*/
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;
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
{
boolean annotationImport = false;
- Sequence seq;
+ SequenceI seq;
AlignFrame alignFrame;
textarea.setText(text);
}
- public void setPDBImport(Sequence seq)
+ public void setPDBImport(SequenceI seq)
{
this.seq = seq;
accept.setLabel(MessageManager.getString("action.accept"));
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);
}
}
git://source.jalview.org / jalview.git / blobdiff