X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=95f1ed19f6fc33535d98855f30ea4893fd866d4d;hb=bf448d3b8794da07525adedec9f1ff04428e84cb;hp=010d52a2b0cbde55009588d15cddcfc74ec3cd58;hpb=06de78be50c3934158fa1d35ec92ad86b54e959f;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 010d52a..95f1ed1 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -88,6 +88,7 @@ import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; +import jalview.util.dialogrunner.RunResponse; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; @@ -122,6 +123,7 @@ import java.awt.event.MouseEvent; import java.awt.print.PageFormat; import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; import java.io.File; import java.io.FileWriter; import java.io.PrintWriter; @@ -136,6 +138,7 @@ import java.util.Vector; import javax.swing.JCheckBoxMenuItem; import javax.swing.JEditorPane; +import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JMenu; @@ -150,7 +153,8 @@ import javax.swing.SwingUtilities; * @version $Revision$ */ public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener + IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener, + PropertyChangeListener { public static final int DEFAULT_WIDTH = 700; @@ -178,6 +182,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ String fileName = null; + File fileObject; + /** * Creates a new AlignFrame object with specific width and height. * @@ -324,6 +330,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, init(); } + @Override + public void propertyChange(PropertyChangeEvent evt) + { + Desktop.getDesktop().propertyChange(evt); + } + + + /** + * BH 2018 + * + * @return true if we have any features + */ + @Override + protected boolean haveAlignmentFeatures() { + AlignmentI alignment = getViewport().getAlignment(); + + for (int i = 0; i < alignment.getHeight(); i++) + { + SequenceI seq = alignment.getSequenceAt(i); + for (String group : seq.getFeatures().getFeatureGroups(true)) + { + if (group != null)return true; + } + } + return false; + } + /** * initalise the alignframe from the underlying viewport data and the * configurations @@ -378,7 +411,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.desktop != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + /** + * BH 2018 ignore service listeners + * + * @j2sNative + * + */ + { addServiceListeners(); + } setGUINucleotide(); } @@ -495,6 +536,16 @@ 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) { + this.fileObject = file; + } /** * Add a KeyListener with handlers for various KeyPressed and KeyReleased @@ -1026,8 +1077,7 @@ 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 @@ -1035,11 +1085,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE; - AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, - protocol, currentFileFormat); + + AlignFrame newframe = null; + + if (fileObject == null) + { + + DataSourceType protocol = (fileName.startsWith("http:") + ? DataSourceType.URL : DataSourceType.FILE); + newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, + currentFileFormat); + } + else + { + newframe = loader.LoadFileWaitTillLoaded(fileObject, DataSourceType.FILE, currentFileFormat); + } newframe.setBounds(bounds); if (featureSettings != null && featureSettings.isShowing()) @@ -1103,41 +1163,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String format = currentFileFormat == null ? null : currentFileFormat.getName(); - JalviewFileChooser chooser = JalviewFileChooser + final JalviewFileChooser chooser = JalviewFileChooser .forWrite(Cache.getProperty("LAST_DIRECTORY"), format); - + final AlignFrame us = this; chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.save_alignment_to_file")); chooser.setToolTipText(MessageManager.getString("action.save")); - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) { - currentFileFormat = chooser.getSelectedFormat(); - while (currentFileFormat == null) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString( - "label.select_file_format_before_saving"), - MessageManager.getString("label.file_format_not_specified"), - JvOptionPane.WARNING_MESSAGE); + @Override + public void run() + { currentFileFormat = chooser.getSelectedFormat(); - value = chooser.showSaveDialog(this); - if (value != JalviewFileChooser.APPROVE_OPTION) + while (currentFileFormat == null) { - return; + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString( + "label.select_file_format_before_saving"), + MessageManager + .getString("label.file_format_not_specified"), + JvOptionPane.WARNING_MESSAGE); + currentFileFormat = chooser.getSelectedFormat(); + chooser.showSaveDialog(us); } - } - fileName = chooser.getSelectedFile().getPath(); + fileName = chooser.getSelectedFile().getPath(); - Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); + Cache.setProperty("DEFAULT_FILE_FORMAT", + currentFileFormat.getName()); - Cache.setProperty("LAST_DIRECTORY", fileName); - saveAlignment(fileName, currentFileFormat); - } + Cache.setProperty("LAST_DIRECTORY", fileName); + saveAlignment(fileName, currentFileFormat); + } + }).showSaveDialog(this); } public boolean saveAlignment(String file, FileFormatI format) @@ -1392,36 +1452,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void exportFeatures_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportFeatures(alignPanel); + new AnnotationExporter(alignPanel).exportFeatures(); } @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations(alignPanel); + new AnnotationExporter(alignPanel).exportAnnotations(); } @Override public void associatedData_actionPerformed(ActionEvent e) { - // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser( + final JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.load_jalview_annotations")); chooser.setToolTipText( MessageManager.getString("label.load_jalview_annotations")); + chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) + { - int value = chooser.showOpenDialog(null); + @Override + public void run() + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); + } - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(choice, null, null, null); - } + }); + chooser.openDialog(this); } /** @@ -1828,7 +1891,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void copy_actionPerformed(ActionEvent e) { - System.gc(); if (viewport.getSelectionGroup() == null) { return; @@ -1864,23 +1926,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new ArrayList<>(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); - ArrayList hiddenRegions = viewport.getAlignment() - .getHiddenColumns().getHiddenColumnsCopy(); - for (int[] region : hiddenRegions) - { - if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) - { - hiddenColumns - .add(new