X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=036bbe362146f80a5d27076439886b33f48d5b1e;hp=21af30157c6037e2cdb421b19c0bf741e4fd944e;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hpb=10e637daad8983c41db8679baabea5563d7371f4 diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java index 21af301..036bbe3 100644 --- a/src/jalview/appletgui/CutAndPasteTransfer.java +++ b/src/jalview/appletgui/CutAndPasteTransfer.java @@ -20,21 +20,12 @@ */ package jalview.appletgui; -import jalview.datamodel.Alignment; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.Sequence; -import jalview.io.AnnotationFile; -import jalview.io.AppletFormatAdapter; -import jalview.io.IdentifyFile; -import jalview.io.TCoffeeScoreFile; -import jalview.schemes.TCoffeeColourScheme; -import jalview.util.MessageManager; - import java.awt.BorderLayout; import java.awt.Button; import java.awt.Dialog; import java.awt.Font; import java.awt.Frame; +import java.awt.Label; import java.awt.Panel; import java.awt.TextArea; import java.awt.event.ActionEvent; @@ -42,6 +33,20 @@ import java.awt.event.ActionListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; +import jalview.analysis.AlignmentUtils; +import jalview.bin.JalviewLite; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.AnnotationFile; +import jalview.io.AppletFormatAdapter; +import jalview.io.IdentifyFile; +import jalview.io.NewickFile; +import jalview.io.TCoffeeScoreFile; +import jalview.schemes.TCoffeeColourScheme; +import jalview.util.MessageManager; + public class CutAndPasteTransfer extends Panel implements ActionListener, MouseListener { @@ -51,7 +56,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, boolean annotationImport = false; - Sequence seq; + SequenceI seq; AlignFrame alignFrame; @@ -83,7 +88,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, textarea.setText(text); } - public void setPDBImport(Sequence seq) + public void setPDBImport(SequenceI seq) { this.seq = seq; accept.setLabel(MessageManager.getString("action.accept")); @@ -142,149 +147,261 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, if (pdbImport) { - PDBEntry pdb = new PDBEntry(); - pdb.setFile(text); + openPdbViewer(text); - if (alignFrame.alignPanel.av.applet.jmolAvailable) - { - new jalview.appletgui.AppletJmol(pdb, new Sequence[] - { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE); - } - else + } + else if (treeImport) + { + if (!loadTree()) { - new MCview.AppletPDBViewer(pdb, new Sequence[] - { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE); + return; } + } + else if (annotationImport) + { + loadAnnotations(); + } + else if (alignFrame != null) + { + loadAlignment(text, newWindow); + } + // TODO: dialog should indicate if data was parsed correctly or not - see + // JAL-1102 + if (this.getParent() instanceof Frame) + { + ((Frame) this.getParent()).setVisible(false); } - else if (treeImport) + else { - try - { - jalview.io.NewickFile fin = new jalview.io.NewickFile( - textarea.getText(), "Paste"); + ((Dialog) this.getParent()).setVisible(false); + } + } - fin.parse(); - if (fin.getTree() != null) - { - alignFrame.loadTree(fin, "Pasted tree file"); - } + /** + * Parses text as Newick Tree format, and loads on to the alignment. Returns + * true if successful, else false. + */ + protected boolean loadTree() + { + try + { + NewickFile fin = new NewickFile(textarea.getText(), "Paste"); - } catch (Exception ex) + fin.parse(); + if (fin.getTree() != null) { - // TODO: JAL-1102 - should have a warning message in dialog, not simply - // overwrite the broken input data with the exception - textarea.setText(MessageManager.formatMessage( - "label.could_not_parse_newick_file", new String[] - { ex.getMessage() })); - return; + alignFrame.loadTree(fin, "Pasted tree file"); + return true; } + } catch (Exception ex) + { + // TODO: JAL-1102 - should have a warning message in dialog, not simply + // overwrite the broken input data with the exception + textarea.setText(MessageManager.formatMessage( + "label.could_not_parse_newick_file", new Object[] + { ex.getMessage() })); + return false; } - else if (annotationImport) + return false; + } + + /** + * Parse text as an alignment file and add to the current or a new window. + * + * @param text + * @param newWindow + */ + protected void loadAlignment(String text, boolean newWindow) + { + Alignment al = null; + + String format = new IdentifyFile().Identify(text, + AppletFormatAdapter.PASTE); + try + { + al = new AppletFormatAdapter().readFile(text, + AppletFormatAdapter.PASTE, format); + } catch (java.io.IOException ex) { - TCoffeeScoreFile tcf = null; - try + ex.printStackTrace(); + } + + if (al != null) + { + al.setDataset(null); // set dataset on alignment/sequences + if (openSplitFrame(al, format)) { - tcf = new TCoffeeScoreFile(textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE); - if (tcf.isValid()) - { - if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), - true)) - { - alignFrame.tcoffeeColour.setEnabled(true); - alignFrame.alignPanel.fontChanged(); - alignFrame.changeColour(new TCoffeeColourScheme( - alignFrame.viewport.getAlignment())); - alignFrame.statusBar - .setText(MessageManager - .