X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=44a2318d42d0f66173755f01cb1f1e6951caa81d;hb=9d7c487b4a2774d380d0807527e365e9002a1fd5;hp=f31a22033ed6194f03b3a1d6c92d7b243826d5e9;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index f31a220..44a2318 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -66,6 +66,7 @@ import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; @@ -75,7 +76,6 @@ import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; -import jalview.io.StructureFile; import jalview.io.TCoffeeScoreFile; import jalview.jbgui.GAlignFrame; import jalview.schemes.Blosum62ColourScheme; @@ -132,6 +132,8 @@ import java.awt.print.PageFormat; import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; import java.io.File; +import java.io.FileWriter; +import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; @@ -147,7 +149,6 @@ import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JRadioButtonMenuItem; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; @@ -859,7 +860,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, modifyConservation.setEnabled(!nucleotide); showGroupConservation.setEnabled(!nucleotide); rnahelicesColour.setEnabled(nucleotide); + nucleotideColour.setEnabled(nucleotide); purinePyrimidineColour.setEnabled(nucleotide); + RNAInteractionColour.setEnabled(nucleotide); showComplementMenuItem.setText(nucleotide ? MessageManager .getString("label.protein") : MessageManager .getString("label.nucleotide")); @@ -891,7 +894,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); + modifyPID.setEnabled(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(av.getConservationSelected()); + modifyConservation.setEnabled(conservationMenuItem.isSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.isRightAlignIds()); centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); @@ -1114,11 +1119,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void saveAs_actionPerformed(ActionEvent e) { + String format = currentFileFormat == null ? null : currentFileFormat + .getName(); JalviewFileChooser chooser = JalviewFileChooser.forWrite( - Cache.getProperty("LAST_DIRECTORY"), - // AppletFormatAdapter.WRITABLE_EXTENSIONS, - // AppletFormatAdapter.WRITABLE_FNAMES, - currentFileFormat.toString(), false); + Cache.getProperty("LAST_DIRECTORY"), format); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -1132,14 +1136,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat = chooser.getSelectedFormat(); while (currentFileFormat == null) { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager .getString("label.select_file_format_before_saving"), MessageManager .getString("label.file_format_not_specified"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); currentFileFormat = chooser.getSelectedFormat(); value = chooser.showSaveDialog(this); if (value != JalviewFileChooser.APPROVE_OPTION) @@ -1150,8 +1154,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fileName = chooser.getSelectedFile().getPath(); - Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat.toString()); + Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); Cache.setProperty("LAST_DIRECTORY", fileName); saveAlignment(fileName, currentFileFormat); @@ -1181,17 +1184,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) - // { - // warningMessage("Cannot save file " + fileName + " using format " - // + format, "Alignment output format not supported"); - // if (!Jalview.isHeadlessMode()) - // { - // saveAs_actionPerformed(null); - // } - // return false; - // } - AlignmentExportData exportData = getAlignmentForExport(format, viewport, null); if (exportData.getSettings().isCancelled()) @@ -1216,15 +1208,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); + PrintWriter out = new PrintWriter(new FileWriter(file)); out.print(output); out.close(); this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", - new Object[] { fileName, format })); + new Object[] { fileName, format.getName() })); } catch (Exception ex) { success = false; @@ -1235,11 +1226,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { - JOptionPane.showInternalMessageDialog(this, MessageManager + JvOptionPane.showInternalMessageDialog(this, MessageManager .formatMessage("label.couldnt_save_file", new Object[] { fileName }), MessageManager .getString("label.error_saving_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } return success; @@ -1254,8 +1245,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - JOptionPane.showInternalMessageDialog(this, warning, title, - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(this, warning, title, + JvOptionPane.WARNING_MESSAGE); } return; } @@ -1269,8 +1260,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void outputText_actionPerformed(ActionEvent e) { - - FileFormatI fileFormat = FileFormat.forName(e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); AlignmentExportData exportData = getAlignmentForExport(fileFormat, viewport, null); if (exportData.getSettings().isCancelled()) @@ -2372,13 +2363,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getAlignment().getWidth()) ? true : false; if (isEntireAlignWidth) { - int confirm = JOptionPane.showConfirmDialog(this, + int confirm = JvOptionPane.showConfirmDialog(this, MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ MessageManager.getString("label.delete_all"), // $NON-NLS-1$ - JOptionPane.OK_CANCEL_OPTION); + JvOptionPane.OK_CANCEL_OPTION); - if (confirm == JOptionPane.CANCEL_OPTION - || confirm == JOptionPane.CLOSED_OPTION) + if (confirm == JvOptionPane.CANCEL_OPTION + || confirm == JvOptionPane.CLOSED_OPTION) { return; } @@ -3509,12 +3500,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! */ @Override - protected void modifyPID_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed() { if (viewport.getAbovePIDThreshold() && viewport.getGlobalColourScheme() != null) @@ -3527,12 +3515,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! */ @Override - protected void modifyConservation_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { if (viewport.getConservationSelected() && viewport.getGlobalColourScheme() != null) @@ -3544,41 +3529,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on selecting or deselecting (Colour) By Conservation */ @Override - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { - viewport.setConservationSelected(conservationMenuItem.isSelected()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setSelected(false); + boolean selected = conservationMenuItem.isSelected(); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); changeColour(viewport.getGlobalColourScheme()); - - modifyConservation_actionPerformed(null); + if (selected) + { + modifyConservation_actionPerformed(); + } + else + { + SliderPanel.hideConservationSlider(); + } } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on selecting or deselecting (Colour) Above PID Threshold */ @Override - public void