From 3cea8af5f3d2849ebe7062972c0865af1f86c5f7 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Fri, 13 Nov 2020 18:09:28 +0000 Subject: [PATCH] JAL-3775 Eclipse re-formatting commit --- src/jalview/gui/AlignFrame.java | 5 +- src/jalview/gui/Desktop.java | 161 +++++++++--------- src/jalview/gui/Preferences.java | 44 +++-- src/jalview/io/BackupFiles.java | 12 +- src/jalview/jbgui/GPreferences.java | 55 +++--- src/jalview/project/Jalview2XML.java | 312 +++++++++++++++++----------------- 6 files changed, 293 insertions(+), 296 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index e886ad0..5370437 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1079,9 +1079,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (fileObject == null) { - DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName) - ? DataSourceType.URL - : DataSourceType.FILE; + DataSourceType protocol = HttpUtils.startsWithHttpOrHttps( + fileName) ? DataSourceType.URL : DataSourceType.FILE; newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); } diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 67d273c..21092e6 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -395,11 +395,9 @@ public class Desktop extends jalview.jbgui.GDesktop } }); - boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", - false); + boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false); - boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", - false); + boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false); desktop = new MyDesktopPane(selmemusage); showMemusage.setSelected(selmemusage); @@ -558,10 +556,10 @@ public class Desktop extends jalview.jbgui.GDesktop .getStructureSelectionManager(this); if (Cache.getDefault(Preferences.ADD_SS_ANN, true)) { - ssm.setAddTempFacAnnot(Cache - .getDefault(Preferences.ADD_TEMPFACT_ANN, true)); - ssm.setProcessSecondaryStructure(Cache - .getDefault(Preferences.STRUCT_FROM_PDB, true)); + ssm.setAddTempFacAnnot( + Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true)); + ssm.setProcessSecondaryStructure( + Cache.getDefault(Preferences.STRUCT_FROM_PDB, true)); ssm.setSecStructServices( Cache.getDefault(Preferences.USE_RNAVIEW, true)); } @@ -610,7 +608,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } }).start(); - + } @Override @@ -655,10 +653,8 @@ public class Desktop extends jalview.jbgui.GDesktop Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); String x = Cache.getProperty(windowName + "SCREEN_X"); String y = Cache.getProperty(windowName + "SCREEN_Y"); - String width = Cache - .getProperty(windowName + "SCREEN_WIDTH"); - String height = Cache - .getProperty(windowName + "SCREEN_HEIGHT"); + String width = Cache.getProperty(windowName + "SCREEN_WIDTH"); + String height = Cache.getProperty(windowName + "SCREEN_HEIGHT"); if ((x != null) && (y != null) && (width != null) && (height != null)) { int ix = Integer.parseInt(x), iy = Integer.parseInt(y), @@ -668,10 +664,10 @@ public class Desktop extends jalview.jbgui.GDesktop // attempt #1 - try to cope with change in screen geometry - this // version doesn't preserve original jv aspect ratio. // take ratio of current screen size vs original screen size. - double sw = ((1f * screenSize.width) / (1f * Integer.parseInt( - Cache.getProperty("SCREENGEOMETRY_WIDTH")))); - double sh = ((1f * screenSize.height) / (1f * Integer.parseInt( - Cache.getProperty("SCREENGEOMETRY_HEIGHT")))); + double sw = ((1f * screenSize.width) / (1f * Integer + .parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH")))); + double sh = ((1f * screenSize.height) / (1f * Integer + .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT")))); // rescale the bounds depending upon the current screen geometry. ix = (int) (ix * sw); iw = (int) (iw * sw); @@ -962,8 +958,8 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the - * window + * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close + * the window * * @param frame */ @@ -1103,8 +1099,9 @@ public class Desktop extends jalview.jbgui.GDesktop public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); - JalviewFileChooser chooser = JalviewFileChooser - .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled()); + JalviewFileChooser chooser = JalviewFileChooser.forRead( + Cache.getProperty("LAST_DIRECTORY"), fileFormat, + BackupFiles.getEnabled()); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( @@ -1290,10 +1287,8 @@ public class Desktop extends jalview.jbgui.GDesktop public void quit() { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); - Cache.setProperty("SCREENGEOMETRY_WIDTH", - screen.width + ""); - Cache.setProperty("SCREENGEOMETRY_HEIGHT", - screen.height + ""); + Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); + Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, getWidth(), getHeight())); @@ -1324,9 +1319,9 @@ public class Desktop extends jalview.jbgui.GDesktop private void storeLastKnownDimensions(String string, Rectangle jc) { - Cache.log.debug("Storing last known dimensions for " - + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width - + " height:" + jc.height); + Cache.log.debug("Storing last known dimensions for " + string + ": x:" + + jc.x + " y:" + jc.y + " width:" + jc.width + " height:" + + jc.height); Cache.setProperty(string + "SCREEN_X", jc.x + ""); Cache.setProperty(string + "SCREEN_Y", jc.y + ""); @@ -1681,16 +1676,17 @@ public class Desktop extends jalview.jbgui.GDesktop setProgressBar(MessageManager.formatMessage( "label.saving_jalview_project", new Object[] { chosenFile.getName() }), chosenFile.hashCode()); - Cache.setProperty("LAST_DIRECTORY", - chosenFile.getParent()); + Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent()); // TODO catch and handle errors for savestate // TODO prevent user from messing with the Desktop whilst we're saving try { - boolean doBackup = BackupFiles.getEnabled(); - BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null; + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) + : null; - new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile); + new Jalview2XML().saveState( + doBackup ? backupfiles.getTempFile() : chosenFile); if (doBackup) { @@ -1716,7 +1712,7 @@ public class Desktop extends jalview.jbgui.GDesktop setProgressBar(null, chosenFile.hashCode()); } }).start(); - } + } } @Override @@ -1747,8 +1743,10 @@ public class Desktop extends jalview.jbgui.GDesktop "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY"), suffix, desc, - "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles, - // allowBackupFiles + "Jalview Project", true, BackupFiles.getEnabled()); // last two + // booleans: + // allFiles, + // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); chooser.setResponseHandler(0, new Runnable() @@ -1765,29 +1763,30 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void run() { - try + try { new Jalview2XML().loadJalviewAlign(selectedFile); } catch (OutOfMemoryError oom) - { - new OOMWarning("Whilst loading project from " + choice, oom); - } catch (Exception ex) - { - Cache.log.error( - "Problems whilst loading project from " + choice, ex); - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.error_whilst_loading_project_from", - new Object[] - { choice }), - MessageManager.getString("label.couldnt_load_project"), - JvOptionPane.WARNING_MESSAGE); - } + { + new OOMWarning("Whilst loading project from " + choice, oom); + } catch (Exception ex) + { + Cache.log.error( + "Problems whilst loading project from " + choice, ex); + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.error_whilst_loading_project_from", + new Object[] + { choice }), + MessageManager + .getString("label.couldnt_load_project"), + JvOptionPane.WARNING_MESSAGE); + } } }, "Project Loader").start(); } }); - + chooser.showOpenDialog(this); } @@ -1976,9 +1975,7 @@ public class Desktop extends jalview.jbgui.GDesktop // FIXME: ideally should use UI interface API FeatureSettings viewFeatureSettings = (af.featureSettings != null - && af.featureSettings.isOpen()) - ? af.featureSettings - : null; + && af.featureSettings.isOpen()) ? af.featureSettings : null; Rectangle fsBounds = af.getFeatureSettingsGeometry(); for (int i = 0; i < size; i++) { @@ -2011,7 +2008,8 @@ public class Desktop extends jalview.jbgui.GDesktop addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - // and materialise a new feature settings dialog instance for the new alignframe + // and materialise a new feature settings dialog instance for the new + // alignframe // (closes the old as if 'OK' was pressed) if (ap == af.alignPanel && newaf.featureSettings != null && newaf.featureSettings.isOpen() @@ -2029,9 +2027,9 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Gather expanded views (separate AlignFrame's) with the same sequence set - * identifier back in to this frame as additional views, and close the expanded - * views. Note the expanded frames may themselves have multiple views. We take - * the lot. + * identifier back in to this frame as additional views, and close the + * expanded views. Note the expanded frames may themselves have multiple + * views. We take the lot. * * @param source */ @@ -2083,8 +2081,7 @@ public class Desktop extends jalview.jbgui.GDesktop } // refresh the feature setting UI for the source frame if it exists - if (source.featureSettings != null - && source.featureSettings.isOpen()) + if (source.featureSettings != null && source.featureSettings.isOpen()) { source.showFeatureSettingsUI(); } @@ -2189,12 +2186,12 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Proxy class for JDesktopPane which optionally displays the current memory - * usage and highlights the desktop area with a red bar if free memory runs low. + * usage and highlights the desktop area with a red bar if free memory runs + * low. * * @author AMW */ - public class MyDesktopPane extends JDesktopPane - implements Runnable + public class MyDesktopPane extends JDesktopPane implements Runnable { private static final float ONE_MB = 1048576f; @@ -2431,14 +2428,17 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding - * when opened + * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this + * binding when opened */ protected void addQuitHandler() { - getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW) - .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()), + getRootPane() + .