int[] - { region[0] - hiddenOffset, region[1] - hiddenOffset }); - } - } + + // create new HiddenColumns object with copy of hidden regions + // between startRes and endRes, offset by startRes + hiddenColumns = new HiddenColumns( + viewport.getAlignment().getHiddenColumns(), hiddenOffset, + hiddenCutoff, hiddenOffset); } Desktop.jalviewClipboard = new Object[] { seqs, @@ -2209,11 +2265,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int[] region : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is @@ -2268,11 +2321,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int region[] : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is @@ -2714,8 +2764,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * Create a new AlignmentPanel (with its own, new Viewport) */ - AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, - true); + AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel); if (!copyAnnotation) { /* @@ -3274,6 +3323,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setOverviewPanel(null); }; }); + if (getKeyListeners().length > 0) + { + frame.addKeyListener(getKeyListeners()[0]); + } alignPanel.setOverviewPanel(overview); } @@ -3889,33 +3942,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); - int value = chooser.showOpenDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String filePath = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", filePath); - NewickFile fin = null; - try - { - fin = new NewickFile(filePath, 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); - } - } + 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) @@ -4335,13 +4395,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Try to load a features file onto the alignment. * * @param file - * contents or path to retrieve file + * contents or path to retrieve file or a File object * @param sourceType * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed correctly. */ - public boolean parseFeaturesFile(String file, DataSourceType sourceType) + public boolean parseFeaturesFile(Object file, DataSourceType sourceType) { + // BH 2018 return avc.parseFeaturesFile(file, sourceType, Cache.getDefault("RELAXEDSEQIDMATCHING", false)); @@ -4388,8 +4449,10 @@ 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<>(); + final List files = new ArrayList<>(); List protocols = new ArrayList<>(); try @@ -4417,20 +4480,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Object[] { String,SequenceI} */ ArrayList filesmatched = new ArrayList<>(); - ArrayList filesnotmatched = new ArrayList<>(); + ArrayList filesnotmatched = new ArrayList<>(); for (int i = 0; i < files.size(); i++) { - String file = files.get(i).toString(); + // BH 2018 + Object file = files.get(i); + String fileName = file.toString(); String pdbfn = ""; - DataSourceType protocol = FormatAdapter.checkProtocol(file); + DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName)); if (protocol == DataSourceType.FILE) { - File fl = new File(file); + File fl = (file instanceof File ? (File) file : new File(fileName)); pdbfn = fl.getName(); } else if (protocol == DataSourceType.URL) { - URL url = new URL(file); + URL url = new URL(fileName); pdbfn = url.getFile(); } if (pdbfn.length() > 0) @@ -4452,7 +4517,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (mtch != null) { - FileFormatI type = null; + FileFormatI type; try { type = new IdentifyFile().identify(file, protocol); @@ -4474,17 +4539,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int assocfiles = 0; if (filesmatched.size() > 0) { - if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JvOptionPane.showConfirmDialog(thisaf, - MessageManager.formatMessage( - "label.automatically_associate_structure_files_with_sequences_same_name", - new Object[] - { Integer.valueOf(filesmatched.size()) - .toString() }), - MessageManager.getString( - "label.automatically_associate_structure_files_by_name"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) - + boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false); + if (!autoAssociate) + { + String msg = MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()) + .toString() }); + String ttl = MessageManager.getString( + "label.automatically_associate_structure_files_by_name"); + int choice = JvOptionPane.showConfirmDialog(thisaf, msg, + ttl, JvOptionPane.YES_NO_OPTION); + autoAssociate = choice == JvOptionPane.YES_OPTION; + } + if (autoAssociate) { for (Object[] fm : filesmatched) { @@ -4510,6 +4579,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true, false); } } + else + { + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) + { + filesnotmatched.add(o[0]); + } + } } if (filesnotmatched.size() > 0) { @@ -4529,7 +4608,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return; } - for (String fn : filesnotmatched) + for (Object fn : filesnotmatched) { loadJalviewDataFile(fn, null, null, null); } @@ -4556,9 +4635,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param file * either a filename or a URL string. */ - public void loadJalviewDataFile(String file, DataSourceType sourceType, + public void loadJalviewDataFile(Object file, DataSourceType sourceType, FileFormatI format, SequenceI assocSeq) { + // BH 2018 was String file try { if (sourceType == null) @@ -4642,11 +4722,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); - SequenceI repseq = viewport.getAlignment().getSequenceAt(0); - viewport.getAlignment().setSeqrep(repseq); - HiddenColumns cs = new HiddenColumns(); - cs.hideInsertionsFor(repseq); - viewport.getAlignment().setHiddenColumns(cs); + viewport.getAlignment().setupJPredAlignment(); isAnnotation = true; } // else if (IdentifyFile.FeaturesFile.equals(format)) @@ -4868,14 +4944,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, MessageManager.getString("option.trim_retrieved_seqs")); trimrs.setToolTipText( MessageManager.getString("label.trim_retrieved_sequences")); - trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); + trimrs.setSelected( + Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); - Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", + Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); }; }); @@ -5597,17 +5674,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); + final AlignFrame us = this; + chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) + { + @Override + public void run() + { - int value = chooser.showOpenDialog(null); + { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + new VCFLoader(choice).loadVCF(seqs, us); + } - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", choice); - new VCFLoader(viewport.getAlignment()).loadVCF(choice, this); - } + }; + }).openDialog(null); } + } class PrintThread extends Thread