-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-\r
-public class CutAndPasteTransfer extends Panel implements ActionListener, MouseListener\r
-{\r
- boolean pdbImport = false;\r
- boolean treeImport = false;\r
- Sequence seq;\r
- AlignFrame alignFrame;\r
-\r
- public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)\r
- {\r
- try {\r
- jbInit();\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
-\r
- this.alignFrame = alignFrame;\r
-\r
- if (!forImport)\r
- {\r
-\r
- buttonPanel.setVisible(false);\r
- }\r
- }\r
-\r
- public String getText()\r
- {\r
- return textarea.getText();\r
- }\r
-\r
- public void setText(String text)\r
- {\r
- textarea.setText(text);\r
- }\r
-\r
- public void setPDBImport(Sequence seq)\r
- {\r
- this.seq = seq;\r
- pdbImport = true;\r
- }\r
-\r
- public void setTreeImport()\r
- {\r
- treeImport = true;\r
- ok.setLabel("Accept");\r
- }\r
-\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- if(evt.getSource()==ok)\r
- ok_actionPerformed();\r
- else if(evt.getSource()==cancel)\r
- cancel_actionPerformed();\r
- }\r
-\r
- protected void ok_actionPerformed()\r
- {\r
- String text = getText();\r
- int length = text.length();\r
- textarea.append("\n");\r
- if(textarea.getText().length()==length)\r
- {\r
- String warning = "\n\n#################################################\n"\r
- +"WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"\r
- +"\nCAN'T INPUT FULL ALIGNMENT"\r
- +"\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"\r
- +"\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"\r
- +"\n#################################################\n";\r
- textarea.setText(text.substring(0, text.length()-warning.length())\r
- +warning);\r
-\r
- textarea.setCaretPosition(text.length());\r
- }\r
-\r
- if(pdbImport)\r
- {\r
- new MCview.AppletPDBViewer(text, AppletFormatAdapter.PASTE,\r
- seq,\r
- alignFrame.getSeqcanvas());\r
- }\r
- else if(treeImport)\r
- {\r
- try{\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),\r
- "Paste");\r
-\r
- fin.parse();\r
- if(fin.getTree()!=null)\r
- alignFrame.loadTree(fin, "Pasted tree file");\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- textarea.setText("Could not parse Newick file!\n" + ex);\r
- return;\r
- }\r
- }\r
- else if(alignFrame!=null)\r
- {\r
- SequenceI[] sequences = null;\r
-\r
- String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);\r
- try{\r
- sequences = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE, format);\r
- }catch(java.io.IOException ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- if (sequences != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences), alignFrame.viewport.applet,\r
- "Cut & Paste input - " + format,\r
- false);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
- }\r
- }\r
-\r
- if(this.getParent() instanceof Frame)\r
- ((Frame)this.getParent()).setVisible(false);\r
- else\r
- ((Dialog)this.getParent()).setVisible(false);\r
- }\r
-\r
- protected void cancel_actionPerformed()\r
- {\r
- textarea.setText("");\r
- if(this.getParent() instanceof Frame)\r
- ((Frame)this.getParent()).setVisible(false);\r
- else\r
- ((Dialog)this.getParent()).setVisible(false);\r
- }\r
-\r
- protected TextArea textarea = new TextArea();\r
- Button ok = new Button();\r
- Button cancel = new Button();\r
- protected Panel buttonPanel = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
-\r
-\r
- private void jbInit() throws Exception {\r
- textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));\r
- textarea.setText("Paste your alignment file here");\r
- textarea.addMouseListener(this);\r
- this.setLayout(borderLayout1);\r
- ok.setLabel("New Window");\r
- ok.addActionListener(this);\r
- cancel.setLabel("Close");\r
- cancel.addActionListener(this);\r
- this.add(buttonPanel, BorderLayout.SOUTH);\r
- buttonPanel.add(ok, null);\r
- buttonPanel.add(cancel, null);\r
- this.add(textarea, java.awt.BorderLayout.CENTER);\r
- }\r
-\r
- public void mousePressed(MouseEvent evt) {\r
- if (textarea.getText().startsWith("Paste your")) {\r
- textarea.setText("");\r
- }\r
- }\r
- public void mouseReleased(MouseEvent evt){}\r
- public void mouseClicked(MouseEvent evt){}\r
- public void mouseEntered(MouseEvent evt){}\r
- public void mouseExited(MouseEvent evt){}\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.api.ComplexAlignFile;
+import jalview.bin.JalviewLite;
+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.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
+{
+ boolean pdbImport = false;
+
+ boolean treeImport = false;
+
+ boolean annotationImport = false;
+
+ SequenceI seq;
+
+ AlignFrame alignFrame;
+
+ FileParse source = null;
+
+ public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ this.alignFrame = alignFrame;
+
+ if (!forImport)
+ {
+ buttonPanel.setVisible(false);
+ }
+ }
+
+ public String getText()
+ {
+ return textarea.getText();
+ }
+
+ public void setText(String text)
+ {
+ textarea.setText(text);
+ }
+
+ public void setPDBImport(SequenceI seq)
+ {
+ this.seq = seq;
+ accept.setLabel(MessageManager.getString("action.accept"));
+ addSequences.setVisible(false);
+ pdbImport = true;
+ }
+
+ public void setTreeImport()
+ {
+ treeImport = true;
+ accept.setLabel(MessageManager.getString("action.accept"));