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( + KeyStroke + .getKeyStroke(KeyEvent.VK_Q, + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx()), "Quit"); getRootPane().getActionMap().put("Quit", new AbstractAction() { @@ -2567,8 +2567,9 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * This will return the first AlignFrame holding the given viewport instance. It - * will break if there are more than one AlignFrames viewing a particular av. + * This will return the first AlignFrame holding the given viewport instance. + * It will break if there are more than one AlignFrames viewing a particular + * av. * * @param viewport * @return alignFrame for viewport @@ -2945,8 +2946,8 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Explode the views in the given SplitFrame into separate SplitFrame windows. - * This respects (remembers) any previous 'exploded geometry' i.e. the size and - * location last time the view was expanded (if any). However it does not + * This respects (remembers) any previous 'exploded geometry' i.e. the size + * and location last time the view was expanded (if any). However it does not * remember the split pane divider location - this is set to match the * 'exploding' frame. * @@ -3117,7 +3118,8 @@ public class Desktop extends jalview.jbgui.GDesktop Transferable t) throws Exception { - // BH 2018 changed List to List to allow for File from SwingJS + // BH 2018 changed List to List to allow for File from + // SwingJS // DataFlavor[] flavors = t.getTransferDataFlavors(); // for (int i = 0; i < flavors.length; i++) { @@ -3129,7 +3131,8 @@ public class Desktop extends jalview.jbgui.GDesktop // byte[] data = getDroppedFileBytes(file); // fileName.setText(file.getName() + " - " + data.length + " " + // evt.getLocation()); - // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent(); + // JTextArea target = (JTextArea) ((DropTarget) + // evt.getSource()).getComponent(); // target.setText(new String(data)); // } // dtde.dropComplete(true); @@ -3329,10 +3332,10 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * Answers a (possibly empty) list of any structure viewer frames (currently for - * either Jmol or Chimera) which are currently open. This may optionally be - * restricted to viewers of a specified class, or viewers linked to a specified - * alignment panel. + * Answers a (possibly empty) list of any structure viewer frames (currently + * for either Jmol or Chimera) which are currently open. This may optionally + * be restricted to viewers of a specified class, or viewers linked to a + * specified alignment panel. * * @param apanel * if not null, only return viewers linked to this panel diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 0e04117..6972657 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -374,12 +374,10 @@ public class Preferences extends GPreferences /* * 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)); + 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()); @@ -402,7 +400,8 @@ public class Preferences extends GPreferences * set choice of structure viewer, and path if saved as a preference; * default to Jmol (first choice) if an unexpected value is found */ - String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()); + String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, + ViewerType.JMOL.name()); structViewer.setSelectedItem(viewerType); String viewerPath = ""; ViewerType type = null; @@ -438,10 +437,11 @@ public class Preferences extends GPreferences { if (validateViewerPath()) { - Cache.setProperty(structViewer.getSelectedItem() - .equals(ViewerType.CHIMERAX.name()) - ? CHIMERAX_PATH - : CHIMERA_PATH, structureViewerPath.getText()); + Cache.setProperty( + structViewer.getSelectedItem().equals( + ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH + : CHIMERA_PATH, + structureViewerPath.getText()); } } }); @@ -655,8 +655,7 @@ public class Preferences extends GPreferences annotations_actionPerformed(null); // update the display of the annotation // settings - - + /* * Set Backups tab defaults */ @@ -676,7 +675,7 @@ public class Preferences extends GPreferences comboBox.addItem(promptEachTimeOpt); comboBox.addItem(lineArtOpt); comboBox.addItem(textOpt); - + /* * JalviewJS doesn't support Lineart so force it to Text */ @@ -827,8 +826,7 @@ public class Preferences extends GPreferences Boolean.toString(structFromPdb.isSelected())); String viewer = structViewer.getSelectedItem().toString(); String viewerPath = structureViewerPath.getText(); - Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, - viewer); + Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer); if (viewer.equals(ViewerType.CHIMERA.name())) { Cache.setOrRemove(CHIMERA_PATH, viewerPath); @@ -959,16 +957,16 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty(BackupFiles.ENABLED, Boolean.toString(enableBackupFiles.isSelected())); int preset = getComboIntStringKey(backupfilesPresetsCombo); - Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset)); + Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", + Integer.toString(preset)); if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM) { BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry(); BackupFilesPresetEntry.backupfilesPresetEntriesValues.put( BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE); - Cache.applicationProperties - .