X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=21af30157c6037e2cdb421b19c0bf741e4fd944e;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=6f5498d19647c6d10682f68c01b86f93e9adeddb;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java old mode 100755 new mode 100644 index 6f5498d..21af301 --- a/src/jalview/appletgui/CutAndPasteTransfer.java +++ b/src/jalview/appletgui/CutAndPasteTransfer.java @@ -1,28 +1,46 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * 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.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.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 @@ -68,7 +86,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, public void setPDBImport(Sequence seq) { this.seq = seq; - accept.setLabel("Accept"); + accept.setLabel(MessageManager.getString("action.accept")); addSequences.setVisible(false); pdbImport = true; } @@ -76,14 +94,14 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, public void setTreeImport() { treeImport = true; - accept.setLabel("Accept"); + accept.setLabel(MessageManager.getString("action.accept")); addSequences.setVisible(false); } public void setAnnotationImport() { annotationImport = true; - accept.setLabel("Accept"); + accept.setLabel(MessageManager.getString("action.accept")); addSequences.setVisible(false); } @@ -128,20 +146,23 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, 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"); + jalview.io.NewickFile fin = new jalview.io.NewickFile( + textarea.getText(), "Paste"); fin.parse(); if (fin.getTree() != null) @@ -151,24 +172,75 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, } catch (Exception ex) { - textarea.setText("Could not parse Newick file!\n" + 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) { - if (new AnnotationFile().readAnnotationFile( - alignFrame.viewport.alignment, textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE)) + TCoffeeScoreFile tcf = null; + try { - alignFrame.alignPanel.fontChanged(); - alignFrame.alignPanel.setScrollValues(0, 0); - + 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; } - else + if (tcf == null) { - alignFrame.parseFeaturesFile(textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE); + 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")); + } + } } } else if (alignFrame != null) @@ -192,15 +264,20 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, { AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet, "Cut & Paste input - " + format, false); - af.statusBar.setText("Successfully pasted alignment file"); + 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); @@ -239,7 +316,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, private void jbInit() throws Exception { textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10)); - textarea.setText("Paste your alignment file here"); + textarea.setText(MessageManager + .getString("label.paste_your_alignment_file")); textarea.addMouseListener(this); this.setLayout(borderLayout1); accept.addActionListener(this); @@ -254,7 +332,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, public void mousePressed(MouseEvent evt) { - if (textarea.getText().startsWith("Paste your")) + if (textarea.getText().startsWith( + MessageManager.getString("label.paste_your"))) { textarea.setText(""); }