/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.appletgui;
-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.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-
import jalview.analysis.AlignmentUtils;
+import jalview.api.ComplexAlignFile;
import jalview.bin.JalviewLite;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
+import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
+import jalview.schemes.ColourSchemeI;
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.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
public class CutAndPasteTransfer extends Panel implements ActionListener,
MouseListener
{
AlignFrame alignFrame;
+ FileParse source = null;
+
public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
{
try
}
else if (alignFrame != null)
{
- loadAlignment(text, newWindow);
+ loadAlignment(text, newWindow, alignFrame.getAlignViewport());
}
// TODO: dialog should indicate if data was parsed correctly or not - see
// 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() }));
+ "label.could_not_parse_newick_file",
+ new Object[] { ex.getMessage() }));
return false;
}
return false;
* @param text
* @param newWindow
*/
- protected void loadAlignment(String text, boolean newWindow)
+ protected void loadAlignment(String text, boolean newWindow,
+ AlignViewport viewport)
{
- Alignment al = null;
+ AlignmentI al = null;
String format = new IdentifyFile().Identify(text,
AppletFormatAdapter.PASTE);
+ AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
try
{
- al = new AppletFormatAdapter().readFile(text,
- AppletFormatAdapter.PASTE, format);
+ al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
+ source = afa.getAlignFile();
} catch (java.io.IOException ex)
{
ex.printStackTrace();
}
if (newWindow)
{
- AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
- "Cut & Paste input - " + format, false);
+ AlignFrame af;
+
+ if (source instanceof ComplexAlignFile)
+ {
+ ColumnSelection colSel = ((ComplexAlignFile) source)
+ .getColumnSelection();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ boolean showSeqFeatures = ((ComplexAlignFile) source)
+ .isShowSeqFeatures();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ af = new AlignFrame(al, hiddenSeqs, colSel,
+ alignFrame.viewport.applet, "Cut & Paste input - "
+ + format, false);
+ af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
+ }
+ else
+ {
+ af = new AlignFrame(al, alignFrame.viewport.applet,
+ "Cut & Paste input - " + format, false);
+ }
+
af.statusBar
.setText(MessageManager
.getString("label.successfully_pasted_annotation_to_alignment"));
* @param al
* @return
*/
- protected boolean openSplitFrame(Alignment al, String format)
+ protected boolean openSplitFrame(AlignmentI al, String format)
{
- final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
+ final AlignmentI thisAlignment = this.alignFrame.getAlignViewport()
+ .getAlignment();
if (thisAlignment.isNucleotide() == al.isNucleotide())
{
// both nucleotide or both protein
}
AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
- boolean mapped = AlignmentUtils.mapProteinToCdna(protein, dna);
+ boolean mapped = AlignmentUtils.mapProteinAlignmentToCdna(protein, dna);
if (!mapped)
{
return false;
dialog.setMainPanel(question);
dialog.setVisible(true);
dialog.toFront();
-
+
if (!dialog.accept)
{
return false;
}
/*
+ * 'align' the added alignment to match the current one
+ */
+ al.alignAs(thisAlignment);
+
+ /*
* Open SplitFrame with DNA above and protein below, including the alignment
* from textbox and a copy of the original.
*/
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;
+ AlignFrame proteinFrame = al.isNucleotide() ? copyFrame : newFrame;
SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
sf.addToDisplay(false, applet);
return true;
jalview.io.AppletFormatAdapter.PASTE);
if (tcf.isValid())
{
- if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
- true))
+ if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
{
alignFrame.tcoffeeColour.setEnabled(true);
alignFrame.alignPanel.fontChanged();
// 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
+ new Object[] { (tcf.getWarningMessage() != null ? tcf
.getWarningMessage() : "") }));
}
}
if (tcf == null)
{
if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
- textarea.getText(),
- jalview.io.AppletFormatAdapter.PASTE))
+ textarea.getText(), jalview.io.AppletFormatAdapter.PASTE))
{
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
if (alignFrame.alignPanel.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(pdb, new SequenceI[]
- { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+ new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null,
+ alignFrame.alignPanel, AppletFormatAdapter.PASTE);
}
else
{
- new MCview.AppletPDBViewer(pdb, new SequenceI[]
- { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+ new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
+ alignFrame.alignPanel, AppletFormatAdapter.PASTE);
}
}
git://source.jalview.org / jalview.git / blobdiff