+ addSequences.setVisible(false);
+ }
+
+ public void setAnnotationImport()
+ {
+ annotationImport = true;
+ accept.setLabel(MessageManager.getString("action.accept"));
+ addSequences.setVisible(false);
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == accept)
+ {
+ ok(true);
+ }
+ else if (evt.getSource() == addSequences)
+ {
+ ok(false);
+ }
+ else if (evt.getSource() == cancel)
+ {
+ cancel();
+ }
+ }
+
+ protected void ok(boolean newWindow)
+ {
+ String text = getText();
+ int length = text.length();
+ textarea.append("\n");
+ if (textarea.getText().length() == length)
+ {
+ String warning = "\n\n#################################################\n"
+ + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
+ + "\nCAN'T INPUT FULL ALIGNMENT"
+ + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
+ + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
+ + "\n#################################################\n";
+ textarea.setText(text.substring(0, text.length() - warning.length())
+ + warning);
+
+ textarea.setCaretPosition(text.length());
+ }
+
+ if (pdbImport)
+ {
+ openPdbViewer(text);
+
+ }
+ else if (treeImport)
+ {
+ if (!loadTree())
+ {
+ return;
+ }
+ }
+ else if (annotationImport)
+ {
+ loadAnnotations();
+ }
+ else if (alignFrame != null)
+ {
+ loadAlignment(text, newWindow, alignFrame.getAlignViewport());
+ }
+
+ // 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
+ {
+ ((Dialog) this.getParent()).setVisible(false);
+ }
+ }
+
+ /**
+ * 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");
+
+ fin.parse();
+ if (fin.getTree() != null)
+ {
+ 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;
+ }
+ 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,
+ AlignViewport viewport)
+ {
+ AlignmentI al = null;
+
+ String format = new IdentifyFile().Identify(text,
+ AppletFormatAdapter.PASTE);
+ AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
+ try
+ {
+ al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
+ source = afa.getAlignFile();
+ } catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (al != null)
+ {
+ al.setDataset(null); // set dataset on alignment/sequences
+
+ /*
+ * SplitFrame option dependent on applet parameter for now.
+ */
+ boolean allowSplitFrame = alignFrame.viewport.applet
+ .getDefaultParameter("enableSplitFrame", false);
+ if (allowSplitFrame && openSplitFrame(al, format))
+ {
+ return;
+ }
+ if (newWindow)
+ {
+ AlignFrame af;
+
+ if (source instanceof ComplexAlignFile)
+ {
+ ColumnSelection colSel = ((ComplexAlignFile) source)
+ .getColumnSelection();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ boolean showSeqFeatures = ((ComplexAlignFile) source)
+ .isShowSeqFeatures();
+ ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+ af = new AlignFrame(al, hiddenSeqs, colSel,
+ alignFrame.viewport.applet, "Cut & Paste input - "
+ + format, false);
+ af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
+ 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"));
+ }
+ else
+ {
+ 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(AlignmentI 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.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 Object[] { (tcf.getWarningMessage() != null ? tcf
+ .getWarningMessage() : "") }));
+ }
+ }
+ else
+ {
+ tcf = null;
+ }
+ } catch (Exception x)
+ {
+ tcf = null;
+ }
+ if (tcf == null)
+ {
+ if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
+ textarea.getText(), jalview.io.AppletFormatAdapter.PASTE))
+ {
+ alignFrame.alignPanel.fontChanged();
+ alignFrame.alignPanel.setScrollValues(0, 0);
+ alignFrame.statusBar
+ .setText(MessageManager
+ .getString("label.successfully_pasted_annotation_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"));
+ }
+ }
+ }
+ }
+
+ /**
+ * 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)
+ {
+ 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);
+ }
+ }
+
+ protected void cancel()
+ {
+ textarea.setText("");
+ if (this.getParent() instanceof Frame)
+ {
+ ((Frame) this.getParent()).setVisible(false);
+ }
+ else
+ {
+ ((Dialog) this.getParent()).setVisible(false);
+ }
+ }
+
+ protected TextArea textarea = new TextArea();
+
+ Button accept = new Button("New Window");
+
+ Button addSequences = new Button("Add to Current Alignment");
+
+ Button cancel = new Button("Close");
+
+ protected Panel buttonPanel = new Panel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ private void jbInit() throws Exception
+ {
+ textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
+ textarea.setText(MessageManager
+ .getString("label.paste_your_alignment_file"));
+ textarea.addMouseListener(this);
+ this.setLayout(borderLayout1);
+ accept.addActionListener(this);
+ addSequences.addActionListener(this);
+ cancel.addActionListener(this);
+ this.add(buttonPanel, BorderLayout.SOUTH);
+ buttonPanel.add(accept, null);
+ buttonPanel.add(addSequences);
+ buttonPanel.add(cancel, null);
+ this.add(textarea, java.awt.BorderLayout.CENTER);
+ }
+
+ public void mousePressed(MouseEvent evt)
+ {
+ if (textarea.getText().startsWith(
+ MessageManager.getString("label.paste_your")))
+ {
+ textarea.setText("");
+ }
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+}
git://source.jalview.org / jalview.git / blobdiff