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); - } - else - { - // file valid but didn't get added to alignment for some reason - alignFrame.statusBar.setText(MessageManager.formatMessage( - "label.failed_add_tcoffee_scores", - new String[] - { (tcf.getWarningMessage() != null ? tcf - .getWarningMessage() : "") })); - } - } - else - { - tcf = null; - } - } catch (Exception x) + return; + } + if (newWindow) { - tcf = null; + AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet, + "Cut & Paste input - " + format, false); + af.statusBar + .setText(MessageManager + .getString("label.successfully_pasted_annotation_to_alignment")); } - if (tcf == null) + else { - if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, - textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE)) + alignFrame.addSequences(al.getSequencesArray()); + alignFrame.statusBar.setText(MessageManager + .getString("label.successfully_pasted_alignment_file")); + } + } + } + + /** + * Check whether the new alignment could be mapped to the current one as + * cDNA/protein, if so offer the option to open as split frame view. Returns + * true if a split frame view is opened, false if not. + * + * @param al + * @return + */ + protected boolean openSplitFrame(Alignment al, String format) + { + final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment(); + if (thisAlignment.isNucleotide() == al.isNucleotide()) + { + // both nucleotide or both protein + return false; + } + AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment; + AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al; + boolean mapped = AlignmentUtils.mapProteinToCdna(protein, dna); + if (!mapped) + { + return false; + } + + /* + * A mapping is possible; ask user if they want a split frame. + */ + String title = MessageManager.getString("label.open_split_window"); + final JVDialog dialog = new JVDialog((Frame) this.getParent(), title, + true, 100, 400); + dialog.ok.setLabel(MessageManager.getString("action.yes")); + dialog.cancel.setLabel(MessageManager.getString("action.no")); + Panel question = new Panel(new BorderLayout()); + final String text = MessageManager + .getString("label.open_split_window?"); + question.add(new Label(text, Label.CENTER), BorderLayout.CENTER); + dialog.setMainPanel(question); + dialog.setVisible(true); + dialog.toFront(); + + if (!dialog.accept) + { + return false; + } + + /* + * Open SplitFrame with DNA above and protein below, including the alignment + * from textbox and a copy of the original. + */ + final JalviewLite applet = this.alignFrame.viewport.applet; + AlignFrame copyFrame = new AlignFrame( + this.alignFrame.viewport.getAlignment(), applet, + alignFrame.getTitle(), false, false); + AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet, + "Cut & Paste input - " + format, false, false); + AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame; + AlignFrame proteinFrame = al.isNucleotide() ? copyFrame + : newFrame; + SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame); + sf.addToDisplay(false, applet); + return true; + } + + /** + * Parse the text as a TCoffee score file, if successful add scores as + * alignment annotations. + */ + protected void loadAnnotations() + { + TCoffeeScoreFile tcf = null; + try + { + tcf = new TCoffeeScoreFile(textarea.getText(), + jalview.io.AppletFormatAdapter.PASTE); + if (tcf.isValid()) + { + if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), + true)) { + alignFrame.tcoffeeColour.setEnabled(true); alignFrame.alignPanel.fontChanged(); - alignFrame.alignPanel.setScrollValues(0, 0); + alignFrame.changeColour(new TCoffeeColourScheme( + alignFrame.viewport.getAlignment())); alignFrame.statusBar .setText(MessageManager - .getString("label.successfully_pasted_annotation_to_alignment")); - + .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); } else { - if (!alignFrame.parseFeaturesFile(textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE)) - { - alignFrame.statusBar - .setText(MessageManager - .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file")); - } + // file valid but didn't get added to alignment for some reason + alignFrame.statusBar.setText(MessageManager.formatMessage( + "label.failed_add_tcoffee_scores", + new Object[] + { (tcf.getWarningMessage() != null ? tcf + .getWarningMessage() : "") })); } } + else + { + tcf = null; + } + } catch (Exception x) + { + tcf = null; } - else if (alignFrame != null) + if (tcf == null) { - Alignment al = null; - - String format = new IdentifyFile().Identify(text, - AppletFormatAdapter.PASTE); - try - { - al = new AppletFormatAdapter().readFile(text, - AppletFormatAdapter.PASTE, format); - } catch (java.io.IOException ex) + if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, + textarea.getText(), + jalview.io.AppletFormatAdapter.PASTE)) { - ex.printStackTrace(); - } + alignFrame.alignPanel.fontChanged(); + alignFrame.alignPanel.setScrollValues(0, 0); + alignFrame.statusBar + .setText(MessageManager + .getString("label.successfully_pasted_annotation_to_alignment")); - if (al != null) + } + else { - if (newWindow) + if (!alignFrame.parseFeaturesFile(textarea.getText(), + jalview.io.AppletFormatAdapter.PASTE)) { - AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet, - "Cut & Paste input - " + format, false); - af.statusBar + alignFrame.statusBar .setText(MessageManager - .getString("label.successfully_pasted_annotation_to_alignment")); - } - else - { - alignFrame.addSequences(al.getSequencesArray()); - alignFrame.statusBar.setText(MessageManager - .getString("label.successfully_pasted_alignment_file")); + .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file")); } } } - // TODO: dialog should indicate if data was parsed correctly or not - see - // JAL-1102 - if (this.getParent() instanceof Frame) + } + + /** + * Open a Jmol viewer (if available), failing that the built-in PDB viewer, + * passing the input text as the PDB file data. + * + * @param text + */ + protected void openPdbViewer(String text) + { + PDBEntry pdb = new PDBEntry(); + pdb.setFile(text); + + if (alignFrame.alignPanel.av.applet.jmolAvailable) { - ((Frame) this.getParent()).setVisible(false); + new jalview.appletgui.AppletJmol(pdb, new SequenceI[] + { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE); } else { - ((Dialog) this.getParent()).setVisible(false); + new MCview.AppletPDBViewer(pdb, new SequenceI[] + { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE); } }