the path to the file + * @return + */ + public boolean canExecute(String path) + { + File file = new File(path); + if (!file.canExecute()) + { + file = new File(path + ".exe"); + { + if (!file.canExecute()) + { + return false; + } + } + } + return true; + } /** * If Chimera is selected, check it can be found on default or user-specified @@ -1418,6 +1595,18 @@ 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;