From: Jim Procter Date: Wed, 11 Jul 2018 13:50:07 +0000 (+0100) Subject: Merge branch 'Jalview-BH/JAL-3048_exportSettingsrefactor' into Jalview-BH/JAL-3026 X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~548 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ac782d365838ae95fc6bbf6164e763a1e6893e72;hp=2cbf9d005db462396fa1dc0750aa63a2e6cd0735;p=jalview.git Merge branch 'Jalview-BH/JAL-3048_exportSettingsrefactor' into Jalview-BH/JAL-3026 --- diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 1401a28..b18d33c 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -336,14 +336,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.getDesktop().propertyChange(evt); } - /** - * BH 2018 - * + * BH 2018 + * * @return true if we have any features */ @Override - protected boolean haveAlignmentFeatures() { + protected boolean haveAlignmentFeatures() + { AlignmentI alignment = getViewport().getAlignment(); for (int i = 0; i < alignment.getHeight(); i++) @@ -351,12 +351,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI seq = alignment.getSequenceAt(i); for (String group : seq.getFeatures().getFeatureGroups(true)) { - if (group != null)return true; + if (group != null) + return true; } } - return false; + return false; } - + /** * initalise the alignframe from the underlying viewport data and the * configurations @@ -418,7 +419,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * */ { - addServiceListeners(); + addServiceListeners(); } setGUINucleotide(); } @@ -536,14 +537,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setFileFormat(format); reload.setEnabled(true); } - + /** * JavaScript will have this, maybe others. More dependable than a file name * and maintains a reference to the actual bytes loaded. * * @param file */ - public void setFileObject(File file) { + public void setFileObject(File file) + { this.fileObject = file; } @@ -1077,7 +1079,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, FileLoader loader = new FileLoader(); DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL : DataSourceType.FILE; + ? DataSourceType.URL + : DataSourceType.FILE; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } else @@ -1092,13 +1095,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { DataSourceType protocol = (fileName.startsWith("http:") - ? DataSourceType.URL : DataSourceType.FILE); + ? DataSourceType.URL + : DataSourceType.FILE); newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); } else { - newframe = loader.LoadFileWaitTillLoaded(fileObject, DataSourceType.FILE, currentFileFormat); + newframe = loader.LoadFileWaitTillLoaded(fileObject, + DataSourceType.FILE, currentFileFormat); } newframe.setBounds(bounds); @@ -1175,7 +1180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { @Override public void run() - { + { currentFileFormat = chooser.getSelectedFormat(); while (currentFileFormat == null) { @@ -1467,17 +1472,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText( MessageManager.getString("label.load_jalview_annotations")); chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) - { + { - @Override - public void run() - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); - } + @Override + public void run() + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); + } - }); + }); chooser.openDialog(this); } @@ -3937,40 +3942,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); - chooser.response( - new jalview.util.dialogrunner.RunResponse(JalviewFileChooser.APPROVE_OPTION) - { - @Override - public void run() - { - String filePath = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", filePath); - NewickFile fin = null; - try - { - fin = new NewickFile(new FileParse( - chooser.getSelectedFile(), DataSourceType.FILE)); - viewport.setCurrentTree( - showNewickTree(fin, filePath).getTree()); - } catch (Exception ex) - { - JvOptionPane.showMessageDialog(Desktop.desktop, - ex.getMessage(), - MessageManager.getString( - "label.problem_reading_tree_file"), - JvOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - if (fin != null && fin.hasWarningMessage()) - { - JvOptionPane.showMessageDialog(Desktop.desktop, - fin.getWarningMessage(), - MessageManager.getString( - "label.possible_problem_with_tree_file"), - JvOptionPane.WARNING_MESSAGE); - } - } - }).openDialog(this); + chooser.response(new jalview.util.dialogrunner.RunResponse( + JalviewFileChooser.APPROVE_OPTION) + { + @Override + public void run() + { + String filePath = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", filePath); + NewickFile fin = null; + try + { + fin = new NewickFile(new FileParse(chooser.getSelectedFile(), + DataSourceType.FILE)); + viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); + } catch (Exception ex) + { + JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), + MessageManager + .getString("label.problem_reading_tree_file"), + JvOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + if (fin != null && fin.hasWarningMessage()) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + fin.getWarningMessage(), + MessageManager.getString( + "label.possible_problem_with_tree_file"), + JvOptionPane.WARNING_MESSAGE); + } + } + }).openDialog(this); } public TreePanel showNewickTree(NewickFile nf, String treeTitle) @@ -4397,7 +4400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public boolean parseFeaturesFile(Object file, DataSourceType sourceType) { - // BH 2018 + // BH 2018 return avc.parseFeaturesFile(file, sourceType, Cache.getDefault("RELAXEDSEQIDMATCHING", false)); @@ -4444,8 +4447,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - - + final AlignFrame thisaf = this; final List files = new ArrayList<>(); List protocols = new ArrayList<>(); @@ -4478,14 +4480,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ArrayList filesnotmatched = new ArrayList<>(); for (int i = 0; i < files.size(); i++) { - // BH 2018 + // BH 2018 Object file = files.get(i); String fileName = file.toString(); String pdbfn = ""; - DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName)); + DataSourceType protocol = (file instanceof File + ? DataSourceType.FILE + : FormatAdapter.checkProtocol(fileName)); if (protocol == DataSourceType.FILE) { - File fl = (file instanceof File ? (File) file : new File(fileName)); + File fl = (file instanceof File ? (File) file + : new File(fileName)); pdbfn = fl.getName(); } else if (protocol == DataSourceType.URL) @@ -4534,7 +4539,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int assocfiles = 0; if (filesmatched.size() > 0) { - boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false); + boolean autoAssociate = Cache + .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); if (!autoAssociate) { String msg = MessageManager.formatMessage(