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG, - customBFPE.toString()); + Cache.applicationProperties.setProperty( + BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString()); } BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues @@ -1278,8 +1276,7 @@ public class Preferences extends GPreferences if (!useLegacyGap.isSelected()) { JalviewColourChooser.showColourChooser(this, - MessageManager.getString("label.select_gap_colour"), - gap); + MessageManager.getString("label.select_gap_colour"), gap); } } @@ -1287,8 +1284,7 @@ public class Preferences extends GPreferences public void hiddenColour_actionPerformed(JPanel hidden) { JalviewColourChooser.showColourChooser(this, - MessageManager.getString("label.select_hidden_colour"), - hidden); + MessageManager.getString("label.select_hidden_colour"), hidden); } @Override diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java index 6e80578..2b6147f 100644 --- a/src/jalview/io/BackupFiles.java +++ b/src/jalview/io/BackupFiles.java @@ -380,8 +380,8 @@ public class BackupFiles boolean delete = confirmNewerDeleteFile(fileToBeDeleted, replacementFile, true); - Cache.trace("BACKUPFILES " - + (delete ? "confirmed" : "not") + " deleting file " + Cache.trace("BACKUPFILES " + (delete ? "confirmed" : "not") + + " deleting file " + fileToBeDeleted.getAbsolutePath() + " which is newer than " + replacementFile.getAbsolutePath()); @@ -460,8 +460,8 @@ public class BackupFiles // noMax == true means keep all backup files if ((!noMax) && bfTreeMap.size() >= max) { - Cache.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " - + max + ", " + "bfTreeMap.size(): " + bfTreeMap.size()); + Cache.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " + max + + ", " + "bfTreeMap.size(): " + bfTreeMap.size()); // need to delete some files to keep number of backups to designated // max. // Note that if the suffix is not numbered then do not delete any @@ -898,8 +898,8 @@ public class BackupFiles // delete destination file - not usually necessary but Just In Case... Cache.trace("BACKUPFILES deleting " + newFile.getAbsolutePath()); newFile.delete(); - Cache.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() - + " to " + newFile.getAbsolutePath()); + Cache.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() + " to " + + newFile.getAbsolutePath()); Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING); ret = true; Cache.trace("BACKUPFILES move seems to have succeeded"); diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index f1a94fc..38a4732 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -427,11 +427,11 @@ public class GPreferences extends JPanel tabbedPane.add(initConnectionsTab(), MessageManager.getString("label.connections")); - if (!Platform.isJS()) - { - tabbedPane.add(initBackupsTab(), - MessageManager.getString("label.backups")); - } + if (!Platform.isJS()) + { + tabbedPane.add(initBackupsTab(), + MessageManager.getString("label.backups")); + } tabbedPane.add(initLinksTab(), MessageManager.getString("label.urllinks")); @@ -1693,11 +1693,13 @@ public class GPreferences extends JPanel ypos += lineSpacing; structureViewerPathLabel = new JLabel(); - structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, 11)); + structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, + // 11)); structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT); structureViewerPathLabel.setText(MessageManager .formatMessage("label.viewer_path", "Chimera(X)")); - structureViewerPathLabel.setBounds(new Rectangle(10, ypos, 170, height)); + structureViewerPathLabel + .setBounds(new Rectangle(10, ypos, 170, height)); structureViewerPathLabel.setEnabled(false); structureTab.add(structureViewerPathLabel); @@ -1755,14 +1757,14 @@ public class GPreferences extends JPanel /* * hide Chimera options in JalviewJS */ - if (Platform.isJS()) + if (Platform.isJS()) { structureViewerPathLabel.setVisible(false); structureViewerPath.setVisible(false); viewerLabel.setVisible(false); structViewer.setVisible(false); } - + return structureTab; } @@ -2139,13 +2141,13 @@ public class GPreferences extends JPanel visualTab.add(fontNameCB); visualTab.add(fontSizeCB); visualTab.add(fontStyleCB); - + if (Platform.isJS()) { startupCheckbox.setVisible(false); startupFileTextfield.setVisible(false); } - + return visualTab; } @@ -2157,8 +2159,8 @@ public class GPreferences extends JPanel { BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry .getSavedBackupEntry(); - enableBackupFiles - .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS())); + enableBackupFiles.setSelected( + Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS())); BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry .createBackupFilesPresetEntry(Cache @@ -2235,7 +2237,6 @@ public class GPreferences extends JPanel } }); - // enable checkbox 1 col gbc.gridwidth = 1; gbc.gridheight = 1; @@ -2308,8 +2309,8 @@ public class GPreferences extends JPanel presetsComboLabel = new JLabel(title + ":"); presetsPanel.add(presetsComboLabel, gbc); - List entries = Arrays - .