abovePIDThreshold_actionPerformed(ActionEvent e) + public void abovePIDThreshold_actionPerformed() { - viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); - - conservationMenuItem.setSelected(false); - viewport.setConservationSelected(false); + boolean selected = abovePIDThreshold.isSelected(); + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); changeColour(viewport.getGlobalColourScheme()); - - modifyPID_actionPerformed(null); + if (selected) + { + modifyPID_actionPerformed(); + } + else + { + SliderPanel.hidePIDSlider(); + } } /** @@ -3655,13 +3644,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { radioItem.removeActionListener(radioItem.getActionListeners()[0]); - int option = JOptionPane.showInternalConfirmDialog( + int option = JvOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, MessageManager .getString("label.remove_from_default_list"), MessageManager .getString("label.remove_user_defined_colour"), - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) + JvOptionPane.YES_NO_OPTION); + if (option == JvOptionPane.YES_OPTION) { jalview.gui.UserDefinedColours .removeColourFromDefaults(radioItem.getText()); @@ -3809,10 +3798,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if ((viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { - JOptionPane.showInternalMessageDialog(this, MessageManager + JvOptionPane.showInternalMessageDialog(this, MessageManager .getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } else { @@ -3838,14 +3827,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getSelectionGroup().getSize() > 0)) || (viewport.getAlignment().getHeight() < 4)) { - JOptionPane + JvOptionPane .showInternalMessageDialog( this, MessageManager .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), MessageManager .getString("label.sequence_selection_insufficient"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -3943,14 +3932,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.getSelectionGroup().getSize() < 3) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.you_need_more_two_sequences_selected_build_tree"), MessageManager .getString("label.not_enough_sequences"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -3961,14 +3950,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (_s.getLength() < sg.getEndRes()) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), MessageManager .getString("label.sequences_selection_not_aligned"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -3982,14 +3971,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // are the visible sequences aligned? if (!viewport.getAlignment().isAligned(false)) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.sequences_must_be_aligned_before_creating_tree"), MessageManager .getString("label.sequences_not_aligned"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -4254,11 +4243,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() == 1) { - int option = JOptionPane.showConfirmDialog(this, + int option = JvOptionPane.showConfirmDialog(this, MessageManager.getString("warn.oneseq_msainput_selection"), MessageManager.getString("label.invalid_selection"), - JOptionPane.OK_CANCEL_OPTION); - if (option == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION); + if (option == JvOptionPane.OK_OPTION) { msa = viewport.getAlignmentView(false); } @@ -4334,21 +4323,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, ex.getMessage(), MessageManager .getString("label.problem_reading_tree_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin != null && fin.hasWarningMessage()) { - JOptionPane.showMessageDialog(Desktop.desktop, fin + JvOptionPane.showMessageDialog(Desktop.desktop, fin .getWarningMessage(), MessageManager .getString("label.possible_problem_with_tree_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } } @@ -4733,8 +4722,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final String errorTitle = MessageManager .getString("label.implementation_error") + MessageManager.getString("label.translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JOptionPane.ERROR_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JvOptionPane.ERROR_MESSAGE); return; } if (al == null || al.getHeight() == 0) @@ -4743,8 +4732,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); final String errorTitle = MessageManager .getString("label.translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JvOptionPane.WARNING_MESSAGE); } else { @@ -4899,13 +4888,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { type = null; } - if (type != null) + if (type != null && type.isStructureFile()) { - if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type)) - { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; - } + filesmatched.add(new Object[] { file, protocol, mtch }); + continue; } } // File wasn't named like one of the sequences or wasn't a PDB file. @@ -4916,7 +4902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (filesmatched.size() > 0) { if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JOptionPane + || JvOptionPane .showConfirmDialog( this, MessageManager @@ -4929,7 +4915,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .toString() }), MessageManager .getString("label.automatically_associate_structure_files_by_name"), - JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) { for (Object[] fm : filesmatched) @@ -4959,7 +4945,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (assocfiles > 0 && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane .showConfirmDialog( this, "" @@ -4974,7 +4960,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + "", MessageManager .getString("label.ignore_unmatched_dropped_files"), - JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) { return; } @@ -5039,7 +5025,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // some problem - if no warning its probable that the ID matching // process didn't work - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, tcf.getWarningMessage() == null ? MessageManager @@ -5047,7 +5033,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, : tcf.getWarningMessage(), MessageManager .getString("label.problem_reading_tcoffee_score_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } else @@ -5169,8 +5155,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (e.isPopupTrigger()) { String msg = MessageManager.getString("label.enter_view_name"); - String reply = JOptionPane.showInternalInputDialog(this, msg, msg, - JOptionPane.QUESTION_MESSAGE); + String reply = JvOptionPane.showInternalInputDialog(this, msg, msg, + JvOptionPane.QUESTION_MESSAGE); if (reply != null) { @@ -5909,12 +5895,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { System.err.println((ex.toString())); - JOptionPane + JvOptionPane .showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.couldnt_run_groovy_script"), MessageManager .getString("label.groovy_support_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } else