-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
-import jalview.jbappletgui.*;\r
-\r
-public class CutAndPasteTransfer\r
- extends GCutAndPasteTransfer\r
-{\r
- public CutAndPasteTransfer(boolean forImport)\r
- {\r
- super();\r
-\r
- if (!forImport)\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
- protected void ok_actionPerformed(ActionEvent e)\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
- return;\r
- }\r
-\r
- SequenceI[] sequences = null;\r
-\r
- String format = IdentifyFile.Identify(text, "Paste");\r
- sequences = FormatAdapter.readFile(text, "Paste", format);\r
-\r
- if (sequences != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- jalview.bin.JalviewLite.addFrame(af, "Cut & Paste input - " + format,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
- }\r
-\r
- Frame frame = (Frame)this.getParent();\r
- frame.setVisible(false);\r
- }\r
-\r
- protected void cancel_actionPerformed(ActionEvent e)\r
- {\r
- Frame frame = (Frame)this.getParent();\r
- frame.setVisible(false);\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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 java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.MessageManager;
+
+public class CutAndPasteTransfer extends Panel implements ActionListener,
+ MouseListener
+{
+ boolean pdbImport = false;
+
+ boolean treeImport = false;
+
+ boolean annotationImport = false;
+
+ Sequence seq;
+
+ AlignFrame alignFrame;
+
+ 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(Sequence 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)
+ {
+ PDBEntry pdb = new PDBEntry();
+ pdb.setFile(text);
+
+ if (alignFrame.alignPanel.av.applet.jmolAvailable)
+ new jalview.appletgui.AppletJmol(pdb, new Sequence[]
+ { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+ else
+
+ new MCview.AppletPDBViewer(pdb, new Sequence[]
+ { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+
+ }
+ else if (treeImport)
+ {
+ try
+ {
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(
+ textarea.getText(), "Paste");
+
+ fin.parse();
+ if (fin.getTree() != null)
+ {
+ alignFrame.loadTree(fin, "Pasted tree file");
+ }
+
+ } 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 String[]{ex.getMessage()}));
+ return;
+ }
+ }
+ else if (annotationImport)
+ {
+ 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 String[]{(tcf.getWarningMessage() != null ? tcf.getWarningMessage() : "")}));
+ }
+ }
+ else
+ {
+ tcf = null;
+ }
+ } catch (Exception x)
+ {
+ tcf = null;
+ }
+ if (tcf == null)
+ {
+ if (new AnnotationFile().readAnnotationFile(
+ alignFrame.viewport.getAlignment(), 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"));
+ }
+ }
+ }
+ }
+ else if (alignFrame != 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)
+ {
+ ex.printStackTrace();
+ }
+
+ if (al != null)
+ {
+ if (newWindow)
+ {
+ AlignFrame 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"));
+ }
+ }
+ }
+ // 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);
+ }
+ }
+
+ 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