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries); + List entries = Arrays.asList( + (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries); List tooltips = Arrays.asList( BackupFilesPresetEntry.backupfilesPresetEntryDescriptions); backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries, @@ -2336,7 +2337,8 @@ public class GPreferences extends JPanel { if (customiseCheckbox.isSelected()) { - // got here by clicking on customiseCheckbox so don't change the values + // got here by clicking on customiseCheckbox so don't change the + // values backupfilesCustomOptionsSetEnabled(); } else @@ -2415,13 +2417,11 @@ public class GPreferences extends JPanel private JPanel initBackupsTabFilenameExamplesPanel() { - String title = MessageManager - .getString("label.scheme_examples"); + String title = MessageManager.getString("label.scheme_examples"); TitledBorder tb = new TitledBorder(title); exampleFilesPanel.setBorder(tb); exampleFilesPanel.setLayout(new GridBagLayout()); - backupfilesExampleLabel.setEditable(false); backupfilesExampleLabel .setBackground(exampleFilesPanel.getBackground()); @@ -2482,8 +2482,7 @@ public class GPreferences extends JPanel } protected void setComboIntStringKey( - JComboBox backupfilesPresetsCombo2, - int key) + JComboBox backupfilesPresetsCombo2, int key) { for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++) { @@ -2753,9 +2752,8 @@ public class GPreferences extends JPanel JPanel jp = new JPanel(); jp.setLayout(new FlowLayout()); - oldBackupFilesLabel - .setText(MessageManager - .getString("label.autodelete_old_backup_files")); + oldBackupFilesLabel.setText( + MessageManager.getString("label.autodelete_old_backup_files")); oldBackupFilesLabel.setFont(LABEL_FONT); oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT); jp.add(oldBackupFilesLabel); @@ -2915,7 +2913,8 @@ public class GPreferences extends JPanel } - // add some extra empty lines to pad out the example files box. ugh, please tell + // add some extra empty lines to pad out the example files box. ugh, please + // tell // me how to do this better int remainingLines = lowersurround + uppersurround + 1 - lineNumber; if (remainingLines > 0) @@ -2994,8 +2993,7 @@ public class GPreferences extends JPanel private void backupfilesKeepAllSetEnabled(boolean tryEnabled) { boolean enabled = tryEnabled && enableBackupFiles.isSelected() - && customiseCheckbox.isSelected() - && suffixTemplate.getText() + && customiseCheckbox.isSelected() && suffixTemplate.getText() .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1; keepfilesPanel.setEnabled(enabled); backupfilesKeepAll.setEnabled(enabled); @@ -3320,4 +3318,3 @@ public class GPreferences extends JPanel } } - diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index aa4cd6c..64b3a9c 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -29,8 +29,6 @@ import java.awt.Font; import java.awt.Rectangle; import java.io.BufferedReader; import java.io.ByteArrayInputStream; -import java.io.DataInputStream; -import java.io.DataOutputStream; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; @@ -109,7 +107,6 @@ import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.AlignmentPanel; import jalview.gui.AppVarna; -import jalview.gui.ChimeraViewFrame; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; import jalview.gui.OOMWarning; @@ -761,8 +758,8 @@ public class Jalview2XML // create backupfiles object and get new temp filename destination boolean doBackup = BackupFiles.getEnabled(); BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null; - FileOutputStream fos = new FileOutputStream(doBackup ? - backupfiles.getTempFilePath() : jarFile); + FileOutputStream fos = new FileOutputStream( + doBackup ? backupfiles.getTempFilePath() : jarFile); JarOutputStream jout = new JarOutputStream(fos); List frames = new ArrayList<>(); @@ -1092,8 +1089,8 @@ public class Jalview2XML if (frames[f] instanceof StructureViewerBase) { StructureViewerBase viewFrame = (StructureViewerBase) frames[f]; - matchedFile = saveStructureViewer(ap, jds, pdb, entry, viewIds, - matchedFile, viewFrame); + matchedFile = saveStructureViewer(ap, jds, pdb, entry, + viewIds, matchedFile, viewFrame); /* * Only store each structure viewer's state once in the project * jar. First time through only (storeDS==false) @@ -1111,9 +1108,8 @@ public class Jalview2XML } else { - Cache.log.error("Failed to save viewer state for " - + - viewerType); + Cache.log.error( + "Failed to save viewer state for " + viewerType); } } } @@ -1357,9 +1353,8 @@ public class Jalview2XML if (colourScheme instanceof jalview.schemes.UserColourScheme) { - jGroup.setColour( - setUserColourScheme(colourScheme, userColours, - object)); + jGroup.setColour(setUserColourScheme(colourScheme, + userColours, object)); } else { @@ -1542,11 +1537,13 @@ public class Jalview2XML * save any filter for the feature type */ FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); - if (filter != null) { - Iterator filters = filter.getMatchers().iterator(); + if (filter != null) + { + Iterator filters = filter.getMatchers() + .iterator(); FeatureMatcherI firstFilter = filters.next(); - setting.setMatcherSet(Jalview2XML.marshalFilter( - firstFilter, filters, filter.isAnded())); + setting.setMatcherSet(Jalview2XML.marshalFilter(firstFilter, + filters, filter.isAnded())); } /* @@ -1595,8 +1592,7 @@ public class Jalview2XML setting.setDisplay( av.getFeaturesDisplayed().isVisible(featureType)); - float rorder = fr - .getOrder(featureType); + float rorder = fr.getOrder(featureType); if (rorder > -1) { setting.setOrder(rorder); @@ -1620,7 +1616,7 @@ public class Jalview2XML Group g = new Group(); g.setName(grp); g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false)) - .booleanValue()); + .booleanValue()); // fs.addGroup(g); fs.getGroup().add(g); groupsAdded.addElement(grp); @@ -2377,7 +2373,8 @@ public class Jalview2XML { if (calcIdParam.getVersion().equals("1.0")) { - final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]); + final String[] calcIds = calcIdParam.getServiceURL() + .toArray(new String[0]); Jws2Instance service = Jws2Discoverer.getDiscoverer() .getPreferredServiceFor(calcIds); if (service != null) @@ -2538,8 +2535,8 @@ public class Jalview2XML } if (ref.hasMap()) { - Mapping mp = createVamsasMapping(ref.getMap(), parentseq, - jds, recurse); + Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds, + recurse); dbref.setMapping(mp); } vamsasSeq.getDBRef().add(dbref); @@ -2663,12 +2660,12 @@ public class Jalview2XML return id; } - jalview.schemes.UserColourScheme getUserColourScheme( - JalviewModel jm, String id) + jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm, + String id) { List uc = jm.getUserColours(); UserColours colours = null; -/* + /* for (int i = 0; i < uc.length; i++) { if (uc[i].getId().equals(id)) @@ -2677,7 +2674,7 @@ public class Jalview2XML break; } } -*/ + */ for (UserColours c : uc) { if (c.getId().equals(id)) @@ -2705,10 +2702,9 @@ public class Jalview2XML newColours = new java.awt.Color[23]; for (int i = 0; i < 23; i++) { - newColours[i] = new java.awt.Color(Integer.parseInt( - colours.getUserColourScheme().getColour().get(i + 24) - .getRGB(), - 16)); + newColours[i] = new java.awt.Color( + Integer.parseInt(colours.getUserColourScheme().getColour() + .get(i + 24).getRGB(), 16)); } ucs.setLowerCaseColours(newColours); } @@ -2777,54 +2773,69 @@ public class Jalview2XML return af; } - @SuppressWarnings("unused") - private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException { + @SuppressWarnings("unused") + private jarInputStreamProvider createjarInputStreamProvider( + final Object ofile) throws MalformedURLException + { - // BH 2018 allow for bytes already attached to File object - try { - String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString()); + // BH 2018 allow for bytes already attached to File object + try + { + String file = (ofile instanceof File + ? ((File) ofile).getCanonicalPath() + : ofile.toString()); byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile) : null; - URL url = null; - errorMessage = null; - uniqueSetSuffix = null; - seqRefIds = null; - viewportsAdded.clear(); - frefedSequence = null; - - if (HttpUtils.startsWithHttpOrHttps(file)) - { - url = new URL(file); - } - final URL _url = url; - return new jarInputStreamProvider() - { - - @Override - public JarInputStream getJarInputStream() throws IOException { - if (bytes != null) { -// System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length); - return new JarInputStream(new ByteArrayInputStream(bytes)); - } - if (_url != null) { -// System.out.println("Jalview2XML: opening url jarInputStream for " + _url); - return new JarInputStream(_url.openStream()); - } else { -// System.out.println("Jalview2XML: opening file jarInputStream for " + file); - return new JarInputStream(new FileInputStream(file)); - } - } - - @Override - public String getFilename() { - return file; - } - }; - } catch (IOException e) { - e.printStackTrace(); - return null; - } - } + URL url = null; + errorMessage = null; + uniqueSetSuffix = null; + seqRefIds = null; + viewportsAdded.clear(); + frefedSequence = null; + + if (HttpUtils.startsWithHttpOrHttps(file)) + { + url = new URL(file); + } + final URL _url = url; + return new jarInputStreamProvider() + { + + @Override + public JarInputStream getJarInputStream() throws IOException + { + if (bytes != null) + { + // System.out.println("Jalview2XML: opening byte jarInputStream for + // bytes.length=" + bytes.length); + return new JarInputStream(new ByteArrayInputStream(bytes)); + } + if (_url != null) + { + // System.out.println("Jalview2XML: opening url jarInputStream for " + // + _url); + return new JarInputStream(_url.openStream()); + } + else + { + // System.out.println("Jalview2XML: opening file jarInputStream for + // " + file); + return new JarInputStream(new FileInputStream(file)); + } + } + + @Override + public String getFilename() + { + return file; + } + }; + } catch (IOException e) + { + e.printStackTrace(); + return null; + } + } /** * Recover jalview session from a jalview project archive. Caller may @@ -2871,8 +2882,8 @@ public class Jalview2XML XMLStreamReader streamReader = XMLInputFactory.newInstance() .createXMLStreamReader(jin); javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); - JAXBElement jbe = um - .unmarshal(streamReader, JalviewModel.class); + JAXBElement jbe = um.unmarshal(streamReader, + JalviewModel.class); JalviewModel object = jbe.getValue(); if (true) // !skipViewport(object)) @@ -3260,7 +3271,8 @@ public class Jalview2XML AlignFrame loadFromObject(JalviewModel jalviewModel, String file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider) { - SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0); + SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet() + .get(0); List vamsasSeqs = vamsasSet.getSequence(); // JalviewModelSequence jms = object.getJalviewModelSequence(); @@ -3319,11 +3331,10 @@ public class Jalview2XML if (tmpSeq.getStart() != jseq.getStart() || tmpSeq.getEnd() != jseq.getEnd()) { - System.err.println( - String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d", - tmpSeq.getName(), tmpSeq.getStart(), - tmpSeq.getEnd(), jseq.getStart(), - jseq.getEnd())); + System.err.println(String.format( + "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d", + tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(), + jseq.getStart(), jseq.getEnd())); } } else @@ -3606,8 +3617,8 @@ public class Jalview2XML else { // defer to later - frefedSequence.add( - newAlcodMapRef(map.getDnasq(), cf, mapping)); + frefedSequence + .add(newAlcodMapRef(map.getDnasq(), cf, mapping)); } } } @@ -3815,8 +3826,7 @@ public class Jalview2XML jaa.setCalcId(annotation.getCalcId()); if (annotation.getProperty().size() > 0) { - for (Annotation.Property prop : annotation - .getProperty()) + for (Annotation.Property prop : annotation.getProperty()) { jaa.setProperty(prop.getName(), prop.getValue()); } @@ -3897,9 +3907,9 @@ public class Jalview2XML sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved())); sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold()); // attributes with a default in the schema are never null - sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); - sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); - sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); + sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); + sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); + sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus()); if (jGroup.getConsThreshold() != null && jGroup.getConsThreshold().intValue() != 0) @@ -3943,8 +3953,9 @@ public class Jalview2XML if (addAnnotSchemeGroup) { // reconstruct the annotation colourscheme - sg.setColourScheme(constructAnnotationColour( - jGroup.getAnnotationColours(), null, al, jalviewModel, false)); + sg.setColourScheme( + constructAnnotationColour(jGroup.getAnnotationColours(), + null, al, jalviewModel, false)); } } } @@ -4150,8 +4161,8 @@ public class Jalview2XML * @param av * @param ap */ - protected void loadTrees(JalviewModel jm, Viewport view, - AlignFrame af, AlignViewport av, AlignmentPanel ap) + protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af, + AlignViewport av, AlignmentPanel ap) { // TODO result of automated refactoring - are all these parameters needed? try @@ -4259,8 +4270,8 @@ public class Jalview2XML for (int s = 0; s < structureStateCount; s++) { // check to see if we haven't already created this structure view - final StructureState structureState = pdbid - .getStructureState().get(s); + final StructureState structureState = pdbid.getStructureState() + .get(s); String sviewid = (structureState.getViewId() == null) ? null : structureState.getViewId() + uniqueSetSuffix; jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); @@ -4328,8 +4339,8 @@ public class Jalview2XML colourByViewer &= structureState.isColourByJmol(); jmoldat.setColourByViewer(colourByViewer); - if (jmoldat.getStateData().length() < structureState - .getValue()/*Content()*/.length()) + if (jmoldat.getStateData().length() < structureState.getValue() + /*Content()*/.length()) { jmoldat.setStateData(structureState.getValue());// Content()); } @@ -4407,8 +4418,7 @@ public class Jalview2XML } catch (IllegalArgumentException | NullPointerException e) { // TODO JAL-3619 show error dialog / offer an alternative viewer - Cache.log.error( - "Invalid structure viewer type: " + type); + Cache.log.error("Invalid structure viewer type: " + type); } } @@ -4608,23 +4618,23 @@ public class Jalview2XML } AlignFrame loadViewport(String file, List JSEQ, - List hiddenSeqs, AlignmentI al, - JalviewModel jm, Viewport view, String uniqueSeqSetId, - String viewId, List autoAlan) + List hiddenSeqs, AlignmentI al, JalviewModel jm, + Viewport view, String uniqueSeqSetId, String viewId, + List autoAlan) { AlignFrame af = null; af = new AlignFrame(al, safeInt(view.getWidth()), - safeInt(view.getHeight()), uniqueSeqSetId, viewId) -// { -// -// @Override -// protected void processKeyEvent(java.awt.event.KeyEvent e) { -// System.out.println("Jalview2XML AF " + e); -// super.processKeyEvent(e); -// -// } -// -// } + safeInt(view.getHeight()), uniqueSeqSetId, viewId) + // { + // + // @Override + // protected void processKeyEvent(java.awt.event.KeyEvent e) { + // System.out.println("Jalview2XML AF " + e); + // super.processKeyEvent(e); + // + // } + // + // } ; af.setFileName(file, FileFormat.Jalview); @@ -4702,9 +4712,8 @@ public class Jalview2XML viewport.setColourText(safeBoolean(view.isShowColourText())); - viewport - .setConservationSelected( - safeBoolean(view.isConservationSelected())); + viewport.setConservationSelected( + safeBoolean(view.isConservationSelected())); viewport.setIncrement(safeInt(view.getConsThreshold())); viewport.setShowJVSuffix(safeBoolean(view.isShowFullId())); viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds())); @@ -4780,9 +4789,8 @@ public class Jalview2XML af.changeColour(cs); viewport.setColourAppliesToAllGroups(true); - viewport - .setShowSequenceFeatures( - safeBoolean(view.isShowSequenceFeatures())); + viewport.setShowSequenceFeatures( + safeBoolean(view.isShowSequenceFeatures())); viewport.setCentreColumnLabels(view.isCentreColumnLabels()); viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null); @@ -4806,13 +4814,13 @@ public class Jalview2XML .getFeatureRenderer(); FeaturesDisplayed fdi; viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); - String[] renderOrder = new String[jm.getFeatureSettings() - .getSetting().size()]; + String[] renderOrder = new String[jm.getFeatureSettings().getSetting() + .size()]; Map featureColours = new Hashtable<>(); Map featureOrder = new Hashtable<>(); - for (int fs = 0; fs < jm.getFeatureSettings() - .getSetting().size(); fs++) + for (int fs = 0; fs < jm.getFeatureSettings().getSetting() + .size(); fs++) { Setting setting = jm.getFeatureSettings().getSetting().get(fs); String featureType = setting.getType(); @@ -4824,8 +4832,8 @@ public class Jalview2XML .getMatcherSet(); if (filters != null) { - FeatureMatcherSetI filter = Jalview2XML - .parseFilter(featureType, filters); + FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType, + filters); if (!filter.isEmpty()) { fr.setFeatureFilter(featureType, filter); @@ -4857,8 +4865,7 @@ public class Jalview2XML float max = setting.getMax() == null ? 