X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=99a761bfc193c41353ef9473118419a41bc3439e;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=51d8d7f07b27027b11256a9361df476be836633c;hpb=8d3d3b4edf47e543b8b352c1b2c247cfc59122a4;p=jalview.git diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java index 51d8d7f..99a761b 100755 --- a/src/jalview/appletgui/CutAndPasteTransfer.java +++ b/src/jalview/appletgui/CutAndPasteTransfer.java @@ -1,159 +1,277 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.appletgui; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; -import jalview.io.*; - -public class CutAndPasteTransfer extends Panel implements ActionListener, MouseListener -{ - jalview.bin.JalviewLite applet; - - boolean pdbImport = false; - Sequence seq; - SeqCanvas seqcanvas; - - public CutAndPasteTransfer(boolean forImport, jalview.bin.JalviewLite mainApplet) - { - try { - jbInit(); - } catch (Exception e) { - e.printStackTrace(); - } - - applet = mainApplet; - - if (!forImport) - { - buttonPanel.setVisible(false); - } - } - - public void setPDBImport(Sequence seq, SeqCanvas seqcanvas) - { - this.seq = seq; - this.seqcanvas = seqcanvas; - pdbImport = true; - } - - - public String getText() - { - return textarea.getText(); - } - - public void setText(String text) - { - textarea.setText(text); - } - - public void actionPerformed(ActionEvent evt) - { - if(evt.getSource()==ok) - ok_actionPerformed(); - else if(evt.getSource()==cancel) - cancel_actionPerformed(); - } - - protected void ok_actionPerformed() - { - 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) - { - new MCview.AppletPDBViewer(text, "Paste", seq, seqcanvas); - } - else - { - SequenceI[] sequences = null; - - String format = IdentifyFile.Identify(text, "Paste"); - try{ - sequences = new AppletFormatAdapter().readFile(text, "Paste", format); - }catch(java.io.IOException ex) - { - ex.printStackTrace(); - } - if (sequences != null) - { - AlignFrame af = new AlignFrame(new Alignment(sequences), applet, - "Cut & Paste input - " + format); - af.statusBar.setText("Successfully pasted alignment file"); - } - } - - ((Frame)this.getParent()).setVisible(false); - } - - protected void cancel_actionPerformed() - { - ((Frame)this.getParent()).setVisible(false); - } - - protected TextArea textarea = new TextArea(); - Button ok = new Button(); - Button cancel = new Button(); - 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("Paste your alignment file here"); - textarea.addMouseListener(this); - this.setLayout(borderLayout1); - ok.setLabel("OK"); - ok.addActionListener(this); - cancel.setLabel("Cancel"); - cancel.addActionListener(this); - this.add(buttonPanel, BorderLayout.SOUTH); - buttonPanel.add(ok, null); - buttonPanel.add(cancel, null); - this.add(textarea, java.awt.BorderLayout.CENTER); - } - - public void mousePressed(MouseEvent evt) { - if (textarea.getText().startsWith("Paste your")) { - textarea.setText(""); - } - } - public void mouseReleased(MouseEvent evt){} - public void mouseClicked(MouseEvent evt){} - public void mouseEntered(MouseEvent evt){} - public void mouseExited(MouseEvent evt){} -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . + */ +package jalview.appletgui; + +import java.awt.*; +import java.awt.event.*; + +import jalview.datamodel.*; +import jalview.io.*; + +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("Accept"); + addSequences.setVisible(false); + pdbImport = true; + } + + public void setTreeImport() + { + treeImport = true; + accept.setLabel("Accept"); + addSequences.setVisible(false); + } + + public void setAnnotationImport() + { + annotationImport = true; + accept.setLabel("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) + { + textarea.setText("Could not parse Newick file!\n" + ex); + return; + } + } + else if (annotationImport) + { + if (new AnnotationFile().readAnnotationFile( + alignFrame.viewport.alignment, textarea.getText(), + jalview.io.AppletFormatAdapter.PASTE)) + { + alignFrame.alignPanel.fontChanged(); + alignFrame.alignPanel.setScrollValues(0, 0); + + } + else + { + alignFrame.parseFeaturesFile(textarea.getText(), + jalview.io.AppletFormatAdapter.PASTE); + } + } + 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("Successfully pasted alignment file"); + } + else + { + alignFrame.addSequences(al.getSequencesArray()); + } + } + } + + 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("Paste your alignment file here"); + 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("Paste your")) + { + textarea.setText(""); + } + } + + public void mouseReleased(MouseEvent evt) + { + } + + public void mouseClicked(MouseEvent evt) + { + } + + public void mouseEntered(MouseEvent evt) + { + } + + public void mouseExited(MouseEvent evt) + { + } +}