1f : setting.getMax().floatValue(); FeatureColourI gc = new FeatureColour(maxColour, minColour, - maxColour, - noValueColour, min, max); + maxColour, noValueColour, min, max); if (setting.getAttributeName().size() > 0) { gc.setAttributeName(setting.getAttributeName().toArray( @@ -4892,8 +4899,7 @@ public class Jalview2XML } else { - featureColours.put(featureType, - new FeatureColour(maxColour)); + featureColours.put(featureType, new FeatureColour(maxColour)); } renderOrder[fs] = featureType; if (setting.getOrder() != null) @@ -5366,6 +5372,7 @@ public class Jalview2XML } } } + /** * * @param vamsasSeq @@ -6114,8 +6121,8 @@ public class Jalview2XML * @param af * @param jprovider */ - protected void createStructureViewer( - ViewerType viewerType, final Entry viewerData, + protected void createStructureViewer(ViewerType viewerType, + final Entry viewerData, AlignFrame af, jarInputStreamProvider jprovider) { final StructureViewerModel viewerModel = viewerData.getValue(); @@ -6129,8 +6136,7 @@ public class Jalview2XML { String viewerJarEntryName = getViewerJarEntryName( viewerModel.getViewId()); - sessionFilePath = copyJarEntry(jprovider, - viewerJarEntryName, + sessionFilePath = copyJarEntry(jprovider, viewerJarEntryName, "viewerSession", ".tmp"); } final String sessionPath = sessionFilePath; @@ -6150,8 +6156,7 @@ public class Jalview2XML addNewStructureViewer(sview); } catch (OutOfMemoryError ex) { - new OOMWarning("Restoring structure view for " - + viewerType, + new OOMWarning("Restoring structure view for " + viewerType, (OutOfMemoryError) ex.getCause()); if (sview != null && sview.isVisible()) { @@ -6211,8 +6216,7 @@ public class Jalview2XML String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\"); filedat = oldFiles.get(new File(reformatedOldFilename)); } - rewritten - .append(Platform.escapeBackslashes(filedat.getFilePath())); + rewritten.append(Platform.escapeBackslashes(filedat.getFilePath())); rewritten.append("\""); cp = ecp + 1; // advance beyond last \" and set cursor so we can // look for next file statement. @@ -6284,8 +6288,8 @@ public class Jalview2XML * @param fcol * @return */ - public static Colour marshalColour( - String featureType, FeatureColourI fcol) + public static Colour marshalColour(String featureType, + FeatureColourI fcol) { Colour col = new Colour(); if (fcol.isSimpleColour()) @@ -6346,7 +6350,7 @@ public class Jalview2XML boolean and) { jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet(); - + if (filters.hasNext()) { /* @@ -6396,7 +6400,7 @@ public class Jalview2XML } result.setMatchCondition(matcherModel); } - + return result; } @@ -6407,8 +6411,7 @@ public class Jalview2XML * @param matcherSetModel * @return */ - public static FeatureMatcherSetI parseFilter( - String featureType, + public static FeatureMatcherSetI parseFilter(String featureType, jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel) { FeatureMatcherSetI result = new FeatureMatcherSet(); @@ -6423,7 +6426,7 @@ public class Jalview2XML featureType, e.getMessage())); // return as much as was parsed up to the error } - + return result; } @@ -6438,8 +6441,7 @@ public class Jalview2XML * @throws IllegalStateException * if AND and OR conditions are mixed */ - protected static void parseFilterConditions( - FeatureMatcherSetI matcherSet, + protected static void parseFilterConditions(FeatureMatcherSetI matcherSet, jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel, boolean and) { @@ -6461,7 +6463,7 @@ public class Jalview2XML else if (filterBy == FilterBy.BY_SCORE) { matchCondition = FeatureMatcher.byScore(cond, pattern); - + } else if (filterBy == FilterBy.BY_ATTRIBUTE) { @@ -6471,7 +6473,7 @@ public class Jalview2XML matchCondition = FeatureMatcher.byAttribute(cond, pattern, attNames); } - + /* * note this throws IllegalStateException if AND-ing to a * previously OR-ed compound condition, or vice versa @@ -6514,13 +6516,13 @@ public class Jalview2XML public static FeatureColourI parseColour(Colour colourModel) { FeatureColourI colour = null; - + if (colourModel.getMax() != null) { Color mincol = null; Color maxcol = null; Color noValueColour = null; - + try { mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16)); @@ -6529,7 +6531,7 @@ public class Jalview2XML { Cache.log.warn("Couldn't parse out graduated feature color.", e); } - + NoValueColour noCol = colourModel.getNoValueColour(); if (noCol == NoValueColour.MIN) { @@ -6539,7 +6541,7 @@ public class Jalview2XML { noValueColour = maxcol; } - + colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour, safeFloat(colourModel.getMin()), safeFloat(colourModel.getMax())); @@ -6578,7 +6580,7 @@ public class Jalview2XML Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16)); colour = new FeatureColour(color); } - + return colour; } } -- 1.7.10.2